The Biotechnology Information System Network in India
PROCEEDINGS XXIV ANNUAL BIOINFORMATICS COORDINATORS MEETING FEBRUARY 3rd – 4th, 2013
Focal Theme: New Paradigms in Bioinformatics Research
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CSIR-CIMAP DEPARTMENT OF BIOTECHNOLOGY MINISTRY OF SCIENCE AND TECHNOLOGY GOVERNMENT OF INDIA
BIOINFORMATICS CENTRE CSIR- CENTRAL INSTITUTE OF MEDICINAL AND AROMATIC PLANTS, LUCKNOW-226015, INDIA
CSIR-Central Institute of Medicinal and Aromatic Plants CSIR-CIMAP, Lucknow (Headquarters)
CSIR-CIMAP Research Centre, Pantnagar
CSIR-CIMAP Research Centre, Hyderabad
CSIR-CIMAP Research Centre, Purara, Bageshwar
CSIR-CIMAP Research Centre, Bengaluru
The Biotechnology Information System Network in India
PROCEEDINGS XXIV ANNUAL BIOINFORMATICS COORDINATORS MEETING FEBRUARY 3rd – 4th, 2013
Focal Theme: New Paradigms in Bioinformatics Research
DEPARTMENT OF BIOTECHNOLOGY MINISTRY OF SCIENCE AND TECHNOLOGY GOVERNMENT OF INDIA
Host : CSIR- CENTRAL INSTITUTE OF MEDICINAL AND AROMATIC PLANTS, LUCKNOW-226015, INDIA
XXIV ANNUAL BTISNet COORDINATORS MEETING CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow Focal Theme: New Paradigms in Bioinformatics Research 15:15-16:30 hrs
Technical Session-III Presented by Coordinators of DICs (8 minutes each) Chairperson : Prof. Deepti Deobagkar Rapporteur
: Dr. Asad U Khan
DICs 1.
Anna university, Chennai
2.
CCMB, Hyderabad
3.
IARI, New Delhi
4.
IMT, Chandigarh
5.
KAU, Thrissur
6.
MSUB, Baroda
7.
NBRC, Manesar
8.
NII, New Delhi
9.
Pondicherry University , Pondicherry
10. University of Calcutta, Kolkatta 11. NEHU, Shillong 16:30-16:45 hrs
Tea Break
17:30-18:30 hrs
Technical Session-IV Presentation by Coordinators Chairperson : Dr. AK Shasany Rapporteur : Dr. Ashok K Verma Sub-DICs 1.
IIAR, Gandhinagar
2.
IIIM, Jammu-Tawi
3.
KVAFS, Mangalore
4.
MSSRF, Chennai
5.
MGIMS, Wardha
6.
NBRI, Lucknow
XXIV ANNUAL BTISNet COORDINATORS MEETING CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow Focal Theme: New Paradigms in Bioinformatics Research 7.
NDRI, Karnal
8.
NIPGR, New Delhi
9.
NIO, Dona Paula, Goa
10. Punjab Agricultural University, Ludhiana 11. RGCB, Thiruvananthapuram 12. T.M. Bhagalpur University, Bhagalpur 13. Tamilnadu Agricultural University, Coimbatore 14. Tamilnadu Veterinary and Animal Science University, Madras 15. TBGRI, Thiruvananthapuram 16. University of Delhi South Campus, New Delhi 17. University of Kashmir, Kashmir 18:00-19:00 hrs
Cultural Programme Followed by Dinner
MONDAY 04th FEBRUARY, 2013 10:00-11:30 hrs
Technical Session-V Presentation by Coordinators and NEBInet Report (5 minutes each) Chairperson : Prof. UN Dwivedi Rapporteur
: Dr. PS Solanki
BIFs 1.
NIT, Rourkela
2.
North Orissa University, Baripada
3.
Orissa University of Agriculture & Technology, Bhubaneswar
4.
Presidency College, Chennai
5.
Presidency College, Kolkata
6.
Queen Mary's College, Chennai
7.
St. Aloysius College, Mangalore
8.
SGBA University, Amravati
9.
SGPGI, Lucknow
XXIV ANNUAL BTISNet COORDINATORS MEETING CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow Focal Theme: New Paradigms in Bioinformatics Research 10. SVNIT, Surat 11. SVBPUAT University, Meerut 12. Sher-e-Kashmir University, Srinagar 13. SPMV, Tirupati 14. SMVDU, Jammu 15. SKU, Anantpur 16. SSSU, Prasanthi Nilayam 17. SVC, New Delhi 18. SVIMS, Chittoor 19. SVU, Tirupati 20. University of Allahabad, Allahabad 11:30-12:00 hrs
TEA BREAK
12:00-12:30 hrs
Technical Session-VI Discussion on the theme & recommendations
Speakers
: Prof. M. Vijayan, IISC, Bangalore Dr. T. Madhan Mohan, DBT, New Delhi
Rapporteur 13:30-14:30
LUNCH
: Dr. Peeyush Goyel
Contents CENTRES OF EXCELLENCE (COES) Bose Institute, Kolkata
3
Indian Institute of Science, Bangalore
7
Jawaharlal Nehru University, New Delhi
8
Madurai Kamaraj University, Madurai
14
Supercomputing Facility for Bioinformatics & Computational Biology (SCFBio), IIT Delhi, New Delhi
19
University of Pune, Pune
21
DISTRIBUTED INFORMATION CENTRES (DICS) Anna University, Chennai
29
Centre for Cellular and Molecular Biology, Hyderabad
31
Indian Agricultural Research Institute, New Delhi
36
Institute of Microbial Technology, Chandigarh
39
Kerala Agricultural University, Thrissur
41
National Brain Research Centre, Manesar
43
National Institute of Immunology, New Delhi
46
Pondicherry University, Pondicherry
48
University of Calcutta, Kolkata
54
DISTRIBUTED INFORMATION SUB CENTRES (DISCS) Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Kharghar, Navi-Mumbai
59
Aligarh Muslim University, Aligarh
63
All India Institute of Medical Sciences, New Delhi
68
Banaras Hindu University, Varanasi
71
Banasthali Vidyapith, Banasthali
75
Barkatullah University, Bhopal
80
Bharathidasan University, Tiruchirappalli
83
Biotech Consortium India Limited, New Delhi
86
Biotech Park in Biotechnology City, Lucknow
90
Birla Institute of Scientific Research, Jaipur
93
Birla Institute of Technology, Mesra, Ranchi
95
Central Agricultural Research Institute, Port Blair
99
Central Drug Research Institute, Lucknow
100
Central Institute of Medicinal and Aromatic Plants
104
Central Institute of Freshwater Aquaculture, Bhubaneswar
108
Central Plantation Crops Research Institute, Kasaragod
110
Central Sericultural Research and Training Institute, Mysore
113
CSK Himachal Pradesh Krishi Vishvavidyalaya, Palampur
117
Devi Ahilya University, Indore
120
Dr. Y S Parmar University of Horticulture and Forestry, Nauni-Solan
124
G. B. Pant University of Agriculture & Technology, Pantnagar
128
Guru Nanak Dev University, Amritsar
130
Himachal Pradesh University, Shimla
136
Indian Institute of Advanced Research, Gandhinagar
138
Indian Institute of Integrative Medicine
140
Indian Institute of Technology (IIT) Delhi, New Delhi
142
Indian Institute of Technology, Kharagpur
146
Indian Veterinary Research Institute, Izatnagar
148
Institute of Life Sciences, Bhubaneswar
151
Karnataka Veterinary, Animal & Fisheries Science University, Mangalore
154
Mahatma Gandhi Institute of Medical Sciences, Wardha
161
National Botanical Research Institute, Lucknow
165
National Dairy Research Institute, Karnal
167
National Institute of Oceanography, Goa
171
National Institute of Plant Genome Research, New Delhi
174
National Institute of Technology, Raipur
176
Rajiv Gandhi Centre for Biotechnology, Thriuvananthapuram
178
T.M. Bhagalpur University, Bhagalpur
180
Tamil Nadu Agricultural University, Coimbatore
183
Tamilnadu Veterinary and Animal Sciences University, Chennai
186
Tropical Botanic Garden and Research Institute, Thiruvananthapuram
192
University of Kashmir, Kashmir
195
BIOINFORMATICS INFRASTRUCTURE FACILITY(BIFS) Acharya Nagarjuna University, Nagarjuna Nagar, Guntur
199
Alagappa University, Karaikudi
201
Andhra University, Visakhapatnam
206
Assam Agricultural University, Jorhat
210
Assam University, Silchar
213
Awadhesh Pratap Singh University, Rewa
216
Berhampur University, Berhampur
220
Bharathiar University, Coimbatore
222
CCS Haryana Agricultural University, Hisar
226
Ch. Charan Singh University, Meerut
228
College of Agricultural Biotechnology, Latur
231
College of Veterinary Science, Assam Agricultural University, Guwahati
232
Cotton College, Guwahati
237
Dr. B. R. Ambedkar Center for Biomedical Research, Delhi
239
Forest Research Institute, Dehradun
243
Gargi College, New Delhi
246
Gauhati University, Guwahati
248
Guru Jambheshwar University of Science & Technology, Hisar
251
Gurucharan College, Silchar
253
Holy Cross College for Women, Tiruchirappalli
256
Indian Institute of Technology, Guwahati
260
Indian Institute of Technology, Madras
263
Institute of Bioresources and Sustainable Development (IBSD), Imphal
266
CSIR- Institute of Himalayan Bioresource Technology
268
International Centre for Genetic Engineering and Biotechnology, New Delhi
269
Jamia Hamdard University, New Delhi
272
Bioinformatics Centre, Jiwaji University, Gwalior
274
Karnatak University, Dharwad
277
Karnataka State Women’s University, Bijapur
280
Kumaun University, Bhimtal
281
Lady Doak College, Madurai
283
Lucknow University, Lucknow
285
Madras Christian College, Chennai
289
Maharani Lakshmi Ammanni College for Women, Bangalore
291
Maharani’s Science College for Women, Bangalore
294
Maharshi Dayanand University, Rohtak
297
Manipur University, Canchipur
300
Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu
304
Maulana Azad National Institute of Technology, Bhopal
306
Mizoram University, Aizawal
309
Nagaland University, Kohima
314
Narendra Deva University of Agriculture & Technology, Faizabad
316
National Research Centre on Equines, Hisar
318
National Research Centre on Mithun (ICAR), Dimapur, Nagaland
320
North East Institute of Science and Technology (NEIST), Jorhat
322
North Eastern Hill University, Nehu Campus, Shillong
325
North Eastern Regional Institute of Science & Technology (Deemed University), Nirjuli
330
North Orissa University, Baripada
332
Orissa University of Agriculture & Technology, Bhubaneswar
335
Presidency University, Kolkata
339
Queen Mary’s College, Chennai
342
Rajiv Gandhi University, Itanagar
343
S. Kula Women’s College, Nambol
345
Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow
348
Sant Gadge Baba Amravati University, Amravati
351
Sardar Vallabhbhai Patel University of Agriculture & Technology, Meerut
353
Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar
355
Shri Mata Vaishno Devi University, Katra
358
Sri Padmavati Mahila Visva Vidyalayam (Women’s University), Tirupati
360
Sri Krishnadevaraya University, Anantapur
363
Sikkim State Council of Science and Technology, Gangtok
366
Sri Venkateswara College, New Delhi
370
Sri Venkateswara Institute of Medical Sciences University, Tirupati
373
Sir Venkateswara University, Tirupati
378
St. Aloysius College, Mangalore
381
St. Edmund’s College, Shillong
383
Tezpur University, Tezpur
386
Tripura University, Suryamani Nagar
390
University of Allahabad
393
University of Hyderabad, Hyderabad
397
University of Jammu, Jammu
400
University of Kalyani, Kalyani
403
University of Kerala, Thiruvananthapuram
405
University of Madras, Chennai
409
University of North Bengal, Siliguri
413
University of Rajasthan, Jaipur
417
Vidyasagar University, Midnapore
419
West Bengal University of Technology, Kolkata
423
LATEARRIVALS Sardar Vallabhbhai National Institute of Technology, SURAT:
429
Bif Centre, D. M. College of Science, Imphal
431
Bioinformatics Infrastructure facility, University of Hyderabad
434
Centres of Excellence (COEs)
XXIVnd All India BTISnet Coordinators’ Meeting
February 03-04, 2013
Bose Institute, Kolkata Coordinator: Professor Pinak Chakrabarti Summary of the progress made by the centre from its inception: The Bioinformatics Centre of Bose institute, established in 1988 as one of the ten nodal centres under the programme, BTIS of the Department of Biotechnology, has been recognized in 2004 as a “Centre of Excellence” in Bioinformatics to undertake research in the following areas: modeling of proteins structures; molecular interaction and docking; drug design; chromosomal dynamics; stress biology of plants; functional genomics and host-pathogen interactions.
Major research activities in biotechnology and its related fields : The computational infrastructure developed at the Centre has provided the impetus for thriving research activities in bioinformatics and computational biology, as can be seen from a large number of publications made over the years and its recognition as the Centre of Excellence in Bioinformatics by DBT in 2004 and awards received by staff and students working at the Centre.
Area of specialization: Genome analysis; Genetic engineering; Regulatory RNA, stem cell & oncogenomics; structural bioinformatics, molecular modeling and dynamics, ligand design
Infrastructure facilities in the bioinformatics centre: Computer Hardware (functional): TFlop performance, HP cluster one with 0.8 Tflop and another with 2.6 TFlop performance, IBM X206(4 servers), four Dell TFlops performance, GPU computing facility (workstation fitted with Nvidia Tesla card), 3D visualization facility (with Nvidia Qadro 5000 graphics card and Dell alienware monitor) in multiple workstations IBM 226 (two servers), IBM X255 (two servers), HP MFP(Color), HP MFP(Black & White), Pentium IV PC (twenty five nos), HP Scanner, HP Laser Printer, Cisco Switch, Linksys Switches, Xerox photocopier. Communication facilities: BIC has a 4mbps leased lined connectivity to internet through Tata Communication and is also connected to the Bose Institute LAN which connected to internet by 4mbps leased line through ERNET, India.
Scientific Software Packages: A few webservers pertaining to computational biology have been developed. These are: 1)
ProFace, for dissecting protein-protein interfaces and deriving various physicochemical parameters.
2)
IntGeom, for calculating the geometry of interaction between planar side chains in protein structures.
3)
ConfPlot, for the graphical representation of the salient conformational features of protein residues.
4)
ContPlot, for the graphical display of accessible surface areas and contact numbers of individual residues along a polypeptide chain.
The web-servers are available at: http://www.boseinst.ernet.in/resources/bioinfo/stag.html. Softwares for molecular modeling and simulations (such as Bio-suite, Accelyrs, CHARMM, Gaussian, etc.), microarray data analyzing software, graphics and docking programs are available at the Centre.
Centres of Excellence (COEs)
3
February 03-04, 2013
XXIVnd All India BTISnet Coordinators’ Meeting
Details about Staff members working in the centre: Sl.No. Name 1. Pinak Chakrabarti 2. 3.
Designation Senior Professor
Specialization Crystallography, molecular modeling, & biophysics
Professor Evolutionary bioinformatics Assistant Professor Structural dynamics of biomolecules Stem Cells, microRNA, Zhumur Ghosh Faculty fellow Cancer & regulatory networks Ramalinwaswami Computational Proteomics, Sudipto Saha fellow Drug-Drug/Food-Drug Interactions, Pathogen-Host Interactions Molay Das CSIR Pool Officer Plant Genomics Perform administrative duties Tushar Kanti Bhattacharya Sr. Technical Officer and maintain the accounts needed Sujata Roy (Majumder) Technical Officer Documentation of project,comprehensive informatics support etc. Sanjib Kumar Gupta Technical Officer LAN, Website, Server maintenance
1994 2011
Permanent Permanent
2010
Permanent
2012
Permanent
2012 1991
Temporary Permanent
1993
Permanent
1994
Permanent
Official Documents Handling
1990
Permanent
Tapash Chandra Ghosh Shubhra Ghosh Dastidar
4. 5.
6. 7.
8.
9. 10.
Working Since Status 1997 Permanent
J.N. Mandal
Sr. Attendant
Educational Activities BIC provides project work to students undergoing B.Tech/M.Tech/MCA courses from a large number of institutes/universities. It offers a one-semester course in bioinformatics to the PhD students in the institute. It also offers Bioinformatics courses to the integrated MSc-PhD students of Bose Institute. Presently, three students are being trained under the studentship/traineeship programme for a period of 6 months.
Papers published:
4
1.
Hu S, Wilson KD, Ghosh Z, Han L, Wang Y,Lan F,Ransohoff KJ, and Wu JC (2012). MicroRNA-302 increases reprogramming efficiency via repression of NR2F2,. Stem Cells. Nov 8. doi: 10.1002/stem.1278. [Epub ahead of print].
2.
Kumar R, Halder P, Sahu SK, Kumar M, Kumari M, Jana K, Ghosh Z, Sharma P, Kundu M, and Basu J (2012). Identification of a novel role of ESAT-6-dependent miR-155 induction during infection of macrophages with Mycobacterium tuberculosis. Cell Microbiol. 14(10):1620-1631.
3.
Reddy S, Zhao M, Hu D-Q, Fajardo GA, Hu S, , Rajagopalan V, Wu JC, and Bernstein D (2012). Dynamic microRNA expression during the transition from right ventricular hypertrophy to failure, Physiological Genomics 44(10):562-575.
4.
Mallick B and Ghosh Z (2012). Probing Evolutionary Biography of MicroRNAs and Associated Factors. Current Genomics., 13:1-9.
5.
Chakraborti S, Chakravarty D, Gupta S, Chatterji BP, Dhar G, Poddar A, Panda D, Chakrabarti P, Ghosh Dastidar S, Bhattacharyya B (2012). Biochemistry. Sep 11;51(36):7138-48.
6.
Dastidar SG, Lane DP, Verma CS (2012). Why is F19Ap53 unable to bind MDM2? Simulations suggest crack propagation modulates binding. Cell Cycle.. Jun 15;11(12):2239-47.
Centres of Excellence (COEs)
XXIVnd All India BTISnet Coordinators’ Meeting
February 03-04, 2013
7.
Kahali B, Ghosh TC (2012) Disorderness in Escherichia coli proteome: perception of folding fidelity and proteinprotein interactions. J Biomol Struct Dyn. Aug 13. [Epub ahead of print]
8.
Podder S, Ghosh TC (2012) Evolutionary dynamics of human autoimmune disease genes and malfunctioned immunological genes. BMC Evolutionary Biology, 12:10.
9.
Sen K, Ghosh TC (2012) Evolutionary conservation and disease gene association of the human genes composing pseudogenes. Gene..,Jun 15;501(2):164-70. doi: 10.1016/j.gene.2012.04.013. Epub 2012 Apr 13.
10.
Panda A, Begum T, Ghosh TC (2012) Insights into the Evolutionary Features of Human Neurodegenerative Diseases. Human Neurodegenerative Diseases. PLoS ONE 7(10): e48336. doi:10.1371/journal.pone.0048336
11.
Chatterjee T, Pal A, Chakravarty D, Dey S, Saha RP and Chakrabarti P. Protein L-isoaspartyl-O-methyltransferase of Vibrio cholerae: Interaction with cofactors and effects of osmolytes on unfolding. Biochimie (in press).
12.
Chakraborti S, Joshi P, Chakravarty D, Shanker V, Ansari ZA, Singh SP and Chakrabarti P (2012). Interaction of polyethyleneimine functionalized ZnO nanoparticles with bovine serum albumin. Langmuir, 28, 11142-11152.
13.
Dey S, Pal A, Guharoy M, Sonavane S and Chakrabarti P (2012). Characterization and prediction of the binding site in DNA-binding proteins: improvement of accuracy by combining residue composition, evolutionary conservation and structural parameters. Nucleic Acids Res. 40, 7150-7161.
14.
Chatterjee T, Pal A, Dey S, Chatterjee BK and Chakrabarti P (2012). Interaction of virstatin with human serum albumin: spectroscopic analysis and molecular modeling. PLoS ONE, 7(5): e37468.
15.
Mazumder A, Bandyopadhyay S, Dhar A, Lewis DEA, Deb S, Dey S, Chakrabarti P and Roy S (2012). A genetic network that balances two outcomes utilizes asymmetric recognition of operator sites. Biophys. J. 102, 15801589.
16.
Ganguly HK, Majumder B, Chattopadhyay S, Chakrabarti P and Basu G (2012). Direct evidence for CH···p interaction mediated stabilization of Pro-cisPro bond in peptides with Pro-Pro-Aromatic motifs. J. Amer. Chem. Soc. 134, 4661-4669.
17.
Das M and Basu G (2012) . Glycine rescue of â-sheets from cis-proline. J. Amer. Chem. Soc. 134:16536-9.
Books chapter: 1.
Regulatory RNAs: Basics, Methods & Applications (2012) Mallick B. and Ghosh Z. (Eds) Springer-Verlag, Heidelberg, Germany.
Initiation of R&D activities in Bioinformatics: To understand the process of molecular recognition we plan to compare the bound and the unbound forms of protein molecules to delineate the structural changes accompanying the complex formation. Molecular dynamics and normal mode analysis would be carried out to see if the lowest frequency modes can capture the fluctuations occurring in the structure on complexation. Homology modelling, docking and computational studies would be carried out on proteins from Vibrio cholerae and on protein-nanoparticle interactions to corroborate the experimental observations. The research direction in next few years would be in the area of ‘Molecular recognition’ with a focus on the investigation on the dynamics of the molecular structures using atomistically detailed simulations. The atomistic detail of structural dynamics of protein-protein interactions are not only important for the fundamental understating of mechanisms of molecular biology but also important for targeting them for therapeutic benefit. Majority of non-enzymatic protein-protein complexes are characterized with relatively flat and labile interfaces of interactions, which are apparently ‘undruggable’. For them, the difficulty in predicting an inhibitor exits not only due the fact that they might lack well defined hydrophobic pocket, but rather the inherent plasticity and the dynamic nature of the interface of the binding, whose shape can easily change upon the change of environment (even when there is a binding groove), which is non-trivial to predict without simulating the full dynamics of such complxed states. The investigations will be carried out on BCL2 family members as well as p53 pathway, both of which areas are important for cancer therapeutics.
Centres of Excellence (COEs)
5
XXIVnd All India BTISnet Coordinators’ Meeting
February 03-04, 2013
A detailed analysis of the impact of regulatory noncoding RNAs(ncRNAs) on cancer stem cells(CSCs) as well as induced pluripotent stem cells(iPSCs) is one of the main focus of our work. We are elucidating the genes exclusively important for an abnormal cellular reprogramming in CSCs. Thereafter a thorough regulatory network will be constructed to figure out the pathways/phenomenon essential for such transformation. Subsequent wet bench analysis will be performed to validate it. We have started building up a computational pipeline to analyze different types of next generation sequence data incorporating cloud computing techniques. We are also investigating the noncoding RNA mediated regulation of fertilization, cell development and its role in cell fate determination. Further, we shall develop a “Pluripotency Network” based on the different molecular interactions by systemic analysis of the various determinants of pluripotency. We started developing linear motifs (LMs) mediated protein-protein interactions (PPIs) database. Our goal is to discover novel motifs mediating PPIs through analysis of protein interaction networks. PPIs are reported in the literature to be regulated by LMs, which are short elements embedded witin large protein sequences. These short linear peptide sections are often present in disordered regions in eukaryotic proteins and are responsible for thousands of protein-protein interactions. We started a project on understanding macrophage response to Salmonella pathogenic island II (SPI-II) proteins. We will generate host pathogen PPIs data using Affinity Purifaction- Mass Spectrometry (AP-MS) and subsequently construct host- pathogen PPIs network in colloboration with Dr. Santa Sabuj Das lab at NICED, Kolkata. Overall goal of this project is to understand regulatory mechanism of the pathogen in bypassing host protective immune system. Different proteins evolve at different rates. Elucidation of the determinants of the rate of protein sequence evolution is one of the great challenges in evolutionary biology. The main theme of our research goal is to identify and understand the different evolutionary forces by analyzing the genomic and functional data of various organisms.
Details of Training/Workshop organized and total no of user trained Training / Workshop: We had organized a conference entitled “Conference on Informatics & Integrative Biology” from 14th -16th December 2011, with national and international speakers.
Impact shown by the Centre: In 2012, seventeen papers dealing with different aspects of bioinformatics have been published by people working at the Centre. Many other publications have taken the services of the Centre.
Proposed activities for 2013-14 On-going research on understanding protein-protein interactions, the code relating protein sequence to its native fold, evolutionary systems biology, etc. would continue in the coming year. Webservers are being planned for displaying evolutionary conservation of protein interfaces. An international collaborative work has been initiated with Universite Paris-Sud, Orsay, France. Further, we are in the process of analyzing stem cell gene expression data related to disease systems as well as building up a sophisticated computational pipeline for analyzing various types of Next generation sequence data as well as studying complicated gene networks. Application of large scale computing in the investigation and analysis of the biomolecular structure,dynamics and drug design would be one of the major areas of focus and for that expansion of the ‘High Performance Computing’ would be a major goal.
Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
6
Prof. Pinak Chakrabarti Centre of Excellence in Bioinformatics, Bose Institute. P-1/12 CIT Scheme VII-M, Kolkata – 700054 033-23556626/23552816 91-33-2355-3886
[email protected] www.boseinst.ernet.in/bic Prof. Pinak Chakrabarti or Prof. Tapash Chandra Ghosh
Centres of Excellence (COEs)
XXIVnd All India BTISnet Coordinators’ Meeting
February 03-04, 2013
Indian Institute of Science, Bangalore Coordinator: Prof. Saraswathi Vishveshwara Summary of the progress made by the centre from its inception: The Centre was established in the year 1985 as one of the earliest centres for information dissemination and formal teaching in bioinformatics. In tune with the evolving nature of this discipline, there has been a paradigm shift in the focus of the Centre’s activities, which are now directed towards strengthening integrated research programmes in various specialized areas of bioinformatics
Research activities during the year 2012 The major research activities at the centre can be classified into the following areas: (a) Genome sequence and structural analysis, (b) Development of new algorithms in bioinformatics, (c) Internet computing, (d) Integrated database development, (e) Structural analysis of biological macromolecules, (f) Structural pharmacology, including in-silico drug discovery, (g) computational immunology and (h) Modelling and dynamics of protein-ligand interactions, protein folding by graph theoretical methods. While the first four pertain to development of new concepts and resources that often goes back into the public domain, the other areas pertain to application of the existing information to generate new kinds of knowledge that may ultimately lead to useful applications not only in the understanding of basic science but also as useful therapeutic pointers.
Facilities at the centre The centre, which is funded by the Department of Biotechnology (DBT), has been successfully providing continuous, upto-date information and access to software and databases. Softwares available at the centre enable sophisticated analysis, manipulation and visualization of biomolecular sequences and structures. Further, the centre also has Cambridge Structural Database (CSD), which contains more than 625,000 (up to November 2012) small molecule structures.
Educational activities and placement A total of 73 project assistants, 19 project trainees and 89 summer trainees have been trained during the last plan period (2007-2012). Most of them are now well placed in IT and Biotech companies and in reputed academic institutions in India as well as abroad. In addition, the centre offers three courses (Bioinformatics, Computational approaches to Drug Discovery and Chemoinformatics) to the Ph.D. students of the institute.
Collaborative works/initiatives The faculty members of the centre are actively engaged in several collaborative projects such as (a) Institute wide computational genomics project funded by DBT, (b) joint project using genetics aided systems biology for identifying interactions between genes involved in E.Coli protein biosynthesis funded by DBT, (c) participant in centre of excellence on molecular strains of mycobacteria funded by DBT and (d) participant in the Institute wide mathematical biology program funded by DST.
R & D activities in Bioinformatics The faculty members have published several papers (about 29 in the year 2012-2013) in the international journals of high impact factor. Further, they have provided consultancy, advice and training to the biotechnology institutions/ industries. In addition, the faculty members have guided several students from other colleges and universities. Another major outcome of the usage of the resources is the large number of databases and software tools that are made available through the worldwide-web. The tools and databases contain up-to-date information and they use the in-house archives, Protein Data Bank and Genome Database.
Proposed activities The faculty members plan to work on the following main thrust areas: systems biology, structural biology and bioinformatics, molecular design, molecular modelling, structural pharmacology and computational immunology and human resource development.
Contact details : Professor K. Sekar, Indian Institute of Science, Bangalore 560 012, India. (Phone: 080-22933059 and 080-22933060; E-mail:
[email protected]). Centres of Excellence (COEs)
7
XXIVnd All India BTISnet Coordinators’ Meeting
February 03-04, 2013
Jawaharlal Nehru University, New Delhi Coordinator: Prof Indira Ghosh Summary of the progress made by the centre from its inception: School of Computational and Integrative Sciences(SC&IS) presently consists of three centers, namely, Centre for Computational Biology and Bioinformatics (CCBB), High Performance Computing Center (HPCF) and Centre for Complex Systems Study. Our main objective is development of human resource through teaching and research in the frontier areas of Computational biology, Bioinformatics and Systems biology. At present our strength is ten faculty members in our school and 8 faculty positions are advertised for recruitment in 20122013. One G.N.Ramachandran Fellow and one technical person are assisting to keep the teaching and facilities working. Dr. Jean-Numa Gillet from Belgium was appointed as a visiting faculty at our school from May 2012 to July 2013. His research interest is Theoretical Biophysics and Molecular Dynamic Simulations. A novel characteristic of SC&IS is its emphasis on inter-disciplinary research like Computational Genomics, Development of Tools for Bioinformatics, Structure based Bioinformatics and in silico Drug Discovery, Chemoinformatics, Database Management, Microarray Analysis and Datamining, Systems biology and Evolutionary biology. I.
Major Research Projects :
Major research projects and field of research in CCBB presently, is focused towards the application of computational biology in infectious diseases like Mycobactera, Leishmani, Amoeba, Malaria, etc. and development of analytical tools to study biology. A.
Mycobacterium tuberculosis: (TB consortium project supported by DBT)
Genomic Comparison tools for Strain identification : Mycobacterium tuberculosis is a major cause of morbidity and mortality throughout the world. Genomic variations in this organism have been used to type pathogenic strains in a limited scale [Journal of Bacteriology (2002) 184(19):5479-90]. There is not yet any attempt to generate a comprehensive database of all the genomic variations of M. tuberculosis though some attempts have been made in this direction. For example, MTBreg (http://www.doe-mbi.ucla.edu/Services/MTBreg/) covers variations that are detected using spoligotyping) and MycoDB (http://xbase.bham.ac.uk/mycodb/about.pl) has some features that allows comparison between two genomes in a limited manner. A comprehensive database has been generated containing genomic difference of different strain and species of Mycobacteria belonging to M. tuberculosis complex. The variations have been identified using ABWGAT (http://ccbb.jnu.ac.in/tools.html), a comparative genomic tool developed in the project (see paper #5). B.
Metabolic pathway analysis for validating drug targets in M.Tb :
As metabolism is a fundamental determinant of physiology, metabolic model can predict the phenotypic changes. There is one type of model that has shown a surprising ability to simulate the growth of living cells — namely stoichiometric Flux balance models. Therefore, the important steps in developing and disseminating the metabolic model are (i) Physiological and Phenotypic characterization of the bacteria; (ii) genome annotations; (iii) metabolic reconstruction; (iv) Flux balance analysis. Use of Publicly accessible software tools has made it possible to identify and analyze the important metabolite with their relevant reactions & involved enzymes which could possibly are used as drug targets. Such applications have been conducted which resulted in identification of a set of proteins which are to be included as important drug targets. Last year M.Tech project entitled “Studying the role of selective gene set in Mycobacterium tuberculosis metabolic pathway using flux balance analysis” identified a set of genes for double knockout using new protocol of FBA . C.
Knowledge based compound design against M.Tb:
A novel method has been developed in-house to identify a set of chemical compounds with combinatorial motif by the study of known database, having minimum common bioactive substructure (MCBS). Application of data mining procedure to identify the ‘relaxed’ common pattern (pharmacophore) present in the diverse set of drug like/lead compounds is proposed. Use of graph theoretical approach to identify the Maximal Common Substructure (MCS) and Fuzzy logic techniques to identify the ‘relaxed’ chemical motifs so that broader pattern can be found is proposed.
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Development of integrated database of drug targets and antimalarial compounds of Plasmodium falciparum (http:/ /pfal.scisjnu.ernet.in).
This database contains most of the information about possible drug targets of malarial parasite. Information regarding structure of protein, their function, domain, sequences, expression stages etc is available in this database. Uniqueness of this database is the active information and homology modeled structures of malaria targets whose structures has not been solved by X-ray techniques.. It also contains detailed description of chemical compounds showing inhibitory assay against Plasmodium falciparum organism or their known drug targets. This project was supported by Ministry of Communication and Information Technology (MCIT). E.
Identification of new drug targets in Leishmenia
Leishmania major, a protozoan parasite, is the causative agent of cutaneous leishmaniasis. Due to the development of resistance against the currently available anti-leishmanial drugs, there is a growing need for specific inhibitors and novel drug targets. In this regards, aminoacyl tRNA synthetases, the linchpins of protein synthesis, have received recent attention among the kinetoplastid research community. This is the first comprehensive survey of the aminoacyl tRNA synthetases, their paralogs and other associated proteins from L. major. A total of 26 aminoacyl tRNA synthetases were identified using various computational and bioinformatics tools. Phylogenetic analysis and domain architectures of the L. major aminoacyl tRNA synthetases suggest a probable archeal/eukaryotic origin. Presence of additional domains or N- or C-terminal extensions in 11 aminoacyl tRNA synthetases from L .major suggests possibilities such as additional tRNA binding or oligomerization or editing activity. Four freestanding editing domains were identified in L. major. Domain assignment revealed a novel asparagine tRNA Synthetase paralog, asparagine synthetase A which has been so far reported from prokaryotes and archea.(see paper #19) F.
Computational study of Tumor Suppressor protein
Studying p53-MDM2 interactions and also exploring the possibility of identifying suitable drug targets to break this interaction. Well compiled drug databases and screening algorithms are used to select suitable targets and their energetic are also studied in depth. We are also interested in looking at p53-DNA interactions through response elements and we are making efforts to understand the role of p63 and p73 in p53 related pathway. G.
A neurocomputational approach to automaticity in motor skill learning
The first is in the area of multiple robot coalition formation, to find novel algorithms for multiple robot coordination/ cooperation. This is being done in collaboration with colleagues at Delhi University. The second is in the area of cognitive modeling for robotic applications. In collaboration with faculty from Vanderbilt University, a model had been developed for mimicking the automaticity that humans exhibit during learning. The groups at JNU pursuing models that better explain various phenomena associated with acquisition and extinction. II.
New Tools Development
A.
Computational study of replication origins:
DNA replication is a complex process and crucial for the life cycle of any organism. Protein-DNA interactions play a major role and understanding this complex process is a tremendous challenge to biologists and computational biologists. Modes of replication are not same in prokaryotes and in eukaryotes. We are making an effort to study the origin of replication sequences, its distribution, its prediction and functioning using computational approaches. A method to predict OriC sites in bacteria using a correlation measures and also explored its applicability to higher organisms has been published recently in Biosystems(see paper #17 ). B.
Information theoretic analysis:
For analysis purposes DNA is viewed as a long one dimensional symbolic sequences and the information embedded is important for understanding the biological functions. Information theoretic measures such as Shannon entropy, Renyi entropy and Tsallis entropy are increasingly used to identify variable segments in the DNA sequences. In addition, divergence measures are also applied to DNA for getting evolutionary insights. We employ these IT measures and other techniques to individual genes and genomes sequences as well as multiple aligned sequences to identify biologically interesting motifs ( see paper #18 ).
Centres of Excellence (COEs)
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Current Academic Activities (2012-2013). See Website for more details http://ccbb.jnu.ac.in
82 Post Graduate Diploma M.Phil (equivalent)in Bioinformatics during 2001-2006
During 2006-2012 Forty five M.Tech students passed.
Fourteen research fellows have been awarded PhD in Computational Biology & Bioinformatics.
Ten students have done their 6 month projects as long term trainees and five short term trainees including summer trainees at our school during 2012.
Training & Visitors: http://ccbb.jnu.ac.in/training.html Seven visitors had given lectures at our school during 2012. http://ccbb.jnu.ac.in/events.html Supported Fellows & Associates:
http://ccbb.jnu.ac.in/fellows_associates.html
Mr Surajit Mishra was supported to develop CTEP software in collaboration with DBT.
Mr Adarsh Tayal is working COE project as System Analyst
Dr V. Gowri as Research Associate 2011-2012
Kushal Shaw as GN Ramachandran Fellow 2012
Dr Rashi Gupta as Teaching Associate for course teaching (2012 Winter)
Dr V.K.Jayram for lectures in Machine Learning ( during Feb-March 2012)
BINC Examination : SC&IS, JNU successfully conducted BINC Exam 2011-2012 during February 26th and 27th 2012. Out of 800 appeared, 38 were awarded BINC fellowships and top ten students were given Cash awards of Rs 10000 each. Bioinformatics National certificate award ceremony was organized in May 2012. DBT secretary Prof M.K.Bhan attended as Chief Guest. BINC 2013 examination will be held from Feb 23th -24th 2013. Now expanded to nine centers namely, Jawaharlal Nehru University, New Delhi; Pune University, Pune; Anna University, Chennai; University of Kerla, Thiruvanthapuram; Calcutta University, Kolkata; Institute of Bioinformatics & Applied Biotechnology, Bangalore; University of Hyderabad, Hyderabad. North Eastern Hill University, Shillong and Assam Agricultural University, Gauhati BINC-2012 DBT was supported by ERNET connectivity as the major host of online system of registration and communication. In addition to that PfalDB, OpenTox and other online servers are hosted via ERNET connectivity.
Please visit : 1.
http://binc.scisjnu.ac.in
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http://pfal.scisjnu.ernet.in/Malaria/HomeinLink
3.
http://www.opentox.org/
Current Research Projects http://ccbb.jnu.ac.in/research.html
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1.
MCIT project on “Designing novel antimalarials using target based pharmacophore approach” Ministry of Information Technology, Govt of India, Aug 2009-2012 Extended upto May 2013. PI: Professor Indira Ghosh and Co-PI : N.Subba Rao.
2.
DST project on “Development and application of a Biased Monte Carlo simulation technique: Exploring and characterizing potential energy surfaces of large molecules”. 2010-2015.PI: Pradipta Bandhyopadhyay
3.
Bioinformatics National Certificate Exam 2011-2013 PI: Prof Indira Ghosh
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XXIVnd All India BTISnet Coordinators’ Meeting
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Projects in collaboration with academia 4.
DBT Project on “Establishment of National Database on Tuberculosis(TB) Phase II TB Consortium”: Prof. Alok Bhattacharya and Prof Indira Ghosh 2011-2013
5.
DBT project on “Computational Core for Plant Metabolomics” Prof Indira Ghosh with IIIT, Hyderabad, 20112015
6.
DBT Builder Project, Coordinator: Prof R.Bhat, SBT, JNU (SLS, SCMM and SBT and SCIS faculty of JNU) 20122017
Conference and workshop organized during 2012 http://ccbb.jnu.ac.in/events.html 1.
Biomolecules in Motion: Theory and Simulations January 4-6 2013, 16 speakers and Participants:55
2.
One Day Meeting of Synthetic Biology, December 21st 2012 : participated by DBT and NIH representative along with 8 speakers and 25 participants.
3.
Latest Advances in computational Drug Discovery 29th October 2012 Participants:35
4.
National Conference-cum-workshop on “Search for Antimalarials: Mechanism based Approach” 27-29th April 2012. 20 speakers & Participants: 40
4.
Annual Open Day on 21st January 2012
Publications 2012 (20 +2)
http://ccbb.jnu.ac.in/publications.html
1.
Kamaldeep Gill, Abhay K. Singh, Vaishali Kapoor, Lokesh Nigam, Rahul Kumar, Prasida Holla, Satya N. Das, Savita Yadav, Naidu Subbarao, Bidhu Kalyan Mohanti, Sharmistha Dey, Development of peptide inhibitor as a therapeutic agent against head and neck squamous cell carcinoma (HNSCC) targeting p38á MAP kinase, Accepted for Publication in Biochimica et Biophysica Acta(2012)
2.
Ashish Gupta, Lovekesh Vig and David C. Noelle «A Cognitive Model for Automaticity in Motor Skill Learning», Journal of Robotic and Intelligent Systems, 2012 (In Press)
3.
Shikha Pal, Madhur Mishra, D. Raja Sudhakar, Mohammed Haris Siddiqui, In silico designing of a potent analogue against HIV-1 Nef protein and protease by predicting its interaction network with host cell proteins, Journal of Pharmacy and Bioallied Sciences January-March 2013 Vol 5 Issue 1
4.
Singh P and Sengupta S, Phylogenetic analysis and comparative genomics of purine riboswitch distribution in prokaryotes.Evol Bioinform Online. 2012;8:589-609. doi: 10.4137/EBO.S10048. Epub 2012 Nov 6.
5.
Sarbashis Das, Priyanka Duggal, Rahul Roy, Vithal P. Myneedu, Digamber Behera, Hanumanthappa K. Prasad & Alok Bhattacharya Identification of Hot and Cold spots in genome of Mycobacterium tuberculosis using Shewhart Control Charts Nature Scientific Reports - http://dx.doi.org/10.1038/srep00297
6.
Chung-Chau Hon, Christian Weber. Odile Sismeiro, Caroline Proux, Mikael Koutero, Marc Deloger, Sarbais Das, Mridula Agrahari, Marie-Agnes Dillies, Bernd Jagla,Jean-Yves-Coppee, Alok Bhattacharya and Nancy Guillen Quantification of stochastic noise of splicing and polyadenylation in Entamoeba histolytic, Nucleic Acid Research (2012) 1-17, doi: 10.1093/nar/gks1271
7.
Jonathan P. Furado, Anuja P Rahalkar, Sudhanshu Shankar, Pradipa Bandhyopadhyay and Sridhar R Godre, Facilitating minima search for large water clusters at MP2 level via Molecular tailoring, J.Phy.Chem. Letters(2012)
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Biswaranjan Meher, Mattaparthi Venkata Satish Kumar, Smriti Sharma and Pradipta Bandhyopadhyay, Conformational Dynamics of HIV-1 protease: a comparative dynamic simulation study with multiple amber force fields, Journal of Bioinformatics and computational biology(2012)
9.
Sudhanshu Shankar and Pradipta Bandhyopadhyay Determination of low energy structures of a small RNA hairpin using Monte Carlo based techniques, J.Biosciences 37(3) 533-538
Centres of Excellence (COEs)
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Uddipan Sarma, Archana Sareen, Moitrayee Maiti, Vanita Kamat, Raki Sudan, Sushmita Pahari,Neetu Srivastava, Somenath Roy, Sitabhra Sinha, Indira Ghosh, Ajit G. Chande, Robin Mukhopadhyaya, Bhaskar Saha, “Modeling and Experimental Analyses Reveals Signaling Plasticity in a Bi-Modular Assembly of CD40 Receptor Activated Kinases” PLoS ONE (2012),7: July 2012 e39898 doi:10.1371/journal.pone.0039898
11.
Uddipan Sarma & Indira Ghosh, “Oscillations in MAPK cascade triggered by two distinct designs of coupled positive and negative feedback loops” BMC Research Notes. (2012) 5:287 DOI:10.1186/1756-0500-5-2872012.
12.
Uddipan Sarma & Indira Ghosh , “Different designs of kinase-phosphatase interactions and phosphatase sequestration shapes the robustness and signal flow in the MAPK cascade” BMC Systems Biology. (2012 ) 6:82 DOI:10.1186/1752-0509-6-82.
13.
Rithvik Vinekar, Chandra Verma, Indira Ghosh , “Functional relevance of dynamic properties of dimeric NADPdependent isocitrate dehydrogenases” BMC Bioinformatics (2012) Volume 13 Supplement 17, S 2.
14.
Mobashar Hussain Urf Turabe Fazil, Sunil Kumar, Naidu Subba Rao , Chandrabose Selvaraj, Sanjeev Kumar Singh, Haushila Prasad Pandey & Durg Vijai Singh, “Comparative structural analysis of two proteins belonging to quorum sensing system in Vibrio cholerae , Journal of Biomolecular Structure and Dynamics”, DOI:10.1080/ 07391102.2012.687523
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Smriti Sharma and Pradipta Bandyopadhyay, Investigation of the acylation mechanism of class C beta-lactamase: pKa calculation, molecular dynamics simulation and quantum mechanical calculation, Journal of molecular modeling(2012), v18, 481-492
16.
Rupesh Kumar, Amitabha Bose, Birendra Nath Mallick A Mathematical Model towards Understanding the Mechanism of Neuronal Regulation of Wake-NREMS-REMS States, PLOSOne(2012), 7(8), : e42059. doi:10.1371/ journal.pone.0042059
17.
Kushal Shah and A. Krishnamachari. “Nucleotide correlation based measure for identifying origin of replication in genomic sequences”, BioSystems vol. 107 (1), 52-55,2012
18.
Kushal Shah and A. Krishnamachari. “On the origin of three base periodicity in genomes”, BioSystems, vol.103(3) 142-144,2012.
19.
Rentala Madhubala, V S Gowri, Indira Ghosh, Amit Sharma. “Unusual domain architecture of aminoacyl tRNA synthetases and their paralogs from Leishmania major” in BMC Genomics ( 2013).
20.
Jean-Numa Gillet and Indira Ghosh. “Concepts on the protein folding problem” in Journal of Biomolecular Structure and Dynamics, in press (2013).
Book Chapters: Kushwaha Hemant Ritturaj and Ghosh Indira, “Bioinformatics Approach for Finding Target Protein in Infectious Disease” In Bioinformatics of Human Proteomics,Translational Bioinformatics, DOI 10.1007/978-94-007-5811-7_10, X. Wang (ed.), © Springer Science+Business Media Dordrecht 2013. Kushwaha Hemant Ritturaj and Ghosh Indira. ”Target Identification using Systems Approach in Infectious Diseases” . In TRANSLATIONAL RESEARCH IN NEW DRUG DEVELOPMENT. Ed. Ray Arunabha & Gulati Kavita ( V.P, India ), 2012.
Future Plans
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Relocation of School of Computational and Integrative Science to New Building by end of 2013
One Professors, five Associate Professors and two Assistant Professors are to be recruited under UGC IX Plan during 2013. Two GN Ramachandran fellowships funded by COE will be appointed very soon
Building up of the research activities in the Center for Complex Systems Studies (CCSS).
Proposal for Two year M.Sc course(computational and Integrative sciences)
Research focus on Infectious Diseases and understanding of large systems in biology.
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Contact detaills Prof Indira Ghosh Coorindator, Centre of Excellence in Bioinformatics Centre for Computational Biology and Bioinformatics School of Computational and Integrative Sciences Jawaharlal Nehru University, New Delhi-110067 E-mail:
[email protected] /
[email protected] Ph: 011-26738707
Appendix List of students who have completed their M.Tech and Ph.D successfully & Degree submitted/awarded during 2012 (M.Tech and Ph.D. Thesis Titles) Ph.D. Students http://ccbb.jnu.ac.in/thesis-p-2011-2012.html M.Tech. Thesis Titles (2010-2012) Sr. No. 1
Name of the Students Sanjeev Kumar
2
Sahil Moza
3
Tanmaya Meher
4
Neha Aggarwal
5
Sonia Verma
6
Gulrez Chahal
7
Riti Roy
8
Ashish Kumar Singh
9
Md. Sultan Alam
10
Navneet Chandra Verma
11.
Sarbashis Das
12.
Md. Rehan
Thesis Title Computational Study of Origin of Replication and ARS Sequences in Few Genomes. Stochastic Modeling of Calcium Initiated Phagocytosis in Entamoeba Histolytica. Data generation and Data analysis of virtual high throughput screening (vHTS) in Plasmodium falciparum proteins Early (Pre-Luca) Evolution of Genetic Code: A finite Population Study Analysis of Nucleotide Binding Domain Structure and Phylogeny of Fungal Tranaporters. Structural Identification & comparison of Protein Binding sides using graph Theoretical Methods. (Clique Detection) Analysis of transcriptome and retrotransposable elements LINEx/SINEx of Entamoeba histolytica Studying the role of selective gene set in Mycobacterium Tubercuiosis metabolic pathway using flux balance analysis. Analysis of sequence polymorphism of LINEs and SINEx in Entamoeba Histolytica Density of states simulations for protein system study of ww-domain. Ph.D – Submitted/awarded during 2012 Compatative Analysis and Study of Mutations in Bacterial Genomes. Information Theoretic Methods for Identification of Functional Residues in Proteins.
Centres of Excellence (COEs)
Supervisor Dr. A Krishnamachari Prof. Ram Ramaswamy and Prof. Alok Bhattacharya Prof. Indira Ghosh
Dr. Supratim Sengupta Dr. Andrew M. Lynn Naidu Subbarao
Prof. Alok Bhattacharya Prof. Indira Ghosh
Prof. Alok Bhattacharya & Prof. Ram Ramaswamy Dr. Pradipta Bandyopadhyay
Prof. Alok Bhattacharya Dr. Andrew M.Lynn
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Madurai Kamaraj University, Madurai Coordinator: Prof. S. Krishnaswamy Progress made by the centre from its inception The Distributed Information Centre (DIC) at Madurai Kamaraj University (MKU) was started in 1986. To promote human resource development activity, an Advance Diploma one year course in Bioinformatics was started in 1996 to cater to the need of trained man power in Bioinformatics. Students from varied backgrounds like Physics, Chemistry, Computer Science and Life Sciences had enrolled in the course and gained basic and advance knowledge in Bioinformatics. Meanwhile, the centre was upgraded to a Centre of Excellence in Bioinformatics in 2003. Recently, in 2010, with the support from DBT, the advance diploma course was upgraded to a post graduate course in M.Sc. Computational Biology. This course is a network teaching programme involving MKU (State University), Anna University (Technical University) and Pondicherry University (Central University). Three new faculties have also been recruited in MKU in 2010 for this teaching program. Apart from imparting higher education in the realm of Bioinformatics, other main activity of the centre focuses on research and providing services in the major thrust areas such as structural bioinformatics, proteomics, creation of bioinformatics databases, data mining, molecular modelling, molecular dynamics simulations and computer aided drug design. Also, the resources at the centre are efficiently utilized by the teachers and researchers in this region. The faculty at the centre together with the faculty of School of Biotechnology, MKU performs collaborative research work and teaching. The centre has played an important role in the growth of Bioinformatics in this region and has made a significant contribution to the manpower development.
Major Research Activities There have been many ongoing research programmes at MKU. The major areas of research at the Bioinformatics centre at MKU includes, proteomics of infectious diseases, structural bioinformatics of membrane proteins, structural genomics of prophage proteins, structural genomics of Mycobacterium tuberculosis, structural biology of macromolecules in microbial stress response pathways, computational analysis of protein-protein interaction in chemokines and its receptors, largescale sequence analysis, molecular modelling, molecular docking, molecular dynamics simulations, data mining and text mining, systems biology of two component systems. Area of Specialization: Structural Bioinformatics and Genetic Engineering.
Major activities (2012-13) Manpower development
On going MSc Computational Biology program.
Six PhD students have completed and 10 PhD students have registered.
Project trainees, MSc and MPhil project guidance
Participation in local workshops and academic staff training.
In house seminars and workshops related to Bioinformatics.
Elective courses as part of CBCS on Programming for Computational Biology: Centre offers elective courses like Structural Biology, Sequence analysis, Systems biology etc., to post graduate courses and Structural genomics, proteomics, Biophysics and Bioinformatics for M.Phil courses in the University.
Infrastructure facilities
Computers and Communication Facility Systems Centre has a wealth of high performance computation (HPC) and high end interactive graphics facilities. The HPC includes a HCL 4-node 32 Processor cluster, SGI ALTIX 350 with 6 INTEL Itanium Processors and a DELL T3500 series workstation. The T3500 workstation is loaded with a Quad-Core Intel Xeon processor, 4GB RAM, 2TB hard disk and NVIDIA Quadro 4000 graphics card with integrated NVIDIA 3D stereovision. Also, one of the
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XXIVnd All India BTISnet Coordinators’ Meeting
quad core machines has a similar NVIDIA Quadro 4000 graphics card. It is to be noted that NVIDIA Quadro4000 graphics cards can render ultra high resolution (2560 x 1600 pixels which is highly efficient than HD graphics pixels) and 3D. These graphics card also have 256 CUDA cores capable of doing further high performance computing. In addition to the above, the centre also has Desktop-PCs, SGI workstations, Sun workstation, Linux workstations, database servers, Web-servers, Mail-server, Network-server, file-server and file-backup server. The centre has high speed internet connectivity from BSNL. It also has a structured intranet network connecting systems that connect entire School of Biotechnology with Computers, Printers and UPS facilities through LAN and Wi-Fi.
Scientific Software Packages The centre is equipped with software packages for performing various computational and analyses tools, viz., sequence analysis, structure analysis, phylogenetic analysis, molecular modelling, docking and molecular dynamics simulations of macromolecules. Commercial:, Biosym, GCG Accelrys Discovery Studio, Clementine-10.0, MATLAB, CCDC and GOLD, Licensed version of AMBER11. Non-Commercial: BioUbuntu, BioPERL, ClustalW, Phylip, Tree-Puzzle, Treeview, Dendrogram, RasMol, VMD, PyMOL-0.9v, Chimera, Modeller, Autodock, Gramm, Latest version of GROMACS (v4.5.4), CCP4(v6.1.13), Phenix (v1.7.2-869) and many more bioinformatics and crystallographic softwares.
Servers Databases, Software tools and other information resources Servers: PRNDS, Aggregation Propensity Calculator, Prophage detection Databases: Prophage-db, sRNAbase, Glaucoma-db, HNH-db, aggregation database Software tools: sRNAscanner, PsRNA, Intergenics, PCR primer design for whole genome, Structure analysis of Porins, Consensus based validation of porins and a tool to detect Non-coding RNAs, DRAD for prophage detection. Information Resources: Information calculation for genomes, HNH domain sub classification.
Teaching Staff Name Dr. K. Dharmalingam Dr. S. Krishnaswamy Dr. R. Sankaranarayanan Dr. S. Thiyagarajan Dr. K. Kanagarajadurai
Designation DBT Distinguished National Professor Sr. Professor and Coordinator Reader Assistant Professor Assistant Professor
E-mail Id
[email protected] [email protected] [email protected] [email protected] [email protected]
Services provided Service Centre provides easy accessibility to existing databases, servers, information resources and tools to retrieve the data. It is also providing guidance for utilizing the software tools, such as sequence and structure analyses software packages for molecular modelling, docking and molecular dynamics simulations. The faculty at the centre provides assistance on designing the research projects giving a Bioinformatics plug-in to the potential Biotechnology projects.
Manpower Development The centre has on going MSc Computational Biology program and 3rd batch of students have enrolled. Our centre is offering elective and core courses under Choice Based Credit System (CBCS) to MSc and MPhil biotechnolgy students of School of Biotechnology. Moreover, in-house workshops/seminars are being organized frequently. We recruit 2 project trainees and 2 student trainees every year
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Online Bioinformatics resources The existing databases, servers and other Bioinformatics resources available at the centre could be accessible at http:// bicmku.in:8081.
Research In addition to the ongoing research program, the centre also provides research exposure to college teachers and students of other Universities and Industries.
Educational activities & placements A total of 15 students (both 1st and 2nd Year together) enrolled in MSc computational Biology networking program. Among five students in the first batch who have successfully completed MSc computational Biology, three of them went for higher studies. The faculty in our centre provides guidance to students of various colleges and Universities for their final semester projects. As a part of the exchange program, MSc computational biology students from Anna University and Pondicherry University are given opportunity to do summer projects in our centre and vice versa.
Initiative to validate the outcome of Bioinformatics resources The industries and other academic institutions utilize the bioinformatics services provided by the centre. The industrial consultancy is done through the University. The research findings are published in peer reviewed national and international journals.
Collaborative work / initiatives Centre has both International & National collaboration in the field of bioinformatics with Weizmann Institute, Israel; University of Utah, USA; University of Aarhus, Denmark; Aravind Eye Hosptial - Medical Research Foundation, Madurai; NCBS, Bangalore; IISc, Bangalore; AIIMS, New Delhi; Genotypic Technologies, Bangalore.
Initiation of R & D activities in Bioinformatics
Comparison of proteome profile with transcriptome profile in E. coli growing under oxygen stress (K. Dharmalingam)
Infection proteomics of fungal keratitis (K.Dharmalingam)
Structural genomics of prophage proteins (S. Krishnaswamy)
Sub classification of HNH domain proteins (S. Krishnaswamy)
Structural Bioinformatics of membrane proteins and complexes (S. Krishnaswamy)
Structural genomics of M. tuberculosis (R. Sankaranarayanan)
Structure based in silico drug designing (R. Sankaranarayanan)
Structural and computational studies on DNA binding repressors involved in microbial stress response (S. Thiyagarajan)
Functional annotation of structures of unknown proteins from V. cholerae (S. Thiyagarajan)
Functional prediction of chemokines and its receptor sequences (K. Kanagarajadurai)
Computational analysis of Protein-protein interaction study in chemokines (K. Kanagarajadurai)
Training / Workshop
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Dr. K. Kanagarajadurai organized a hands on training cum workshop on “Structural Bioinformatics applications in Drug Discovery” for two days (September 17th & 18th, 2012). More than 40 undergraduate students, post graduate students and research scholars participated in the seminar.
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Papers presented and publications 1.
D. Balasubramaniam, Arulandu Arockiasamy, P.D. Kumar, Amit Sharma, S. Krishnaswamy (2012), Asymmetric pore occupancy in crystal structure of OmpF porin from Salmonella typhi. Journal of Structural Biology, 178: 233244.
2.
K.V. Srividhya, S. Krishnaswamy (2012) Characterization of DLP12 Prophage Membrane Associated Protein: HolinGFP. Indian J. Microbiology DOI 10.1007/s12088-012-0278-7
3.
Santha, S., Pandaranayaka, E.P.J., Rosen, B.P. & Thiyagarajan, S. (2011) Purification, crystallization and preliminary X-ray diffraction studies of an arsenic repressor ArsR from Corynebacterium glutamicum, Acta Crystallogr. F67, pp 1616-1618.
4.
Ananthi S, Santhosh RS, Valarnila M, Prajna NV, Lalitha P, Dharmalingam, K. (2011) Comparative proteomics of human male and female tears by Two-dimensional electrophoresis. Exp Eye Res. 92; 454-463.
5.
Paul Pown Raj. I, Krishnadas. SR, Sundaresan P, Dharmalingam, K (2011) Understanding Primary Open Angle Glaucoma using aqueous humor: a proteomics approach, at The Indian Proteomics Conference, IPCON 2011, New Delhi, India Poster.
6.
Varun Bhaskar, Manoj Kumar, Sankar Manica, Sunil Tripathi, Aparna Venkatraman and Krishnaswamy, S. (2011): Identification of Biochemical and Putative Biological Role of a Xenolog from Escherichia coli using structural analysis Proteins Str Function Bioinformatics 79: 1132-1142.
7.
Rangachari K, Dhivya M, Eswari Pandaranayaka PJ., Prashanthi N, Sundaresan P, Krishnadas SR, Krishnaswamy, S. (2011) Glaucoma Database. Bioinformation 5(9):398-399
8.
Shafreen B, Eswari Pandaranayaka, Krishnaswamy, S. Shakila HS (2011) Homology modeling of cobra C3 and comparative analysis with human bovine serum proteins. J. Biotechnology and Bioinformatics, 2: 100-109.
9.
Anne-Laure Todeschini, Aurelie Dipietromaria, David L’Hote, Fatima Zohr Boucham, Adrien B. Georges, P.J. Eswari Pandaranayaka, S. Krishnaswamy, Isabelle Rivals, Claude Bazin, Reiner A. Veitia (2011) Mutational probing of the forkhead domain of the transcription factor FOXL2 provides insights into the pathogenicity of naturally occurring mutations. Human Molecular Genetics 20: 1-10.
10.
Srividhya K.V, Krishnaswamy, S. (2011) Detection and classification of two component regulatory systems. Online J of Bioinformatics 12:167-174.
11.
T. Madhuranayaki, Krishnaswamy, S. (2011) Protein Engineering of Yellow Fluorescent Protein Insertion in Outer Membrane Protein OmpF from Salmonella typhi. ISABB Journal of Biotechnology and Bioinformatics 1: 10-14.
12.
Packialakshmi, R.M. & Usha, R. (2011). A simple and efficient method for agroinfection of Vernonia cinerea with infectious clones of Vernonia yellow vein virus. Virus Genes 43, 465-470.
13.
Jebasingh, T., Jose, M., Yadunandam, A.K., Backiyarani, S., Srividhya, K.V., Krishnaswamy, S. & Usha, R. (2011). Molecular modeling and conformational analysis of native and refolded viral genome-linked protein of Cardamom mosaic virus Indian Journal of Biochemistry & Biophysics 48, 336-340.
14.
Jebasingh, T., Backiyarani, S., Manohari, C. & Usha, R. (2011). Detection of cardamom mosaic virus- related sequences in plant genomes. Indian Journal of Biotechnology 10, 369-371.
Impact shown The servers and databases present in our centre are being utilized by faculty and students of MKU and students of other universities and colleges which are acknowledged in their publications and presentations. Our outcome is the papers published in the peer-reviewed journals, PhD students and project dissertations along with the training given to students.
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Future activities (2013-2014)
Systems modelling
Large scale sequence and structure analysis centre
Development of annotation tools
E-learning tools, courses
Contact details: Name of the Coordinator: Prof. S. Krishnaswamy Postal Address: School of Biotechnology, Madurai Kamaraj University, Madurai-625021 Phone Number: 0452 2459141, Fax No.:0452 2459105 Email:
[email protected] Website: www.biotechmku.org , http://bicmku.in:8081 Name of Contact Person(s): Prof. S. Krishnaswamy,
[email protected] Dr. R. Sankaranarayanan,
[email protected]
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Supercomputing Facility for Bioinformatics & Computational Biology (SCFBio), IIT Delhi, New Delhi Coordinator: Prof. B. Jayaram A Few Scientific Accomplishments of SCFBio during 2012-2013
Chemegenome in Chemical & Engineering News: “DNA-water interactions distinguish messenger RNA genes from transfer RNA genes (J. Am. Chem. Soc., 2012, 134 (21), pp 8814–8816; DOI: 10.1021/ja3020956)” is featured in C&EN (May, 2012) as DNA’s destiny lies in its solvation.
Bhageerath in CASP 10: In the just completed protein structure prediction Olympics CASP 10 held from 1st May to July 17th 2012, the Bhageerath-H software-the only participant from India-is seen to be among the best servers in the world.
Sanjeevini for Anticancer and Antimalarial Molecules: The drug design (Sanjeevini) methodologies have led to a new molecule for breast cancer which is being processed for patenting. Work is in progress on synthesis and testing of a few antimalarial molecules designed.
BAITOC (Bioactivity information to organic chemist) an application developed by SCFBio enfielded in Code for Science India competition (2012) organized by Elsevier in collaboration with Institute of Bioinformatics, Bangalore, has been declared as one of the winners in both concept formulation and application development rounds.
Over 16 publications in refereed national/international journals have been published from SCFBio (http:// www.scfbioiitd.res.in/publication/publication.htm) during the year 2012.
Other Accomplishments/Activities
10 day long short-term training programmes in Bioinformatics were conducted for a total 125 students spreads over a period of one and a half month during August-October 2012.
Strengthened the services component by providing 24x7 free access to a tera scale computational facility on a consistent basis for Bioinformaticians.
The accessibility and world-wide usage of the in house developed softwares and other services facilitated by SCFBio have gone higher and reached a significant number of 16000 hits per day (on an average) through the facility’s website.(www.scfbio-iitd.res.in/usage)
Conference organized by SCFBio in 2012 On the occasion of 10th Anniversary of the facility, SCFBio organized a two day National Conference (July 30th & 31st, 2012) on “New Trends in Bioinformatics” sponsored by Department of Biotechnology. The conference brought together several leading experts from the country in Bioinformatics to address what has been solved and what remains to be conquered in some key areas on the pathway from Genome to developing in silico suggestions of personalized medicine. The conference featured, 25 leading scientists from the country sharing the latest from their Laboratories, and around 150 students participating/presenting posters on their discoveries. During the conference an indigenous software suite “Dhanvantari” developed by SCFBio team which integrates the latest versions of Chemgenome, Bhageerath & Sanjeevini for genome annotation, protein tertiary structure prediction and target directed lead molecule design respectively, into a pipeline in a high performance computing environment was inaugurated by Dr. T. Ramasami (secretary, DST), in the presence of Dr. Manju Sharma (Former Secretary, DBT), Dr. T. Madhan Mohan(Adviser, DBT), & Prof. R. K. Shevgaonkar (Director, IIT Delhi) .
Proposed Activities in the year 2013-2014
It is proposed to collaborate with synthetic chemistry and biology partners/laboratories in order to give the computational techniques much required impetus by creating new molecules in the physical form using the Gene2Drug (Dhanvantari) methodology.
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It is proposed to upgrade the Computational facilities to a higher level (at least 50 Tera Flops (compute) and 500 Tera Bytes (storage)) in order to serve the scientific community more effectively by providing uninterrupted compute time on its Supercomputers.
It is proposed to give more emphasis on the short term training programmes in Bioinformatics and also to launch a certificate course (6 months long) in order to delve more expertise to the students interested and passionate in the area of Bioinformatics.
It is proposed to extend the research work carried out in the facility in all the three major areas of Bioinformatics viz; Genomics, Proteomics and Drug Design at the cutting edge and to provide top class services.
Contact details: Professor B. Jayaram Coordinator, School of Biological Sciences & Coordinator, Supercomputing Facility for Bioinformatics & Computational Biology Indian Institute of Technology, Hauz Khas, New Delhi - 110016, India. Phone : +91-11-26591505, Fax : +91-11-26582037 Email:
[email protected]
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University of Pune, Pune Coordinator : Prof. Deepti Deobagkar Summary of the progress made by the centre from its inception The Bioinformatics Centre at University of Pune is one of the few DICs that were initiated in 1987. The mandate of the Centre includes:
To develop state of the art infrastructure and expertise for data warehousing and data mining
To develop derived databases and algorithms for knowledge discovery in the areas of Life Sciences
To carry out R&D activities with special emphasis on virology, infectious & parasitic diseases, metabolic pathway engineering, drug development, chemoinformatics & immunoinformatics
To provide short-term & long-term training in the area of Bioinformatics
Center of Excellence in bioinformatics Bioinformatics center has been recognized as Center of Excellence (CoE) by two national funding agencies, viz., Department of Biotechnology (DBT), Govt. of India (2002 onwards) and Ministry of Communications and Information Technology (MCIT), Govt. of India (2007 onwards).
Human Resource Development
More than 46 short-term training programs (workshops) have been organized by the Bioinfromatics Centre since 1987 till date in which 696 scientists, teachers, research students and industry professionals have participated. The centre has conducted in house and on site training programmes in Bioinformatics for industry professionals.
The Centre was a pioneer in launching one of the first formal training programmes in Bioinformatics in 1997, viz. Advanced Diploma in Bioinformatics (ADB). It was a one-year post-graduate diploma that was funded by DBT, Govt. of India. Subsequently, M. Sc. programme in Bioinformatics was launched in the year 2002 and has been running successfully till date. This programme is also funded by DBT, Govt of India. The M. Sc. and ADB courses were being run simultaneously during the years 2002-2006. The ADB programme has been kept on hold since academic year 2006-2007. Detailed information about the Bioinformatics training activities is available on the web-site of the Centre (http://115.111.37.201/courses/IndexMSC.html).
The Centre also offers Ph.D. degree in Bioinformatics. A total of five Ph. D. degrees in Bioinformatics have been awarded so far.
The Centre hosted a six months Certificate course in Clinical Research and Clinical Data Management (CRCDM) during 2005-2010 implemented through an industry-academia partnership model.
Initiation of R&D activities in bioinformatics
Identification and Characterization of Phenobarbitone Induced Yeast Mitochondrial Proteins, a Computational Approach: To analyze the MS- data of phenobarbitone induced yeast mitochondrial proteins to identify and characterize them and to understand the role played by over-expressed proteins/ enzymes/ peptides in their respective cellular pathway using computaional approaches.
Identifying novel human DNA Methyl Transferase 1 inhibitors by incorporating receptor flexibility in small molecule database searches.
Identifying specific inhibitors of eIF2-alpha kinases using computational approaches.
Symmetric and non-symmetric amino acid substitution matrices were re-compiled for E. histolytica, which possesses a compositionally biased genome. This study would be continued to annotate hypothetical proteins of E. histolytica.
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With the objective of providing comprehensive information on the parasite genome and proteome resources as well as the analytical tools for the parasite research community, the parasite genome and proteome resources as well as the analytical tools were reviewed and the process is being continued now.
Absence of a suitable drug for treatment of hepatitis E necessitates design and development of a new drug. Helicases are known to be important antiviral drug targets. A study to design suitable drug molecule/s targeted against helicases using structure-based drug design approach was initiated and is being continued.
Prediction of 3-D structures of viral proteins for which no experimental structure available in PDB using homology-modeling approach.
Extending the applications of return time distribution based method for the genotyping and molecular phylogeny.
Functional metagenomics, Epigenetics and regulatory networks in connection with miRNA and DNA methylation. Structure function relationship in Plasmodium DBL alpha domain molecule with receptors and Targets.
Area of specialization Bioinformatics, Computaitonal Biology, Genomics, Epigenomics and Mi RNA, Phyloinformatics, Comparative Genomics, Molecular modeling and simulations, Chemoinformatics, Structural Bioinformatics, Metabolic pathway engineering, Immunoinformatics etc.
Major achievements made during 2012
Prof. Deobagkar has been appointed as a Chairman, Board of Studies and in RR committee, in Bioinformatics, University of Pune, Pune for next two years, Advisory Committee of KEMHRC Research center. MOES, GOI PAMBC, IBSC, Serum Institute of India, etc
Prof. Deepti Deobagkar’s talk on ‘Stem Cells’ broadcasted by All India Radio on 25th July at 8.15 p.m. She delivered V G Bhidey and Diwan Memmorial lectures. She delivered talks in MRDG IISc, Center for Human Genetics, etc.
Prof. Deobagkar was invited to write one marathi article ‘Jaiva Tantrache Samarthya – (meaning -Power of Biotechnology) published in marathi monthly magazine ‘Lokrajya’ October-2012 issue, Page No. 19-26.
Mr. Pandurang Kolekar(PhD student) was awarded as the ‘Young Researcher’ (FIRST prize) in the National Symposium “Accelerating Biology” organized by CDAC during Feb 15-17, 2012. oral presentation on “Return time distribution based alignment-free novel algorithm for multi-locus sequence typing: case study of ‘Typhimurium’ complex of Salmonella strains” during the symposium.
Dr. Sangeeta Sawant, Dr. Urmila Kulkarni- Kale and Dr. Deepti Deobagkar invited to Oslo and Telemark in Norway to conduct Bioinformatics workshop, deliver lectures and attended International Conference on Personalised Cancer Care in Oslo.
Infrastructure facilities in the Bioinformatics Centre: The centre is equipped with state-of-art facilitates in terms of hardware, software, and internet connectivity. Infrastructure and the expertise available at this centre facilitate the users from academia and industry in every possible way.
Hardware facility
4 Server HP Pro Liant DL 580 G5 (16 processors), HP ML 57084 (16 processors), Altix 350 (12 processors), Wipro Net server (8 processors), IBM 236 Server (2 processors), 2 SGI Fuel Workstations, IBM E Server X series, IBMx3500M2 tower server, 100 Branded PC/Desktop (some of them Core 2 duo).
Communication Network facility
The centre has 25 Mbps(1:1) (DBT paid) Internet connectivity through Tata Communications, Pune.
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Software facility(other than public domain softwares)
MOE, DS-toolkit (modeling + SBD +Gene), InsightII, AMBER, MDL® ISIS/Base, WHAT IF, The Cambridge Structural Database (CSD), SLIM 21LX
New Softwares purchased:
Accelrys: Upgradation of Discovery Studio from version 2.5 to version 3.5 and purchase of the fourth bundle for Cheminformatics (perpetual licenses)
Schrodinger products: Glide and Prime, 30 tokens for 3 years
Matlab: 15 licenses of matlab base and simbiology (perpetual licenses)
GRID software (Linux version) from Moleular Discovery Ltd. for 3 years
New Databases/server development
MuV genotyping server
Dengue subtyper
HRV Typer
West Nile virus genotyping server
Protfract: Fractal properties of proteins
Aeromonas MLSTyper server
BioDB Extractor
The web-servers and online databases are available at : http://bioinfo.net.in
Details about Staff members working in the centre: S.No.
Name
Designation
Working Since
1.
Prof. Deepti Deobagkar
Director & Prof. of Zoology
8.11.2010 (as Director)
2.
Dr. Sangeeta Sawant
Assistant Professor (Reader)
20.12.2010
3.
Dr. V. B. Baladhye
Assistant Professor
24.12.2010
4.
Dr. Manali Joshi
Assistant Professor
01.01.2011
5.
Dr. Abhijeet Kulkarni
Assistant Professor
17.01.2011
6.
Mrs. Smita Saxena
Assistant Professor
01.03.2012
7.
Dr. Urmila Kulkarni-Kale
Sr. Information Scientist
26.11.1993
8.
Mr. Sanjay Londhe
Information Scientist, Gr. I
20.04.1994
9.
Mr. Dattatraya Desai
Information Scientist, Gr. II
25.07.2008
10.
Mr. Rahul Khandare
Sr. Technical Assistant
15.02.1999
11.
Ms. Sunita Jagtap
Jr. Technical Assistant
21.10.1993
12.
Mrs. Vijaya B. Dahiphale
Data Ent. Operator Gr. I
31.01.1989
13.
Mr. Raghavandra K. Wade
Data Ent. Operator Gr. I
31.01.1989
14.
Mr. Vishwanath R. Limbkar
Data Ent. Operator Gr. II
01.09.1989
15.
Ms. Pranali Khoje
Accounts Assistant
08.09.2003
16.
Ms. Surekha Ingwale
Library Assistant
13.08.2012
17.
Mr. Vijaya More
Peon
02.06.2007
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Educational activities (Jan 2011-Dec 2012)
No of registered students: M.Sc. I - 29, M.Sc. II - 28; Total 57
No of registered research students: JRFs: 3, SRFs: 3, RA: 4, TA: 1; Total 4
No of students qualifying examinations: BINC: 8; CSIR JRF/lectureship:1 & GATE: 4.
Bioinformatics courses conducted for M Sc Zoology and M Sc Bioinformatics.
Number of faculty members and research students participated / presented oral & poster presentations in 20 international / National conferences / symposia / workshops.
Students’ achievements
Three students of M.Sc. Bioinformatics(2010-12 batch) have been selected for Ph.D.at IIT – Mumbai, NCBS – Bangalore and University of Iowa, USA.
14 students successfully cleared the BINC 2012 examination. 2 students got the I and II rank.
Mr. Anirban Banerji (guide- Dr. India Ghosh, JNU, Delhi) successfully defended his PhD research work on 5.12.2012. Title of thesis - Theoretical studies on protein interior and Interfaces using the structural and Geometric self-similarity.
The pre-synopsis presentation of Ms. Shweta Kolhi (guide-Prof. Ashok Kolaskar), titled ‘Understanding metabolome of bacteria – A Bioinformatics approach’ was done on 10.12.2012 as a pre-PhD requirement.
Papers published or presented in the conferences :
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Deepti Deobagkar, DNA methylation and Toxicogenomics in a book “Epigenomics and Toxicology” eds Saura Sahu, Publisher Wiley Eastern.
Deobagkar DD, Panikar C, Rajpathak SN, Shaiwale NS, Mukherjee S An immunochemical method for detection and analysis of changes in methylome. ,Methods(2012) 56 260-267. (IF 4.875).
A study on bacteria associated with the intestinal tract of farmed yellow seahorse, Hippocampus kuda (Bleeker, 1852): characterization and extracellular enzymes” Tanu, D. Deobagkar, R. Khandeparker, R. A. Sreepada, S. V. Sanaye and H. B. Pawar (2012) *Aquaculture Research* 43 386-394 (IF 1.925).
Radhakrishnan A, Raju R, Tuladhar N, Subbannayya T, Thomas JK, Goel R, Telikicherla D, Palapetta SM, Rahiman BA, Venkatesh DD, Urmila KK, Harsha HC, Mathur PP, Prasad TS, Pandey A, Shemanko C, Chatterjee A. A pathway map of prolactin signaling. J Cell Commun Signal. 2012 [Jun 9].
Kulkarni-Kale, U., Waman V., Raskar S., Mehta S., & Saxena S. Genome To Vaccinome: Role of Bioinformatics, Immunoinformatics & Comparative Genomics. Current Bioinformatics (CBIO). special Hot Topic issue titled “Contemporary Trends in Bioinformatics Relevant for Some Important Biomedical Problems”. 7:454-66, Impact Factor 0.976
Kolekar, P.S., Kale, M.M., Kulkarni-Kale, U. (2012). Alignment-free distance measure based on return time distribution for sequence analysis: Applications to clustering, molecular phylogeny and subtyping. Molecular Phylogenetics and Evolution, 65(2):510-522. PMID: 22820020
Saxena S. Using Pig for data analysis in Hadoop. International Journal of Advanced Research in computer Science 2012 Vol 3(7):240-245.
Kolhi S and Kolaskar A.S, Categorization of metabolome in bacterial systems. Bioinformation, 2012;8:309-15.
Kolhi S and Kolaskar A.S, Metabolic Network Analysis: Current Status and Way Forward. Current Bioinformatics Vol. 8, 2013. In press
Banerji A., Magarkar A.; “How happy is your web browsing? A model to quantify satisfaction of an Internet user searching for desired information”; Physica A: Statistical Mechanics and its Applications, 391 (2012) : 4215-4224
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Subhajit Basu, Deepti D Deobagkar, SG Prabhu Matondkar and Irene Furtado, Culturable Bacterial Flora Associated with the Dinoflagellate Green Noctiluca miliaris During Active and Declining Bloom Phases in the Northern Arabian Sea Microbial Ecology (2013) Microbial Ecology (published online 3rd January
Papers accepted
Yadav, A., Jayaraman, V.K., Kale M.M., Kulkarni-Kale, U. Phylogenetic clustering of protein sequences using Recurrence Quantification Analysis. Accepted for publication in the Advanced Science Letters (ISSN: 19366612) and for oral presentation in the international conference ICAEE 2012.
Exposure to heat stress modulates DNA methyltransferase activity in the embryonic S2 cell line of Drosophila melanogaster. Sania Deshmukh, Chitra Panniker, Deepti Deobagkar ,Drosophila Information service 2012 95 (in press)
Book Chapter communicated:
Kadam Kiran, Sawant Sangeeta, Kulkarni-Kale Urmila, Jayaraman Valadi K. Prediction of Protein Function based on Machine Learning Methods: An Overview. Book Chapter submitted to iConcept Press. Book Title: Introduction to Sequence and Genome Analysis.
Details of Training/Workshop organized and total no. of users trained Silver Jubilee Bioinformatics Conference and Alumni meet – during 6th to 9th December 2012. No of participants: 33
DBT-sponsored (under Center of Excellence (CoE) programme):
Workshop and Mini Symposium on Cancer Informatics – (in Collaboration with NCCS- DBT) on 13th and 14th September 2012, No. of participants: 415 participants in Mini-symposium and 30 participants in workshop.
Joint workshop (University of Pune Bioinformatics Centre and Telemark University Norway) was conducted on Basic Bioinformatics during 4th to 6th September 2012. No. of participants :18 participants from Norway.
Second international next generation sequencing data analysis workshop (in Collaboration with Persistent Systems Ltd.) was organized during December, 10-13, 2012. No of participants: 41
Impact shown by the Centre:
The faculty members and research students have published several papers in reputed international journals.
The faculty members are regularly being invited for talks at various national and international conferences, seminars, universities and colleges.
Dr. Manali Joshi (Rs. 3 lakhs), Dr. Vijay Baladhye (Rs 1.4 lakhs) and Dr. Abhijit Kulkarni (Rs. 3 lakhs) received grant from BCUD, UOP
The Centre has been identified as a Centre of Excellence both by DBT and MCIT DeitY.
HRD programs offered by the centre are well recognized in India and abroad.
The students qualify various prestigious certification courses and are very well absorbed in research and placements both in academia and industry.
Proposed activities 2013-14:
Carrying out high-quality research in newly emerging areas.
Further Develop and design new databases & servers, update and maintain existing ones.
Setting up wet-lab facility.
Organizing workshops and modular courses for professionals under the CoE programmes of DBT & MCIT.
It is aimed to create general awareness among students and professionals about bioinformatics.
Follow up with university administrations for recruitment of vacant faculty positions.
Persuing the state and central govt. to create permanent faculty positions at the Centre.
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Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
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Prof. Deepti D. Deobagkar Director, Bioinformatics Centre, University of Pune, Pune 411 007 020 2569 0195, 020 2569 2039 020 2569 0087
[email protected],
[email protected] http://bioinfo.net.in Dr. Sangeeta Sawant, Assistant Professor (Reader) Email:
[email protected]
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Anna University, Chennai Coordinator: Prof. P. Gautam Summary of the progress made by the centre from its inception: The Distributed Information Centre (DIC), Biotechnology Information System (BTIS) at Centre for Biotechnology, Anna University was started in 1989 with grants from DBT and functioned as SubDIC till March, 2002. During April 2002 it has been promoted as a Distributed Information Centre by the DBT, Government of India. The DIC-BTIS at Anna University has good infrastructure facility with Dell Power Edge R610 Cluster, Dell, HCL and IBM PCs. Three Credit courses in Bioinformatics and Computational Biology are being offered to the Undergraduate and Postgraduate students of the University. In the past six years we have published several papers in good impact international journals.
Major research activities in biotechnology and its related fields : Immunotechnology, Chemical Biology, Protein Biotechnology, Molecular Biology, Bioprocess Engineering, Tissue Culture and Drug Discovery, Genomics and Proteomics, Computational Biology, Bioinformatics, Toxicology and Bioremediation.
Area of specialization: Major research areas of the Centre in Bioinformatics and Computational Biology include Molecular Dynamics Simulation, Enzyme Structure Function studies, Protein Protein interactions, Comparative Genomics. MD Simulations and Quantum Mechanics of small molecules are also being done.
Major achievements made during 2012-13:
Ph.D awarded - titled “Studies on Understanding Domain Movements and Interactions of Pseudomonas aeruginosa lipase, Rhizomucor miehei lipase and Candida rugosa lipase with a Lipid Molecule: A Molecular Dynamics Approach” by Ms. T.Kothai (Part-Time), August 2012.
M.Sc Computational Biology II year Projects 7 nos ( Dec 2011 – May 2012)
Infrastructure facilities in the Bioinformatics Centre: Dell systems – 10 nos; MAC Workstations – 2nos; Laserjet Printers 2 nos; NVIDIA GPU Tesla Server connected with Dell Cluster to enhance the Cluster Computing power – 1no. Cluster Server : Dell Power Edge R610 Rack Mount Server with 2 x Quad Core Xeon CPU With 2 Nodes – 1no; Apple G5 64Bit Cluster Computing System-1no; Dell Optiplex Intel V Pro Systems – 5 nos; G5 Apple Mac-1no; HCL Intel V Systems – 4 nos; IBM Intel Pentium IV – 5 nos; HP 24 port 100Mbps Switch-1no, Colour Laserjet Printer-1no. Scientific Software: GROMACS, AutoDock, EXOME, Visualization Softwares, GAMESS
Details about staff members working in the centre: Sl.No. Name 1. Dr. T.Kothai
Designation Member Research Staff
2.
Documentation Assistant
Mrs. Vijayalakshmi Narayanan
Specialization Molecular Dynamics Simulation Digital Library
Working Since 1996 onwards
Status Contract Basis
2006 onwards
Contract Basis
Educational activities Courses in Bioinformatics, Computational Biology, Computer Aided Drug Design, Perl, Unix and C are being offered to the Undergraduate and Postgraduate students of the University. We also provide Summer term Projects and Curriculum Based Projects for Undergraduates and Postgraduate students.
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Papers/ published or presented in the conferences : 1.
Suganya Selvaraj, Vaishnavi Sambandam, Dipasri Sardar, Sharmila Anishetty. 2012. Insilico analysis of DosR regulon proteins of Mycobacterium tuberculosis. Gene 506(1):233-41
2.
Baskaran SK, Goswami N, Selvaraj S, Muthusamy VS, Lakshmi BS. 2012. Molecular dynamics approach to probe the allosteric inhibition of PTP1B by chlorogenic and cichoric acid. J Chem Inf Model. 52(8), pp 2004-12.
Initiation of R & D activities in bioinformatics: Projects Undertaken:
PG project works have been carried over in Docking, Homology Modeling and MD Simulation.
Details of Training/Workshop organized and total no of user trained No. 1.
Workshop Title
Period
Workshop on Sequence Analysis and Molecular Simulation
th
No. of Participants th
December 12 – 15 , 2012
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Impact shown by the Centre: We have published more than 14 papers in good impact international journals in the past six years. M.Sc. (Computational Biology) Course has commenced from October 2010, jointly offered with the Bioinformatics Centres of Madurai Kamaraj University and Pondicherry University. Two of the First batch passed out students (201012 – 7 students) are doing Ph.D in International and National Universities.
Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person(s)
Prof. P. Gautam Centre for Biotechnology, Anna University, Chennai – 600025. 091-44-22350772 091-44-22350299
[email protected],
[email protected] http://www.annauniv.edu Dr.T.Kothai, Dr.Sharmila Anishetty Email:
[email protected];
[email protected]
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Centre for Cellular and Molecular Biology, Hyderabad Coordinator: Dr. Rakesh K Mishra Summary of the progress made by the centre from its inception: Bioinformatics centre was initiated in the eighties in CCMB, being first among such activities, and has been immensely benefitted by the DBT support in subsequent years. Number of research program have been supplemented and supported by this centre in addition to setting up strong bioinformatics programs that have started generating high impact publications and value addition to the other ongoing activities. Several PhDs and other trained manpower has been generated that is supporting and leading the programs in different institutions and establishments in the country.
Major research activities in biotechnology and its related fields: The CCMB is mandated to conduct basic research in frontier and multidisciplinary areas of modern biology and to seek potential applications of this work. Research at CCMB can be grouped under the following five broad areas: i.
Cell functions in normal and disease states; cytoskeleton reorganization and regulation of cell functions; nuclear organization and the molecular basis of laminopathies; cell biology of signaling; metabolism and gene regulation in brain disorders; cold adaptation in bacteria; and structure, composition and function of nuclear architecture in chromatin organization and regulation.
ii.
Protein folding to understand its various facets, misfolding consequences, chaperone functions and how ions modulate folding; translational proofreading, a process by which incorrect amino acids are removed from tRNA, taking biochemical, structural & in-vivo approaches; and understanding the mechanistic basis of functioning of membrane proteins with a particular focus on receptors. The research activity also includes peptide-membrane interactions to understand biological processes such as sorting of proteins in cells and mechanism of action of membrane-active peptide toxins; structural studies on RNAi machinery; and calcium binding proteins, etc.
iii.
Biology in the genome context and to apply this knowledge to uncover the mechanism of epigenetic regulation. Major activities in this area aim to understand: how is the genome packaged with consequences regulation of gene expression; what epigenetic mechanisms are involved in differentiation, growth and regeneration; what implications do sequence variations in Indian populations have in diseases; and what is the role of micronutrients in complex diseases and clinical phenotypes.
iv.
Plants have unique developmental processes and strategies to deal with biotic and abiotic stresses. Current activity in this are include: Plant reproductive development, plant chromosome organization and control of meiosis, Plant adaptation to stresses, Plant immunity, Molecular markers and map development in crops.
v.
Infectious organisms such as Leishmania, plasmodium, Mtb, HCV and HIV are responsible for the major load of morbidity and mortality in India. The biology and evolution of these organisms and their interaction with their host is being investigated.
vi.
CCMB is also actively involved in using molecular markers to ascertain the inter- and intra-specific genetic makeup of species and assisted reproductive techniques are being developed in CCMB. Ongoing molecular evolutionary studies will give in-depth knowledge of the phylogenetic relationships among the wild species and help in developing strategies to protect and conserve wild and endangered species and maintain the balance in the ecosystem.
Activities related to bioinformatics: i.
Genome organization and epigenetic regulation: Genomics of non-coding part of genomes, Bioinformatics of the epigenetic regulatory system.
ii.
Structural Bioinformatics: Towards understanding the mechanism of Type III Polyketide Synthases, Bioinformatics of proteins involved in lipid metabolism in Mycobacterium tuberculosis, Bioinformatic Studies on a Unique Cell Wall-Degrading Esterase, Bioinformatic analysis on archael tRNA synthetases.
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Sequence-Structure Relatedness in Proteins: Single Amino Acid Periodicity Peptides in Proteins, Heteroatom Groups and their Neighbors in Proteins, Disulphide Bridge Connectivity Patterns in Proteins, Analysis, Detection and the Prediction of Structual Motifs in Proteins, Protein Three-dimensional Models.
iv.
Functional Genomics and development of tools for HTP analysis and proteomics.
Area of specialization: i.
Biology of Cells and Subcellular Complexes
ii.
Protein and Macromolecular Assemblies
iii.
Genetic Analysis and Genomics
iv.
Biology of Plant Development and Disease
v.
Molecular Basis of Infection and Disease
vi.
Bioinformatics
Major achievements made during 2012-13: Genome organization and epigenetic regulation: Development of a Chromatin domain boundary element search tool for insect genomes: Chromatin domain boundary elements prevent inappropriate interaction between distant or closely spaced regulatory elements and restrict enhancers and silencers to correct target promoters. In spite of having such a general role and expected frequent occurrence genome wide, there is no DNA sequence analysis based tool to identify boundary elements. Here, we report chromatin domain Boundary Element Search Tool (cdBEST), to identify boundary elements. cdBEST uses known recognition sequences of boundary interacting proteins and looks for ‘motif clusters’. Using cdBEST, we identified boundary sequences across 12 Drosophila species. Of the 4576 boundary sequences identified in Drosophila melanogaster genome, >170 sequences are repetitive in nature and have sequence homology to transposable elements. Analysis of such sequences across 12 Drosophila genomes showed that the occurrence of repetitive sequences in the context of boundaries is a common feature of drosophilids. We use a variety of genome organization criteria and also experimental test on a subset of the cdBEST boundaries in an enhancer-blocking assay and show that 80% of them indeed function as boundaries in vivo. These observations highlight the role of cdBEST in better understanding of chromatin domain boundaries in Drosophila and setting the stage for comparative analysis of boundaries across closely related species.
Functional genomics: Analyses of non-coding RNA to establish their role as putative piRNAs, analyses of miRNAs targeting cancer genes to eventually create a database containing information about the miRNAs involvement in different cancers, including the target gene, the pathway affected, the interaction with other miRNAs, etc., and compilation of synonymous human SNPs, where the SNP changes a rare codon to a frequently used codon of vice-versa, using the 1000 genome data
Infrastructure facilities in the Bioinformatics Centre: Hardware:
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Mid-Range Servers
6
Low End Servers
11
Desktops
600
Workstations
50
High Performance Servers / Workstations
9
Clusters
1 (5 node cluster)
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Network Resources: Dedicated 40 Mbps leased line connectivity for Internet access. Connected to National Knowledge network – An ultra high 100 Mbps bandwidth that seamlessly interconnects the leading Scientific and Technological institutions. Nation-wide computational grid, GARUDA is also connected through NKN LAN with 10 Gbps backbone and switched 1 Gbps to desktops. Security infrastructure for LAN and WAN. Proxy and caching device for faster browsing and data transfer speeds. Wireless connectivity in all floors. Exclusive 60KV UPS with redundancy for uninterrupted power supply. The Laboratory is also equipped with Modern Video Conferencing Facility.
Applications and other resource: BLAST, CLUSTALW, EMBOSS, Phylip, Repeat Masker, Phrap, SIFT, Polyphen, Mfold, MEME, MIRANDA, Sigma Plot 9.0, Discovery Studio Modeling, SPSS 11.0, Reference Manager 11.0.1, MATLAB, Avadis NT, NR, Swissprot, PDB, EST, human genome (chromosome-wise), chimp genome, mouse genome etc. for BLAST, PBD structures, Human Genome, Chimp genome, cattle genome, DSSP (Dictionary of Secondary Structure of Proteins), Nonredundant databases of nucleic acid and protein sequences and translated protein sequences, GeneCards, Protein and Molecular Biology Protocols CD’s, CCMB Microarray clone Anotation Systems, Proteomics Database and Integrated Data mining Module for CCMB Glioma Proteomics.
Details about staff members working in the centre: Sl. No. Name Rakesh K Mishra
Designation Sr Principal Scientist
Rajan Sankaranarayanan Sr Principal Scientist
Specialization Epigenetics & genomics
Since 2001
Structural bioinformatics
2001
Status Group Leader, Coordinator of bioinformatics centre and Head IT Group Group Leader
K Guruprasad
Principal Scientist Protein structure modeling
2002
Project Leader
Shrish Tiwari Geetha Thanu
Principal Scientist Functional genomics Scientist Information Technology Junior Scientist Information Technology Junior Scientist Information Technology Junior Scientist Information Technology
1999 2009
Project Leader IT Group support
2009
IT Group support
2009
IT Group support
2009
IT Group support
S Balaraju Biswajit Roy Aparna Kumari
Educational activities i.
Continuous Training Program in Bioinformatics
ii.
Lecture course in the PhD course work program.
Papers published: 1.
A. Chattopadhyay, Y.D. Paila, S. Shrivastava, S. Tiwari, P. Singh and J. Fantini (2012). Sphingolipid-binding domain in the serotonin1A receptor, Adv. Exp. Med. Biol. 749, 279-93.
2.
Sajad Ahanger, A Srinivasan, D Vasanthi, Y Shouche and Rakesh K Mishra (2012). Conserved boundary elements from the Hox complex of mosquito, Anopheles gambiae., Nucleic Acids Res. (2012) doi:10.1093/nar/ gks1178
3.
A Mamillapalli, Rashmi U Pathak, Hita Sony G and Rakesh K Mishra (2012). Transposable element ‘roo’ attaches to nuclear matrix of the Drosophila melanogaster, Journal of Insect Science (in press)
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4.
E. Sreesankar, R. Senthilkumar, Vellaichamy Bharathi, Rakesh K Mishra and Krishnaveni Mishra (2012). Functional diversification of yeast telomere associated protein, Rif1, in higher eukaryotes, BMC Genomics 13:255
5.
A Srinivasan and Rakesh K Mishra (2012). Chromatin domain boundary element search tool for Drosophila, Nucleic Acids Res. 40(10), 4385-95.
6.
Singh NP, Madabhushi SR, Srivastava S, Senthilkumar R, Neeraja C, Khosla S, Rakesh K. Mishra (2011). Epigenetic profile of the euchromatic region of human Y chromosome, Nucleic Acids Res. 39, 3594-606
7.
H. Sultana, S. Verma, Rakesh K. Mishra (2011). A BEAF dependent chromatin domain boundary separates myoglianin and eyeless genes of Drosophila melanogaster, Nucleic Acids Res. 39, 3543-57
8.
A. Chaturvedi, S. Tiwari and R.A. Jesudasan (2011) “RiDs db: Repeats in diseases database”, Bioinformation 7, 96-97.
Initiation of R&D activities in bioinformatics: i.
Extensive use of NGS data analysis and development of tools for genomics and proteomics analysis.
ii.
Analysis of genome scale epigenetic profiles in complex organisms and search for cis elements controlling epigenetic modifications.
iii.
Structural bioinformatics and analysis of proteins structural dynamics.
Details of Training/Workshop organized and total no of user trained Continuous training program in Bioinformatics: BIC@CCMB has a training program which is running throughout the year. CCMB faculty interested in this program will contribute the training and will have trainees working on ideas suggested by them. Major computational/bioinformatics project can be planned to make teamwork involving a group of trainees. Training program will also involve general talks given by CCMB scientists / invited speakers. Guidelines for trainees will be prepared and modified by BIC from time to time to ensure smooth conduct of the training program. About 10 trainees go through this program every year.
Impact shown by the Centre: There are three kinds of impact that can be associated with the BiC@CCMB i.
Quality publications in leading journals of the related fields
ii.
Creation of tools to assist in-house research activities
iii.
Trained manpower generation
Proposed activities for 2013-14
34
a.
Continuous Bioinformatics Training program.
b.
Development of databases and tools for proteomics and genomics.
c.
Acquisition of expertise of NGS and other HTP data handling and analysis.
d.
Comparative genomics & annotation of complex genomes for regulatory elements.
e.
Mapping of synonymous SNPs on the protein secondary structure
f.
Sequence repeats in the human proteome and their association with diseases.
g.
Analysis of protein structures related to certain sequence-specific features.
h.
Databases for protein structure bioinformatics.
i.
Development of software “CCMBprot”: Analysis of mass spectrometry data
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Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
Dr. Rakesh K Mishra CCMB, Uppal Road, Hyderabad 500007 (40) 27192658 (40) 27160591
[email protected] www.ccmb.res.in Dr. Rakesh K Mishra
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Indian Agricultural Research Institute, New Delhi Coordinator: Dr. H. Chandrasekharan Summary of the progress made by the centre from its inception: Bioinformatics Centre at IARI, New Delhi was established in 1989 under Biotechnology Information System (BTIS) Network to function as a computerized information base in fields related to Agricultural Biotechnology in particular and fields allied to agriculture in general. The Centre became a part of Unit of Simulation and Informatics (USI) in November 2003. The USI is entrusted with the additional responsibility of maintaining the Institute’s campus network, the website development and the web server administration. Since its inception, the Centre has provided various services, such as online and offline bibliographic search through network and CDROM server, electronic mail, internet, creation and update of database, statistical analysis of research data, biological sequence analysis, Genomic and proteomics data analysis to the researchers, students and farmers. A number of Bioinformatics tools and techniques were developed and updated at the centre. Crop database along with information retrieval system are functional at the centre. Work has been initiated for application and validation of various bioinformatics resources for nucleotide and protein sequence alignment, gene prediction, RNA/ protein structure prediction, biological data mining and modeling.
Major research activities in biotechnology and its related fields at your institution (a)
Structural and functional comparison of Deoxy-Hypusine Synthase in wheat and Homo sapiens.
(b)
Structure prediction through comparative modeling of wheat stripe rust protein.
(c)
Structure and functional site prediction of SMV (sterility mosaic virus) protein.
(d)
In-silico analysis of Blast resistance /susceptible protein of pi-ta.
(e)
Development of prediction model to classify wheat protein.
Area of specialization of the center Agri-Informatics (Comprising Computerized Information Systems in various branches of agricultural sciences with special reference to Agricultural Bioinformatics).
Infrastructure facilities in the Bioinformatics Centre A.
Computer & Communication facility: ILL from both NKN and ERNET are available for various web related activities.
B.
Scientific Software packages: Centre is in possession of certain scientific software packages, which have been procured / developed over the years. These include Advanced Sequence Analysis Software Genocluster, SAS, Infocrop and a number of crop information systems.
Details about staff members working in the centre
Dr. H. Chandrasekharan, Co-ordinator cum Principal Investigator- Permanent
Dr. A. K. Mishra, Deputy Co-ordinator cum Co Principal Investigator – Permanent
Types of services provided
36
Software and algorithm development
Creation and updation of databases (Agri-informatics and bioinformatics)
Statistical analysis of biological research data (students and scientists of the institute)
Human resource development in Bioinformatics & Computational biology (Studentship and Traineeship)
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Educational activities M.Sc. and PhD students of IARI are being guided in their research by scientists of this Centre. The Centre provides facilities for attachment training for a limited number of M.Sc (Bioinformatics) final year students for completing their short-term projects.
Collaborative works/ initiatives Our Centre has collaboration with National Research Centre on Plant Biotechnology (NRCPB), National Bureau of Plant Genetic Resources (NBPGR), Indian Agricultural Statistics Research Institute (IASRI) and a score of other research and development organizations.
Papers/ published or presented in the conferences
Jethra G, Mishra A K, Pandey P S, Chandrasekharan H (2011) Structure and Function Prediction of unknown wheat protein using: LOMETS and I-TASSER. Indian journal of Agricultural sciences.
H. Chandrasekharan, Sarita Patle, A.K. Mishra “CeRA-The e-journal consortium National Agricultural Research System, Vol. 102 No. 5 (10 March 2012).
A.K. Mishra and H. Chandrasekharan “Structure based Analysis and Functional Classification of Plant miRNAs” International Conference on Recent Prospective in Macromolecular Structure and Function, 27-28 January 2012 at CARI Port Blair.
A.K. Mishra and H. Chandrasekharan “Classification and Feature based analysis of Plant microRNA” National Symposium on Bioinformatics: Challenges in the post-genomic era February 2012, Jammu.
A.K. Mishra and H. Chandrasekharan “Deriving gene similarities using Phylogenetic analysis for Fusarium Head Blight in Wheat and Barley” National Conference on Computing for Nation Development at Bhartiya Vidyapith New Delhi March 2012.
H. Chandrasekharan, A.K. Mishra et al. Consortium for e-Resources in Agricultural (CeRA) Current Status at National Conference of Agricultural Libraries and User Community 2012 at ANGRU Hyderabad.
Details of Training/Workshop organized and total no. of user trained A 3 day training programme Bioinformatics Applications in Agriculture was conducted during 14th to 16th December 2011. 20 participants from different institutes/universities had participated in this programme.
Impact shown by the Centre The web based application ‘Wheat Informatics’ and Rice Portal has been developed which enables the target user to retrieve general, scientific, bioinformatics and other information about these crops. These applications are user’s friendly and will help the students, researchers and even the farmers to know complete detail related to wheat and rice. The RKMP portal (http://rkrnp. iari.res. in) Is a getaway for providing rice knowledge to the stake holders. The portal consists of several information systems and decision support modules to give a unified solution for a particular query. A case study has also been taken for states of Haryana, Punjab and Uttrakhand by integrating the state specific content collected from these states. The portal provides many specific queries for rice research and cultivation, such as queries related to variety selection, management of disease, insect, pest of rice, rice statistics, site specific frequently asked questions (FAQ). Development of SNP Prédictions Tool: ‘SNPredictor’ by EST data, and making it user friendly. This is tool for the prediction of all potential SNP’s i.e. Single Nucleotide Polymorphs. These are helpful in predicting the causes of mutation in the organisms. This tool can also predict the potential contigs. Prediction of stress related genes, gene profiling, prediction of co-regulated/co-expressed genes group; gene network creation and gene ontology analysis were performed using R language for Triticum aestivum.
Proposed activities for 2013-14
To carry out new research initiative for machine learning applications in Bioinformatics.
Bioinformatics application development for Wheat, Rice and Maize.
Structure and function prediction of various proteins of major crops in India.
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Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
38
Dr. H. Chandrasekharan Unit of Simulation & Informatics A-0 Block, LBS Building, IARI, New Delhi-110012 011-25841255, 011-25842490 011-25843719
[email protected],
[email protected] Dr. H. Chandrasekharan
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Institute of Microbial Technology, Chandigarh Coordinator: Dr G P S Raghava Summary of the progress made by the centre from its inception: Bioinformatics centre (BIC) at IMTECH has shown consistent growth in the different areas of bioinformatics. Centre has developed databases and software both for in house use and for scientist’s world over. BIC has developed a number of web servers based on peer-reviewed research carried out at the bioinformatics centre. BIC staff has published more than 150 research papers in reputed international journals and more than 70 abstract/poster/papers presented in national and international conferences. Our servers are getting more than 80,000 hits per day.
Major research activities in biotechnology and its related fields at your institution:
Fermentation Technology & Applied Microbiology
Cell Biology & Immunology
Molecular Biology and Microbial Genetics
Protein Science & Engineering
Area of Specialization: Protein Modeling and Protein Engineering Major activities of the centre during the year 2011-12: This year our centre has been involved in the development of I. Method for prediction of N- and O-glycosites in prokaryotic protein sequences II. Databases of a. CPPsite: a curated database of cell penetrating peptides; b. TumorHoPe: A database of tumor homing peptide; c. PolysacDB: A comprehensive database of microbial polysaccharide antigens and their antibodies; d. ccPDB: compilation and creation of data sets from Protein Data Bank; e. ProGlycProt: a repository of experimentally characterized prokaryotic glycoproteins; f. AVPpred: Collection and Prediction of highly effective antiviral peptides. Centre has also acquired expertise and presented (draft) genome sequences of a number of industrially important microorganisms.
Staff members working in the centre: S. No. 1. 2. 3. 4. 5. 6. 7.
Name of staff Dr. GPS Raghava Dr. Balvinder Singh Dr. Manoj Kumar Sh. Harvinder Jassal Sh. Harminder Singh Sh. Sandeep Kumar Sh. Paramjit Lal
Designation Sr. Principal Scientist Principal Scientist Scientist Jr. Scientist J.T.A. J.T.A. J.T.A.
Specialization Bioinformatics Bioinformatics Bioinformatics Computers Computers Computers Computers
Types of services provided: Biocomputing, Consultation Services, Installation and commissioning of new local area network points, Maintenance of network related hardware and software, Development and maintenance of web sites.
Educational activities:
Guiding Ph.D. students and others that are using facilities at BIC or those provided by BIC.
Regular workshops/training programmes in Bioinformatics.
BIC staff participates in the pre Ph.D. course at IMTECH.
Initiative to validate the outcome of bioinformatics resources: The research work is published in peer-reviewed journals and is available on world-wide-web. Servers developed at the centre are receiving more than 30,000 hits per day.
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Collaborative works / initiatives: BIC staff has a number of collaborative projects including major projects like OSDD, see http://crdd.osdd.net/ Databases / Software packages: More than 20 databases and 170 web servers. Databases are available online.
Papers published or presented in the conferences with reference: The BIC staff of this centre has published more than 150 research papers in reputed international journals. Fourteen peer reviewed research papers were published by staff of bioinformatics centre during 2012-13 and a few are being reviewed. Initiation of R&D activities in Bioinformatics: As above Details of Training / Workshop organized and total no. of user trained: BIC organizes minimum one workshop every year with average 30 participants per workshop. Impact shown by your centre: Solely based upon Bioinformatics approach or in silico methods, the number of publication of research papers from the centre are more than 150. Manpower Trained: Manpower is being trained by organizing workshops/training programmes, Tools Developed: As described above. Proposed activities of the centre during the year 2013-14: Staff of the bioinformatics centre will continue to develop new databases and prediction methods in area of molecular biology. Research efforts will be on to publish new (draft) genome sequences of industrially and economically important microorganisms. Staff of centre will be actively engaged in the research work of molecular modeling and simulations in collaboration and otherwise.
Contact detail Name of the Coordinator: Dr G P S Raghava, Scientist (
[email protected]) Scientific staff: Dr. Balvinder Singh (
[email protected]), Dr. Manoj Kumar (
[email protected]), Sh Harvinder Jassal (
[email protected]). Postal Address: Bioinformatics Centre, Institute of Microbial Technology, Sector 39A, Chandigarh-160 036, INDIA Phone Number: +91-172-2690557 & +91-172-6665450 Fax No.: +91-172-2690632 & +91-172-2690585 Website: http://www.imtech.res.in/bic/
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Kerala Agricultural University, Thrissur Coordinator: Dr P.A. Nazeem About the Centre The Bioinformatics Centre at KAU, Thrissur is funded by the Department of Biotechnology, New Delhi under the Biotechnology Information System Network (BTISnet) programme. The Centre was upgraded to DIC during 2004 with the objective to support Plant Biotechnology research. The Centre is involved in a wide range of research work on plant responses to biotic and abiotic stresses, plant metabolomics using systems biology approaches, plant-pathogen interaction studies and study of active compounds of medicinal plants. In addition to this, the Centre offers a credit course in Bioinformatics to post graduate Plant Biotechnology students conducts training programmes in Bioinformatics and maintains various databases relevant to agriculture.
Major activities of the centre during the year 2012-13
Organized [2+1] credit course in Bioinformatics for M.Sc Plant Biotechnology students.
Conducted various training programme for researchers, scientists and students.
Carrying out R & D activities like gene analysis, structure prediction, interaction studies, evolutionary biology, data mining and Gel documentation for molecular marker data.
Publishing quarterly e-news letters named ‘Biobits’.
Creation and maintenance of databases.
Infrastructure facilities in bioinformatics centre: A.
Computer and Communication facility
The Centre has one Dell Server with Microsoft Windows Vista, one IBM Server with Microsoft Windows Server 2003, ISA Server for networking, and 24 Personal Computers with Local Area Networking facility. Networking: The Centre has established a leased line connectivity of 20 Mbps speed from Reliance. B.
Scientific software packages
Accelrys Discovery Studio, Omiga 2.0, NTSYSpc 2.1, Rasmol , Cn3D , VMD , Chimera , Swiss PDB Viewer, Modeller 7v7 , Hex, Argus lab , Clustal X , Clustal W, Treemap , Tree Explorer , Phylip, Mega, Bioedit , Oligotes , Primer 3, Marvin Sketch, ISIS Draw. C.
Databases and other information resources
The Centre provides CD-ROM search facility for databases acquired like DERWENT, AGRISEARCH, and AGRICOLA. The library has a collection of more than 300 books.
Types of services provided:
Training programmes for agricultural scientists, technical staffs and students.
Literature search by means of CD ROM and Internet.
Offering courses in Bioinformatics for PG and Ph.D students.
Support to R&D activities for PG projects in Biotechnology.
Papers published or presented in the conference
Parvathi Sudha.K.K, Priyanka James and R.Keshavachandran, Homology Modeling and Phylogenetic analysis of Plant Defensins from Capsicum annuum L. Proceedings of the National Symposium on Bioinformatics: Challenges in post-genomic era- BTISNET in India (1986-2012). P-59.
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Renu Kushwah, P.A. Nazeem, S. Manjula, R. Keshavachandran and Sherin Jose (2011). Differential gene expression in relation to drought tolerance in black pepper (Piper nigrum L.). Journal of Plantation Crops, 2011, 39 (1).
Harish C, Abida PS, Nazeem PA, Vasanth Nirmal Boscoa, Genetic diversity of Pseudomonas strains using RAPDAn approach for comparative study between in-silico and in-vitro. International Journal of Integrative Biology, 2011. Vol(12).
Tirthkar.M.B., Abida.P.S., and Nazeem.P.A. Differential Expression of SOS pathway genes in water stress tolerance in rice and its validation by electronic Northern. Manuscript submitted as Book Chapter in “Advances in Bioinformatics”
Future activities:
Offer new training courses in Bioinformatics.
Further improvement of infrastructural facilities.
Continuation of teaching of Bioinformatics to M.Sc Plant Biotechnology students.
To enable an E print facility to act as a repository for research articles by integrating data generated from Biotechnology division and other affiliated research stations.
Development of new databases and updation of existing ones.
In Silico studies on plant derived compounds against various diseases.
In Silico studies on plant defense mechanisms.
Development of a KAU Agri portal.
Establishment of Agri Bioinformatics Centre
Contact details:
42
Name of the Coordinator Postal address
: :
Phone number Mobile Email Website Name of contact person Email
: : : : : :
Dr P.A. Nazeem Bioinformatics Centre, (DIC) Kerala Agricultural University Vellanikkara,Thrissur, Kerala-680 656. 0487-2371994 +919447126917
[email protected] www.kaubic.in Dr P.A. Nazeem
[email protected]
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National Brain Research Centre, Manesar Coordinator: Dr. Nandini C Singh Summary of progress of the centre since its inception Since its inception in 1999 the Distributed Information Centre is continuously upgrading the network and computing requirement of the centre. High end multiprocessor servers are used to maintain the IT infrastructure services viz. email servers/ web servers/ FTP servers etc. apart from managing application compute servers for growing requirement of the computing power. The centre also has upgraded the central storage to 50TB for aiding in growing research activities of the centre. The centre is connected with National Knowledge Network at 1 Gbps connectivity which is immensely helping in many ongoing collaborative projects with collaborators in India and abroad involving huge processing and transfer of research data in real-time for multiple research objectives. The campus LAN has constantly been upgraded and is running on manageable L3 switches over 10 Gbps fibre backbone. The DIC staff works as a team and focuses on in-house development, assists in technical problem solving, in addition to helping scientists, handling the servers and the network.
Major research activities: The major research area at NBRC is Neural Information Processing. The objective of DIC is to provide technical support to scientists 1)
During collection of data during different neurophysiological and neruoimaging experiments
2)
To assist in management and storage of experimental data
3)
To develop algorithms in the processing of neural data
4)
To provide platforms for better archival and sharing of research data
5)
To ensure data security.
A few highlights of the research and training at NBRC in this area have been summarized below Magnetic Resonance Spectroscopy – Integration of medical physics and technology (MRI, MRS and fMRI) to understand brain disorders and identification of causal molecular process are the focus area of Dr. Mandal’s laboratory. Eventually that could lead to therapeutic discovery/development. Imaging and Image analysis: Novel techniques of image acquisition and image analysis for more efficient application of diagnostic and therapeutic neuroimaging methodology are being developed by Prof. Prasun Roy’s laboratory. The laboratory utilizes MRI based strain analysis to estimate the stress in flowing blood to estimate cerebrovascular deficits, as also to delineate elastoplastic deformation of brain for early diagnosis and differentiation of Mild Cognitive Impairment and Alzheimer’s disease. Cognitive Neuroscience and language processing– The Speech and Language Laboratory (SALLY) records brain activity in the form of Blood Oxygen Level Dependent signal to study and understand how different region of the brain network together to read different scripts and how this is altered in children with dyslexia. Area of specialization: NEURAL INFORMATION PROCESSING
Major achievements made during 2012-13: BRAIN GRID project - Under the leadership of Dr. P K Roy, The initiation of a collaborative project with Montreal Neurological Institute, Canada to develop a brain image analysis platform that will integrate MRI images and genomic data across different countries, at different sites to enable participation from India in global clinical trails.
Infrastructure facilities in the Bioinformatics Centre: Servers: The centre has a pool (20-25) of servers for various infrastructure applications and application servers for computational and research activities. Storage: The central storage provide online centralized 50 TB storage facility to users
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Network: The centre is connected with National Knowledge Network (NKN) with 1 Gbps fibre connectivity; it also has a redundant 10 Mbps RF link. The campus wide LAN is implemented over a 10 Gbps backbone with manageable L3 switches and Firewall/UTM appliances.
Details about staff members working in the centre: Sl.No. Name
Designation
Specialization
Working Since
Status
1.
Dr. Nandini C Singh
Scientist & coordinator Speech and Language DIC Laboratory, FMRI
2.
Mahender Kumar Singh
Information Scientist
ICT, Bioinformatics, System Analyst
2005
Core
3.
Kedar Singh Bajetha
Computer Operator
IT , Technical Support
2003
Core
4.
Reema Saxena
Computer Operator
IT
2000
DIC-Project
5.
Ganesh Gurmurthy
Computer Operator
Technical Support
2009
DIC- Project
6.
Amit Kumar
Computer Operator
2009
DIC-Project
7.
Sunita
Computer Operator
2008
DIC-Project
Core
Educational activities NBRC is also a deemed University and has two educational programmes in Neuroscience namely Ph.D & Integrated Ph.D in neurosciences.
Papers/ published or presented in the conferences:
44
1.
Pal, S., Roy, P. The effect of stochastic fluctuation in radiation dose-rate on cell survival following fractionated radiotherapy, Physics in Medicine and Biology, 57, 1561-70, 2012.
2.
Chandrasekhar, S, Kapoor, S, Rallabandi, S, Padhi, R, Roy, P (2012). Automated Treatment of Melanoma with Chemoimmunotherapy using Optimal Dynamic Inversion, Advances in Control and Optimization of Dynamical Systems, vol. 2, 930-35.
3.
Raghunathan, P., Roy, P. (2012) Neuroimaging Studies of Human Cognition: Measurement Techniques and Recent Developments, Tripathi, R (ed). Expanding Horizons of the Mind Sciences, Nova Science Publishers, New York, 33-47.
4.
Chaitra Rao, Avantika Mathur and Nandini C Singh. ‘Cost in Transliteration’ – The Neurocognitive Processing of Romanized Writing. Brain and Language (2012, in press).
5.
Nandini Chatterjee Singh (2012) The developing biliterate brain. ISSBD Bulletin 1(61), 22 – 26.
6.
M. Sharda and N. C. Singh (2012) Auditory Perception of Natural Sound Categories – An fMRI Study. Neuroscience, 214 49–58
7.
Chakraborty, T. A. Sumathi, V. S. Mehta & N. C. Singh (2012) Picture-naming in patients with left frontal lobe tumor – a functional neuroimaging study, Brain Imaging and Behavior. 6(3), 462-471.
8.
Chaitra Rao, Shweta Soni and Nandini Chatterjee Singh (2012). The Case of the Neglected Alphasyllabary: Orthographic Processing in Devanagari, Peer Commentary in Brain and Behavioural Sciences. Volume 35, 5, 302303.
9.
Pravat K. mandal*, H. Akolkar, and Manjari Tripathi “Mapping of Hippocampal pH and Neurochemicals from in vivo Multi-Voxel 31P Experiments in Healthy Normal Young Male/Female, Mild Cognitive Impairment, and Alzheimer’s Disease” Journal of Alzheimer Disease (2012)
10.
Pravat K. Mandal*, Rashima Mahajan, Ivo D. Dinov “Structural Brain Atlases: Design, Rationale and Applications in Normal and Pathological Cohorts” Journal of Alzheimer’s Disease (2012, In Press)
Distributed Information Centres (DICs)
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February 03-04, 2013
11.
Pravat K mandal, Jitesh Joshi, Sumiti Saharan “Visuospatial Perception: An Emerging Biomarker for Alzheimer’s Disease. Journal of Alzheimer’s Disease. (2012, in PRESS)
12.
Pravat K Mandal* “Proton Magnetic Resonance Spectroscopic Signal Processing for the Quantitation of Neurometabolites” European Journal of Radiology 653– 664, 81(2012).
13.
Pravat K. mandal*, Manjari Tripathi and Sreedevi Sugunan “Brain oxidative stress: Detection and mapping of anti-oxidant marker ‘Glutathione’ in different brain regions of healthy male/female, MCI and Alzheimer patients using non-invasive magnetic resonance spectroscopy” Biochemical Biophysical Research Communications 4347, 417(2012)
14.
Pravat K. Mandal* “Predictive Biomarkers for Alzheimer’s Disease using State-of-the-Art Brain Imaging Techniques “ Journal of Alzheimer’s Disease (In Press, 2012)
15.
Ramaswamy, R, Khanna, R, Roy, P. A method to estimate topographical connectivity and elastometric tissue stress performance from MRI brain images, and enable differentiation between normal subjects, mild cognitive impairment and dementia patients. [Patent]
Initiation of R&D activities in Bioinformatics: We have recently initiated an online research study to collect responses on emotion perception in music wherein North Indian Classical Music Ragas have been used as stimuli.
Details of Training/Workshop organized and total no of user trained
Training/Workshops in the area of Neuroinformatics / Computational neuroscience are organized by NBRC every year and nearly 400 students have been trained in previous years.
CNS Course at NBRC – Students enrolled in Integrated Ph.D and Ph.D programme at NBRC undergo 8 week course on computational neuroscience which also includes teaching, tutorial and laboratory sessions
Impact shown by the Centre:
The computational neuroscience group at NBRC has published/submitted around 15 publications and patent applications in 2012
DBT Biotech Consortia for digital library access throughout the country is currently being coordinated by NBRC.
NBRC also offers short term training opportunities to students of diverse academics backgrounds through summer training and project internships which give students vast exposure to these emerging areas of neurosciences.
Proposed activities for 2013-14 The centre intends to upgrade the IT infrastructure by adding SAN and blade servers for high performance data processing and upgrade network and communication services. On the research front may projects involving FMRI, MRS and upcoming MEG facility are planned.
Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
Dr. Nandini C Singh National Brain Research Centre, NH-8, Manesar, Gurgaon - 122051 +91-124-2845-333 +91-124-2338-928
[email protected] http://www.nbrc.ac.in Dr. Nandini C Singh (Scientist & coordinator, DIC)
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XXIVnd All India BTISnet Coordinators’ Meeting
National Institute of Immunology, New Delhi Coordinator: Dr. Debasisa Mohanty Summary of the progress made by the centre from its inception: Bioinformatics Center (BIC) at NII is engaged in advanced research in the area of computational and structural biology. The progress made by the center is reflected in publications from the center in the area of computational biology. The center also facilitates usage of bioinformatics resources in large number of publications from other experimental research groups at NII.
Major activities in biotechnology and its related fields: The research interests of the various research groups at NII coalesce in six major areas; Chemical Biology, Genetics & Cell Signaling, Immunity & Infection, Molecular & Cell Biology, Reproduction & Development, and Structural & Computational Biology.
Area of specialization: Computational & Structural Biology
Major achievements made during 2012-13: During the year 2012-2013, the most notable achievements by the researchers working at the center has been identification of a novel family of putative phosphothreonine lyases by in silico genome analysis, development of a novel computational tool for deciphering phosphorylation networks, deciphering the binding modes of small molecule modulators of proteinprotein interactions and structure based analysis of microRNA-protein interactions.
Infrastructure facilities in the Bioinformatics Centre: High performance computing: CPU and GPU clusters Bioinformatics & Molecular modeling softwares: MOE, AMBER, CHARMM & CSD
Web servers developed by the center: Construction of phospho-networks
http://www.nii.ac.in/phosnetconstruct.html
Analysis of enzymes catalyzing novel PTMs
http://www.nii.ac.in/novPMenzy.html
Analysis of PKS/NRPS
http://www.nii.ac.in/sbspks.html
Motif Discovery
http://www.nii.ac.in/~deepak/RegAnalyst
Substrates for MHCs & Kinases
http://www.nii.res.in/modpropep.html
Substrate Specificity of ACS
http://www.nii.res.in/pred_acs_substr.html
Software for analysis of GTr
http://www.nii.res.in/searchgtr.html
Solvent Accessibility of phosphosites
http://www.nii.res.in/paccess.html
Details about staff members working in the centre: S. N. 1. 2. 3. 4.
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Name Dr. Madhumalar Ms S. Sachdeva Mr M.S. Rao Mr. Naveen
Designation DBT Scientist Technical Officer II Technical Officer II Technical Assistant
Specialization Comp. Biophys. IT Sys Adm IT Sys Adm Comp. Operator
Distributed Information Centres (DICs)
Working Since 2012 1989 1989 1993
Status Project Staff NII Core NII Core NII Core
XXIVnd All India BTISnet Coordinators’ Meeting
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Educational activities Currently six students are enrolled for Ph.D. degree and one student has been awarded Ph.D. degree during the reporting year.
Papers/ published or presented in the conferences : 1.
Yadav G, Anand S and Mohanty D* (2013) Prediction of inter domain interactions in modular Polyketide Synthases by docking & correlated mutation analysis J Biomol. Struct. Dynam. 31, 17-29.
2.
Anand S and Mohanty D* (2012) Modeling holo-ACP:DH and holo-ACP:KR complexes of modular polyketide synthases: A docking and molecular dynamics study. BMC Struct Biol 12:10.
3.
Vats A, Singh AK, Mukherjee R, Chopra T, Ravindran MS, Mohanty D, Chatterji D, Reyrat JM, Gokhale RS* (2012) Retrobiosynthetic approach delineates the biosynthetic pathway and the structure of the acyl chain of mycobacterial glycopeptidolipids. J Biol Chem. 287(36):30677-87.
4.
Ahmed A, Gaadhe K, Sharma G P, Kumar N, Neculai M, Hui R, Mohanty D and Sharma P* (2012) Novel insights into the regulation of malarial Calcium Dependent Protein Kinase 1 FASEB J 26:3212-3221.
5.
De S, Kumari J, Mudgal R, Modi P, Gupta S, Futami K, Goto H, Lindor NM, Furuichi Y, Mohanty D and Sengupta S (2012) RECQL4 is essential for the transport of p53 to mitochondria in normal human cells in the absence of exogenous stress. J Cell Sci. 125:2509-2522.
6.
Khater S and Mohanty D* (2013) Structural bioinformatics approaches for deciphering biosynthetic code of secondary metabolites. In BIOMOLECULAR FORMS AND FUNCTIONS: A Celebration of 50 years of the Ramachandran Map (Eds. Manju Bansal and N Srinivasan) IISc Press-WSPC Publication, Singapore 596224.
R & D activities in bioinformatics: The center also has a number of ongoing research projects focused on analysis of secondary metabolite biosynthetic pathways, protein interaction networks, microRNA target identification and novel post translational modifications.
Details of Training/Workshop organized and total no of user trained During the current reporting year, three students have carried out their project training at the center for periods ranging from two to six months. Faculties of the center have also delivered 15 lectures in the area of computational and structural biology for new researchers.
Impact shown by the Centre: The impact of the center on the research at NII is reflected in large number of publications every year in peer reviewed journals.
Proposed activities for 2013-14 The center plans to expand the scope of the existing research projects to address questions on small molecule modulators of protein interaction networks, disease associated kinase mutations, analysis of NGS data and development of computational tools for retro-biosynthetic enumeration of enzymatic reactions.
Contact details: Name of the Coordinator Name of the Co-Coordinator Postal Address Phone Number Fax No. Email Website
Dr. Debasisa Mohanty Dr. Bichitra K. Biswal NII, Aruna Asaf Ali Marg, New Delhi-67 011-26703749, 011-26715016 011-26742125
[email protected],
[email protected],
[email protected] http://www.nii.res.in
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Pondicherry University, Pondicherry Coordinator: Prof. Priya Davidar Summary of the progress made by the centre from its inception: The Centre for Bioinformatics in Pondicherry University was started as Sub Distributed Information Centre of the Department of Biotechnology, Govt. of India (DBT) in 1991. The mandate of the Centre is to train manpower and conduct research in various areas of Bioinformatics. Recognizing the progress made by the Centre, DBT upgraded the Centre to a full Centre level in 2002 and several new positions were sanctioned and additional funding was allocated. The Centre is identified as a Centre of Excellence for Research and Training in the field of Bioinformatics by the Department of Information Technology, Govt. of India, New Delhi in 2007 and awarded a special grant of ‘ 3.69 crores. The Centre has taken up several research projects and has been offering modular courses in Bioinformatics under this Grant. The Centre is offering an M.Sc., program in Bioinformatics in 2007 supported by the University Grants Commission (UGC) under the scheme of “Innovative Programme - Teaching & Research in Interdisciplinary and Emerging Areas”. To advance research in Bioinformatics, the Centre started Ph.D. Programme in 2009. The Centre started offering a Network M.Sc., Computational Biology teaching programme fully funded by DBT in collaboration with Madurai Kamaraj University, Madurai and Anna University, Chennai in 2010. This programme will be first of its kind in the country. The Centre has also signed an MoU with Institute of Bioinformatics (IoB), Bangalore and University of Sienna, Italy for collaborative research and Ph.D. guidance. The Ph.D. students can visit these labs for collaborative research and the details are available at www.bicpu.edu.in. The Centre has so far organized 37 National Level Seminars and Training Programs and took a lead in organizing National Seminars in emerging fields like Intellectual Property Rights in Bioinformatics and Biotechnology and Nanosciences & Nanobiotechnology. All students, research scholars and faculty are provided round-the-clock computing facility with a separate 11 Mbps dedicated internet connectivity in addition to the regular internet connectivity provided by the University. The Centre has established a separate wet lab facility with sophisticated equipments. Most of the past students were placed in various leading research institutions and industries. In the past few years, Centre has taken up research activities in the areas of sequence analysis, molecular modeling, structural biology, database development etc., and several papers have been published in peer-reviewed International and National Journals. The faculty and students have received projects/fellowships from various funding agencies like Department of Biotechnology, Department of Information Technology, University Grants Commission, Council of Scientific and Industrial Research-JRF/SRF, Department of Science and Technology, Bioinformatics National Certificate (BINC), DSTInnovation in Science pursuit for Inspired Research (INSPIRE) and Rajiv Gandhi Fellowship. The University is extending full support for the development of the Centre by providing a new state of the art building. From 2012, through UGC Special Assistance Program (SAP) at the DRS-I level, the Centre received ‘ 27,50,000 lakhs + 1 project fellow.
Major research activities in biotechnology and its related fields: Some of the important areas are genomics, proteomics, DNA Protein Interactions, X-ray Crystallography of Macromolecules (Proteins), Molecular Modeling / Simulation of Biomolecules for targeted Drug Discovery, Computational Biology, Molecular Dynamics Simulation, Comparative Genomics, Database & Software Development and Development of Bioinformatics Educational Materials
Area of specialization: Molecular Biology, Systems biology, DNA-Protein Interactions, Genome Sequence analysis, Protein Structure Modeling, Molecular modeling, X-ray Crystallography, Drug Design, Metabolic Pathways and re-constitution, Cell Signaling, Single particle analysis, Medicinal Chemistry, Computational Biology
Major achievements made during 2012-13:
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The Ministry of Human Research & Development (MHRD) has considered our Centre for the Centre of Excellence in Structural Biology.
University approved a separate state of the art building for Bioinformatics Centre now under construction.
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XXIVnd All India BTISnet Coordinators’ Meeting
The Centre has conducted various training programs in Bioinformatics and organized several invited lectures from the experts of India and abroad.
Infrastructure facilities in the Bioinformatics Centre: Computers facility
Tesla GPU Server, Xeon Quad Core-Web Server, Xeon Quad Core-Database Server, Xeon Quad Core-Proxy Server, Xeon Cluster Server, Itanium-Email Server, AMD Opteron-Domain Control Server, Wipro Xeon-Domain Name Server, HP Workstations, Silicon Graphics Fuel Machine, Apple iMac Systems, HCL Laptops, HCL Intel Core i5/Core 2 Duo Workstations (145 nos.)– Works on both Windows and Linux Operating Systems. Communication facility
In addition to the facility provided by the University our Centre has,(i)Dedicated 11 Mbps Leased Line Internet connectivity from BSNL, managed by Cisco 2800, 1800 series routers and by 12 manageable Switches. (ii) Backbone network, which is being operated in 1000baseT technology (IEEE 802.3ab Standard). (iii) LAN each end user is connected to the backbone network at 1000baseT/100baseT standards. (iv) Wi-Fi IEEE 802.11g standard access point is made available in our centre. Wet lab facility
The Centre has developed a separate wet lab facility. The lab is functional with the following equipments: Bio–safety cabinet, Bench Top Freeze Dryer, Cold cabinet, Sonicator, HPLC System, ELISA Reader, Deep Freezers -80°C, UV-Visible Spectrophotometer, Thermo Cycler, Electrophoresis unit, Refrigerated Centrifuge, Quartz Distillation Unit, pH meter, Vertical Gel apparatus, Horizontal Gel apparatus, Western blot apparatus, -20°C Freezer, UV illuminator, Table Top Centrifuge, Thermal Cycler, Gel Documentation System, and Water purification system. The Centre is in a process of establishing a cell culture facility. Scientific Software packages
VLife, Schrodinger Maestro, Tripos Sybyl 8.1, Discovery Studio 3.0, Kaspersky, Amber10, Gromacs, SPSS, Autodock, Dock, Modeller, Gromos 96, Whatif, EMBOSS, BioEdit, Phred, Consed, GeneScan, Statistica, Endnote, R. Resources & Services
A separate in-house designed website is available at www.bicpu.edu.in and is being maintained by the Centre for information about courses, admissions, syllabus, seminar notifications & various opportunities for traineeship/ studentship/ JRF that are updated periodically. Bioinformatics related tools can be downloaded from the site. Databases & other information resources in the Centre
Books: 600 books available in the reference library of the Centre Journals: Science, Nature, Scientific American, Briefings in Bioinformatics, Bioinformatics, Nature Structural and Molecular Biology, Nature Chemical Biology, Cell, Current Science. Magazines : Linux for U, PC Quest, Chip, Biospectrum. Access to E-Journals: UGC Infonet Journals, Science Direct, Blackwell Publishers, EBSCO
Details about staff members working in the centre: Sl.No. Name 1.
Prof. Priya Davidar
2.
Prof. P.P. Mathur
3.
Dr. Basant K. Tiwary
Designation
Specialization
Centre Head
Spatial Ecology & Biodiversity informatics Professor & Head Biochemistry of Reproduction, Molecular Biology, Environmental Endocrinology and Bioinformatics Associate Molecular Evolution, Professor Bioinformatics & Systems Biology
Distributed Information Centres (DICs)
Working Since Aug. 2012
Status Continuing
1991
Aug. 2012
Sep. 2010
Continuing
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February 03-04, 2013
XXIVnd All India BTISnet Coordinators’ Meeting 4.
Dr. Dinakar R. Ampasala
Reader
Biochemistry, Molecular Entomology & Signal transduction
Sep. 2010
Continuing
5.
Dr. P.T.V. Lakshmi
Reader
Phytomatics, Genomics & Proteomics, Biofuel production
Sep. 2010
Continuing
6.
Dr. R. Krishna
Assistant Professor
X-ray Crystallography (Proteins), Molecular Modeling (Protein & DNA)
Dec. 2007
Continuing
7.
Dr. M. Suresh Kumar
Assistant Professor
Structural Studies on Viral Proteins, Promiscuity of Antibodies, Inhibitors for Viral Proteases
Dec. 2007
Continuing
8.
Dr. Archana Pan
Assistant Professor
Comparative Genomics, Proteome Analysis
Apr. 2009
Continuing
9.
Dr. R. Amutha
Assistant Professor
Computational Biology, Molecular Dynamics Simulation
Jul. 2009
Continuing
10.
Dr. B. Syed Ibrahim
Assistant Professor
Structural studies on venom proteins and proteases, Methyl Transferase and Transcription Factor - drug designing
Aug. 2010
Continuing
11.
Dr. A. Murali
Assistant Professor
Structural Biology, Transmission electron microscope, Single particle analysis & Nano Biotechnology
Aug. 2010
Continuing
12.
Dr. S. Mohane Coumar
Assistant Professor
Medicinal Chemistry, Drug Design & Discovery
Sep. 2010
Continuing
13.
Dr. V. Amouda
Assistant Professor
Database Management, Algorithms, Computer Networks
March 1992
Continuing
14.
Mr. M. Sundara Mohan
Information Officer
Internet Technologies, Web Development
Mar. 1992
Continuing
15.
Mr. E. Malanco
Sr. Technical Assistant Internetworking, Operating system, Programming Languages
Nov. 2008
Continuing
16.
Mr. P. Elavarasan
Sr. Technical Assistant Web Programming, Computer Networks
Feb. 2009
Continuing
17.
Mr. S. Manikandan
Sr. Technical Assistant Web Programming, Computer Networks
Jan. 2009
Continuing
18.
Ms. R. Jeyakodi
Teaching Assistant
Networks, DBMS, Programming Languages and Algorithms
Mar. 2010
Continuing
19.
Ms. D. Venmathi
Computer Assistant
-
Nov. 2007
Continuing
29.
Ms. N. Bhanumathi
Data Entry Operator
-
Jan. 2007
Continuing
Educational activities Some of the Institutions/ Industries who have recruited our students are as follows:
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Industry Placements: HCL Infosystems, Tata Consultancy Services, Wipro Technologies Molecular Connections, Bangalore, Institute of Bioinformatics, Bangalore, Protein Lounge, Bhubaneswar, Genemines, Chennai, BIOBASE Databases Indian Pvt. Ltd., Bangalore, Computational Reseach Lab, Pune, Jubilant BioSys, Bangalore, Persistent Systems Limited, Pune
Teaching/ Research Placements: Stony Brook University, New York, Pusan National University, South Korea, Sungkyunkwan University, South Korea, University of Madras, Chennai, Central Sericulture Research & Training Institute, Mysore, Institute of Microbial Technology Institute, Chandigarh, Madurai, Indian Institute of Technology, Chennai, Jawaharlal Nehru University, New Delhi, Kumaun University, Nainital, MANIT, Bhopal, Amity University
Distributed Information Centres (DICs)
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February 03-04, 2013
Papers/ published or presented in the conferences : 1.
Bhattacharjee M, Raju R, Radhakrishnan A, Nanjappa V, Muthusamy B, Singh K, Kuppusamy D, Lingala BT, Pan A, P.P. Mathur, Harsha HC, Prasad TSK, Atkins GJ, Pandey A, and Chatterjee1 A. A Bioinformatics Resource for TWEAK-Fn14 Signaling Pathway, Journal of Signal Transduction, 2012: 376470. doi:10.1155/2012/376470
2.
T. S. K. Prasad, H. C. Harsha, S. Keerthikumar, N. R. Sekhar, L. D. N. Selvan, P. Kumar, S. M. Pinto, B. Muthusamy, Y. Subbannayya, S. Renuse, R. Chaerkady, P. P. Mathur, R. Ravikumar and A. Pandey Proteogenomic analysis of Candida glabrata using high resolution mass spectrometry. J. PROTEOME RESEARCH 11: 247-260, 2012. IF: 5.460
3.
S. Cynthia D’Cruz, R. Jubendradass, M. Jayakanthan, S.J. Amala Rani and P.P. Mathur Bisphenol A impairs insulin signaling and glucose homeostasis and decreases steroidogenesis in rat testis: an in vivo and in silico study. FOOD CHEM. TOXICOL. 50: 1124-1133, 2012. IF: 2.602
4.
R. Muthukumaran, B. Sangeetha, R. Amutha and P.P. Mathur Development of anti-HIV activity models of lysine sulfonamide analogues: A QSAR perspective. CURR. COMPUT.AIDED DRUG DES. 8: 70-82, 2012. IF: 1.521
5.
O.P. Sharma, A. Pan, S.L. Hoti, A. Jadhav, M. Kannan and P.P. Mathur Modelling, docking, simulation and inhibitory activity of the Benzimidazole analogue against ?-tubulin protein from Brugia malayi for treating lymphatic filariasis. MEDICINAL CHEM. RES., 2012 (in press) DOI: 10.1007/s00044-011-9763-5. IF: 1.058
6.
Basant K. Tiwary. The coordinated expression, interaction and evolution of the neuroendocrine genes. Integrative Biology 4, 1377-1385. IF: 4.509
7.
Basant K. Tiwary. The severity of mental disorders is linked to interaction among candidate genes. Integrative Biology 4, 1096-1101. IF: 4.509
8.
Basant K. Tiwary. Correlated evolution of Gonadotropin-Releasing Hormone and Gonadotropin-Inhibitory Hormone and their receptors in mammals. Neuroendocrinology DOI:10.1159/000342694. IF:2.376
9.
Annamalai A, Christina P, Christina V, and Lakshmi P.T.V. Green synthesis and Characteristics of Ag NPs using aqueous Extract of Phyllanthus maderaspatensis L. Journal of Experimental Nano Science. (Manuscript ID TJEN-2011-0061), 2012 (In press). IF:1.011
10.
Subhashini R and Lakshmi P.T.V. Comparative Computational Analysis of Cystic Fibrosis Transmembrane Conductance Regulator Protein to Treat Lung Infections. International Journal of Medical Engineering and Informatics. Int. J. Medical Engineering and Informatics, 4(4):351-361, (DOI: 10.1504/IJMEI.2012.050276), 2012.
11.
R.Sathiskumar, P.T.V.Lakshmi and A. Annamalai. Estimation of biomass contents and phytoconstituent analysis of Enicostemma littorale blume. Int. J. Pharma and Bio Sciences, 3(3):(B) 506-522, July, 2012. IF: 0.47
12.
Saravanan Vijayakumar and P.T.V.Lakshmi. SLocP Tool Box-An integrated platform for predicting sub cellular localization of proteins. Journal of Computational Intelligence in Bioinformatics, 5(2):133-140. (ISSN: 0973385X), 2012.
13.
Ponmari Guruvaiah, Annamalai Arunachalam and Lakshmi Palanisamy Thanga Velan. Evaluation of phytochemical constituents and antioxidant activities of successive solvent extracts of leaves of Indigofera caerulea Roxb using various in vitro antioxidant assay systems, Asian Pacific Journal of Tropical Disease, 2(1):S118-S123, (DOI: 10.1016/S2222-1808(12)60136-4), 2012.
14.
Jayaprakash Chinnappan and Palanisamy Thangavelan Lakshmi. High-throughput virtual screening for novel DHFR inhibitors of P.Jiroveci from the zinc database. Int. J. Applied biology and pharmaceutical technology, 3(4):425-438. ISSN 0976-4550, 2012.
15.
Annamalai A, Christina V.L., and Lakshmi P.T.V. (2012). Evaluation of Genetic Diversity in Cardiospermum halicacabum based on Geographical Variation using RAPD Markers. PHARMACOGNOSY COMMUNICATION. Vol.2 (1) : 62-65, 2012. IF: 0.432.
16.
Lakshmi P.T.V. (2012). Medicinal Plant Informatics. PHARMACOGNOSY COMMUNICATION. Vol.2 (1) : 5-11, 2012. IF: 0.432
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XXIVnd All India BTISnet Coordinators’ Meeting
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17.
J. Muthukumaran, A. Parthiban, H. Surya Prakash Rao andR. Krishna (2012). 6-Ethyl-N-methyl-3-nitro-4nitromethyl-4H-chromen-2-amine.ACTA CRYST. E68, o180-o181. IF: 0.411
18.
M. Kannan, P. Manivel , K. Geetha, J. Muthukumaran, H. Surya Prakash Rao and R. Krishna. Synthesis and in silico evaluation of 1N-methyl-1S-methyl-2-nitroethylene (NMSM) derivatives against Alzheimer disease: to understand their interacting mechanism with Acetylcholinesterase (2012) Journal of Chemical Biology , Volume 5, Issue 4, pp 151-166, doi: 10.1007/s12154-012-0084-z. IF:1.90
19.
Kannan Muthu, Manivel Panneerselvam, Muthukumaran Jayaraman, Nishith Saurav Topno, Arindam Atanu Das & Ramadas Krishna. Structural insights into interacting mechanism of ID1 protein with an antagonist ID1/3-PA7 and agonist ETS-1 in treatment of ovarian cancer: molecular docking and dynamics studies (2012) J Mol Model , Volume 18, Issue 11, pp 4865-4884doi: 10.1007/s00894-012-1489-x
20.
O.P. Sharma, A.A. Das, R. Krishna, M. Suresh Kumar, and P.P. Mathur Structural Epitope Database (SEDB): A Web-based Database for the Epitope, and its Intermolecular Interaction Along with the Tertiary Structure Information. J PROTEOMICS BIOINFORM., 5: 084-089, 2012. doi:10.4172/jpb.1000217
21.
Vijayalakshmi E., O.P. Sharma, Archana Pan In silico identification of potential drug targets in Clostridium difficile R20291: Modeling and virtual screening analysis of a candidate enzyme MurG, Med. Chem. Res. (2012) (in press)
22.
Aditya Sharma and Archana Pan Identification of potential drug targets in Yersinia pestis using metabolic pathway analysis: MurE ligase as a case study, Eur. J. Med. Chem. (2012), vol. 57, 185-195.
23.
M Kohitosh, S Vanessa, A Mikhai, L Eveline, R Helmut, F Mathy, R Amutha, C Arnout, M Andreas, H Piet Solution Structure and Conformational Dynamics of Deoxyxylonucleic Acid (dXNA): An Orthogonal Nucleic Acid Candidate, Chemistry - A European Journal, Vol 18,No.3, pp. 869-879, 2012.
24.
Sangeetha Balasubramanian, Muthukumaran Rajagopalan & Amutha Ramaswamy Structural Dynamics Of Full Length Retroviral Integrase: a molecular dynamics analysis, Journal of Biomolecular Structure & Dynamics, Vol 29, No.6, pp. 659-670, 2012.
25.
Jiann-Yih Yeh, Mohane Selvaraj Coumar, Hui-Yi Shiao, Ta-Jen Lin, Yen-Chun Lee, Hui-Chen Hung, Shengkai Ko, Fu-Ming Kuo, Ming-Yu Fang, Yu-Lin Huang, John T. A. Hsu, Teng-Kuang Yeh, Shin-Ru Shih, Yu-Sheng Chao, Jim-Tong Horng, and Hsing-Pang Hsieh. Anti-Influenza Drug Discovery: Identification Of Orally Bioavailable Quinoline Derivative Through Activity And Property Guided Lead Optimization. ChemMedChem 2012,7,15461550. IF: 3.1
26.
Subhalaxmi Mohanty, Amouda Nizam & Monalisha Biswal IntDb: A Comprehensive Database for Classified Introns of Saccharomyces & Human, Journal of Bioinformation, Volume:8(5), pp-233-236. (2012)
Initiation of R&D activities in Bioinformatics: A number of sponsored research projects are carried out by the faculty of the Centre from various funding agencies like DBT, DIT, and UGC etc.
Details of Training/Workshop organized and total no of user trained
52
National Seminar Cum Workshop on Perspectives Of Chemoinformatics For Drug Discovery February 21 & 22, 2013(proposed)
National Seminar Cum Workshop on Drug Discovery and Translational Research February 14 & 15, 2013 (proposed)
National Seminar on Emerging Trends in Structural Biology & Bioinformatics between September 26-28, 2012
National Seminar cum Workshop on Drug Design and Industrial Applications between March 7-9, 2012
National Workshop on Statistical Computing in Life Sciences between February 27 - March 4, 2012
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XXIVnd All India BTISnet Coordinators’ Meeting
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Impact shown by the Centre:
The Centre started offering a Master’s program in Computational Biology under DBT Network Program in 2010.
The Centre started offering a Master’s program in Bioinformatics in 2007, which is funded by the University Grants Commission (UGC) under its scheme of Innovative Program in Emerging Areas in Teaching and Research.
The Centre has been identified as a Centre for Excellence in Bioinformatics Teaching and Research by the Department of Information Technology, Ministry of Communication & Information Technology, New Delhi.
The Centre has been able to achieve many targets towards training and manpower development in bioinformatics.
The Centre has been able to fill the teaching and non-teaching positions.
Projects in the areas of comparative genomics, structural analysis, homology modeling, molecular docking and E-learning module in Bioinformatics are being completed.
The Centre has created a big impact in Pondicherry University and surrounding institutions towards teaching and research in Bioinformatics.
Our Centre is collaborating with many other institutions like Vector Control Research Centre, IICT, Hyderabad and Industries in some projects.
Conducted various training programmes in Bioinformatics and arranged several invited lectures.
The Centre has helped various Universities/ Colleges for curriculum development & training.
Proposed activities for 2013-14
Strengthen the existing programmes and strive to get continuation of the Centre of Excellence from DIT and would get Centre of Excellence from DBT.
We would like the start the following new programmes,
a)
Ph.D in Computational Biology
b)
Diploma Course in Bioinformatics as add on course
c)
The Centre will conduct Special Lectures/ Training in Bioinformatics and Computational Biology through video conferencing
d)
Establishment of potential of Excellence in Structural Biology
Strengthen the existing research program & aggressively pursue research in various areas like Structural Biology, Genomics & Proteomics, Molecular Modelling, Drug Design, Computational Biology, Translational Research and Synthetic Biology.
Contact details: Name of the Coordinator Postal Address
Phone Number Fax No. Email Website Name of Contact Person
Prof. Priya Davidar Prof. Priya Davidar, Centre Head, Centre for Bioinformatics Pondicherry University, Pondicherry – 605 014 +91-413-2655212 +91-413-2655211
[email protected] [email protected] www.bicpu.edu.in Prof. Priya Davidar
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University of Calcutta, Kolkata Coordinator: Prof. Subhasis Mukhopadhyay Summary of the progress made by the centre from its inception: The Centre has become a hub of the Bioinformatics related activities of the host institute and acts as a major resource center for the extra-mural support as regards teaching, research and related activities.
Major research activities in biotechnology and its related fields: The center has the following three major groups in the area of in-silico biology and a small collaboration with developmental biology and plant biotechnology groups of the host institute. a)
Computational Linguistics, Comparative Genomics and QSAR studies,
b)
Simulation of modified RNA, Structural Analysis of Protein DNA interaction and simulation of cellular pattern formation and dynamics.
c)
To understand the regulatory principle of A. Thaliana and O. Sativa, to identify the genetic blueprint and their regulation in spinal chord regeneration of Zebrafish, to identify the potential structural and functional units of metabolic and transcriptional regulatory pathways, to reconstruct and analyze the genome scale metabolism of rice.
Area of specialization: Human Resource Development
Major achievements made during 2012-13: Induction of new human resource development strategy and opening up of new research area.
Infrastructure facilities in the Bioinformatics Centre: The center is equipped with state-of-the-art computational facility, buttressed with a 5mbps out-going internet highway.
Details about Staff members working in the centre: Sl.No. Name 1. Subhasis Mukhopadhyay
Designation Professor
2.
Sudip Kundu
Associate Professor
3. 4. 5.
Ansuman Lahiri Assistant Professor Ms Sutapa Dutta Trainne Ms Rachana Banerjee Trainee
Specialization Computational Biology and Bioinformatics Computational Biology and Bioinformatics Do Do Do
Working Since 2001
Status Permanent
2001
Do
2001 2010 2010
Redeployed Temporary Do
Educational activities Invited Lectures:
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1.
Sudip Kundu - Modeling the rice leaf metabolism at various conditions, Indo-US Workshop on Cyanobacteria: Molecular Networks to Biofuels, Dec, 2012
2.
Sudip Kundu - Application of Elementary Modes to Real Systems, Workshop on Metabolic Modeling, ICGEB, 2012
3.
Sudip Kundu - Modeling rice metabolism and its regulation, SBC India, 2012
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Award: DBT-CREST Award to Sudip Kundu (March-July, 2012) Sudip Kundu - BBSRC India-UK Partnering Award on Predictive modelling of the rice metabolic network, 2009-13
Papers/ published or presented in the conferences : Papers published: 1.
Dhriti Sengupta and Sudip Kundu*, Role of long- and short-range hydrophobic, hydrophilic and charged residues contact network in protein’s structural organization, BMC Bioinformatics 2012, 13:142 doi:10.1186/ 1471-2105-13-142
2.
Dhriti Sengupta and Sudip Kundu*, Do topological parameters of amino acids within protein contact networks depend on their physico-chemical properties?, Physica A 391(17), 4266–4278, 2012
3.
Rahul Shaw, Suma DebSarma and Sudip Kundu*, An algorithm for removing stoichiometric discrepancies in biochemical reaction databases, Current Science, 103, 1328-1334, 2012
4.
Dhriti Sengupta and Sudip Kundu*, Role of physico-chemical properties of amino acids in protein’s structural organization: A Network perspective, M.A. Lones et al. (Eds) IPCAT 2012, LNCS 7223, pp74-81, Springer-Verlag Berlin
5.
Rachana Banerjee* & Subhasis Mukhopadhyay , Niche specific amino acid features within the core genes of the genus Shewanella, Bioinformation 8(19): 938-942 , 2012
6.
Sutapa Datta and Subhasis Mukhopadhyay, An in silico identification of human promoters: a soft computing based approach, Current Bioinformatics, 2013, in press
7.
Sutapa Datta and Subhasis Mukhopadhyay, A composite method based on formal grammar and DNA structural features in detecting human polymerase II promoter region, PLOS ONE 2013, in press
Conference Presentation: 1.
Aditya Kumar Sarkar and Ansuman Lahiri “Structural insight into ABF1-ABRE interaction: a model building approach” at IBS 2012, Chennai, 19-21 January 2012.
2.
Aditya Kumar Sarkar and Ansuman Lahiri “Understanding ABFs :Dimerization and Interaction with ABREs” at Two day national seminarcum workshop on “Probing Biology: in vitro, in vivo, in silico -II”.venue- Department of Botany, Visvabharati, Santiniketon, 3-4 December 2011. Awarded a prize for the poster.
3.
Saikat Dutta Chowdhury and Ansuman Lahiri “Simulating shape transtions in pavement cells” at Mesoscopic origin of cell behaviours during tissue morphogenesis Carghese, 29 April - 5 May, 2012
4.
Indrajit Deb “Structural and dynamical aspects of modified ribonucleosides in tRNA : The role of 2'-Omethylcytidine (OMC) and 2'-O- methylguanosine (OMG) at the anticodon stem loop (ASL) of yeast tRNAPhe” during the Annual Symposium of the Indian Biophysical Society (IBS-2012) organized by Madras School of Biophysics, Department of Crystallography and Biophysics, University of Madras, January 19-21, 2012.
5.
Saikat Dutta Chowdhury and Ansuman Lahiri “Pavement Cell Shape: An Analysis.” Annual Meeting of The Indian Biophysical Society; January 19-21 (2012)
6.
Saikat Dutta Chowdhury and Ansuman Lahiri “Pavement Cell Shape: An Analysis.” Recent Advances in Chemical & Physical Biology; SINP, India and Mechanobiology Institute, Singapore. March 5-7 (2012)
Initiation of R&D activities in Bioinformatics: Systems Biochemistry The group has 15 registered Ph. D students and two students had obtained their Ph.D degree during the year.
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Details of Training/Workshop organized and total no of user trained We are going to organize an International conference on Systems Biology of Plants and Microbes on 21st and 22nd January, 2013. The four European and seven Indian scientists had confirmed their participation to give their talks.
Impact shown by the Centre: We have reconstructed a genome scale metabolic model of rice (Oryza sativa) which can generate the biomass from its inorganic nutrients with the help of light energy. The result of preliminary analysis of metabolic response of rice under different conditions are already presented in several international conferences and the manuscripts are under preparation. This model would help the rice biotechnologist to design the more efficient rice cultivars.
Proposed activities for 2013-14 We plan to expand our teaching and research activities by introducing novel areas of studies and improving collaboration.
Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
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Dr Subhasis Mukhopadhyay Dept of biophysics, Calcutta University, 92 A P C Road, Kolkata 700 009 033-23510359
[email protected] Dr Subhasis Mukhopadhyay
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Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Kharghar, Navi-Mumbai Coordinator: Dr. Ashok K Varma Summary of the progress made by the centre from its inception The Department of Biotechnology (DBT), Government of India, funded to establish the Biotechnology Information Service (BTIS)/Bioinformatics Centre at the Cancer Research Institute in 1989. Since its inception DBT is continuously funding the centre to support infrastructure and softwares. TMC-ACTREC also supports as and when required for gradual maturation of the facility. In addition to expansion of the institutional infrastructure, there is increase in number of full- time users also. In year 2012-13 we have procured one high-end workstation with 24GB RAM for NGS data analysis. Presently, the softwares available in the centre are extensively used by six Principal Investigators which comprise senior and middle level scientists, Ph. D students from ACTREC and number of project trainees from various academic institutes of India. The main theme of the centre is to provide infrastructure, training and software support to the scientists and young investigators working on Basic or translational research projects using bioinformatics based approaches to fulfil the mandate of DBT for setting up the SubDIC centre at ACTREC. BTIS at ACTREC organizes every year a two-day workshop to train faculties/Ph.D. students from various colleges/universities. We provide them training from basic knowledge of bioinformatics to modern approaches/ tools in molecular modelling & drug discovery. This helps them in teaching bioinformatics related subjects in their home institute.
Major research activities in biotechnology and its related fields:
The major focus of the institute is basic and translational research in cancer biology.
The detailed list of scientists working on different aspects of cancer biology and translational research are available in http://www.actrec.gov.in/basic_main.htm.
Activities on data-base analysis, structural bioinformatics, molecular modeling, and structure based drug design.
Molecular profiling of oral, cervix, lung, breast, gastric and brain cancer, hematological malignancies using genomics and proteomics technologies
Molecular imaging for targeting cancer specific genes/proteins
Cancer Immunology
Basic research investigations on cell proliferation, differentiation and metastasis and aberrations in cancer are also ongoing towards identifying molecular targets.
Structural Biology approaches towards understanding proteosomal dynamics, apoptosis and BRACA1 interacting partners
This year centre has started Macromolecular crystallography using X-ray diffraction analysis and Next-GenSequencing based projects.
Area of specialization of the center
Cancer Biology
Basic and Translational research
Structural Biology and Bioinformatics
Medical Imaging in small animals
Cancer Genomics & proteomics
Next -Gen Sequencing
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Major achievements made during year 2012-13
Inhibitor designing for of Gankyrin-ATPase complex.
ATP binding site analysis in 14-3-3 zeta.
Binding partners for Protease HtrA2.
A data base is being made of basic research scientists working on Oral cancer in India. The database will provide information via appropriate links of their ongoing work.
SNPs and Indels analysis of deep sequencing data of brain tumor exomes.
Identification of leads from marine seaweeds against human â-tubulin
Targeting Pim1 kinase for potential drug-development using 3D-QSAR.
Organization of two days workshop.
Training of new JRF (batch 2011-12) of Institute registering for their Ph. D degree.
Training of M. Sc., M. Tech., Ph.D. students of neighboring Institute so that they can use the bioinformatics based approaches in enhancing their carrier/research work.
Elucidation of MAPK pathways using in-silico tools.
Checkpoint kinases and anti-cancer drug design.
Infrastructure facilities in the Bioinformatics Centre A.
Computer & Communication facility:
This year one-high end graphics workstation with 24GB RAM has been added. In addition, we have very good Linux based IBM servers, purchased using DBT grant, and are used as the Internet and mail servers. Total we have six workstations for Molecular dynamics and NGS data analysis. B.
Scientific Software packages: Sybyl from Coordinator grant.
C.
Databases & other information resources: Database on oral cancer genes and Histone database (See 11 below)
Details about Staff members working in the centre All staff on DBT funding was absorbed by the institute way back in 1994. The centre has one full time Scientist D, Mr. Nikhil Gadewal, with a post graduate degree in Biotechnology and a diploma in Bioinformatics who provides full support to users. Centre is also supported by staff from IT department of Institute and biostatistics personnel who are permanent staff of the Institute as and when required. However A support staff is needed to assist the permanent staff for bioinformatics based calculation, analyzing the data from recently started activities like proteomics, microarray, and next-generation sequence data analysis. 2.
Types of services provided:
Training from basics tools to modern approaches in bioinformatics to scientific staff/doctoral students of Institute and also neighboring institutes;
Special emphasis is to train scientific staff, and post graduate students of basic sciences from academic institutes in the state.
Institute organizes two days open day, on this day we call most of the colleges of Mumbai and make them aware of the latest technologies and research on Cancer.
Educational activities : Nil Initiative to validate the outcome of bioinformatics resources:
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Each year there are about ~ 50 short- term trainees from different parts of the country who undertake their B.Tech/M.Tech/M Sc dissertation with the faculty at ACTREC and utilize the facility.
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Good numbers of students/academic staff members from Mumbai and nearby institutes also regularly access the facility/take suggestions relevant to their work from BTIS staff.
Collaborative works/ initiatives: Nil
Databases/ Software packages developed: The Oral cancer data-base of genes involved in oral cancer. The new markers (genes) were also identified by comparing the gene lists from published articles
A new database was developed here and uploaded on our website. (URL-http://www.actrec.gov.in/OCDB/ index.htm).
A new Histone database was uploaded on our website (http://www.actrec.gov.in/histome/index.php)
Papers/ published or presented in the conferences
Pruthvi Raj Bejugam, Raja R Kuppili, Nitu Singh, Nikhil Gadewal, Lalith K. Chaganti, G. Madhavi Sastry, Kakoli Bose, Allosteric regulation of serine protease HtrA2 through a novel non canonical substrate binding pocket. PloS One. 2013 (Accepted)
Selvaa KC, Gadewal NS, Mohammed SM. Identification of leads from marine seaweeds against human â-tubulin. Letters in Drug Discovery, 2013, 10:67-74.
Gadewal NS and Varma AK. Targeting Pim1 kinase for potential drug-development, Int J Comput Biol Drug Des., 2012; 5(2):137-151.
Badjugar DC, Sawant U, Mahadik H, Gadewal NS, Varma AK. Pathogenicity of mutations discovered in BRCA1 BRCT domains is characterized by destabilizing the hydrophobic interactions. J Cancer Sci Ther, 2012, 4(11): 386-393.
Satyajeet P. Khare, Farhat Habib, Rahul Sharma, Nikhil Gadewal, Sanjay Gupta, and Sanjeev Galande, HIstome— a relational knowledgebase of human histone proteins and histone modifying enzymes, Nucleic Acids Research, D337–D342, (40) 2012
Nikhil S Gadewal & Narendra N Joshi, In silico analysis of peptide binding features of HLA-B*4006, Indian Journal of Experimental Biology, Vol.50, January 2012,
Initiation of R&D activities in Bioinformatics
Bioinformatics based approaches for retrieval of scientific information and further validation.
Protein-protein interactions, protein-drug interactions, molecular modeling and structure based receptor design are an integrated approach of this centre.
Genomics and Proteomics data analysis for oral cancer, cervical cancer, brain cancer and hematological malignancies using bioinformatics.
Recently in 2011, Expertise in Next- Gen-Sequencing has been introduced.
Details of Training/Workshop organized and total no. of user trained
ACTREC, Tata Memorial Centre-SubDIC center provides two days lectures cum hands- on- training workshop, targeting colleges/universities lecturers and research scholars. For this calendar year, the workshop was on February 9th-10th 2012. There were 14 participates. The lectures were from scientists having expertise on basic bioinformatics, proteomics, biological databases, sequence analysis, structural bioinformatics and drug designing. The workshop started with the welcome remark from Dr. Rajiv Sarin (Director) and Dr. Surekha Zingde (Dy. Director) followed by talk entitled ‘Study of Antisense PNA targeted to primer template complex of HIV-1 and Effect of modified bases present in the tRNALys3’ from Dr. Uddhavesh Sonawane - CDAC, Pune. The basics of bioinformatics were covered by Nikhil Gadewal on Database, sequence and structure analysis. Dr. Ashok Varma delivered talk on ‘Structural bioinformatics and translational research’. An expert in bioinformatics was invited from other academic/industrial institutes to deliver a special lecture every year. In the year 2012 the key note
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speaker for first day was Dr. Petety Balaji from IIT Bombay, Mumbai who presented a case study for annotations of hypothetical proteins. Next day key note speaker was Dr. V. N. Balaji, Jubilant Biosys Ltd., Banglore entitled ‘Development of docking screening protocol for enzyme inhibitor hit identification and lead optimization: A case study for HIV Protease Inhibitors’. Dr. Shailza Singh from NCCS covered detailed talk on homology modeling. The other speakers were Amit Dutt, Prasanna Venkatraman, K, Bose, R Govekar from ACTREC. The morning session was for lectures and afternoon was hands –on- workshop. Hands on session covered data bases retrieval, protein structure visualization, prediction of secondary and tertiary structures, its validation, molecular modeling and dynamics.
A special program for the Bioinformatics faculty/coordinator from North-East Region of the country was organized by the centre. Each faculty got hands- on -training on gene cloning, protein purifications and crystalliza tion. The training details will be provided separately to DBT. ~7 students were provided six months training on Database development, protein modeling and structure activity relationship, microarray analysis, next- gen data analysis.
Impact shown by the Centre
Papers published from the center-90, Book chapter-2 ;
Invited lectures by the scientists of BTIS-ACTREC in neighboring Universities/colleges and other part of country .
There is a growing demand from many city colleges/institutes to hold the bioinformatics workshop twice in a year for three days.
Increasing demand from students from various part of country to undertake projects at the centre
Proposed activities for 2013-14:
Organizing
Workshop on Cancer Informatics workshop using NGS data analysis on 28-30 Jan 2013
Workshop on Basics of Bioinformatics on February 21st -22nd, 2013 and January 30th -31st, 2014.
Infrastructure and expertise development in molecular-dynamics, Microarray data analysis, Next- Gen Sequencing.
Structural dynamics of nucleosome core particle containing homomorphous histone variants:
National Cancer Data Base for Translational Research
Proteomics of metastasis
Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
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Dr. Ashok K Varma Bioinformatics Centre, Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Kharghar, Navi Mumbai - 410 210. 022-2740 5112 022-2740 5085
[email protected];
[email protected] www.actrec.gov.in Dr. Ashok K Varma
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Aligarh Muslim University, Aligarh Coordinator: Dr. Asad Ullah Khan Summary of the progress made by the centre from its inception: The Distributed Information Sub-Centre was established by the DBT, New Delhi at Aligarh Muslim University, Aligarh in the academic session 1988-89. The main function of the Centre is to act as a member of Bioinformatics Network System for providing information to the interested users on topics pertaining to the relevant areas of Biotechnology specially protein folding and design, protein structure and protein engineering. The functions of the Centre include, among others, acquisition, creation and development of programmes and databases needed by the users. For the last several years, Centre is contributing significantly for the manpower development by organizing workshops and courses in the field of bioinformatics. Since its inception the Centre has organized 17 national level bioinformatics workshops and trained more than 400 participants from different universities and institutions. Centre is regularly organizing seminar lecture for the benefit of students, researchers and scientists working the area of biotechnology or in the areas related to biotechnology. Centre is regularly providing Internet facility for its users since 1994. Recently a dedicated 512 kbps BSNL leased line and a 2 mbps broadband connection has been installed and is functioning satisfactorily in providing online literature search etc.
Major research activities in biotechnology and its related fields: Right from its establishment, the unit has been concentrating on research in various aspects of protein biotechnology and efforts continue in this direction, in addition to those in immunology and molecular biology. One aspect that is being actively pursued is the stabilization of enzymes with the help of polyclonal antibodies. Attempts are currently being made to identify regions of the enzyme that are crucial for enzyme stability and raise antibodies against the regions in experimental animals. Another group is actively engaged in the study of pathways leading to various folding intermediate of proteins, which involves the characterization of various intermediates. Moreover development of liposome-based vaccines to project against various antifungal diseases are also in pipeline. Mechanism of ESBL and MBL among E. coli and Klebsiella pneumonia with special reference to CTX-M and NDM-1 enzymes has been characterized. Synthetic and natural molecules are screened and designed by computational approach and validated their interaction with recombinant enzymes. Moreover, novel compounds from plant sources and Nanoparticles of various biomaterials have been characterized as antimicrobial, anti-adherence and anti-biofilm against microbial infections. Role of drugs in transcription regulation via histone modulation has also been studied. Area of Specialization of the centre : Basic Biotechnology
Major activities of the centre during the year 2012-13: Distributed Informatics Sub-Center is involved in bioinformatics research in the fields of drug designing and drug-protein interaction. Dr. Asad Ullah Khan, Associate Professor and Coordinator is working in this area and received a project entitled “ Designing inhibitors against betalactamases :Putative drug candidates against drug resistant bacterial strains of infectious diseases’’ from DBT, New Delhi with a total sanctioned grant of Rs. 36.2 lakhs from 2010 to2013. Workshops on Bioinformatics : Workshop on “Bioinformatics in Drug Discovery” held during March 21-22, 2012 in which 25 participants were trained. E-Mail and Internet Facility : The Centre is regularly providing INTERNET facility to the users through BSNL dedicated 512 kbps leased line and BSNL 2 mbps Broad Band Connection which has recently been procured by the Centre. CD-ROM Databases Facility : The CD-ROM databases facility of the Centre is being regularly used by the students, researchers and teachers of this University for the retrieval of scientific information. Scientific Software Facility : Among others, Centre has procured few scientific softwares like Sigma Plot, DTMM, Reference Manager, Enzfitter, Instat, Peakfit, which are being regularly used by the students and researchers of this University.
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Bioinformatics teaching: A paper entitled “Biostatistics & Computer Applications” has been introduced in the curriculum offered to M.Sc. Biotechnology course. Inhouse Databases: These are Proteolytic enzyme database, Immobilized metal affinity chromatography database, Human Vaccine database. Databases/ Software packages developed: Resently Dr. Asad’s lab has developed two data bases (1) BLAD for Betalactamase (unpublished) and (2) AMDD: Anti-Microbial Drug Database (published) Collaborative works/ initiatives: we are collaborating with JNU, New Delhi, ICGEB, New Delhi, JALMA, Agra
Infrastructure facilities in the Bioinformatics Centre: a.
Computer & Communication facility: The Bioinformatics Centre is now fully equipped with BSNL dedicated 512 kbps leased line and BSNL 2 mbps Broad Band Connection, One servers, 25 Pentium IV systemss with two dot matrix printers, three laser printers, one scanner, one photocopier and a fax machine.
b.
Scientific Software packages: Sigma plot, Grafit, Reference Manager, DTMM, Instat, Buffer Maker
c.
Databases & other information resources: Medline and Biotechnology Abstracts
d.
Journals: European Journal of Biochemistry, Science, New Scientist, Trends in Biochemical Sciences and Trends in Biotechnology, Nature, New Scientist, Nature Biotechnology etc.
Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Sl. No. 1. 2. 3.
Name S. Faisal Maqbool Parveen Salahuddin S. Aqtedar Husain
Designation Sr. Scientific Officer Sr. Res. Assistant Data Entry Operator
Working Since 23 years 22 years 22 years
Status Absorbed Absorbed Absorbed
Educational activities:
Bioinformatics teaching:
Multimedia and E-learning initiatives:
Long term research training programmed for fresh M.Sc/ PG Diploma bioinformatics students.
Papers/published or presented in the conferences:
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1.
Khan AU. (2012) “Nanodrugs: optimism for emerging trend of multi-drug resistance” International Journal of Nanomedicine :4323-4. (IF: 3.2).
2.
Khan, SN, Danishuddin, M, Varshney, B, Lal, SK and Khan, AU (2012) “Inhibition of N-terminal lysines acetylation and transcription factor assembly by epirubicin induced deranged cell homeostasis” PloS ONE 7(12): e51850. doi:10.1371/journal.pone.0051850 (IF: 4.4).
3.
Khan, S, Alam F, Azam A, and Khan AU. (2012) “Gold nanoparticles enhance methylene blue induced photodynamic therapy: A novel therapeutic approach to inhibit Candida albicans biofilm” International Journal of Nanomedicine 7: 3245-57 (IF: 3.2).
4.
Khan AU and Ali SZ (2012) “Quick screening and easy detection method of NDM-gene in clinical isolates: A need of the time” Asian Pas. J Trop Med. 5(10):839-40.
5.
Hasan, S., Danishuddin, M., Adil, M., Singh, K., Verma, P.K, Khan, A.U.(2012) “ Efficacy of E. officinalis on the cariogenic properties of Streptococcus mutans: a novel and alternative approach to suppress quorum-sensing mechanism” PloS ONE 7(7):e40319. (IF: 4.4).
6.
Parveen M., Ali A., Alam M, Khan AU., Ahmad A. (2012) “Synthesis, characterization, biological evaluation and in silico screening of oxadiazinanones” Med Chem Res ( in press) (IF: 1.3)
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7.
Ahmad A, Khan AU, Rauf, A. (2012) “Synthesis and evaluation of in vitro antimicrobial activity of novel 2,3disubstituted-4-thiazolidinones from fatty acid hydrazides” Med Chem Res. ( In press) (IF: 1.3)
8.
Latif A., Ahmad S, Khan, AU., and Rehman, S (2012) “In-vitro antibacterial screening of swertia chirayita linn. against some gram negative pathogenic strains” Internattional Journal of Pharmaceutical Research and Development. 4(4-0974-9446):188-194.
9.
Khan AU, (2012) “ Medicine at nanoscale: a new horizon” International Journal of Nanomedicine 7: 2997-98. (IF: 3.2)
10.
Khan R, Adil M, Danishuddin M, Verma P and Khan A U. (2012) “ In vitro and in vivo inhibition of Streptococcus mutans biofilm by Trachyspermum ammi seeds: an approach of alternative medicine” Phytomedicine 19(89):747-55. (IF: 3.2)
11.
Khan AU, Nordmann, P (2012) “Spread of carbapenemase NDM-1 producers: the situation in India and what may be proposed” Scand. J Infec Diseases 44(7):531-5. (IF: 2).
12.
Khan, A and Khan AU. (2012)“ Biomarker discovery and drug developmemt: aproteomic Approach” Journal of Proteomics and Bioinformatics 5: 3-4 (IF: 2.2)
13.
Danishuddin M and Khan AU. (2012) “Molecular modeling and docking analysis of Beta-lactamases with known inhibitors: a comparative study” In Silico Biology 11(5):273-80.
14.
Tabassum S, Parveen M, Ali A, Alam M, Ahmad A, Khan, A U, Khan, RA (2012) “ Synthesis of Aryl-1,2,4,5tetrazinane-3-thiones, in-vitro DNA Binding Studies, Nuclease Activity and its Antimicrobial activity” Journal Molecular Structure 1020: 33-40 (IF: 1.7)
15.
Danishuddin M, kaushal L, Beig M H and Khan A U. (2012) “AMDD: Anti-Microbial Drug Database” Genomics Proteomics and Bioinformatics in press. (IF: 1.0)
16.
Khan AU and Nordmann, P. (2012) “ NDM-1 producing E cloacae and K pneumonia from diabetic foot ulcer in India” J Med Microbiology 61(Pt 3):454-6. (IF: 2.5)
17.
Haque, S F , Ali, SZ, Mohammed TP1, Khan, A.U. (2012) “Prevalence of plasmid mediated blaTEM-1 and blaCTXM-15 type Extended spectrum beta-lactamases (ESBL) in patients with sepsis” Asian Pacific Journal of Tropical Medicine (2012) 5: 412-420. 1. Khan AU. “Nanodrugs: optimism for emerging trend of multi-drug resistance” International Journal of Nanomedicine 7:4323-4. (IF: 3.2).
18.
Qadeer A, Rabbani G, Zaidi N, Ahmad E, Khan JM, Khan RH. (2012) 1-Anilino-8-Naphthalene Sulfonate (ANS) Is Not a Desirable Probe for Determining the Molten Globule State of Chymopapain. PLoS One. 2012;7(11):e50633. doi: 10.1371/journal.pone.0050633.
19.
Naqvi Z, Ahmad E, Khan RH, Saleemuddin M. (2012) Non-native States of Bovine Beta-Lactoglobulin Induced by Acetonitrile: pH-Dependent Unfolding of the Two Genetic Variants A and B. Cell Biochem Biophys. [Epub ahead of print]
20.
Kumar S, Ahmad E, Kumar S, Khan RH, Gourinath S. (2012) Flexibility of EF-hand motifs: structural and thermodynamic studies of Calcium Binding Protein-1 from Entamoeba histolytica with Pb2+, Ba2+, and Sr2+. BMC Biophys. 5(1):15. doi: 10.1186/2046-1682-5-15.
21.
Ahmad E, Rabbani G, Zaidi N, Khan MA, Qadeer A, Ishtikhar M, Singh S, Khan RH. (2012) Revisiting ligandinduced conformational changes in proteins: essence, advancements, implications and future challenges. J Biomol Struct Dyn. 2012 Aug 13. [Epub ahead of print
22.
Tabassum S, Al-Asbahy WM, Afzal M, Arjmand F, Khan RH. (2012) Interaction and photo-induced cleavage studies of a copper based chemotherapeutic drug with human serum albumin: spectroscopic and molecular docking study. Mol Biosyst. 8(9):2424-33.
23.
Khan AB, Khan JM, Ali MS, Khan RH, Kabir-Ud-Din. (2012) Interaction of amphiphilic drugs with human and bovine serum albumins.Spectrochim Acta A Mol Biomol Spectrosc. 2012 Nov;97:119-24. doi: 10.1016/ j.saa.2012.05.060. Epub 2012 Jun 7.
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Haque, R., Anwar, S., Alam, M.F., Younus, H., (2012) Effect of divalent cations on the activity and conformation of yeast alcohol dehydrogenase. J. Proteins and proteomics 3 (2012) 111-116.
Initiation of R&D activities in Bioinformatics: NO
Initiative to validate the outcome of bioinformatics resources
Organizing workshop in bioinformatics for manpower development.
Providing online services through BSNL dedicated 512 kbps leased line and BSNL 2 mbps Broad Band Connection for literature search etc.
Providing offline services using CD-ROM database (Medline, Life Science Collection and Biotechnology Abstracts).
Providing scientific softwares like Sigma plot, Grafit, Reference Manager, DTMM, Instat, Buffer Maker and a number of word processing softwares for the routine use of researchers and teachers.
Details of Training/ Workshop organized and total no. of user trained The centre has organized 19 workshops since 1994 and has trained more than 450 users so far. Impact shown by your centre: Centre is involved in bioinformatics research in the fields of genome and proteome analysis. Faculties are in process of elucidating mechanism of multiple drug resistance in bacteria with special reference to ESBL (extended spectrum beta lactamase) and recently known enzyme, NDM-1 among E. coli and Klebsiella pneumonia isolated from Hospital infections. Whole family of CTX-M genes was characterized by PCR amplification and sequencing. Genetic features (Tn and IS elements) associated with these resistant markers were also studied using shotgun sequencing approach and PCR amplification. This basic research provided a significant information to design the lead molecules (Drug candidate). The new inhibitors have been designed against NDM-1 and CTX-M variants. Many synthetic molecules after being screened by virtual screening from Zinc Database, were tested against multidrug resistant clinical strains. Different in silico tools were used to map the drug/inhibitor binding sites on these enzymes. Moreover, these enzymes were cloned from clinical multidrug-resistant strains and expressed protein was studied for the interaction with putative drug candidate in vitro using various spectroscopic approaches. This study has concluded a significant molecules which may be a future drug candidate against multidrug resistant strains including NDM-1 Superbug. My group has also revealed mode of action of natural and synthetic molecules including, Nanoparticles against biofilm and adherence of S. mutans and Candida as an alternative approach to control infections. Gene expression of biofilm forming genes and other virulence factors were also studied using quantitative RT-PCR. Biochemical as well as microscopic characterization (confocal, SEM and TEM) has also been performed to understand the mode of mechanism of inhibition of Biofilm. We have also identified interaction of drugs on Basal Transcription Machinery. A hypothesis was proposed whether drugs interact transcriptional machinery via interfering with histone modulation. To prove this hypothesis in vitro histone modulation assays were performed in the presence of different drugs. Furthermore, we have confirmed inhibition of acetylation (as key regulator) by many biochemical and immunochemical approaches using monoclonal antibodies against H3K14 (Histone 3 Lysine 14 position). Moreover, binding sites were also characterized using several bioinformatics tools, biophysical techniques and autoradiagraphy. More than 24 papers have been published using bioinformatics facilities(see above list). Databases: (i) Proteolytic enzyme database (ii) Immobilized metal affinity chromatography database (iii) Human Vaccine database Software: AMACAN: An hydrophobicity analysing software for protein and amino acid sequences developed in visual basic and MS-Access for the routine use of students and teachers.
Proposed activities for 2013-14:
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Data base development (1) BLAD for Betalactamase (unpublished) and (2) AMDD: Anti-Microbial Drug Database (published).
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Organising workshops on bioinformatics. Organising seminar lecture programmes in the areas of bioinformatics and biotechnology Online access to E-journals, softwares etc.
Contact details: Name of the Coordinator Postal Address Phone Number Fax No.
Dr. Asad Ullah Khan Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh – 202 002. 0571-2720388, 0571-2721776
Email Name of Contact Person
[email protected],
[email protected] Dr. Asad Ullah Khan
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All India Institute of Medical Sciences, New Delhi Coordinator: Prof. Y.D. Sharma Major activities of the centre during the year 2012-13 BTIS provided support for three major activities of our department namely (i) Teaching: All practical classes of Bioinformatics and Computers module of M.Biotechnology (ii) Research: Active research was carried out in the field of infectious diseases including malaria & tuberculosis, cancer and cardiac diseases culminating in (iii) Publications, diagnostics and patents.
Infrastructure & Scientific software packages: We have one Sun server with Xenon processor and GcG software for research and teaching in Bioinformatics. Students, research scholars and faculty are using various scientific software like Labwork for Gel Analysis, GraphPad Prism for data analysis and End Note etc. Access to computers and accessories including round the clock internet facility for teaching, scientific research and publication to students, research scholars, office staff and faculty is being provided. Teaching of Bioinformatics: A 4.5 credit point course module in bioinformatics is being run for M,Biotechnology students. The students are imparted with hands on training in the use of various bioinformatics tools and packages. Experts are invited from various academic institutes/centres for delivering lectures on various topics in Bioinformatics to M.Biotech. students. Some of the collaborating institutes/centres include IGIB, New Delhi, SIT, JNU New Delhi, IIT Delhi, Deptt. of Biophysics, AIIMS, Computer Facility, AIIMS and Dept. Of NMR, AIIMS. Software developed: The two-software packages Spectral Repeat Finder and My Pattern Finder developed by us are being used by students for in silico analysis of research hypotheses and are finding support in experimental results.
Initiation of R&D activities in Bioinformatics: In silico analysis of wet-lab. Data and hypothesis formulation using bioinformatics tools available on-line is an integral part of all R&D activities being carried out in our department. Manpower trained: BTIS is providing support to the M.Biotech. Teaching Programme, PhD scholars, MD/MS trainees, WHO fellows, DBT Associates and summer trainees. The total strength of manpower trained is, therefore, greater than 447 till to-date. Impact shown by centre on the growth of biotechnology and allied areas: No. of M.Biotech students trained:
225
No. of PhD scholars passed out
42
No. of PhD scholars enrolled currently
16
No. of Post MD/MS professionals trained
> 17
No. of summer trainees
> 152
No. of WHO fellows trained
21
No. of papers published in 2012
18
No. of patents
16
Publications in 2012:
Papers published in peer-reviewed (Pub-Med indexed) journals in 2012:
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1.
R.K. Tyagi, Y.D. Sharma. Erythrocyte binding activity displayed by a selective group of Plasmodium vivax tryptophan rich antigens is inhibited by patients’ antibodies. PLoS One, 7, e50754 (2012).
2.
M. Zeeshan, H. Bora, Y.D. Sharma. Presence of memory T cells and naturally acquired antibodies in Plasmodium vivax malaria-exposed individuals against a group of tryptophan-rich antigens with conserved sequences. J. Infect. Dis., 207, 175-85 (2012).
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3.
S. Garg, V. Saxena, V. Lumb, D. Pakalapati, P.A. Boopathi, A.K. Subudhi, S. Chowdhury, S.K. Kochar, D.K. Kochar, Y.D. Sharma, A. Das. Novel mutations in the antifolate drug resistance marker genes among Plasmodium vivax isolates exhibiting severe manifestations. Exp. Parasitol., 132, 410–6 (2012).
4.
M. Zeeshan, M.T. Alam, S. Vinayak, H. Bora, R.K. Tyagi, M.S. Alam, V. Choudhary, P. Mittra, V. Lumb, P.K. Bharti, V. Udhayakumar, N. Singh, V. Jain, P.P. Singh, Y.D. Sharma. Genetic variation in the Plasmodium falciparum circumsporozoite protein in India and its relevance to RTS,S malaria vaccine. PloS One 7, e43430 (2012).
5.
P.K. Bharti, M.M. Shukla, Y.D. Sharma and Neeru Singh. Genetic diversity in the block 2 region of the merozoite surface protein-1 of Plasmodium falciparum in central India. Malaria J., 11, 78 (2012).
6.
Y.D. Sharma. Molecular surveillance of drug resistant malaria in India. Curr. Sci., 102, 696-703 (2012).
7.
V. Lumb, R. Madan, M.K. Das, V. Rawat, V. Dev, W. Khan, H. Khan and Y.D. Sharma. Differential genetic hitchhiking around mutant pfcrt alleles in Indian Plasmodium falciparum population. J. Antimicrob. Chemother., 67, 600-8 (2012).
8.
S. Dhingra, K. Kaur, N.K. Taneja and J.S .Tyagi. DevR (DosR) binding peptide inhibits adaptation of Mycobacterium tuberculosis under hypoxia. FEMS Microbiol. Lett., 330, 66–71 (2012).
9.
S. Haldar, N. Sankhyan, N. Sharma, A. Bansal, V. Jain, V.K. Gupta, M. Juneja, D. Mishra, A. Kapil, U.B. Singh, S. Gulati, V. Kalra, J.S. Tyagi. Detection of Mycobacterium tuberculosis GlcB or HspX Antigens or devR DNA Impacts the Rapid Diagnosis of Tuberculous Meningitis in Children. PLoS ONE, 7, e44630 (2012).
10.
S. D. Majumdar, A. Vashist, S. Dhingra, R. Gupta, A. Singh, V. K. Challu, V. D. Ramanathan, P. Kumar and J. S. Tyagi. Appropriate DevR (DosR)-mediated signaling determines transcriptional response, hypoxic viability and virulence of Mycobacterium tuberculosis. PLoS One 7, e35847 (2012).
11.
S. Das, P. Duggal, R. Roy, V. P. Myneedu, D. Behera, H. K. Prasad and A. Bhattacharya. Identification of Hot and Cold spots in genome of Mycobacterium tuberculosis using Shewhart Control Charts. Sci Rep., 2, 297 (2012).
12.
M. Chaduvula, A. Murtaza, N. Misra, N. P. Narayan, V. Ramesh, H. K. Prasad, R. Rani, R. K. Chinnadurai and I. Nath. Lsr2 peptides of Mycobacterium leprae show hierarchical responses in lymphoproliferative assays, with selective recognition by patients with anergic lepromatous leprosy. Infect. Immun., 80, 742-52 (2012).
13.
V. K. Verma, V. Taneja, A. Jaiswal, S. Sharma, D. Behera, V. Sreenivas, S. S. Chauhan and H. K. Prasad. Prevalence, distribution and functional significance of the -237C to T polymorphism in the IL-12Rbeta2 promoter in Indian tuberculosis patients. PLoS One 7, e34355 (2012).
14.
P. Gaur, G.A. Qadir, S. Upadhyay, A.K. Singh, N.K. Shukla and S.N. Das. Skewed immunological balance between Th17 (CD4+IL17A+) and Treg (CD4+CD25+ FOXP3+) cells in human oral squamous cell carcinoma. Cell. Oncol. 35, 335-43 (2012).
15.
M.Y. Karimi , V. Kapoor, S.C. Sharma, S.N. Das. Genetic polymorphisms in FAS (CD95) and FAS ligand (CD178) promoters and risk of tobacco-related oral carcinoma: gene-gene interactions in high-risk Indians., Cancer Invest,1-6 (2012).
16.
V. Kapoor, D. Paliwal, S.B. Singh, B.K. Mohanti, S.N. Das. Deregulated expression of Beclin 1 in patients with tobacco-related oral squamous cell carcinoma. Biochem Biophys Res Commun., 422, 764-9 (2012).
17.
V. Bharti, B. K. Mohanti and S. N. Das. Functional genetic variants of CTLA-4 and risk of tobacco-related oral carcinoma in high-risk North Indian population. Hum. Immuno,l, (2012).
18.
R. Garg, V. Kapoor, M. Mittal, M. K. Singh, N. K. Shukla and S. N. Das. Abnormal expression of PI3K isoforms in patients with tobacco-related oral squamous cell carcinoma. Clin. Chim. Acta 416, 100-6 (2012).
Future activities: The conditions for learning and teaching of Bioinformatics shall be optimized based on the articulated needs and concerns of the students carrying out research in the field of biomedical sciences. Upgradation of Infrastructure Facility will be carried out for teaching purposes. Refurbishing of the website will be carried out.
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Contact details:
Name of the Coordinator: Prof. Y.D. Sharma Postal Address: Dept. of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi-110029. Phone Number:26594609 Mobile: 9868397964 Fax: 26589286 Email:
[email protected] Website:
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www.aiims.edu/aiims/departments/biotechnology
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Banaras Hindu University, Varanasi Coordinator: Prof. A. M. Kayastha Area of Specialization of the Centre: Bioinformatics applications in medical and agricultural sciences. Major Research Activities in biotechnology and its Related Fields : Comparative and Functional Genomics: Complete genome of different species such as plants and microbes are being analyzed for the regulatory cascades and networks that control signal perception, transduction and change in gene expression. Homology Modeling, Protein-Protein Interaction and Protein-Drug Interaction: Structures of enzymes such as -amylase, b-amylase, asparaginase, b-galactosidase, b-lactamase etc are generated by homology modeling. In silico Protein-Protein, DNA-Protein and Protein-ligand interactions to understand the systems biology. Molecular Microbial Diversity: Phylogenetic classification of nucleotide sequence of 16S rRNA genes and protein coding genes to investigate microbial diversity. Bioinformatics study of gene isolated from pathogenic organism characterized from human tissues samples, aquatic, desert plants, coalbeds and contaminated sites. Bioprospecting of Novel Genes by Metagenomics: Clone library from the DNA from the metagenome of the coalbed microbes has been prepared and sequenced to find novel genes that might produce industrially important enzymes. Biomedical Genomics: Protein-Drug interaction, Active binding residues correlation with structural and functional motif.
Educational Activities and Collaborative Initiatives: A course on Bioinformatics and Biostatistics is offered to M.Sc. Biotechnology students. The facility is also used by M.Sc. Bioinformatics students of Mahila Maha Vidyalaya, B.H.U. It is also closely interacting with the Structural Biology group of CDRI, Lucknow; Department of Biotechnology, IIT Guwahati, Biotechnology Unit, Aligarh Muslim University and Hyderabad Central University.
Papers Published in Peer-Reviewed Journals: 1.
Pratyush, D.D., Tiwari, S., Kumar, A. and Singh, S.K. (2012): A new approach to touch down method using betaine as co-solvent for increased specificity and intensity of GC rich gene amplification. Gene, 497: 269-272.
2.
Singh, D.N., Kumar, A., Sarbhai, M.P. and Tripathi, A.K. (2012): Cultivation independent analysis of archaeal and bacterial communities of the formation water in an Indian coal bed to enhance biotransformation of coal into methane. Applied Microbiology and Biotechnology, 93:1337-1350.
3.
Kumari, A., Singh, K. and Kayastha, A.M. (2012): An overview on á-amylases: General properties, mechanism and various perspectives on biotechnological applications. Current Biotechnology, 1: 98-107.
4.
Kumar, S. and Kayastha, A.M. (2012): Characterization of histidine residues of active site of Soybean (Glycine max) urease by chemical modification. Protein and Peptide Letters, 19: 656-661.
5.
Singh, N. and Kayastha, A.M. (2012): Purification and characterization of á-galactosidase from white chick pea (Cicer arietinum). Journal of Agricultural and Food Chemestry, 60: 3253-3259.
6.
Kishore, D. and Kayastha, A.M. (2012): A â-galactosidase from chick pea (Cicer arietinum) seeds: Its purification, biochemical properties and structural aspects. Food Chemistry, 134: 1113-1122.
7.
Kishore, D., Kundu, S. and Kayastha, A.M. (2012) Thermal, chemical and pH induced denaturation of a multimeric â-galactosidase reveals multiple unfolding pathways. PLoS ONE, 7(11): e50380.
8.
Verma, S., Bahorun, T. and Kumar, A. (2012): N-methyl N-nitroso Urea induced altered DNA structure initiate hepatocarcinogenesis. Preventive Medicine, 54: 130-136.
9.
Tripathi, M.K., Kumar M., Singh, V.K., Nath, G. and Asthana, R.K. (2012): Use of enterobacterial repetitive intergenic consensus PCR in detecting Target(s) of Hapalindole-T, from a cyanobacterium, in Escherichia coli: In-silico validation. American Journal of Bioinformatics, 1: 30-40.
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10.
Marla, S.S. and Singh, V.K. (2012): LOX genes in blast fungus (Magnaporthe grisea) resistance in rice. Functional Integrative Genomics, 12: 265-275.
11.
Yadav, S.S., Singh, V.K., Liebau, E. and Rathaur, S. (2012): Molecular modelling and docking of Brugia malayi glutathione reductase. Online Journal of Bioinformatics, 13: 59-79.
12.
Singh, R., Chaturvedi, N. and Singh, V.K. (2012): In-silico study of herbal compounds (baicalin, curcumin and dronabinol) as novel MAO inhibitors for parkinson’s disease treatment. International Journal of Life science and Pharma Research, 2: 81-98
13.
Arora, N., Singh, V.K., Shah, K. and Pandey-Rai S. (2012): Qualitative and Quantitative analysis of 3D predicted Arachidonate 15-Lipoxygenase-B (15-LOX-2) from Homo sapiens. Bioinformation, 8: 555-561.
14.
Singh, V.K., Singh, A.K., Chand, R. and Singh, B.D. (2012): Genome wide analysis of disease resistance MLO gene family in sorghum [Sorghum bicolor (L.) Moench]. Journal of Plant Genomics, 2: 18-27.
15.
Yadav, S.S., Singh, V.K., Liebau, E. and Rathaur, S. (2012): Amplification, In-silico classification, characterization and molecular modeling of Histone H2B gene from Setaria cervi. Online Journal of Bioinformatics, 13:232-245.
16.
Pandey, S., Shrivastava, A.K., Singh, V.K., Rai, R., Singh, P.K. and Rai, S. (2012): A new arsenate reductase involved in arsenic detoxification in Anabaena sp. PCC7120. Rai L.C., Functional Integrative Genomics, PMID: 23086594.
17.
Shahi, S.K., Singh, V.K., Kumar, A., Gupta, S.K. and Singh, S.K. (2012): Interaction of dihydrofolate reductase and aminoglycoside adenyltransferase enzyme from Klebsiella pneumoniae multidrug resistant strain DF12SA with clindamycin: a molecular modelling and docking study. Journal of Molecular Modeling, PMID: 23097003.
Sequence Deposited in NCBI/DDBJ/EMBL: 1.
1 ribosomal RNA gene from Nematoctonus robustus. Singh, R.K. and Singh, V.K. Acc. No. JX866679.
2.
3 TIR domain protein gene form Cajanus cajan cultivars. Singh, V.K., Singh, A.K., Singh, S., Kayastha, A.M., Singh, N.K. and Singh, B.D. Acc. No. JX667781-JX667783.
3.
6 genes from Anabaena species Babele, P.K., Singh, G., Kumar, A. and Singh, V.K. Acc. No. JX481174- JX481179.
4.
6 beta-lactamase genes from Escherichia coli. Shahi, S.K., Kumar, A. and Singh, V.K. Acc. No. JX294479JX294484.
5.
10 ribosomal RNA genes from Nostoc species Singh, G., Babele, P.K., Singh, V.K. and Kumar, A. Acc. No. JX075257-JX075266.
6.
8 genes from Cercospora canescens. Chand, R., Singh, V., Kumar, M., Pal, C., Kumar, P. and Singh, V.K. Acc. No. JX020730 - JX020736.
7.
Dimethyladenosine transferase gene from Escherichia coli. Shahi, S.K., Kumar, A. and Singh, V.K. Acc. No. JX017293.
8.
2 ribosomal RNA gene from Anabaena sp. Babele, P.K., Singh, G., Singh, V.K. and Kumar, A. Acc. No. JQ964321JQ964322
9.
Histone H2B and galectin genes form Setaria cervi. Yadav, S.S., Singh, V.K., Liebau, E. and Rathaur, S. Acc. No. JQ622388 - JQ622389.
10.
Cathepsin B gene from Brugia malayi. Yadav, S.S., Elesela, S., Singh, V.K., Liebau, E. and Rathaur, S. Acc. No. JQ622390.
De novo whole genome sequencing of Cercospora canescens: In collaboration with Mycology and Plant Pathology Department, Institute of Agricultural Sciences, Banaras Hindu University, whole genome shotgun sequences of Cercospora canescens has been deposited at DDBJ/EMBL/GenBank. Chand, R., Singh, V., Singh, V.K., Kumar, M., Pal, C., Kumar, P. and Chowdappa, P., Accession No. ANSM00000000. The version described first version, ANSM01000000. BioProject: PRJNA183604; BioSample accession: SAMN01828531.
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Structures Deposited in PMDB: 1.
Structures of TIR, NB-ARC and LRR domains form Cajanus cajan. Singh, V.K., Singh, A.K., Singh, S., Kayastha, A.M., Singh, N.K. and Singh, B.D. PMDB ID: PM0078097, PM0078232 and PM0078100.
2.
Structures of Beta lactamase proteins (TEM, SHV and OXA) from Escherichia coli. Shahi, S.K., Kumar, A. and Singh, V.K. PMDB ID: PM0078524 - PM0078526; docking complex of OXA, SHV and TEM protein structures with clindamycin and piperacillin-tazobactam were deposited with PMDB ID: PM0078676 - PM0078681.
3.
Structures of Lanosterol synthase and HMG CO A from Mus musculus. Yadav, N., Singh, V. K., Singh, B., Mishra, A. K., Chuttani K. PMDB ID: PM0078335 and PM0078482. Docking complex of both protein structures with macrocyclic aza compounds were deposited with PMDB ID: PM0078597- PM0078600, PM0078606 - PM0078608, PM0078613.
4.
Structures for PAX gene family members from Homo sapiens. Rashmi, Singh, V.K., Gangopadhayay, A. N., Shah, G.L., Rai, S.K., Pandey V., Sarita, Khanna, A., Mohapatra, T. M., Singh, R. PMDB ID: PM0078614, PM0078618 PM0078623.
Database Development: S.No Database Name 1. Lactabase
Description A database for Antibiotic Resistance genes PLANTR A database for Resistance http://www.insilicogenomics.in/r/PLANTR.html gene family Electronic File for MAP http://www.insilicogenomics.in/mapk/mapgenes.ht A database for MAP KINASE GENES Kinase gene family of ml Cajanus cajan LEG-MLO A database for Mlo gene http://www.insilicogenomics.in/mlofamily.html family from legume plants CCWRKY A database for WRKY http://www.insilicogenomics.in/wrky/wrky.html Transcription Factor in Pigeonpea
2. 3.
4. 5.
URL http://www.insilicogenomics.in/general-info.asp
Details of Training Workshop Organized and Total No. of Users Trained: (1) Practical training course on “Bioinformatics Application in Agriculture & Medical Sciences” February 9-11, 2012. Participants: 18 In addition Ms. Meghna Shah, B. Tech Biotechnology, MNNIT, Allahabad, Ms. Lazeena Rizvi and Ms. Sakshi Singh, M.Sc. Bioinformatics students from Banaras Hindu University and Allahabad University, respectively have carried out their 1 month training on the following topics. 1.
WRKY Gene family: Evolution in Pigeonpea
2.
Electronic File for Cajanus cajan Map Kinase Genes
3.
In-silico identification of TNL gene family from Pigeonpea
Furthermore, a large number of M.Sc. and Ph.D students from various Departments of B.H.U visit us to use the softwares available in Bioinformatics centre and seek guidance from Information officer, Mr. Vinay Singh.
Future activities of 2013-2014: The Centre proposes to organize two short training courses annually and development of tool and databases for the benefit of researchers involved in biosciences. The Centre will also be playing an important role in the bioinformatics related needs of various departments of faculty of Science, Institute of Agricultural Science and Institute of Medical Sciences and also involved in the DBT-BHU Interdisciplinary School of Life Sciences.
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Details about staff members working in the centre Name of the staff Mr. Vinay Kumar Singh Mrs. Savita Rani Mr. Dinesh Chaudhary Mr. Raghuveer Sharan Awasthi Mr. Rajendra Prasad
Designation Information officer Programmer Data Entry Operator Data Entry Operator Attendant
Contact details: Name of the Coordinator:
Prof. A. M. Kayastha
Postal Address:
School of Biotechnology, Faculty of Science Banaras Hindu University, Varanasi 221 005
Phone Number: 0542-2368364 Fax No.0542- 2368693/2368174 Email:
[email protected] Website: http://bioinformaticsbhu.tripod.com, www.insilicogenomics.in Name of Contact Person(s): Mr. Vinay Kumar Singh (
[email protected]) Email:
[email protected],
[email protected]
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Banasthali Vidyapith, Banasthali Coordinator: Prof. Vinay Sharma Summary of the progress made by the centre from its inception: In view of rapidly growing importance of Information Technology in Biotechnology teaching and research, communication etc., Centre for Bioinformatics (a sub-DIC under BTIS programme) at Banasthali University was sanctioned by Department of Biotechnology, Govt. of India in November, 1998. Over the last forteen years, this centre has acquired many databases and software’s and has round the clock Internet connectivity.
Major research activities in Biotechnology and its related fields :
To cater the regional and national needs development of specific databases.
The R & D activities in Bioinformatics.
To provide services for the analysis of biological data, bibliographic references to published literature in science and technology (including databases and patents).
Training programmes in Bioinformatics.
Interactions made with Bioinformatics Industries
Area of specialization: Information Dissemination in Biotechnology Bioinformatics R&D & Human Resource Development
Major achievements made during 2012-13:
Published 9 research papers in core bioinformatics and 29 others in biological sciences
Increased number of Sub-DIC including interaction with other departments.
Acquired additional infrastructure facilities including hardware’s, software’s and database.
Infrastructure facilities in the Bioinformatics Centre:
Branded Dell/HP – 4 Nos.
Branded Apple iMac – 2 Nos.
HP Elite Book 8560w Notebook – 1 No
Blu-Ray Disc Writer Internal – 2 Nos.
HP color LaserJet M 451 DN – 1 No
Digital Heavy duty Photocopier make Sharp Ar-5623N build in duplex with complete accessories and stabilizer.1 No
Switch 24 port D-Link – 2 Nos.
Software’s Adobe CS6 Design Premium 6.0 DVD Academic, Red Hat Enterprise Linux Server- AP Standard, Red hat Desktop 1 year basic, Media for Red Hat Products, Oracle 11 g Standard ONE Edition.
Databases Agricola Database (12 month subscription with Quarterly Updates 1984+)
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Details about Staff members working in the centre: Sl.No. 1. 2. 3. 4. 5.
Name Designation Mrs. Shweta Jain Information Officer Mrs. Kiran Shanti Technical Assistant Mr. S.R. Choudhary Computer Operator Mr. Amit Goyal Data Entry Operator Mr. Chandresh Kumar Junior Technical Assistant
Specialization MCA M.Sc. Botany, PGDCA MCA, M.sc Bioinformatics MCSE,CCNA, ‘O’ level MCA
Working Since July 2012 January, 1999 October, 2000 June, 2004 January, 2013
Status Non-Regular Regular Non-Regular Non-Regular Non-Regular
Educational activities M.Sc. Bioinformatics
Papers/ published or presented in the conferences: Research Publications: Core Bioinformatics 1.
Sharma, V., Sekhwal, M.K., Swami, A.K. and Sarin, R. 2012. Identification of drought responsive proteins using gene ontology hierarchy. Bioinformation, 8(13): 595-599
2.
Sharma V, Kuntal H, Katara P, Sharma S. Identification of SSRs in EST sequences of Lolium and Agrostis species. International Journal of Integrative Research (In Press).
3.
Shanker, A. and Sharma, V. 2012. Efficacy of maximum likelihood method and longer sequences in phylogenetic analysis. Res. J. Biotech. 7: 114-118.
4.
Shanker A and Sharma V. 2012. Chloroplast genome analysis to detect transition link between bryophytes and pteridophytes: A Bioinformatics Approach. Archive for Bryology. 121: 1-8.
5.
Katara P and Sharma V. 2012. In Silico Approaches to Predict Gene Distribution Patterns. International Journal of Biomedical Research. 5 (2): 71-74.
6.
Katara P, Grover A and Sharma V. 2012. In Silico Prediction of Drug Targets in Phytopathogenic Pseudomonas syringae pv. phaseolicola: Charting a Course for Agrigenomics Translation Research. OMICS: A Journal of Integrative Biology. 16(12): 700-706.
7.
Kuntal H, Sharma V and Daniell H. 2012. Microsatellite analysis in organelle genomes of Chlorophyta. Bioinformation. 8(6): 255-259.
8.
Sekhwal, M.K., Swami, A.K., Sarin, R. and Sharma, V. 2012. Identification of salt treated proteins in sorghum using gene ontology linkage. Physiology and Molecular Biology of Plants, 18: 209-216.
9.
Sekhwal, M.K., Sharma, V. and Sarin, R. 2012. Identification of MFS Proteins in Sorghum Using Semantic Similarity. Theory in Biosciences, DOI: 10.1007/s12064-012-0174-z
Other Important Research Publications in Biological Sciences
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1.
Chaudhary, S., Pak, J. E., Gruswitz, F., Newby, Z. E., Sharma, V. and Stroud, S. 2012. Overexpressing Human Membrane Proteins in Stably Transfected and Clonal Human Embryonic Kidney 293S Cells, Nature Protocols, 7(3): 453-466.
2.
Alam, A., Behera, K.K., Vats, S., Sharma, D. and Sharma, V. 2012. Impact of Bryo-Diversity depletion on Land Slides in Nilgiri Hills, Western Ghats (South India) –A Study, Archive for Bryology, 122: 1-7.
3.
Mittal, S., Kumari, N. and Sharma, V. 2012. Differential response of salt stress on Brassica juncea: Photosynthetic performance, pigment, proline, D1 and antioxidant enzymes, Plant Physiology and Biochemistry, 54: 17-26.
4.
Raturi, A., Singh, S.K., Sharma, V. and Pathak, R. 2012. Stability and environmental indices for yield attributing traits in Indian Vigna radiata genotypes under arid conditions. Asian J. Ag. Sciences, 4(2): 126-133
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5.
Jain, R., Saxena, J. and Sharma, V. 2011. Determination of the organic acids in fermentation media by HPLC, International Journal of Biological Sciences and Engineering, 2(4): 561-565.
6.
Gupta, P., Ravi, I. and Sharma, V. 2012. Induction of â-1,3-glucanase and chitinase activity in the defense response of Eruca sativa plants against the fungal pathogen Alternaria brassicicola. Journal of Plant Interactions. DOI:10.1080/17429145.2012.679705)
7.
Alam, A., Sharma, V. and Sharma, S.C. 2012. An Association between Macromitrium sulcatum (Hook.) Brid. and Ulothrix zonata (Weber & Mohr) Kützing. Archive for Bryology, 129: 1-4
8.
Alam, A., Sharma, S.C. and Sharma, V. 2012. In vitro antifungal efficacies of Targionia hypophylla L. against growth of some pathogenic fungi. Int. J. Ayurvedic and Herbal medicine, 2(2): 229-233
9.
Sharma, A., Joshi, N. and Sharma, V. 2012. Induction of defence mechanism in cluster bean using differential method of inoculation. Vegetos, 25(1): 253-260.
10.
Jain, R., Saxena, J. and Sharma, V. 2012. Effect of Phosphate-solubilizing Fungi Aspergillus awamori S29 on Mungbean (Vigna radiata cv. RMG 492) Growth. Folia Microbiologica, DOI: 10.1007/s12223-012-0167-9
11.
Saini, P., Khan, S., Baunthiyal, M. and Sharma, V. 2012. Mapping of Fluoride endemic area and assessment of F1 accumulation in soil and vegetation. Environmental Monitoring and Assessment. DOI: 10.1007/s10661-0122683-0
12.
Verma, S., Prasanna, R., Saxena, J., Sharma, V. and Nain, L. 2012. Deciphering the metabolic capabilities of a lipase producing Pseudomonas aeruginosa SL-72 strain. Folia Microbiologica, 57: 525-531. DOI: 10.1007/s12223-0120163-0
13.
Saini, P., Khan, S., Baunthiyal, M. and Sharma, V. 2012. Organ-wise accumulation of fluoride in Prosopis juliflora and its potential for phytoremediation of fluoride contaminated soil. Chemosphere, 89: 633-635 doi 10.1016/ j.chemosphere.2012.05.034.
14.
Alam, A., Sharma, V., Sharma, S.C. and Tripathi, A. 2012. Bryoflora of Munsyari and Dharchula Tehsil of Pithoragarh, Uttarakhand, Western Himalayas, India, Archives of Bryology, 140: 1-11.
15.
Koul, B., Yadav, R., Sanyal, I., Sawant, S., Sharma, V. and Amla, D.V. 2012. Cis-acting motifs in artificially synthesized expression cassette leads to enhanced transgene expression in tomato (Solanum lycopersicum L.), Plant Physiology and Biochemistry, 1-11 online (in press).
16.
Alam, A., Khan, S., Sharma, V., Sharma, S.C. and Rani, A. 2012. RAPD and morphological analysis of bryophytes - Thuidium tamariscinum (Hedw.) Schimp. and Hyophyla comosa Dixon in P. de la Varde, Researcher, 4(11):98103.
17.
Srivastava, N., Tiwari, N. and Sharma, V. 2012. Effect of Azadirachta indica leaf extract on callus induction and its enhancement for the plantlet regeneration in Carica papaya (var. Pusa Dwarf). J. Cell Tissue Research, 12(3): 2417-2422.
18.
Parwani, L., Bhatnagar, M., Bhatnagar, A. and Sharma, V. 2012. Reactive oxygen species control by plant biopolymers intended to be used in wound dressings. International Journal of Pharmacy and Pharmaceutical Sciences, 4 (S5): 506-510.
19.
Singh, L., Pracheta, Sharma, V., Paliwal R. 2012. Bioprospecting anticarcinogenic potential of plants in Rajasthan, India. Journal of Plant Developmental Sciences, 4(1): 115-123.
20.
Singh A., Dhabhai R., Shanker S. and Chaurasia S. P. 2012. Wheat Straw as a source of renewable energy. International Journal of Environmental Engineering and Management. 3(1):21-23.
21.
Dhabhai R., Chaurasia S. P., and Dalai A. K. 2012. Influence of pretreatment conditions on composition of liquid hydrolysate and subsequent enzymatic saccharification of remaining solids. The Canadian Journal of Chemical Engineering, (in press).
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22.
Dhabhai R., Chaurasia S. P., and Dalai A. K. 2012. Immobilization of Saccharomyces cerevisiae on Canadian pine wood chips and its use in co culture with free Pichia stipitis for conversion of glucose- xylose mixtures to bioethanol. Journal of Biobased Materials and Bioenergy. (in press).
23.
Jana, S. and Shekhawat, G.S. 2012. RAPD analysis, antioxidant study during cell differentiation and standardization of in vitro regeneration protocol of Anethum graveolens: A medicinal herb and spice. Biologia Plantarum, 56 (1): 9-14.
24.
Kundu, S., Chakraborty, D., Das, K. and Pal, A. 2012. An efficient in-gel digestion protocol for mass spectral analysis by MALDI-TOF-MS and MS/MS and its use for proteomic analysis of Vigna mungo leaves. Plant Molecular Biology Reporter, DOI 10.1007/s11105-012-0475-x.
25.
Sharma N and Garg V. 2012 Antihyperglycemic and antioxidant effect of hydroethanolic extract of Butea monosperma bark in diabetic mice, Indian Journal of Biochemistry and Biophysics, 49(1): 55-62.
26.
Srivastava, N., Sharma, A., Misra, S., Behra, K.K. and Bahgyawant, S.S., 2012. Influence of light stress on somatic embryos inducing in-vitro antimicrobial activity in Carthamus tinctorious L. (variety- Mangira). Journal of Pharmacy Research. 5 (5): 2505-2509.
27.
Teotia , P. S., Srivastav, N., Garg, V., Shekhawat, G.S., Sharma, N and Chadha, S. M. 2012. Stevioside: A natural sweetener having potential of controlling glucose levels in diabetic patients. International Journal of Current Research, 4 (4): 83-90.
28.
Tripathi, R. 2012. Stress Related Histopathological Changes in the Sperm Morphology of prawn Macrobrachium dayanum (Crustacea: Decapoda). Journal of Experimental Zoology 15(2)
29.
Yadav, D., Suri, S., Chaudhary, A.A., Hemant, Beg, M.N., Garg, V., Asif, M. and Ahmad, A. 2012. Stimuli Responsive Polymeric Nanoparticles in Regulated Drug Delivery for Cancer, Polish Journal of Chemical technology. 14(1): 57-64.
Monograph Publication 1.
Shanker, A. and Sharma, V. 2012. Evolutionary analysis of plants using chloroplast proteome sequences. LAP Germany, p. 152 (ISBN 978-3-8473-7563-0).
Initiation of R&D activities in Bioinformatics: Within a short span, the centre has made rapid strides in major trust areas of research in Bioinformatics and other Biological sciences. Centre has published various national and international publications.
Details of Training/Workshop organized and total no of user trained A three days workshop on “In silico genome and proteome analysis” is proposed to be organized during February 16-18, 2013. 11.
Impact shown by the Centre:
The centre has published 9 research papers in core Bioinformatics and 29 others in biological sciences.
Proposed activities for 2013-14
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More Interactions with Bioinformatics Industry
Continue to Train Human Resources in Bioinformatics
To cater to the regional and national needs, the work on the specific databases being currently developed by the Center will continue.
The R & D activities will be strengthened in Bioinformatics.
The PG courses in Bioinformatics will be focalized towards offering specializations in future.
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Contact details: Name of the Coordinator Postal Address
Phone Number Fax No. Email Website Name of Contact Person
Professor Vinay Sharma Department of bioscience & Biotechnology Banasthali University, P.O. Banasthali Vidyapith Newai, Tonk, Rajasthan Pin-304022 01438-228302, 01438-228341 Ext. 380 01438-228365
[email protected];
[email protected] www.banasthali.org Professor Vinay Sharma, Shweta Jain (Information Officer)
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Barkatullah University, Bhopal Coordinator: Dr. Ragini Gothalwal Summary of the progress made by the centers from its inception Bioinformatics Center (DICS) was started in the year 2002-03, with an aim to provide computational facility and training in computational Biology and Bioinformatics to the Students, research scholars, faculties and scientists from the UTDs and affiliated colleges of Barkatullah University. Center has enough infrastructure and expertise required for the academics and research in Bioinformatics. Center has provided the expertise in analysis such as phylogenetics, structural analysis, primer designing, diversity analysis and other computational analysis. Numbers of 3-6 months Dissertation/projects with bioinformatics training have been carried out at center. Number of workshops/training has been conducted by the Center besides the national seminar, conferences and scientific meetings. Software and hardware related solutions and expertise are provided. Center is working on CUDBE (Codon Usage DataBase Explorer) and MGT (Microbial Genomics Tools) indicating the specialization in Microbial Genomics and informatics.
Major research activities in biotechnology and its related fields : Biotechnology: 1.
Cyanobacterial Biotechnology
2.
Bioremediation
3.
Mycorrhizal Biofertilisers
4.
Bioactive Compound from Medicinal Plant
5.
Metal Binding Proteins
Bioinformatics: 1.
Microbial Genomics
2.
Computational Microbiology
Major Activities of the Center during the year 2012-2013 1.
Organized a, 6-days Hands-on-Training for M.P. Govt. colleges Lecturers and a 15-days Hands-on-Training for M.Sc. students of MVM College Bhopal, in collaboration with Madhya Pradesh Biotechnology Council Bhopal.
2.
Two National Level Workshops on Diversity analysis and Cheminformatics were organized.
3.
Research oriented training cum dissertation/project for students. (18 in no)
Infrastructure facilities in the Bioinformatics Center A.
Computer & Communication facility Computer and Peripherals: 31 Clients Desktop, 5 Printers and 3 Scanners Internet Facility: Leased line Internet Connection by Barkatullah University Power Supply: UPS: 5 in nos.
B.
Scientific Software Packages:
Licensed Software OS and Packages: Win server Std. 2003, Visual studio .NET, MS-Office 2003 and 2007, Adobe Creative Suite Premium, Macromedia Dreamweaver, MSSQL Server. Licensed Bioinformatics Software: Hyperchem Release 7.5 (1 user) and ExomED research (1 user) and Systat13 (2 user license), Flex
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Details about staff members working in the center (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) S.N.
Name
1
Mr. Kishor K. Shende Information Officer Bioinformatics & Biotechnology Mr. Durgesh Gupta Technical Assistant Bioinformatics and Botany Mrs. Archana Nema Computer Computer Application Professional Mr. Chandan Bisht Data Entry Operator Data entry and Official Work
2 3 4
Designation
Specialization
Period of Working 9 years
Absorption Status Absorbed
7 years 8 years
Absorbed Absorbed
9 years
Absorbed
Types of services provided
Training and teaching in Bioinformatics and Computational Biology.
Computational facility and expertise
Software installation and Configuration
Collaborative Work/initiatives: i.
Collaboration with Madhya Pradesh Council of Biotechnology, Bhopal M.P. for providing Bioinformatics training to students and teachers from State govt. affiliated colleges.
ii.
Initiated collaboration with BIF, MANIT Bhopal
Paper published or personated in the conferences with references: Research articles: 3 communicated Abstracts: 4
Details of Training/Workshop organized and total no. of user trained Workshops Workshop/Training Training Training National Workshop National Workshop
Title of the Workshop 6 days Hands on Training for Teachers “Topics in Bioinformatics for Teachers” 15 days Hands on Training for students “Bioinformatics and Structural Bioinformatics” “Horizon of Bioinformatics in Environmental Management and Biodiversity Conservation” “In-Silico Dimensions of Medico-Cheminformatics”
Date Participants 23-28 July, 2012 17 10-27 Sep, 2012
23
16-19 Oct, 2012
37
15-19 Jan, 2013
30
Long Term Training and Dissertation/Projects: 6 months Dissertation/Projects: 18
(during Jan-Dec 2012)
Computational Facility Provided Data Analysis: 8
(during Jan-June 2012)
Impact shown by your center on the growth of Biotechnology and allied areas. In this you may highlight the details like number of paper published/ number of papers published with the help of you’re your center, how your center is promoting various activities of your organization and neighboring institution, manpower trained, tools developed, patents & copyrights acquired and other services offered etc. iii. iv.
Research scholars and students are visiting center for computational expertise and facility to analyze their data. Bioinformatics knowledge sharing is initiated to the remote colleges of Madhya Pradesh regions and even at high School level.
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XXIVnd All India BTISnet Coordinators’ Meeting v.
Research abstracts Published in Bioinformatics in national conferences/seminars
vi.
Research paper and abstract published with the help of Bioinformatics center:
vii.
Database (CUDBE) Tools Developed: 1 (MGT1.0)
February 03-04, 2013
viii. Resource person provided to other Institute: SGB Amravati University Amravati, SVNIT Surat; Institute for Excellent in Higher Education Bhopal, Shakarlal Khandelwal College Akola M.S., Sant Hiradaram Girls College Bhopal. KRG College Gwalior, PG Govt. College Datia M.P., RDVV Jabalpur. MVM College Bhopal.
Future activities: ix.
To establish the Virtual Learning for the students, faculties, research scholars for remote areas of Madhya Paadesh.
x.
Establishment of MoU and collaboration with other institutes.
xi.
To start M.Sc. Course in Bioinformatics.
xii.
To organize short term module based training for research scholars
xiii. To organize 3 months and 6 months training programs for the students xiv. To promote the introductory Bioinformatics among the high school children
Contact details Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
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Dr. Ragini Gothalwal Bioinformatics Center (SubDIC), Department of Biotechnology, Barkatullah University, Bhopal – 462 026 (Madhya Pradesh) India 91-755-2491848, 2491849 91-755-2491850
[email protected];
[email protected] www.bioinfobubpl.nic.in Dr. Ragini Gothalwal
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Bharathidasan University, Tiruchirappalli Coordinator: Dr. L. Uma Summary of the progress made by the centre from its inception: The Centre was launched in April 2001 as a special purpose centre meant for cyanobacteriology. Training workshops on the basics of bioinformatics are being conducted every year during the month of February / March. The Centre assists the National Facility for Marine Cyanobacteria (DBT, Sponsored Facility) and the Department of Marine Biotechnology faculty scholars and students by providing infrastructural facilities like internet, email, printing and also conducts bioinformatics theory and laboratory courses for M.Sc. and M.Phil programmes and project students. The Bioinformatics Centre at this institute, supported by DBT, has created awareness in cyanobacteria, the primordial organism. The Centre focuses on database generation, data mining and its application in wet lab research in regard to cyanobacteria.
Major research activities in biotechnology and its related fields : The centre assists NFMC in the biotechnological exploitation of marine cyanobacteria through genome wide hunt in the areas of metabolic pathways degradative enzymes molecular markers in addition to identifying the biotechnological potentials.
Area of specialization: Cyanobacteriology - Bioinformatics
Major achievements made during 2012-2013: The leased line internet facility has been upgraded to 1 Mbps, and a pair of 1 Mbps modems has been added to the centre. As part of human resource development, workshop is conducted every year and this year it entitled as “Cyanobacterial Advanced Research Techniques (CART 2012)” which is scheduled from February 27 – March 9, 2012). The wet lab hands on experiments are supported by in silico methods. The manpower trained per year is @50 (students and researchers)
Research in Cyanobacterial bioinformatics: INING
In silico studies on complexation of cyanobacteria hydroxamate siderophores and uranium
Comprehensive analysis on cyanobacterial CO2 fixing enzyme phosphoenolpyruvate carboxylase.
Comparative studies on enzymes associated with fatty acid biosynthesis.
Stress associated enzymes and pathways.
Infrastructure facilities in the Bioinformatics Centre A.
Computer & Communication facility
IBM Xeon Server – 1, Alpha Servers-2, Xeon Server-1, SGI FUEL Workstation-1,Pentium IV Computers-23 (2 Laptops), Scanner -1, Printers-5 (4 + 1 Large format printer), 7.5 KVA UPS-1, 10 KVA UPS – 1, LCD Projector-1, Router-1, Leased Line Modems- One Pair, Lease line- 1 Mbps Leased-line internet connection is available round the clock. B.
Databases & other information resources
Blue Green Database - BGBASE, a database on Cyanobacteriology has been developed at the centre and is available online at www.nfmc.res.in. The database is constantly being updated. A library with about 260 books on Bioinformatics and computer science is available for the researchers. C.
Software Packages
The centre has software packages and tools for sequence analysis, structure analysis, phylogenetic analysis, molecular modelling, docking and molecular dynamics as follows. Clustal W and Omega, Treeview, Mega, Mr. Bayes, RaxmL, Phymol-0.9v, Yasara, Molegro, Chimera, Visual Molecular dynamics, Autodock 4.2, and Gromacs.
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Details about staff members working in the centre: Name Mrs.V.Sangeetha Mrs. R. Renganayagi Ms. M. Shylaja Naciyar
Designation Technical Assistant Technical Assistant Junior Technical Assistant
Specialization Information Technology Computer Application Bioinformatics
Working Since May 2008 October 2004 March 2011
Ms .R. Rajalakshmi
Junior Technical Assistant
Bioinformatics
April 2011
Educational Activities Bioinformatics –as one paper M.Sc - Extra Disciplinary Course, M.Phil - Optional paper
Papers/ published or presented in conferences:
Molecular Characterization of marine cyanobacteria and its potential for biodiesel production. National Conference on Role of microbes in Health, Agriculture and Industry. 26 – 27, March 2012. Organized by Department of Biotechnology, Alagappa University, Karaikudi.
Molecular Characterization and physiological response of psychrophilic and mesophilic Nostoc species to different temperature regimes. Indo-US Workshop on Cyanobacteria – Molecular networks to biofuels. Organized by IIT, Bombay and Purdue University, IN, United States, Lonovola, Pune. December 16 – 20, 2012.
Initiation of R&D activities in bioinformatics:
Cyanobacterial Glutathione S transferases.
Acetyl-coA carboxylase.
Details of Training/ Workshop organized and total no of user trained
Cyanobacterial Advanced Research Techniques (CART 2012) February 27 – March 9, 2012
User trained through workshop – 20
Through regular classes 15
Impact shown by the Centre:
Maintaining our website (www.nfmc.res.in) with GPS data for the Cyanobacterial cultures in the repository
It helps to users can obtain geological data for the cyanobacterial cultures
Cyanobacterial cultures supplied to 38 Institutes across the country.
Paper Published: Vijayaraghavan Rashmi, Mohandass ShylajaNaciyar, Ramamoorthy Rajalakshmi, Stanley.F.D’ Souza, Dharmar Prabaharan and Lakshmanan Uma. “Siderophore mediated uranium sequestration by marine cyanobacterium Synechococcus elongatus BDU 130911”. Bioresource Technology. Accepted on 4th December 2012. (DOI: http:// dx.doi.org/10.1016/j.biortech.2012.12.016). IF: 4.980.
Proposed activities for 2013 – 2014
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Classification of cyanobacterial glutathione S transferases enzymes.
Interaction studies on binding affinity of GST with various substrates.
Comparative analysis of acetyl-coA carboxylase metabolic pathways
Protein-protein interaction
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Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
Dr. L. Uma Bioinformatics Centre, NFMC, Bharathidasan University, Tiruchirappalli – 620 024 0431 2407084 0431 2407084
[email protected],
[email protected] www.nfmc.res.in Dr. L. Uma
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Biotech Consortium India Limited, New Delhi Coordinator: Dr. Purnima Sharma Summary of the progress made by the centre from its inception Since its inception in 1992, the Distributed Information Sub Centre (DISC) at Biotech Consortium India Limited (BCIL) has taken up various activities to facilitate commercialisation of biotechnology. It has brought out a number of publications and periodicals, databases and status reports and has organized several seminars/workshops, events, entrepreneurs’ meets etc. for promotion of commercial biotechnology. Current activities include compilation of databases and directories, preparation of industry specific status reports on different aspect of biotechnology and organizing national and international workshops, seminars, conferences and entrepreneurs’ meets to create awareness on issues relevant to commercialization of biotechnology. The DISC also runs a Biotechnology Club. The biotech club membership is being offered on annual and life memberships basis to individuals, institutions and corporate bodies interested in biotechnology. Members receive BCIL’s publications and, participate in events organized by BCIL, either free of cost or at a discount.
Major research activities in biotechnology and its related fields : BCIL’s main objective is to provide linkages to facilitate commercialization of biotechnology. BCIL has been engaged in technology transfer, consultancy, project management, IPR Facilitation, certification services, information dissemination and manpower training related to biotechnology. In these areas, it has assisted over 200 clients including scientists, technologists, research institutions, universities, first generation entrepreneurs, the corporate sector, government, banks and financial institutions.
Area of specialization of the centre: Technology assessment, valuation and transfer, preparation of commercial databases, biotechnology project specific updates, publication of journals and organization of national and international workshops, seminars and training programmes and Intellectual Property Services.
Major achievements made during the year (2012-13) Focussing on commercial biotechnology, in the year under review, DISC continued to bring out publications and organize events primarily of relevance to industry. The major projects undertaken by DISC were: I.
Development of New Websites DBT has set up a North Eastern Region-Biotechnology Programme Management Cell (NER-BPMC) through Biotech Consortium India Limited (BCIL) for promotion of Biotechnology activities in the North Eastern Region of India. DISC at BCIL is coordinating for development of a comprehensive dynamic website for online submission, review and monitoring of proposals submitted by project investigators from North Eastern Region of India under various schemes of DBT for North Eastern Region. DISC at BCIL has also coordinated development of a Portal for “Review of Mechanisms and Protocols of Teaching (PROMPT)” an online student feedback portal by means of which students enrolled with DBT sponsored programmes can provide their feedback and suggestions pertaining to teaching, laboratory, institution, examination, seminar and dissertation standards of their institute. This portal is ready for hosting on NIC website.
II.
Maintenance of ongoing websites: The following ongoing websites developed during the previous years were regularly updated and maintained by DISC: a) b) c) d)
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Updation & Maintenance of DBT Biosafety website (http://dbtbiosafety.nic.in) Web-based database on Indian GMO Research Information System (IGMORIS) (http://igmoris.nic.in) BCIL website (parent organization) www.bcil.nic.in Website for National Certification Systems for Tissue Culture Raised Plants (NCS-TCP) (http://dbtncstcp.nic.in/)
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Conferences, workshops, seminar-cum-training programmes :
a)
“Workshop on “Commercialisation of Biotechnology”
The annual Workshop on “Commercialisation of Biotechnology” was organized on March 12, 2012 at New Delhi. The programme focussed on business opportunities and issues related to biotechnology commercialization, emerging biosafety issues, enhancing competitiveness through IPR protection and financing options in biotechnology. Eminent speakers from industry and government departments made presentations on the above topics. The event was structured in a highly interactive format through formal presentations as well as open discussions. Around 100 participants consisting of senior representatives from biotechnology industry, research and development institutions, students from various university and colleges, first generation entrepreneurs and financial institutions attended the programme. b)
Workshops on “Effective Grant Writing Skills & Strategic Management of IPR”
A series of Workshops on “Effective Grant Writing Skills & Strategic Management of IPR” were organized by BCIL in New Delhi, Hyderabad, Kolkata and Ahmedabad during the year. The main focus of these workshops was to sensitize researchers, academicians and industry in writing an effective grant proposals and strategies for management of IPR in biotechnology research on the effective use and management of IP tools that were relevant to their R&D. More than 160 participants attended these workshops. IV
Management of DBTt’s e-Library Consortia for NER Institutions
DISC at BCIL assisted in management of DBT’s e-Library Consortia (NER-DeLCON) through which access to online eresources are being provided to 17 institutions from NER. All the institutions/universities under NER-DeLCON are utilizing this facility. V.
Biotechnology club
The Biotechnology Club managed by DISC at BCIL has more than 200 members including life and annual members. Many leading biotech companies are members of the club. VI.
Publication The following periodicals and journals are being published by DISC: a)
Vatis Update: Biotechnology The Value Added Technology Information Services (VATIS) Update, Biotechnology a publication in association with Asian and Pacific Centre for Transfer of Technology (APCTT) was continued during the year.
b)
Biotech Bulletin The in-house bimonthly publication from DISC, “Biotech Bulletin”, consisting of compilation of interesting news clippings on biotechnology from newspapers, magazines and journals for apprising industry on current national/international developments in the area of biotechnology was also continued.
Infrastructure facilities in the Bioinformatics Centre The Centre has two IBM LAN servers. A 3Mbps Internet Lease Line (1:1) has been installed at the centre from SIFY. Besides, the centre has Pentium 4 Laptops, 6 Intel Core-i5 desktops, 2 Core to Dao processor machines, CISCO Router, Firewall, HP color laser printer, HP scanner and related peripherals required for its functioning.
Details about staff members working in the centre: Name Dr. Purnima Sharma
Designation Managing Director
Specialization Ph.D. in Medical Biotechnology
Dr. Vibha Ahuja
General Manager
Ph.D in industrial Biotechnology
Vinod Kumar
Deputy Manager
Project Management, Management of BCIL Biotech Club & VATIS Update, Event Management, Publications
Distributed Information Sub Centres (DISCs)
Working since (years) 22 (Absorbed in BCIL) 20 (Absorbed in BCIL) 12 Absorbed (in BCIL)
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February 03-04, 2013
XXIVnd All India BTISnet Coordinators’ Meeting Mr. Maheep Sharma Mr. Lingesh B.S. Ms. Reetu Saxena Ms. Sharma
Sr. Software Developer Database Development, Website Maintenance Project Executive Database management and information collection Project Executive Information collection and compilation
Deepanshu Computer Operator
Data Entry, Database management
1 Contractual 1 Contractual 2 Contractual 3 Contractual
Educational activities with details of placement: NA Papers published or presented in the conferences with reference: In almost all the workshops, conferences and training programmes, BCIL officers have been presenting papers on various issues related to biotech commercialization such as status of biotech industry in India, IPR issues in biotechnology, regulatory requirements, biosafety issues, business opportunities in biotechnology, etc. The following specific presentations were made by BCIL officers from DISC during the year: Sl. No. Workshop Topic 1 Workshops on “Effective Grant Writing Skills & Strategic Presentations on ‘Relevance of IP for Management of IPR” at New Delhi, Hyderabad, Kolkata and Indian Biotechnology Industry’ Ahmedabad
Initiation on R&D activities in Bioinformatics: NA
Details of Training / Workshop organized and total no. of user trained DISC at BCIL has organized the following workshop during the year. S. No. 1. 2.
Workshops/seminars organized Workshop on “Commercialization of Biotechnology” Workshops on “Effective Grant Writing Skills & Strategic Management of IPR” at New Delhi, Hyderabad, Kolkata and Ahmedabad Total
Participants 100 160 260
Impact shown by your centre on the growth of biotechnology The DISC at BCIL is promoting activities related to commercial biotechnology by organizing workshops on key issues related to commercialization of biotechnology, IPR facilitation, assisting (providing database support) in identifying suitable licensees for transfer of technologies and bringing out publications in biotechnology.
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1)
During the year more than 260 stake holders belonging to diverse background i.e. scientists, industry, academicians and students were trained on different aspects of commercial biotechnology.
2)
Assisted parent organization in transfer of technology on ‘Monoclonal Antibody based Kit for the Detection of Chlamydia trachomatis’ developed by National Institute of Pathology, Delhi to M/s Accurex Biomedical Private Limited, Mumbai
3)
A technology for Neonatal Resuscitation Device developed under Stanford India Biodesign Program of DBT transferred to Windmill Heath Technologies.
4)
Transferred technology for Limb Immobilization Device developed under Stanford India Biodesign Program of DBT to M/s. HLL Lifecare Limited.
5)
Provide support service to the parent organization in placing more than 65 post graduate students in Bioinformatics for 6 months industrial training in leading biotech/bioinformatics companies under Bioinformatics Industrial Training Programme of DBT.
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Proposed activities for 2013-14 The Distributed Information Sub Centre (DISC) at BCIL proposes to take up the following activities: i.
Compilation of Directory of Biotechnology Industries and Institutions in India – 6th Edition.
ii.
Organizing workshops on Commercialisation of Biotechnology
iii.
Organizing workshops on “Management of IPR in Biotechnology”
iv.
Organizing Entrepreneurship Development Programmes in Biotechnology in North Eastern Region of India.
v.
Updation of technology profiles
vi.
Providing value added services to the members of Biotechnology Club of DISC at BCIL
vii.
IPR Facilitation services
Additional Details Name of the Coordinator
:
Address
:
Phone No. Fax No. Email Website Name of the contact person
: : : : :
Dr. Purnima Sharma Managing Director Biotech Consortium India Limited 5th Floor, Anuvrat Bhawan 210, Deen Dayal Upadhyaya Marg New Delhi – 110 002 011-2321 9064/65/66/67 011-2321 9063
[email protected] www.bcil.nic.in Mr. Vinod Kumar, Deputy Manager, BCIL
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Biotech Park in Biotechnology City, Lucknow Coordinator: Prof. P. K. Seth Summary of the progress made by the centre from its inception The Bioinformatics Centre, a cardinal component of the Biobusiness centre of the Biotech Park, Lucknow continues to be a nodal point for industry-academia-public institution interaction and plays an important role in the human resource generation as well as in R&D in the area of bioinformatics and biotechnology. The bioinformatics hands-on training, dissertation training often utilizes a “dual mentor” approach, which combines quantitative/ computational and biological application elements and serves as a single window information platform for technical capabilities and national facilities available in various research institutions of the city. The interdisciplinary graduate training program in bioinformatics and computational biology draws faculty from the various universities working in the field of bioinformatics, College of Engineering, the College of Pharmacy, and the College of Information Technology. The training program of the Bioinformatics Centre adds a capstone of quality to the bioinformatics program’s mission to provide promising students in this highly interdisciplinary domain with the skills and knowledge necessary to launch successful and independent careers in basic and applied research in academia, industry, and government. During the current year the centre has procured all modules of commercial Bioinformatics software SYBLE-X Suite with chemo-informatics modules which are being used in the training program and by several research students from local institutions. Further, two new databases and two online tools, relevant to the need of industries and the researchers were developed and four workshops were conducted. The centre has also taken a new initiative to empower students and researchers with skills required in the application of bioinformatics in drug discovery and drug designing under a Professional Bioinformatics Training Programme. Major highlights of the work undertaken during the current year are given below:
Databases Two new databases namely anti-asthmatic meditational plants and gallbladder cancer and two online tools for SiRNA design and Human mitochondrial haplo group detection tool were developed this year. Thirteen databases under health care, six under agro-based products and eight miscellaneous databases developed earlier were updated. These databases and online tools are on user friendly platforms and out of these six are online on “http://www.biotechpark.org.in/db.html” which are being regularly accessed.
Research Activities The Bioinformatics Centre of Biotech Park, Lucknow has established collaboration with the local institutions for addressing problems of mutual interest. Research students from Lucknow University, King George’s Medical University, Babasaheb Bhimrao Ambedkar University, Lucknow, Chandra Shekhar Azad University of Agriculture & Technology, Kanpur, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGI), Lucknow, National Bureau of Fish Genetic Resources (NBFGR), Lucknow, Amity University, Lucknow, Narendra Deva University Of Agriculture &Technology, Kumarganj, Faizabad and National Bureau of Agriculturally Important Microorganisms, Mau frequently visit the centre for their research work in Bioinformatics. Students from local teaching institutions took small research projects in area of genomics & proteomics, phylogenetic analysis, molecular modeling, docking, molecular dynamics, chemo-informatics and RNAi interference technology, studies on human and plant diseases were undertaken. Structure based drug designing and drug target prediction for Alzhimer, Pneumoniae, HIV virus, Med-cow disease, prion protein, flaviviruses; evolutionary studies of Influenza virus; siRNA designing against hepatitis delta virus, viagra virus of crop plants and potato X virus were also pursued by short term (46 months) trainees. These activities have led to submission of sixteen protein structures in Protein Data Bank and following research publications: 1.
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Saxena S, Singh S, et. al. (2013). Designing of putative siRNA against geminiviral suppressors of RNAi to develop geminivirus resistant Papaya crop. International Journal of Bioinformatics Research and Applications. 9 (1): 3-12. DOI:10.1504/IJBRA.2013.050655. PMID: 23207994.
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XXIVnd All India BTISnet Coordinators’ Meeting 2.
Verma A, Gupta S, et al. (2012) Molecular mechanism of interaction between Shrimp and White Spot Disease Virus through PmRab7 and VP28 proteins: an insight using simulation and docking studies.J Mol Model. DOI 10.1007/s00894-012-1672-0. PMID: 23179770.
3.
Chitranshi N, Gupta S, et al. (2012) New molecular scaffolds for the design of Alzheimer’s acetylcholinesterase inhibitors identified using ligand and receptor based virtual screening. Med Chem Res. DOI 10.1007/s00044-0120227-3.
4.
Gupta S, et al. (2012) Identification of novel potent inhibitors aginst Bcl-XL anti-apoptotic protein using docking studies. Protein Peptide Letters 9. PMID: 22670675.
5.
Singh S, Gupta S K, et al. (2012) Design of potential siRNA molecules for hepatitis delta virus gene silencing, Bioinformation. 8(16):749-757. PMID: 23055625.
6.
Gupta S, et al. (2012) Targeting the Epidermal Growth Factor Receptor: Exploring the potential of Novel Inhibitor N-(3-Ethnylphenyl)-6, 7-bis (2-methoxyethoxy) Quinolin-4-Amine using Docking and Molecular Dynamics Simulation. Protein Peptide letters. 9 PMID: 22486613.
Papers presented NIL
Poster presented 1.
Sunil K Gupta, Sarita Singh, Kamlesh K Pant, Prahlad K Seth “Docking Studies towards Exploring Novel Antiviral Molecule against Envelope Protein of Tick-Borne Encephalitis Virus” presented in 100th Indian Science Congress, 02nd -07th January, 2013 at Indian Science Congress Association, Kolkata, India.
2.
Alok Kumar Pandey, Sarita Singh. “Structure Based Drug designing for Leaf Scald Disease of Sugarcane” presented in National Seminar on Transcriptomics: A Recent Era (NST-2012), 07th, April 2012 at Lucknow, India (Page no: 15)
Training Four DBT sponsored training workshops on (1) Protein Modeling & Rational Drug Design (2) Drug Discovery, Design Methods & Applications and (3) Chemoinformatics were organized in which about 40 persons: scientists, medical doctors, research scholars, graduate and post graduate students form Allahabad, Aligarh, Ajmer, Bhojpur (Bihar), Banasthali, New Delhi, Gorakhpur, Gwalior, Haryana, Jaipur, Jalgaon, Kanpur, Lucknow, Moradabad, Sonebhadra, Varanasi and other places of the country participated. Further 60 persons received short and long-term (I to 6 month) training at the centre. More than 150 persons from different educational institutions viz. Medical colleges, Pharmaceutical institutes, Universities and colleges visited the centre and got acquainted with bioinformatics tools and their applications.
Details of Training/Workshop organized and total no of user trained: S. No. 1. 2. 3.
Workshop Title Protein Modeling & Rational Drug Design Drug Discovery, Design Methods & Applications Chemo-informatics
Date June 21 – 22, 2012 September 11-13, 2012 December 27-28, 2012 Total Participants
Number of participants 14 16 7 37
Proposed activities for the year 2013-2014
The Bioinformatics Centre will continue to conduct more Professional Bioinformatics Training Programme for students, researchers and school teachers, the major thrust areas will be quantitative structure activity relationship (QSAR), pharmacophore generation, lead optimization, molecular dynamics and simulation and computer added drug designing, virtual screening, fingerprinting, chemo-informatics, pharmacogenomics, pharmacogenetics and pharmaco-dynamics etc.
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Develop and design new database & servers, update and maintain existing ones.
The Centre will continue to contribute significantly in the field of bioinformatics, molecular modeling, computational approaches to inhibitor design, and drug designing.
To organize three short-term Training programmes and one national workshop on bioinformatics.
Regular updating of the website of Biotech Park, Lucknow and databases.
Contact details:Name of the Coordinator:
Prof. P. K. Seth Chief Executive Officer
Postal Address:
Biotech Park, Lucknow Sector-G, Jankipuram, Kursi Road, Lucknow-226021
Phone Number:
+91-522- 4053000-20, 4012076.
Fax No:
+91-522-4012081
Email:
[email protected] [email protected]
Website:
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www.biotechpark.org.in
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Birla Institute of Scientific Research, Jaipur Coordinator: Prof. M Krishna Mohan Summary of the progress made by the centre from its inception : Birla Institute of Scientific Research, Jaipur is a leading center for Biotechnology research in Rajasthan. The institute undertakes goal-oriented applied research in the frontier areas of industrial biotechnology sponsored by government and industries as well as in-house research. The BTIS-SubDIC at BISR was established in 1999. This is one of the core facility used by scientist for analysis of data using various Bioinformatics software application for their research work. This facility is also used by other nearby academic institutes and universities. Recently BISR has initiated research in the area of Proteomics, Genomics and Structural Bioinformatics. Besides, efforts are being made to develop various quality information resources in the form of databases and software for professionals in the area of biotechnology and Bioinformatics.
Major activities of the institute Birla Institute of Scientific Research (BISR) is involved in fostering and promoting various aspects of science and technology and has multi functional activities. The research programs of the BISR are concerned primarily with Biotechnology and Natural Resource Management.
Major Activities:
Conduct basic and applied research in established and emerging areas of science and technology.
Organize quality improvement and customer specific training programs in Biotechnology.
Establish and maintain effective linkages with industry, educational and research organizations.
Major activities of the centre during the year 2012 - 13 a)
National workshop on advance areas of Bioinformatics
Bioinformatics: Sequence Analysis, 21 - 23 September 2012
Molecular Modeling and Drug Design, 14 – 16 December 2012.
b)
Research training in Bioinformatics was imparted to 10 students in the form of their dissertation work.
c)
Summer Training was imparted (May-June-July, 2012) to 40 students.
d)
Various features were incorporated into the PIASP (Protein Structure Analyzer and Structure Parser) program for analyzing protein-ligand interaction.
Infrastructure and Scientific Software at Bioinformatics Centre The centre is equipped with the following scientific software packages: Discovery Studio Package from Accelrys, GCG Sequence Analysis Package, Exome Horizon from MASCON, Vector NTI, Reference Manager, Visual Studio, CLC workbench, PDQuest Image Analysis.
Types of services provided The Bioinformatics Centre at BISR has created an infrastructure for providing facilities to the users working in the field of Biological Sciences. The users of Rajasthan, Jaipur in particular, are using facilities available at the Bioinformatics Centre extensively. The centre has leased line Internet connection as well latest Bioinformatics software for sequence and structure analysis. The center provides the following services: a)
Bioinformatics supports to researchers
b)
Customized training in Bioinformatics for researchers and faculty members
c)
Support in Installing, implementing and maintaining software on computer.
d)
Create awareness for taking preventive measure against data security
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XXIVnd All India BTISnet Coordinators’ Meeting e)
Organizing workshops in Bioinformatics
f)
Research Training to students of Biotechnology and Bioinformatics
Biotechnology Impact and Publication The institute is engaged in various research activities and centre provides the Bioinformatics support to the scientists. All scientists and researchers in the institute are regularly accessing the Bioinformatics facility at the centre. During 2008-13 institutes has published more than 20 research articles in peer reviewed journals in the area of Biotechnology and Bioinformatics. Contact details : Coordinator Prof. M Krishna Mohan Head, R& D Biotechnology Mobile: +91-9314509942 Email:
[email protected]
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Dy. Coordinator Dr. P S Solanki Scientist Mobile: +91-9928365838 Email:
[email protected]
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XXIVnd All India BTISnet Coordinators’ Meeting
Birla Institute of Technology, Mesra, Ranchi Coordinator: Dr. A. S. Vidyarthi Summary of the progress made by the center from its inception The Distributed Information Sub-Center (Sub-DIC) was established by the Department of Biotechnology, Government of India at Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi in the year of 2005. Six workshops & training programmes on different aspects of bioinformatics for teachers, scientists, research scholars and PG students have been organized. Two faculty members and six research scholars are being pursuing their doctoral research in the centre. The centre is also actively involved in imparting education (M Sc. Bioinformatics) with the help of the university. Four batches of 20 students have conducted their project/dissertation work in bioinformatics and development of databases. Students of BE Biotechnology and M Tech Biotechnology are also encouraged to do their project/ dissertation in the field of bioinformatics. About 15 out side students belong to national institute/ university have completed their dissertation work/ short term training in the centre. More than 40 research articles have been published in peer reviewed journals of international repute and about 20 research articles have been presented in national / international workshop/ symposia. Five databases have been developed and are available in department website.
Area of specialization of the center Medicinal and Aromatic Plants, Molecular Modeling and Drug design, Database development, Functional Genomics of crop plants, Artificial intelligence and Computational Bioinformatics.
Major activities of the center during the year 2011-12
Doctoral research and projects for M. Sc. Bioinformatics and B. E. Biotechnology students were assigned and conducted in this lab.
Development and up-gradation of standalone software for Homology modelling, Swift Modeller.
Development of web based tool Predict @ Proteommetal for prediction of metal binding site in protein sequences and structures.
Development of artificial Intelligence based tool for early detection of diabetes in Indian population and Pima Indian population.
Development of artificial Intelligence based tool for early detection of thyroid at three stages.
Drug discovery by high throughput screening against target molecules and known homologs from different pharmaceutical compounds and medicinal plants.
Identification of single exon genes and their encoded proteins in rice (Oryza sativa L.) genome
Infrastructure facilities in the Bioinformatics Center Scientific Software packages: GCG 11.0 (Sequence Analysis), Insight II (Molecular Modeling), SYSTAT 11.0, SIGMAPLOT 9.0 (Statistical Analysis), DS GENE STATIC (Sequence search on internet).
Details about staff members working in the center Sl. No.
Name of the Staff
Designation
Specialization
1.
Dr. A. S. Vidyarthi
Professor & HOD
Bioprocess Engineering
2.
Dr. Raju Poddar
Sr. Lecturer
Codon Biasing
3.
Dr. Shankaracharya
Associate Lecturer
Molecular Modelling and Computational Intelligence
Period of working 9 years 6.5 years 6years
Educational activities with details of placement Ph D in Bioinformatics and biotechnology, M. Sc. in Bioinformatics (2 years), M. Tech in Biotechnology (2 years) and B.E. in Biotechnology (4 years). Placement of the students in the institute is more than 70%.
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Databases/ Softwares packages developed
Swift Modeller v1.0 and v2.0
Improvement in rice SEG database
Predict @ Proteommetal
Software for early detection of diabetes in Indian population
Software for early detection of thyroid at three stages
Databases/ Softwares packages in development
Intelligent system for early detection of different types of cancers
Expert system based Graphic User Interface for prediction of cardiovascular diseases
Intelligent system for prediction of Liver diseases
Computational Intelligence based Pre-diabetes detection tool for American population
Papers published
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1.
Jabin D, Vidyarthi AS and Shankaracharya. (2013) In silico analysis of flavopiridol analogues with Cdk2 in cancer therapy. Online J Bioinformatics. 14 (1): 1-8.
2.
Pandey D.M., Vidyarthi A.S., Nigam V.K., Prasad D., Ramani R., Prasad B.C., Das R., Kumar A., Prajapati G.K., Kumari A., Wany A. (2013) Meeting report: International symposium on plant biotechnology towards tolerance to stresses and enhancing crop yield (ISPB-2011). Current Research in Microbiology and Biotechnology 1(1): 16-22.
3.
Mallick, M, Odedra, D, Vidyarthi, AS, Shankaracharya (2013) Meropenem: A potent drug against superbug as unveiled through bioinformatics approaches. Int. J. Bioinformatics Research and Applications. 9(2): 109-120.
4.
Smita S., Katiyar A., Pandey D.M., Chinnusamy V., Archak S., Bansal K.C. (2013) Identification of conserved drought stress responsive gene-network across tissues and developmental stages in rice. Bioinformation 9(2): 072-078.
5.
Kumari A., Kumar A., Pandey D.M. (2013) In silico analysis of some least studied transcription factors/regulators in rice during abiotic stress. International Journal of Computational Bioinformatics and In Silico Modeling 2(1): 72-80.
6.
Shankaracharya, Odedra D, Samanta S and Vidyarthi AS (2012) Computational Intelligence-Based Diagnosis Tool for Detecting Prediabetes and Type 2 Diabetes in India. Rev Diabet Stud.,9(1):55-62 (I.F=2.936)
7.
Shankaracharya, Odedra D, Mallick M, Shukla P, Samanta S and Vidyarthi AS (2012) Java based diabetes type2 prediction tool for better diagnosis. Diabetes Technol Ther. 14(3):251-256. (I.F=2.146)
8.
Mathur A, Shankaracharya and Vidyarthi AS. (2012) SWIFT MODELLER v2.0: A platform independent GUI for homology modeling. J Mol Model 18(7):3021-3023. (I.F=2.224).
9.
Shankaracharya, Kumari S and Vidyarthi AS. (2012) Development of Java based graphical user interface for Diagnosis of Hepatitis Using Mixture of Expert. Nature preceding| doi:10.1038/npre.2012.7093.1.
10.
Pandey D.M., Kim S.-R. (2012) Identification and expression analysis of hypoxia stress inducible CCCH-type zinc finger protein genes in rice. J. Plant Biol. 55:489-497.
11.
Kumbhakar, S., Singh, P. K. and Vidyarthi, A. S. (2012) Screening of root nodule bacteria for the production of polyhydroxyalkanoate (PHA) and the study of parameters influencing the PHA accumulation. African Journal of Biotechnology, 11(31), 7934-7946
12.
Kumari A., Kumar A., Wany A., Prajapati G. K. Pandey D. M. (2012) Identification and annotation of abiotic stress responsive candidate genes in peanut ESTs. Bioinformation 8(24): 1211-1219.
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13.
Pandey B., Sharma P., Pandey D. M., Varshney J., Sheoran S., Singh M., Singh R., Sharma I., Chatrath R. (2012) Comprehensive computational analysis of different classes of Glutathione S-transferases in Triticum aestivum L. Plant Omics Journal 5(6): 518-531 (2012)
14.
Mukherjee K., Pandey D. M. and Vidyarthi A.S. (2012) Molecular Dynamics Simulation of Rap1 Myb-type domain in Saccharomyces cerevisiae. Bioinformation 8(18): 881-885.
15.
Mukherjee, K., Bothra, A.K., Vidyarthi, A.S. (2012). Molecular dynamics simulation of DNA binding domain of hTRF2. Journal of Advanced Bioinformatics Applications and Research. Volume 3(2), 324-327
16.
Katiyar A., Smita S., Pandey D. M., Chinnusamy V. and Bansal K.C. (2012) Identification of miRNAs in sorghum by using bioinformatics approach. Plant Signaling & Behavior 7(2): 1–14.
17.
Chauhan, N., Vidyarthi, A. S., and Poddar, R. (2012) Comparative Analysis of Different DNA Binding Drugs for Leishmaniasis Cure: A Pharmacoinformatics Approach. Chemical Biology & Drug Design. 80 54-63, DOI:10.1111/ j.1747-0285.2012.01329.x
18.
Karthik MVK, Syed H, Goswami T, Shukla P. (2012). Model and molecular docking substrate stabilization of Microsporum canis keratinase. Online J Bioinform . 13(1):33-40
19.
Ranjan, S. K., Mallick, C. B., Saha, D. Vidyarthi, A. S and Ramani, R. (2011) Genetic variation among species, races, forms and inbred lines of lac insects belonging to the genus Kerria (Homoptera, Tachardiidae). Genetics and Molecular Biology, 34, 3, 511-19.
20.
Chauhan, N., Vidyarthi, A. S., and Poddar, R. (2011) Comparative Multivariate Analysis of Codon and Amino Acid Usage in Three Leishmania Genomes Genomics Proteomics Bioinformatics 9(6): 218-228 DOI: 10.1016/ S1672-0229(11)60025-9.
21.
Kumar S, Pathak J, Asha PJ, Bandopadhyay R. (2011). Inhibition of Farnesyl pyrophosphate by allosteric site drug binding. Online J Bioinform 12(1):57-65
22.
Karthik MVK, Shrivastava S, Shukla P.(2011). Molecular docking for substrate stabilization in Thermomyces lanuginosus 11 xylanases. Online J Bioinform. 12(1):107-114
23.
Sahu, D., Kumar, A., Pandey D.M. (2011). In silico analysis of enzyme involved in enrichment of citronella oil, Int. J. Computational Biology and Drug Design, 4332-344.
24.
Shukla, A., Vidyarthi, A. S., Samanta, S. (2011). Computer Aided Drug Design and Studies of Antiviral Drug against H3N2 Influenza Virus World Academy of Science Engineering & Technology 59, 45-48.
Initiation of R & D activities in Bioinformatics 1.
Development of artificial intelligence based advance system for early detection of Non Communicable diseases.
2.
Functional genomic study of differentially expressed proteins induced by the drought in rice plants and
3.
Molecular modeling and drug design for better drug etc.
4.
Metagenomic study on coal.
Details of training/ Workshop organized and total no. of user trained “International Symposium on Plant Biotechnology towards Tolerance to Stresses & Enhancing Crop Yield (ISPB-2011), on 28th Sept. to 1st Oct 2011 (Number of participants 150)
Future activities Research: Development of intelligent system for early detection of non communicable diseases, Functional genomics of Rice, Molecular modeling and drug design as described above. Workshop: A workshop will be conducted on open-source softwares for bioinformatics Training: Students will be allotted under the scheme traineeship and studentship to accomplish the tasks in Bioinformatics
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Contact details : Name of the Coordinator
:
Dr. A. S. Vidyarthi
Postal Address
:
Prof. & Head Dept. of Biotechnology, Birla Institute of Technology, Mesra 835 215,Ranchi, Jharkhand
Phone Number
:
+ 91-651- 2276223, 2276590
Fax No.
:
+ 91-651- 2275401
Email
:
[email protected] [email protected]
Website
:
www.bitmesra.ac.in
Name of the contact person
:
Dr. A. S. Vidyarthi & Mr. Shankaracharya
E-mail
:
[email protected] [email protected]
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Central Agricultural Research Institute, Port Blair Coordinator: Dr. M Balakrishnan The details of the progress report are as follows;
Sixty two species of coral reef of Andaman and Niocbar Islands falling under 26 genera are documented. The database work is in progress.
About 215 species of butterflies of Andaman and Niocbar Islands were classified into two super families and five families and the same were documented. The database work is in progress.
Complied the 34 years of research work in the field of Horticultural and forestry done by CARI
Proposed activities for the during the year 2013-14
Development of database on Flora and Marine faunal biodiversity of Andaman and Niocbar Islands
Compilation of 34 years of research work in Fisheries and Field Crops carried out by CARI, Port Blair.
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Central Drug Research Institute, Lucknow Coordinator : Suman K Mallik Summary of the progress made by the centre from its inception BTIS Centre has been catering to the information requirements of the users working in the area of Biomedical Research. This center has been serving the research community in the area of Drugs & Pharmaceuticals for quite some time. With the establishment of BTIS Center, the user profile of the center widened to those working in the area of Biotechnology in Drug Research and Pharmaceutical Industry.
User profile of the center includes:
Drugs & Pharmaceutical & BiotechIndustry
R&D Institution, CSIR, ICAR, DBT, DOD, State Science & Technology Councils, etc.
Universities/Departments of Biotechnology
Small Entrepreneurs
Students pursuing Courses in Biotechnology and Bioinformatics.
Area of Specialization of the Centre: Biomedical Research
Major research activities in biotechnology and its related fields at your institution Bioinformatics BTIS at CDRI extends hardware/software facilities and provides information resources for the Bioinformatics research work being carried out by CDRI as well as other visiting scientists/students working in the area of Bioinformatics.
Analysis of Progress of Bioinformatics and Computational Biology through the Publications from India BTIS Centre of CDRI has been compiling a list of all the publications in this area from all over the country. We have sent analysis of such data to DBT from time to time so as to assess the output in the form of publications. This year we made a comprehensive compilation of the Indian publications and a report in the form of a book detailed below was published Bioinformatics and Computational Biology : A Compendium of Research Publications from India ( 2002-2010)- Published by CSIR-CDRI and DBT. The Publication was released in the coordinators Meeting held at SMVDU, Jammu on 2nd Feb, 2012
Information Services Being a National Information Centre on Drugs & Pharmaceuticals, our library caters to the information needs of the students, researchers of institutions/universities involved in biomedical research all over the country. A large number of users from Biotech related pharmaceutical Industry asks for and receives information services from the Centre.
Current Awareness Services Current awareness service in the area of Drugs & Pharmaceuticals has been one of the main activities of the CDRI Library, we have been publishing two journals; Drugs & Pharmaceuticals – Industry Highlights (Monthly) and Drugs & Pharmaceuticals — Current R&D Highlights (Quarterly). Recently we have started a new on-line publication - “Recent Patents on Bioinformatics in drug Research” (Bimonthly).
Infrastructure facilities in the Bioinformatics Centre Earlier, we had few computers attached to a server to cater to the users’ information needs. However, the grant made available by the BTIS we have acquired more computers and latest version of a HP cluster server. The The resource procured by CDRI Library includes:
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On-line Databases,
4500 online journals of all major publishers
Periodicals & Books in the area of drug research.
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Efforts are on to carry out more collaborative initiatives on the pattern of Lucknow Special Libraries Consortium. The Centre is a part of DELNET and would like to join hands with other BTIS Centres. Studies on Bioinformatics Publications from India: The Centre continued its efforts in developing a database on the Publications related to bioinformatics and computational biology in the institutions across the country. The data has been compiled and published in the form of a compendium.
Papers/ published or presented in the conferences 1.
Overexpression, purification, crystallization and preliminary X-ray analysis of putative molybdenum cofactor biosynthesis protein C (MoaC2) from Mycobacterium tuberculosis H37Rv.Srivastava, Shubhra; Srivastava, Vijay Kumar; Arora, Ashish; Pratap, J. Venkatesh Acta Crystallographica Section F-Structural Biology And Crystallization Communications 68,Pt 6,687-691.
2.
Role of conserved active site tryptophan-101 in functional activity and stability of phosphoserine aminotransferase from an enteric human parasite. Mishra V, Kumar A, Ali V, Nozaki T, Zhang KYJ, Bhakuni V. Amino Acids 43(1), 483-91.
3.
Novel protein-protein interactions between Entamoeba histolytica d-phosphoglyceratedehydrogenase and phosphoserine aminotransferase Mishra V, Kumar A, Ali V, Nozaki T, Zhang KYJ, Bhakuni V. Biochimie 94(8)16761686.
4.
Heat shock protein 60 of filarial parasite Brugia malayi: cDNA cloning, expression, purification and in silico modeling and analysis of its ATP binding site.R.C. Misra, A.K. Verma, S.K. Verma, V. Kumar, W.A. Siddiqui, M.I. Siddiqi, P.K. Murthy. Experimental Parasitology 132(2) 257-66.
5.
Proteomics approaches for myeloid leukemia drug discovery.Kapoor I, Pal P, Lochab S, Kanaujiya JK, Trivedi AK. Expert Opin Drug Discov 7 (12)1165-75.
6.
Genome wide computational analysis of Brugia malayi helicases: A comparison with human hostTuteja, Renu; Ansari, Abulaish; Anita; Suthar, Manish Kumar; Saxena, Jitendra Kumar. Gene 499(1)202-208.
7.
Deletion of the APOBEC3B gene strongly impacts susceptibility to falciparum malaria Jha, Pankaj; Sinha, Swapnil; Kanchan, Kanika; Qidwai, Tabish; Narang, Ankita; Singh, Prashant Kumar; Pati, Sudhanshu S.; Mohanty, Sanjib; Mishra, Saroj K.; Sharma, Surya K.; Awasthi, Shally; Venkatesh, Vimala; Jain, Sanjeev; Basu, Analabha; Xu, Shuhua; Mukerji, Mitali; Habib, Saman . Infection Genetics and Evolution 12(1)142-148.
8.
RNAi mediated silencing of ATPase RNA helicase gene in adult filarial parasite Brugia malayi impairs in vitro microfilaria release and adult parasite viability.Singh M, Singh PK, Misra-Bhattacharya S. J Biotechnol 157(3)351-8.
9.
Medicarpin, a legume phytoalexin, Stimulates Osteoblast Differentiation And Promotes Peak Bone Mass Achievement In Rats: Evidence For Estrogen Receptor β-Mediated Osteogenic Action Of Medicarpin.Bhargavan B, Singh D, Gautam AK, Mishra JS, Kumar A, Goel A, Dixit M, Pandey R, Manickavasagam L, Dwivedi SD, Chakravarti B, Jain GK, Ramachandran R, Maurya R, Trivedi A, Chattopadhyay N, Sanyal S. J Nutr Biochem 23(1) 27-38
10.
QSAR of 2-(4-methylsulphonylphenyl) pyrimidine derivatives as cyclooxygenase-2 inhibitors: simple structural fragments as potential modulators of activity. Sharma, B. K.; Singh, P.; Pilania, P.; Shekhawat, M.; Prabhakar, Y. S. Journal of Enzyme Inhibition and Medicinal Chemistry. 27(2) 249-260
11.
Development and evaluation of tripalmitin emulsomes for the treatment of experimental visceral leishmaniasis.Pal, Ajay; Gupta, Swati; Jaiswal, Anil; Dube, Anuradha; Vyas, Suresh P. Journal of Liposome Research 22(1)62-71
12.
Medicarpin, a legume phytoalexin, stimulates osteoblast differentiation and promotes peak bone mass achievement in rats: evidence for estrogen receptor beta-mediated osteogenic action of medicarpin. Bhargavan, Biju; Singh, Divya; Gautam, Abnish K.; Mishra, Jay Sharan; Kumar, Amit; Goel, Atul; Dixit, Manish; Pandey, Rashmi; Manickavasagam, Lakshmi; Dwivedi, Shailendra D.; Chakravarti, Bandana; Jain, Girish K.; Ramachandran, Ravishankar; Maurya, Rakesh; Trivedi, Arun; Chattopadhyay, Naibedya; Sanyal, Sabyasachi, Journal of Nutritional Biochemistry 23(1)27-38
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13.
Discovery of a new class of dithiocarbamates and rhodanine scaffolds as potent antifungal agents: synthesis, biology and molecular docking Chauhan, K; Sharma, M; Singh, P; Kumar, V; Shukla, PK; Siddiqi, MI; Chauhan, PMS. Medchemcomm 3(9)1110-1104.
14.
Synthesis and bioevaluation of aryl hydroxamates distinguishing between NAD(+) and ATP-dependent DNA ligases.Kukshal, Vandna; Mishra, Mridul; Ajay, Arya; Khanam, Taran; Sharma, Rahul; Dube, Divya; Chopra, Deepti; Tripathi, Rama Pati; Ramachandran, Ravishankar. Medchemcomm 3(4)453-461
15.
Glu-108 is essential for subunit assembly and dimer stability of D-phosphoglycerate dehydrogenase from Entamoeba histolytica.Mishra, Vibhor; Kumar, Ashutosh; Ali, Vahab; Nozaki, Tomoyoshi; Zhang, Kam Y. J.; Bhakuni, Vinod. Molecular and Biochemical Parasitology 181(2)117-124.
16.
Withania somnifera chemotypes NMITLI 101R, NMITLI 118R, NMITLI 128R and withaferin A protect Mastomys coucha from Brugia malayi infection.Kushwaha, S; Soni, V K; Singh, P K; Bano, N; Kumar, A; Sangwan, R S; Misra-Bhattacharya, S. Parasite immunology 34 (4)199 -209.
17.
mRNA expression of cytokines and its impact on outcomes after infection with lethal and nonlethal Plasmodium vinckei parasites. Siddiqui, Arif J; Bhardwaj, Jyoti; Puri, Sunil K. Parasitology Research 110 (4)1517 -1524.
18.
Leishmania donovani Triose Phosphate Isomerase: A Potential Vaccine Target against Visceral Leishmaniasis. Kushawaha PK, Gupta R, Tripathi CD, Khare P, Jaiswal AK, Sundar S, Dube A. PLoS One 7 (9)e45766.
19.
M. tuberculosis Sliding beta-Clamp Does Not Interact Directly with the NAD(+) -Dependent DNA Ligase.Kukshal, V; Khanam, T; Chopra, D; Singh, N; Sanyal, S; Ramachandran, R. Plos One 7(4) e35702
20.
Molecular Characterization of NAD(+)-Dependent DNA Ligase from Wolbachia Endosymbiont of Lymphatic Filarial Parasite Brugia malayi.Shrivastava N, Nag JK, Misra-Bhattacharya S. PLoS One 7(7) e41113.
21.
IL-4 Haplotype-590T,-34T and Intron-3 VNTR R2 Is Associated with Reduced Malaria Risk among Ancestral Indian Tribal Populations.Jha, AN; Singh, VK; Kumari, N; Singh, A; Antony, J; van Tong, H; Singh, S; Pati, SS; Patra, PK; Singh, R; Toan, NL; Song, LH; Assaf, A; Messias-Reason, IJT; Velavan, TP; Singh, L; Thangaraj, K. Plos One 7(10)
22.
Proteomic identification of E6AP as a molecular target of tamoxifen in MCF7 cells Lochab, Savita; Pal, Pooja; Kanaujiya, Jitendra K.; Tripathi, Shashi B.; Kapoor, Isha; Bhatt, Madan L. B.; Sanyal, Sabyasachi; Behre, Gerhard; Trivedi, Arun K. Proteomics 12(9)1363-1377
23.
Triiodothyronine Acutely Stimulates Glucose Transport into L6 Muscle Cells Without Increasing Surface GLUT4, GLUT1, or GLUT3 Teixeira, SS; Tamrakar, AK; Goulart-Silva, F; Serrano-Nascimento, C; Klip, A; Nunes, MT. Thyroid 22(7)747-754
24.
Mechanism of Inhibition of the ATPase Domain of Human Topoisomerase II alpha by 1,4-Benzoquinone, 1,2Naphthoquinone, 1,4-Naphthoquinone, and 9,10-Phenanthroquinone Gurbani, Deepak; Kukshal, Vandna; Laubenthal, Julian; Kumar, Ashutosh; Pandey, Alok; Tripathi, Sarita; Arora, Ashish; Jain, Swatantra K.; Ramachandran, Ravishankar; Anderson, Diana; Dhawan, Alok Toxicological Sciences 126(2)372-390.
25.
Chemotypical variations in Withania somnifera lead to differentially modulated immune response in BALB/c mice.Kushwaha, Susheela; Roy, Saptarshi; Maity, Rita; Mallick, Asish; Soni, Vishal K.; Singh, Prashant K.; Chaurasiya, Narayan D.; Sangwan, Rajender S.; Misra-Bhattacharya, Shailja; Mandal, Chitra, Vaccine 30(6)10831093.
Proposed activities for 2013-14 With the funds of BTIS, the center plans to:
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Modernize the information base of the centre with introduction of state of the art hardware facilities.
To subscribe to the more user friendly and broader coverage databases,
To develop in-house databases in the areas hitherto untouched by others.
Training in the area of Bioinformatics
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Contact details: Name of the Coordinator Postal Address
Phone Number Fax No. Email Website Name of Contact Person
Dr. Suman K Mallik Sr Principal Scientist & Scientist-in-Charge BTIS-SubDIC & Knowledge Resource Centre Central Drug Research Institute, Lucknow-226 001. 0522-2613812, 9415105084 0522-2623405
[email protected] www.cdriindia.org Dr. Suman K Mallik
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Central Institute of Medicinal and Aromatic Plants Coordinator: Dr. Ashok Sharma Summary of the progress made by the centre from its inception: Bioinformatics Centre, since its inception in 1998 is the backbone of bioinformatics/ computational analysis in R&D activities of CIMAP. The major research activities undertaken include database/ tool development and computational research analysis in the areas of Genomics, Transcriptomics, Proteomics, Metabolomics, Cheminformatics, Pharmacoinformatics, and Virtual High Throughput Screening etc. Centre also continued to provide quality Human Resource Development through its various training programs.
Major research activities in biotechnology and its related fields: 1.
Bioprospecting novel bioactives from plant sources for infectious diseases, metabolic disorders and safety evaluation of MAPs using modern tools.
2.
Expression profiling for metabolic and genetic diversity basis, DNA markers for breeding and identification, genomics for pathway engineering, variety development.
3.
In vitro operations and manipulations in MAPs including micro-cloning, somaclonal breeding, haploid production, protoplast culture and genetic transformation
4.
Computational research analysis in the areas of genomics, proteomics and database/tool development.
Area of specialization: Bioinformatics, Cheminformatics & Pharmacoinformatics studies related to biomolecules/bioactive compounds of Medicinal & Aromatic Plants (MAPs).
Major achievements made during 2012-13: Bioinformatics R&D activities Research analysis related to genomics, transcriptomics, proteomics, metabolomics and machine learning: a.
In silico screening of medicinal plants for phytoremediation capabilities for heavy metals.
b.
Virtual screening of phytomolecules and their mode of action on drug targets with main emphasis on cell wall synthesis enzymes and to identify potential antibacterial leads from medicinal and aromatic plants.
c.
Differential expression analysis of genes responsible for abiotic stress conditions.
d.
Analysis of putative transcription factor binding sites in the genes expressed in stress response.
e.
In silico methods in DNA barcoding.
f.
microRNA prediction in MAPs.
Infrastructure facilities in the Bioinformatics Centre: A.
Computer & Communication facility Fiber optic based LAN with managed switches, 8 MBPS radio link internet connectivity, Silicon Graphics Interface fuel station package, Sun Microsystems, IBM and DELL systems, IBM Quad core Bioinformatics Severs 3400x.
B.
Scientific Software packages General Bioinformatics Tools: VMD 1.8.2 Viewer, Rasmol Viewer, Swiss PDB viewer, Pymol View, BioEdit, MGL Tools - Autodock vinna tools, PMV, Sigmaplot, Cygwin, Modeller 9V8, Clustal X, Matlab R2008b. Bioperl 1.5.1, hmmer 2.1.1, Phylip, Python 2.7, Emboss, Win pep 1.0, Threader, MDL Chime SP6, , Tree View 32, Procheck_NT, SAVES.
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Pattern discovery: BioProspector, CompareProspector, MDscan, Improbizer, Ann-spec, MITRA, GLAM, INCLUSive, Motif Sampler, Toucan, YRSA, YMF, Consensus server, Patser, MEME, YEBIS, Signal Search Analysis Server. Phylogenetic footprinting: Dendroscope, MEGA, PAUP, Mesquite, CompareProspector, Bayesian Phylogenetic Footprint Homepage, FamilyJewels, TRES, FootPrinter, Orthoseq, CRÈME, ConSite, Tools for phylogenetic footprinting purposes and PhyloCon. Software related with IT: MS Visual Studio. Net, OCR Fine Reader, Macromedia MX, Oracle 9i, Application Server, Adobe Acrobat, MS Back Office Server 2000. DNA barcoding: BRONX, ecoPrimers, Spider, CAOS, jMOTU & Taxonerator and OFBG.
Commercial Bioinformatics Softwares: 1.
Sybyl (Comprehensive package)
2.
DNASTAR (DNA and protein sequence analysis, as well as next-gen and third-generation sequence assembly and analysis.)
3.
Biosuite (Comprehensive package)
4.
SYSTAT (For statistical analysis)
Details about Staff members working in the centre: Sl.No. 1. 2. 3. 4.
Name Dr. Ashok Sharma Sudeep Roy Sanchita Amandeep Kaur Kahlon
5. 6. 7. 8.
Mili Bhargawa Shubhandra Tripathi Akhil Srivastava Noopur Singh
Designation Specialization Chief Scientist & Head Bioinformatics SRF-LS Bioinformatics SRF Bioinformatics CIMAP-JNU Ph.D. Pharmacology/ Scholar Pharmaco-informatics Project Assistant Bioinformatics Research Intern Bioinformatics Project Assistant Bioinformatics CIMAP-JNU Ph.D. Bioinformatics Scholar
Working Since Permanent 16-10-2006 17-09-2007 01-11-2008
Status Permanent Contractual CSIR-SRF Contractual
13-09-2011 09-08-2012 21-09-2012 09-10-2012
Contractual Contractual Contractual DST-INSPIRE
Educational activities
CIMAP-JNU and AcSIR Ph.D programme in Life Science (Biotechnology and Bioinformatics).
Papers/ published or presented in conferences: Sanchita, Rashi Chauhan, Garima Soni, Babu Sudhamalla, Ashok Sharma (2012) Docking and molecular dynamics studies of peptide inhibitors of ornithine decarboxylase: a rate-limiting enzyme for the metabolism of Fusarium solani. J Biomol Struct Dyn. Sep 13. DOI:10.1080/07391102.2012.718526. Amandeep Kaur Kahlon, Mahendra P Darokar, Ashok Sharma (2012). Probing the evolutionary conserved regions within functional site of drug-resistant target proteins of Staphylococcus aureus: In silico phylogenetic motif profiling approach. Indian Journal of Biochemistry and Biophysics, 49(6): 442-450. Zahid Rizvi, Pooja Mishra, Sudeep Roy*, AK Kukreja and Ashok Sharma (2012);Application of artificial neural networks for predicting maximum in-vitro shoot biomass production of safed musli (Chlorophytum borivillianium); Journal for proteomics and bioinformatics, 1(10);2012.
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Initiation of R&D activities in bioinformatics: i)
ii)
iii)
Genomics & Proteomics: a)
DNA barcoding of medicinal and aromatic plants.
b)
To analyze hypothetical genes, ESTs sequence assembly and functional annotation of genes.
c)
To identify potential genetic markers such as microsatellite (SSR) related to MAPs.
d)
Statistical analysis of differentially expressed genes under abiotic stress responses.
e)
Over and under expression analysis of genes due to drought stress in Withania somnifera.
f)
Comparative genomics analysis of drug resistant strains of Staphylococcus aureus to identify common and strain specific genes for potential drug targets.
Cheminformatics & Pharmacoinformatics: a)
To identify the active sites of the receptors/targets, binding pockets, interaction energies through docking studies.
b)
To identify potential leads & targets through in silico Virtual High Throughput Screening (VHTS).
c)
To study pharmacokinetics of chemical compound/biomolecules for Drug-likeness/Drugability through Lipinski’s Rule of Five filter, QSAR/QSPR and ADMET analysis.
Development of Bioinformatics Databases/Datawarehouses Terpene synthase pathway genes
Impact shown by the Centre: Bioinformatics Centre of CIMAP, Lucknow is continuously progressing towards the Centre of Excellence in the R&D of Plant Bioinformatics especially Medicinal & Aromatic Plants (MAPs). The extensive work is carried out on the secondary metabolism of MAPs, genomic sequence analysis such as ESTs for SSRs identification in MAPs. Besides this, Bioinformatics centre strengthened the ongoing In-house/Network/Sponsored research projects and successfully organized the Bioinformatics training & teaching, thus contributing to skilled manpower development.
Proposed activities for 2013-14
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Screening of phytomolecules with antibacterial activities through docking studies to find the potential leads and validation through in vitro cell based assays.
Evolutionary analysis of identified pathway enzymes in shikimate pathway of Staphylococcus aureus.
Molecular interaction studies for mode of action of identified synthesized and natural antibacterial from medicinal and aromatic plants against target proteins of Staphylococcus aureus.
Metabolic pathway elucidation and modulation studies in some commercially important medicinal and aromatic plants.
DNA barcoding studies in medicinal and aromatic plants
In silico analysis of regulatory elements of differentially expressed genes in abiotic stresses.
To develop Bioinformatics databases on Terpenes.
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Contact details: Name of the Coordinator
Dr. Ashok Sharma Chief Scientist and Head, Biotechnology Division
Postal Address
Central Institute of Medicinal & Aromatic Plants, (Council of Scientific & Industrial Research) P.O. CIMAP, Kukrail Picnic Spot Road, Lucknow-226015
Phone Number
0522-2718577
Fax No.
0522-2342666
Email
[email protected] [email protected]
Website
www.cimap.res.in
Name of Contact Person
Dr. Ashok Sharma
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Central Institute of Freshwater Aquaculture, Bhubaneswar Coordinator: A.S. Mahapatra Summary of the progress made by the centre from its inception : The Bio-informatics centre of CIFA which is a Sub-DIC under BTIS network is one of the oldest centre in India. It was established during 90s. Since its inception the centre is doing an excellent work with a view to cater to the needs of the scientific community as well as students from eastern as well as other parts of the country. The excellent quality of infrastructure facility set up over the years is being regularly updated both in terms of hardware and software. The centre till date has published 45 research papers, 13 training manuals and 6 books. 16 national level workshop-cum-training on bioinformatics has been done till date. 3 standalone databases related to aquaculture has been developed. The centre till date has trained more than 800 researchers, officials and students. 19 studentship and traineeship were also provided till date. The centre has also acquired databases and has electronic publications to its credit.
Major activities of the centre during the year 2012-13 BTIS at CIFA provided excellent hardware/software facilities and information resources to research workers and students working in the area of bio-informatics. Physical memory of all the computers at the BTIS centre has been upgraded to maximum. New software’s Genius Pro v. 5.6 has been procured. Students have been provided summer training in the area of database development, software development and statistical computing of bio-logical data during this period. 5 postgraduate bio-informatics students also completed their four months project work from the centre on modeling, docking and studies on bio-informatics software’s available and their applications.
Infrastructure facility in the bioinformatics centre Computer and Communication facility: Hardware
Two server
Latest Computers (17)
(1, 3 & 5 KVA) online UPS
DotMatrix / DeskJetPrinters
HP LaserJet 1320 N (Network) Printers (2)
LCD Projector
Colour Scanner
Modem
Switches & Routers
Software
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Window Server-2008
Windows XP, Windows Vista, Windows 7
Novel Netware 4.1, UNIX, LINUX
SPAR1
FoxPro
QPRO
Oracle
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MS Office 97, 2000, 2007 & 2010
MS- Visual Studio 6 – Enterprise Version
MS- Visual Studio 2010 Professional
Systat (Version 12.0)
SPSS (Version 14.0)
SAS (Version 9.2 & 9.3)
Details about staff members working in the centre Name of the staff Mrs. N. Panda Mr. D. P. Rath
Designation T-6 T-5
Specialization Statistics M.C.A
Period of working 2006 1992
Absorption status Permanent Permanent
Proposed activities for 2013-14
Continuation of the Bioinformatics centre: All the hardware, software, facilities etc created in the centre since last 22 years will be maintained.
Support to Biotechnology Research: The BTIS Centre will extend hardware, software, and data base support to the students and scientist involved in the biotechnology research in CIFA and other fisheries Institute.
Workshop on Bioinformatics in Aquaculture: A national level workshop cum training on bioinformatics in aquaculture will be organized during 2013.
Acquiring hardware and software: Old computers will be replaced/upgraded to the latest configuration as well as new systems will be purchased in the BIC as per requirement. There are also plans to acquire new software like Discovery Studio/Gold for modeling and docking.
Project work and summer training: Bio-informatics centre CIFA would continue its support to post-graduate bio-informatics students to undergo their summer training and project work for post graduate bio-informatics students.
Contact details:
Name of the Coordinator
:
Shri. A. S. Mahapatra, Scientist (Computer Application)
Postal address
:
OIC Computer Centre, CIFA, Kausalyaganga, Bhubaneswar - 751002
Phone
:
0674-2465430
Fax no.
:
0674-2465407
Mobile no.
:
+919439364857, +918093382179
E-mail
:
[email protected],
[email protected]
Website
:
www.cifa.in
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Central Plantation Crops Research Institute, Kasaragod Coordinator: Dr. George V Thomas Area of Specialization of the centre Bioinformatics applications in plantation crops (coconut, arecanut and cocoa) and plant growth promoting rhizobacteria
Major activities of the centre during the year 2012-13
Coconut artificial pollination management system
The database meets the two requirements of review of work done and planning of future work. Input data includes bunch opening date, bagging date, dates of pollination, number of flowers pollinated, source of pollen, number of nuts set, date of harvest, number of nuts harvested, name of the pollinator and name of supervisor. Output includes number of bunches pollinated for a palm, number of female flowers pollinated in bunch and in a palm, percentage of nut set, number of nuts harvested from a bunch and a palm, number of pollination effected by a pollinator, number of nuts obtained per pollinator, number of nuts obtained per male parent etc. In addition to these calculations, the database also helps in decision making by analysing the data of the previous year. It is possible to estimate date of emasculation, bagging, pollination, bag removal etc. in advance based on the bunch opening date. Knowing the date on which a particular bunch in a palm has to be emasculated, bagged, pollinated etc., it becomes easier to plan and monitor.
Virtual screening and in vitro evaluation of potential growth regulators against somatic embryogenesis receptor kinase (SERK) in coconut
Homology–based modeling of a coconut SERK protein was carried out for exploring its structural features, characterization of its active sites and binding mechanisms of some plant hormones and growth regulators to the SERK protein by automated docking. 3-D model for coconut SERK was constructed using structure neighbors of the protein in MODELLER. The best model was selected based on overall stereo-chemical quality and minimum energy. The model was refined and used for active site characterization. Twenty one ligands were docked with the target SERK protein using AutoDock server. Homobrassinolide, glutathione and adenine sulphate gave the best docking orientation with coconut SERK protein. An in vitro study was then performed to compare the efficiency of these plant growth regulators in enhancing somatic embryogenesis from plumular explants of coconut. Plumular explants were excised from MGD (Malayan green Dwarf) cultivar of coconut and were inoculated into Y3 media supplemented with TDZ (Thidiazuron, a commonly used growth regulator for plumular studies in coconut) and these plant growth regulators. Plain Y3 medium, without any growth regulator supplementation, served as control. Initial results indicated an enhanced somatic embryogenesis (80-90%) in explants inoculated in Y3 medium supplemented with these plant growth regulators, compared to Y3 medium supplemented with 2,4-D and TDZ (5766%) and control (nil).
Homology modeling deduced 3-D structure of adenylation domain of Pseudomonas fluorescens Pf-5 non-ribosomal peptide synthetases (NRPS)
The 3-D structure of adenylation domain of P. fluorescens Pf-5 NRPS was predicted using MODELLER 9.10. based on templates showing similar identity to the target protein [2AMQ (Brevibacillus brevis), 2VSQ (Bacillus subtilis), 3E7W (Bacillus subtilis) and 3DHV (Bacillus cereus)]. Five models were generated and the model with the discrete optimized potential energy (DOPE) score was chosen. Loop refinement was performed to increase the quality of the model with the best DOPE score. Evaluation and verification of the model, done using Procheck via Ramachandran plot, showed that 86.4% of the residues were in most favorable region and around 9.4% of the residues were in additional allowed regions. Based on the PROMOTIF program, it was found that the percentage of â-strand was 14.7%, percentage of 3, 10 helix was 2.6 % and percentage of á-helix was 31.9 %.
Molecular insights into quorum sensing in Pseudomonas fluorescens using bioinformatics tools
BLAST and CATH result showed that the Phop protein, involved in quorum sensing in Pseudomonas fluorescens, has 3055% identity with three transcriptional regulatory proteins (pdb ID:2PKX,1YS6 & 2Pl1) and these were selected as templates to model its structure. A total of five models were generated and their DOPE score were calculated and the model possessing the minimum score was considered as the best model of Phop protein. Ramachandran plot for the model revealed that out of
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total of 196 residues, 92.9% were in the most favoured region, 6.6% in the additional allowed region, 0.0% in the generously allowed region and 0.5% in the disallowed region, making this model more acceptable. The selected model passed the validation step of Verify_3D program having 92.88% of the residues with averaged 3D-1D score >0.2. Docking studies of four AHL derivatives (C12-AHL, C14-AHL, 3-oxo-C12-AHL and 3-oxo-C14-AHL) with the modeled protein Phop was performed separately. Docking results showed that the ligand C14-AHL ranked one with the minimum glide score of -2.24424 in comparison to other ligands
Upgradation of databses
All databases were updated regularly. These databases are IP restricted and limited accessibility is provided at the website http:// www.bioinfcpcri.org.
Conducting training programmes
A training programme entitled, “Genetic Diversity and Mapping Analysis Using Molecular Marker Data” was conducted from 15st – 20th October 2012, which benefitted 9 researchers and students.
Educational activities with details of placement: One each of studentship and traineeship were awarded during the period.
Databases/ Software packages developed during 2012-13
Coconut artificial pollination management system helps in decision making and tracking the process of artificial pollination. This database meets two requirements, review of work done and planning of future work. It also helps in supervision and monitoring the pollinators which are very important in timely completion of artificial pollination.
Papers published or presented in the conferences: Research papers: a)
Bobby Paul, Rajesh, M.K. and Naresh Kumar S. (2012) Molecular cloning and characterization of a partial mitogen-activated protein kinase cDNA, CnMAPK1 induced in response to water stress in coconut. Indian Journal of Horticulture, 69 (2): 145-150.
b)
Hemalatha N., Rajesh M.K. and Narayanan N. K. (2012) Genome-wide analysis of putative ERF and DREB gene families in indica rice (O. sativa L. subsp. indica). International Journal of Machine Learning and Computing, 2(5): 556-559.
Conference papers: a)
Jamshinath T.P., Rajesh M.K., Joemon K. Jose and George V. Thomas (2012) MAPS (Microsatellite Analysis and Prediction Software): A tool for detection of microsatellites in whole genome sequences. In: Proceedings of “National Symposium on Bioinformatics-Challenges in the Post Genomics Era” held at University of Jammu, Jammu on 2nd February, 2012, pp. 58.
b)
Merin K. Eldo, Rajesh M.K., Jamshinath T.P., Murali Gopal and George V. Thomas (2012) Development of a promoter prediction tool for ó70 in Pseudomonas spp. using SVM and HMM. In: Proceedings of “National Symposium on Bioinformatics-Challenges in the Post Genomics Era” held at University of Jammu, Jammu on 2nd February, 2012, pp. 60.
c)
Jamshinath, T.P., Philip Job, N., Rajesh, M.K., Murali Gopal and George V. Thomas (2012) Homology modeling deduced 3-D structure of adenylation domain of Pseudomonas fluorescens non-ribosomal peptide synthetases (NRPS). In: Abstracts: 22nd Swadeshi Science Congress (Eds. George V. Thomas, Muralidharan, K., Rajesh, M.K., Jayasekhar, S., Mathew, A.C., Subaharan, K., Ravi Bhat, Amarnath, C.H. and Muralikrishna, H.), 6th8th November, 2012, Central Plantation Crops Research Institute, Kasaragod, Kerala, India. pp. 100-101 (B5).
d)
Rachana, K.E., Naganeeswaran, S. and Rajesh, M.K. (2012) Amplification and sequencing of partial–length disease resistant gene homologues coding NBS-LRR type proteins in coconut using comparative genomics. In: Abstracts: 22nd Swadeshi Science Congress (Eds. George V. Thomas, Muralidharan, K., Rajesh,
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M.K., Jayasekhar, S., Mathew, A.C., Subaharan, K., Ravi Bhat, Amarnath, C.H. and Muralikrishna, H.), 6th8th November, 2012, Central Plantation Crops Research Institute, Kasaragod, Kerala, India. pp. 107 (B15). e)
Rajesh M.K., Jamshinath, T.P., Fayas, T.P., Sajini, K.K. and Anitha Karun (2012) Virtual screening and in vitro evaluation of potential growth regulators against somatic embryogenesis receptor kinase in coconut. In: Abstracts of Papers PLACROSYM XX (Eds. Radhakrishnan, B., Raj Kumar, R., Palani, N., Premkumar, R., Victor J. Ilango, R., Muthu Kumar, S., Krishnakumar, V. and Krishnakumar, R.), 12th-15th December, 2012, UPASI Tea Research Foundation, Coimbatore, Tamil Nadu, India. pp. 38-39 (P.56).
f)
Hemalatha N., Rajesh M. K. and Narayanan N. K. (2012) NACSVMPred: A Machine Learning Approach for Prediction of NAC Proteins in Rice using Support Vector Machines. Oral presentation made at the First International Conference on Advanced Information Technologies and Applications (ICAITA-2012) held on December 28, 2012 at Deira, Dubai.
Details of Training/Workshop organized and total no. of user trained: A training programme entitled, “Genetic Diversity and Mapping Analysis Using Molecular Marker Data” was conducted from 15st – 20th October 2012 which benefitted 9 researchers and students.
Future activities:
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Conducting training programmes in development of machine learning algorithms for gene prediction
Development of a web-enabled pipeline for analysis of coconut transcriptomic data
Development of a database of DNA fingerprinting data of coconut and cocoa accessions
Development of a database of phylogenetic studies of indigenous palms using nuclear genes
Decrypting the pathways involved in plant growth promotion in plant growth promoting rhizobacteria.
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Central Sericultural Research and Training Institute, Mysore Coordinator: Dr. S.M.H. Qadri Summary of the progress made by the center from its inception The Bioinformatics Centre at CSRTI, Mysore was established in November, 1999 under the BTIS programme of the DBT, Govt. of India as a Sub-DIC. The website of the center is hosted from the centre’s server with the URL www.btismysore.in. The main focus of the centre is to support biotechnology research pertaining to Sericulture. So far six databases and 2 softwares related to the host plant mulberry and silkworm have been developed, updated and maintained. Infrastructure facilities and support through bioinformatics tools and techniques were provided for the scientists of the Institute for their projects and experiments.
Major research activities in biotechnology and its related fields in your institution Presently, 4 research projects funded by DBT/ DST and 22 projects funded by Central Silk Board are being carried out. Important areas of research like Development of mulberry transgenics over expressing transcription factors associated with drought and epicuticular wax biosynthesis, DNA marker aided analysis of mulberry gene bank towards a core assembly for sustainable conservation, breeding for NPV resistance using BmNOX marker assisted selection, DNA marker assisted breeding for thermotolerance, use of silk fibroin solutions for producing silk films, application of nano-particles for controlling silkworm diseases etc. are covered in the afore said projects.
Area of Specialization of the center The main thrust area of this center is Seri-biotechnology and Seri-bioinformatics
Major activities of the center during the year 2012-13 Databases developed and maintained: 1.
SILKPROT : An Annotated Protein database for Silkworm and Mulberry : SilkProt is a comprehensive, fully annotated, organism specific database for silkworm proteins. SilkProt was developed with MySQL as back-end database and PHP with HTML as front-end. The database contains data about ~1000 silkworm proteins sequences. It has user-friendly interface for accessing the data with Boolean AND based filtering of the results and with easy page navigation. The selected sequences can be viewed as FASTA format. The database has cross reference to other databases like SwissProt, Pubmed, PDB and ModBase.
2.
SilkTF: Silkworm specific transcription factor database. Developed using MySQL and PHP. The database contains 587 protein sequences of mulberry silkworm having the transcription factors.
3.
Mulberry Genome Database : Extensive Molecular marker data on DNA fingerprints, binary scores, similarity, and dissimilarity index matrices, phylogenetic relationship in terms of dendrogram and marker segregation pattern has been compiled and stored using relational database with Visual Basic Platform. The database is also made available in the form of CD and is also being updated regularly.
4.
The Silk e-Lab : The silk e-lab which contains a compendium of sequence information of the silkworm genome, crystal structure data for artificial silk protein and STS markers for RAPD analysis. The same data is being revised, fined and upgraded.
5.
Database of DNA sequences for important plant genes in mulberry : A database has been developed for storing and retrieving DNA sequences of important plant genes responsible for yield, quality, diseases and pest resistance and also some of the mulberry specific genes obtained from the public domain. PCR primers for important plant gene sequences has been designed.
6.
Soilinfo : This database provides the information like type of the soil, physio-chemical properties,micro nutrients etc of the given soil area. The database has been made as online resource for the benefit of the scientist.
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Databases under development: i.
BioinfoLib
Under this Bioinformatics Library information system, one can access specialized bioinformatics centers as well as books, scientific journals, manuals, newsletters and the information on latest research & development in those institutes on bioinformatics and allied areas. This library will be accessible over Internet through the URL of the centre that can be used by all the scientists/research students and the teachers of the research institutes and universities. ii.
Database on Mulberry Pests and Diseases
It provides the information about the various pests and diseases which affects the mulberry plant such time of occurrence, symptoms etc. iii.
Database on Silkworm Pests and Diseases
It provides the information about the various pests and diseases, which affect the silkworm.
Softwares 1.
Sample Web Application for Analysis of Molecular ID.
2.
Construction of growth indices in popular breeds/hybrids of silkworm Bombyx mori L. in relation to nutritional conditions
Infrastructure facilities at the institute and Bioinformatics Centre CSRTI, Mysore has well equipped research laboratories with a wide range of equipments like Electron Microscope (with SEM facilities), Spectrophotometers, High speed Ultracentrifuges, HPLC, PCR machines, Gel Doc System etc. All the sections and laboratories of the Institute are well connected through LAN with 2 Mbps Internet connectivity. The Institute has a library equipped with all the modern facilities, subscribing for 92 national and international journals of repute and having a collection of 9380 books and 200 technical reports, besides 6760 bound back volumes of scientific journals. The Bioinformatics center has 4 Pentium IV, 2 Pentium III desktop computers, 1 Lap top computer, 1 HP Compaq ML 150 Server, Canon laser colour printers, HP Office Jet 6500 printer, HP Officejet 2515, 1 Sony digital Video camera, and 5 KVA UPS. The internet access is through 2 Mbps leased line from BSNL. The scientific software packages available are, PHYLIP, SPSS, Cn3D, Clustal W, PDB – on five CDs, EMBOSS, Artimis – Genome analysis package, Pinnacle DV Studio.
Papers published or presented in the conferences with reference 1.
Sumathy, R.; Gopalakrishnan, V.K. and Ashwath S.K (2012) The prediction of Protein-protein interaction in Silkworm Bombyx mori. Karpagam University 4th Annual Research Congress, Coimbatore.Tamil Nadu, November 29-30, pp.369.
2.
Sumathy, R.; Ashwath, S.K.; Shariff, A.A and Qadri, S.M.H (2012) In silico analysis and modeling of G protein coupled receptors of silkworm, Bombyx mori. National Symposium on Bioinformatics : Challenges in the postgenomic era held at School of Biotechnology, University of Jammu, Jammu, Februvary 02, pp 57
3.
Kantharaj, H.M.; Ashwath, S.K.; Avinash, C.; Shariff, A.A and Qadri, S.M.H (2012) Secondary structure analysis of GP64 protein of BmNPV. National Symposium on Bioinformatics : Challenges in the post-genomic era held at School of Biotechnology, University of Jammu, Jammu, February 02, pp 54.
4.
Sumathy, R.; Avinash C.; Shariff, A.A.; Ashwath, S.K and Qadri, S.M.H (2012) Insilico Structural Analysis of Transmembrane Proteins in Silkworm. International Interdisciplinary Science Conference (IISC- 2012) on Protein Folding and Diseases held at Jamia Milia Islamia University, NewDelhi, December 08-10, pp.23.
Papers published in the Journal
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1.
Sumathy, R.; Ashwath S.K.; Gopalakrishnan V.K 2012. Theoretical modeling and Docking studies of silkworm serotonin receptor, J Proteomics Bioinform 5(9): 230-234.
2.
Kantharaj H.M., Ashwath S.K.; Qadri S.M.H 2012 In silico Structural and Functional Analysis of the P74 Protein Related to the (PDV) Polyhedra Derived Virus Infection of BmNPV into the Silkworm. Adv. Bio Tech:11(9):29-32
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3.
M. Ismail Shareef; S. Leelavathi; Anis Ahmed Shariff. 2012. Inhibition of In Vitro TNF-a Production by Anisomeles malabarica R.Br. Reinforces Its Anti-Rheumatic and Immunomodulatory Properties. Proc. Natl. Acad. Sci., India, Sect. B Biol. Sci. 1(6):1-5.
4.
Kantharaj H. M.; Ashwath, S. K.; Qadri, S. M. H. (2012) Biological databases and Bioinformatics tools-Key resources for advanced research in sericulture biotechnology: An overview. Indian J. Seric. (In Press).
Initiation of R&D activities in Bioinformatics: The centre is involved in protein-protein prediction using computational methods, docking studies of G protein coupled receptor, developing algorithm, designing database structure and modifying the same for the development of databases on silkworm proteins and ESTs.
Details of Training/Workshop organized 32 scientists from CSRTI, Mysore & its nested units have attended the Workshop on Bioinformatics and its Applications conducted on 29-30 November 2012. So far 665 persons have been trained in Bioinformatics.
Students Visit to the centre Students of M.Sc., Biotechnology of local colleges visited this center and lecture sessions were organized to appraise the students in the area of Bioinformatics and its applications. The databases, softwares, tools and techniques developed by the centre were demonstrated.
Impact shown by your centre on the growth of biotechnology and allied areas. During the year a total of 263 Research papers were published by the scientists of the Institute & Nested units (International - 47; National – 35; Presented in Conferences – 128; Popular articles – 52; Books and Booklets - 01). The institute is publishing the Indian Journal of Sericulture ( Biannual), Seridoc (Biannual), Reshme Vahini (Kannada, Bimonthly), Reshme Kiran (Hindi – Half Yearly) and Pattu Vignanam (Telugu, Bimonthly). CSRTI, Mysore is has made a mark as a leading R & D institute on tropical sericulture in the country and is well recognized as centre for higher learning and advanced training on international front. As a major component of the institute mandate, training was provided to a total of 2819 persons under different programmes. Major Sericulture states were covered to impart training in different disciplines of sericulture. During the year, One patent have been filed for Poshan’ – a multi-nutrient formulation for mulberry Further technologies commercialized are Navinya – A bio formulation for control of root rot disease of mulberry and Azotobacter biofertilizer for mulberry plants.
Services provided The centre is equipped with 2 Mbps BSNL MLLN Internet connectivity which provides internet facility to all the research laboratories through LAN. The centre extends the infrastructure facilities and software support to the scientists working in the field of molecular biology & seri-bioinformatics in CSRTI and its allied institutes. Guidance is offered to the students of various universities in India for their dissertation or project work in the field of Seribioinformatics.
Plan of work for the year 2012-13 a)
Research work
Currently various high throughput methods are in vogue to identify protein-protein interaction in silkworm Bombyx mori, but none of these methods are applied specifically to silkworm. Therefore information on protein-protein interaction network in silkworm is essential for further understanding of the cellular processes. The protein-protein interaction of Silkworm, Bombyx mori will be predicted using the computational methods and constructing the protein-protein interaction database for Bombyx mori proteome. b)
Development of new databases/on-line resources
i.
SilkPPI
It provides the information about the protein-protein interaction in Silkworm, Bombyx mori and gives the details about the interactions among selected protein.
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SilkGpcr
It provides the information about the G protein coupled receptor protein of Silkworm, Bombyx mori and classified as Rhodopsin like, Secretin like receptor, Metabotropic glutamate receptors etc. c)
Conducting of Workshop on Bioinformatics and its Application
It is proposed to hold the two workshops on Bioinformatics and its Applications to be funded by DBT. d)
Improvement and maintenance of Website of the centre
The website of the center www.btismysore.in will be updated periodically and maintained. e)
Academics:
Each year this centre is receiving a number of applications for project/dissertation works from students of M.Sc./B.Tech (biotechnology/bioinformatics) from universities/institutions all over India. It is proposed to take up two to three projects/ dissertation works especially in the area of seribioinformatics.
Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
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Dr. S.M.H. Qadri Director and Coordinator, Central Sericultural Research & Training Institute, Manandavadi Road, Srirampura, Mysore 570008, Karnataka. (0821) 2362757, 2362406, 2363440 (0821) 2362845, 2362420
[email protected],
[email protected];
[email protected] www.btismysore.in, www.csrtimys.res.in Dr. S. K. Ashwath, Email :
[email protected]
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CSK Himachal Pradesh Krishi Vishvavidyalaya, Palampur Coordinator: Dr T.R. Sharma Summary of the progress made by the Centre from its inception Distributed Information Sub-Centre (DISC) at the Department of Agricultural Biotechnology, CSK HPKV, Palampur (HP) came into existence in October, 2002. Since its inception, the Centre has developed good infrastructure to cater to the scientific needs of the University. The computers available in the Centre are linked through Local Area Network (LAN) and internet with 256 kbps leased line. During the period under report, the Centre has procured softwares like LINUX, ORACLE, WINDOWS NET SERVER WINDOWS SERVER 2003, BIO-SYSTEMATICA, DNA star, iMAS, GenchekTM, SQL SERVER, ADOBE ACROBAT PROFESSIONAL and VStudio.Net for routine bioinformatics work such as data analysis, software development, database creation and management. The Centre has created 5 databases and one software. The Centre has been catering to the needs of the students and faculty of the Department of Agricultural Biotechnology and from other departments of the University by providing back up support to analyze biological data generated from wet lab experiments. The centre has been providing trainings on various current areas of modern biotechnology and bioinformatics to faculty and students at the national level on regular basis.
Major research activities in biotechnology and its related fields The Department of Agricultural Biotechnology is engaged in research on following areas in Agricultural Biotechnology: I.
Molecular mapping of agriculturally important genes in crops plants such as rice, lentil, maize, horsegram & peas.
II.
Biofortification of cereal crops for enhanced zinc and iron content
III.
Development of DNA-based diagnostics for important plant pathogens
IV.
Development of SNP and SSR markers for genetic mapping in Lens, Phaseolus and Trifolium species
V.
Development of gene-targeted markers (GTMs) for marker assisted selection in rice.
VI.
Isolation and characterization of genes for cold stress in chickpea
VII. Elucidation of genetic diversity in crop plants and pathogens using molecular markers.
Area of specialization of the Centre Bioinformatics & Agricultural Biotechnology Major activities of the centre during the year 1
A two day training on “Computer Applications in Genomics & Proteomics” was organized during 02-03 March 2012 in which 32 students and faculty members from CSKHPKV and other institutions participated.
2
The infrastructure of the Bioinformatics Centre is being used to teach Bioinformatics at Masters/Ph.D. level. A course of 3 credit hours (2+1) is taught to post graduate students. In addition, the faculty, research scholars and students are also trained in the bioinformatics. The students are given hands on training on database development and, use of DNA sequence analysis software in sequence assembly, gene annotation, gene ontology, data retrieval and data processing. The students are also taught about gene prediction, construction of restriction maps, drawing structures of various recombinant molecules and other bioinformatics tools of current and future importance. In addition, analysis of marker and other data to elucidate genetic diversity in crops and microbes is also taught.
Details about staff members working in the Centre Name Dr. T.R. Sharma Dr. K.D. Sharma Dr R.K. Chahota Mr. Mukesh Kumar Ms. Pooja Sharma
Designation Coordinator Deputy Coordinator Bioinformatics Incharge Technical Assistant Studentship
Specialization Plant Genetics and Genomics Transcriptomics, Gene Isolation and Expression Plant Genetics and Genomics Computer Hardware & Software Computer Software
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Types of services provided 1.
Internet and e-mail facility to users
2.
User access to Bioinformatics resources available in the Centre
3.
Trainings in the field of bioinformatics
4.
Teaching Bioinformatics at Masters’ level
5.
Sequence/data analysis
6.
Data retrieval
Initiation of R&D activities in Bioinformatics During preceding year, following R&D activities have been pursued in the area of bioinformatics
Development of isogenic lines of mega rice variety BPT5204 with blast resistance genes Pi-ta, Pi-1 and Pi-54 by marker-assisted background section
Development of new agarose gel-based CAPS marker for assisted selection of blast resistance gene Pi-1.
Development of EST-SSR primers in Horsegram (Macrotyloma uniflorum) using different bioinformatics software: Sequence data at National Centre for Bioinformatics (NCBI) was searched for Expressed Sequence Tags (ESTs) of M. uniflorum, a total of 1025 EST sequences were available as on 20th May 2012. These EST sequences were retrieved and checked, 33 sequences were tagged as contaminants by NCBI so these sequences were excluded for further processing to avoid any failure in later stages of marker characterization. The remaining 992 sequences were assembled into unigenes using DNA Starlagergene software. Six hundred and seventeen unigenes were predicted which were then searched for presence of Simple Sequence Repeat (SSR) and Intron Length Polymorphism (ILP) markers. SSRs having minimum repeat length of 10bp were searched using SSRIT (temnykh et al. 2009) and ILPs were detected with the help of PIP database (refrence). Eighty four SSRs were found out of which 63 were suitable for primer designing. SSR primers were designed using PRIMER 3 software with default settings.
Allele frequency based analyses, Principal coordinate analysis (PCA), Phylogenetic tree constructions, and STRUCTURE analysis were used for data analysis and interpretations in horsegram and Kalazira (Bunium persicum)
Research publications
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1.
Sharma KD, Sharma V, Singh R and Nayyar H. 2011. Control of chickpea blight disease by mixing resistance inducer and contact fungicide. Crop Protection DOI 10.1016/j.cropro.2011.07.003.
2.
Sharma KD, Bindal G, Rathour R and Rana JC. 2011. Carotene and mineral content of different Chenopodium species and the effect of cooking on micronutrient retention. International Journal of Food Sciences and Nutrition 63, (3) 290-295. DOI: 10.3109/09637486.2011.624493.
3.
Chahota RK, Mukai Y, Chaudhary HK, Kishore N and Sharma TR. 2011. Karyotyping and in-situ chromosomal localization of rDNA sites in black cumin Bunium persicum (Boiss) B.Fedtsh.1915 (Apiacea). Comparative Cytogenetics 5:345-353.
4.
Kumar N, Sood BC, Sharma TR, Chahota RK and Sood S. 2011. Determination of gene action for some biometrical traits in Lens culinaris Medik. under mid-hill conditions of northwestern Himalayas. Journal of Genetics 90:493497.
5.
Gupta M, Verma B, Kumar N, Chahota RK, Rathour R, Sharma SK, Bhatia S and Sharma TR. 2012. Construction of intersubspecific molecular genetic map of lentil based on ISSR, RAPD and SSR markers. Journal of Genetics 91:279-287.
6.
Singh VK, Singh A, Singh SP, Ellur EK, Choudhary V, Sarkel S, Singh D, GopalaKrishna S, Nagrajan M, Viono KK, Singh UD, Rathour R, Prasanthi SK, Aggarwal PK, Bhatt JC, Mohapatra T, Prabhu KV and Singh AK. 2011. Incorporation of blast resistance into “PRR78”, an elite Basmati rice restorer line, through marker assisted backcross breeding. Field Crops Research. 128: 8-16.
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Kumar S, Malik J, Thakur P, Kaistha S, Sharma KD, Upadhyaya HD, Berger JD, Nayyar H. 2011. Growth and metabolic responses of contrasting chickpea (Cicer arietinum L.) genotypes to chilling stress at reproductive phase. Acta Physiol Plant 33: 779–787.
Impact shown by Centre on the growth of biotechnology and allied areas during the period under report i.
No. of M.Sc. students trained :4
ii.
No. of summer trainees: 18
Future activities During coming years, the Centre proposes to strengthen infrastructure in terms of software tools for biological data analysis for providing better services to the users and keeping a pace with recent scientific developments. Besides this, the following activities will also be undertaken: 1.
Developing software tools and writing algorithms for extracting information from model genomes and utilizing in biotechnology interventions in resource-poor crops.
2.
Completion of databases: The databases established by the centre will be upgraded in terms of data input.
3.
Further improvement of infrastructural facilities.
4.
To further strengthen the research facilities for bioinformatics.
Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
Dr. T.R. Sharma Dept of Agricultural Biotechnology, CSKHPKV, Palampur HP 176 062 01894-230314 01894-230511
[email protected] [email protected] http://hillagric.ac.in Dr. T.R. Sharma
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Devi Ahilya University, Indore Coordinator: Dr. Anil Kumar Summary of the Progress made by the centre from its inception: The Distributed Information Sub-Centre was established in the School of Biotechnology, Devi Ahilya University, Indore in 1993 under the BTIS Net program of DBT. Since inception we are engaged in bioinformatics research. The centre setup a web server (http://www.biotech.dauniv.ac.in/) having all the software & database developed/ procured by the centre. Our center has a user lab comprising of 35 desktop PCs and 24 hours internet connectivity. This facility is being used by students and faculty of the department for the bioinformatics research.
Major research activities in Biotechnology and its related fields at your institution: We have addressed many complex issues of fundamental biology as: a.
Isolation, purification, characterization, localization synthesis and analysis of many enzymes like starch phosphorylase, glycogen phosphorylase and many others.
b.
Immobilization of industrial enzymes.
c.
Waste water treatment and methane production.
d.
Primer designing of many genes like DREB2A, Endo-1, 4-â-Xylanase and others.
e.
Alkaloids and toxoids in vitro production.
f.
Antidiabetic potential of various chemical compounds, insulin mimetic property and glucosidase inhibition.
g.
Development of new generation therapeutics.
Many papers have been presented in various national and international conferences. Our faculty members of biotechnology also authored books/Chapters in edited books/Encyclopedia.
Area of specialization: Genomics, QSAR Analysis, Database Development, Drug Designing and software development related to medical bioinformatics and human resource development.
Major achievements made during 2012-13: During 2012, we have identified bioswitches in shikimate pathway through computational biology to identify drivers and passengers involved in the synthesis of different secondary metabolites in the plants. 2D QSAR analysis of inositol derivatives to find the inositol monophosphatase inhibitors has been done. In the past few months, we used an interactomic approach for the identification of drug target in Listeria monocytogenes and manual curation of the Whole genome sequence of Corynebacterium pseudotuberculosis strain 162 isolated from camel. We are also analyzing the anti-diabetic effect of glimepiride sulphonamide (a drug intermediate) and naringin by in silico, in vitro and in vivo method. We have developed an integrative omics for identification of Biomarkers in lung cancer. We have also designed primers for starch phosphorylase and many other enzyme proteins.
Infrastructure facilities in the Bioinformatics Centre: a.
Computer & Communication facility:
(i)
Servers : Web Svr: HP Prolient ML 570 (Quad Proc. with 4 GB RAM); Proxy Svr: HP Prolient ML 150 with 1 GB RAM.
(ii)
Desktops Pc’s, Printers, Scanners & Communication facility Firewall System: HP Desktop PIV HP 8540 W Mobile Workstation
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Scientific software packages: MATLAB, Autodock Suite, Reference Manager 11, Chimera, Modeller9v8, Molegro Virtual Docker, Swiss PDB.
c.
Databases & other information resources: We have subscription for Journals like Nature, Journal of Bioscience & Bioengineering & Journal of Cell & Tissue Research.
Details about Staff members working in the centre: Sl. No. Name 1. Ms.Nikita Chordia 2. Mrs.Rachana Tiwari
Designation Information Officer Technical Assistant
Specialization Bioinformatics Biotechnology
Working Since July 2012 July 2007
Status Contractual Contractual
3.
Computer Operator
Computer Engineering
July 2010
Contractual
Mr.Priyesh Hardia
Educational activities : We are offering M.Sc Bioinformatics (2 years bioinformatics program). We also impart bioinformatics training to the researchers and students through dissertation and workshops.
Papers/ published or presented in the conferences (last 5 years): 1.
Pundhir, S., Vijayvargiya, H. and Kumar, A. (2008) PredictBias: a server for the identification of genomic and pathogenicity islands in prokaryotes. In Silico Biology 8, 0019.
2.
Garg, N., Pundhir, S., Prakash, A. and Kumar, A. (2008) Primer designing for DREB1A, A cold induced gene. J. Proteomics Bioinformatics. 1(1), 37-46.
3.
Garg, N., Pundhir, S., Prakash, A. and Kumar, A. (2008) PCR Primer Design: DREB Genes. J. Comp. Sci. Syst. Biol. 1, 21-40.
4.
Barh D. and Kumar, A. (2009) In silico identification of candidate drug and vaccine targets from various pathways in Neiseria gonorrhoeae. In Silico Biology 9, 0019.
5.
Barh D., Kumar, A., Chatterjee S. and Liloglou T. (2009) Molecular features, markers, drug targets and prospective therapeutics in cardiac myxoma. Current Cancer Drug Targets 9, 705-716.
6.
Barh D., Kumar, A. and Misra A.N., (2009) Genomic target database (GTB): A database of potential targets in human pathogenic bacteria. Bioinformation, 4, 50-51.
7.
Barh, D., Misra, A. N. and Kumar, A. (2010) In Silico Identification of dual ability of N. gonorrhoeae ddl for developing drug and vaccine against pathogenic Neisseria and other human pathogens. J. Proteomics Bioinformatics 3, 082-090. doi: 10.4172/jpb.1000125
8.
Barh, D., Misra, A. N., Kumar, A. and Vasco, A. (2010). A novel strategy of epitope design in Neisseria gonorrhoeae. Bioinformation 5, 77-85 .
9.
Barh, D., Tiwari, S., Jain, N., Ali, A., Santos, A.R., Misra, A.N., Azevedo, V. and Kumar, A. (2011) In silico subtractive genomics for target identification in human bacterial pathogens. Drug Development Res. 72, 162-177.
10.
Barh, D., Jain, N., Tiwari, S., D’Afonseca, V., Li, L., Ali, A., Santos, A.R., Guimaraes, L.C., Soares, S.D.C., Miyoshi, A., Bhattacharjee, A., Misra, A.N., Silva, A., Kumar, A. and Azevedo, V. (2011) A novel comparative genomics analysis for common drug and vaccine targets in Cornebacterium pseudotuberculosis and other CMN group of human pathogens. Chemical Biol. Drug Design 78, 73-84.
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11.
Pundhir, S. and Kumar, A. (2011) SSPred: A prediction server based on SVM for the identification and classification of proteins involved in bacterial secretion systems. Bioinformation 6, 380- 382.
12.
Barve, N., Mandloi, P., Kumar, A. and Jain, A. (2012) 2D QSAR analysis of inositol derivatives as inositol monophosphatase inhibitors. Adv. Res. Pharmaceut. Biol. 2, 79 - 87.
13.
Hassan, S., Schneider, M.P., Ramos, R.T., Carneiro, A., Lima, A.R. , Guimarães, L.C., Ali, A., Bakhtiar, S., Pereira, U., Santos, A., Soares, S.C., Dorella, F., Pinto, A., Ribeiro, D., Barbosa, M.S., Almeida, S., Abreu, V.A., Aburjaile, F., Fiaux, K.K., Barbosa, E.G., Diniz, C., Rocha, F., Saxena, R., Tiwari, S., Zambare, V., Ghosh, P., Pacheco, L.G., Dowson, C., Kumar, A., Barh, D., Miyoshi, A., Azevedo, V. and Silva, A. (2012) Whole genome sequence of Corynebacterium pseudotuberculosis strain 162 isolated from camel. J. Bacteriol. 194, 5718-5719.
14.
Barh D, Gupta K, Jain N, Khatri G, León-Sicairos N, Tiwari S, Rahangdale S, Verma A, Hassan SS, Santos AR, Ali A, Ramos RTJ, Miyoshi A, Silva A, Kumavath R, Kumar A, Ghosh P, Blum K, Misra AN, Azevedo V. [2012]. Globally conserved inter-species bacterial PPIs based conserved host-pathogen interactome in C. pseudotuberculosis, C. diphtheriae, M. tuberculosis, and Y. pestis: implementation in broad spectrum drug target identification. Integrative Biology; doi: 10.1039/C2IB20206A
15.
Parmar HS, Jain P, Chauhan DS, Bhinchar MK, Munjal V, Yusuf M, Choube K, Tawani A, Tiwari V, Manivannan E, Kumar A. DPP-IV inhibitory potential of naringin: an in silico, in vitro and in vivo study. Diabetes Res Clin Pract. 2012 Jul;97(1):105-11.
16.
Hollmann, A., Saviello, M., Delfederico, L., Luerce, T.D., Barh, D., Jain, N., Tiwari, S., Chandra, S., Gupta, K.K., Zambare, V., Kumar, A., Christopher, L., Misra, A.N., Kumavath, R.N. Azevedo, V., Semorile, L., Miyoshi, A. (2012) Tight controlled expression and secretion of Lactobacillus brevis SlpA in Lactobacillus lactis. Biotechnology Letters. 34, 1275-1281.
17.
Tyagi, S., Banke, J., Chawda, R. and Kumar, A. (2012) Suppression of glyphosate toxicity in plants following peroxide treatment. Toxicol. Environ. Chem. 94, 1331-1341.
18.
Barh, D., Barve, N., Gupta, K.K., Chandra, S., Jain, N., Tiwari, S., Sicairos, N.L., Canizalez-Roman, A., dos-Santos, A.R., Almeida, S., Ramos, R.T.J., de- Abreu, A.C., Carneiro, A.R., Soares, S.C., Castro, T.L.P., Miyoshi, A., Silva, A., Kumar, A., Misra, A.N., Blum, K., Braverman, E.R. and Azevedo, V. (2012) Exoproteome and secretome derived broad spectrum novel drug and vaccine candidates in Vibrio cholera targeted by Piper betel derived compounds. PLOS One in press.
Initiation of R&D activities in Bioinformatics: We have initiated the following activities:
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a.
Micro RNA and chemical Interaction: In this analysis, we are trying to find an in silico interacting network between transcription factors and miRNA which can help in diagnosis, prognosis and treatment of some very important diseases like cancer, diabetes and neuro degerative diseases like Alzheimer.
b.
Arsenic Toxicity: It is a collaboratory project with Institute of Integrative Omics and Applied Biotechnology (IIOAB) in which we are trying to find key gene regulome that are effected by arsenic.
c.
Reverse Vaccinology: Using in silico methods, we are focusing on identification of potent vaccine targets of some lethal bacteria like Shigella.
d.
Property and Structure based drug Designing: Structure and property of previously known drugs are used to find the new drugs.
e.
Identification of virulence factor with the help of comparative genomics: By comparing the bacterial genomes we are trying to find the common virulence factors that can be used for drug design.
f.
Antidiabetic potential of glimepiride sulphonamide via DPP-IV inhibition, insulin mimetic property and glucosidase inhibition.
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XXIVnd All India BTISnet Coordinators’ Meeting g.
Global protein-protein interaction derived effective targets in most common pathogenic bacteria (Currently working on Vibrio).
h.
Understanding of Th1 and Th2 cytokine paradigm in context to in vivo complexity and in silico network analysis
Details of Training/Workshop organized and total no of user trained (last 5 years): S. No.
Dates
Theme of workshop/Training
No. of participants
1.
Nov 04 – Nov 08, 2008
Machine Learning Techniques for Bioinformatics Data Analysis
21
2.
Nov 25 - Nov 27, 2009
Structural Bioinformatics & Systems Biology
19
3.
Jan 20 - Jan 22, 2011
Computational Biology and Molecular Dynamics
49
Impact shown by the Centre: The Bioinformatics sub Centre plays a leading role in introducing the latest advancements in Bioinformatics and contributing in research activities. There are about 40 papers that are published with the support of centre in various national and international journals from its inception. The Centre also provide information to the students and research scholars of biotechnology as well as to other neighboring departments/institutes by the internet facility, scientific software, database CDs and office automation software.
Proposed activities for 2013-14: We are actively engaged in diversified areas of biology and trying to address various complex issues including micro RNA and its chemical interaction, arsenic toxicity, understanding genomics causing virulence, reverse vaccinology and drug designing for various diseases including listeriosis, leishmaniasis and metabolic disorders. Besides we are also continuing work on Th1 and Th2 cytokine paradigm and associated network studies. To address afore said problems protein-protein interaction and various interactome studies will be conducted.
Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
Prof. Dr. Anil Kumar Head, School of Biotechnology, Devi Ahilya University Khandwa Road, INDORE - 452001, INDIA. +91-731-2470372, 2470373 +91-731-2470372.
[email protected] http://www.biotech.dauniv.ac.in Ms. Nikita Chordia, Information Officer, (
[email protected])
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Dr. Y S Parmar University of Horticulture and Forestry, Nauni-Solan Coordinator: Dr S V Bhardwaj Summary of the Progress made by the centre from its inception:
The Distributed Information Sub Centre (Sub-DIC), at YSPUHF, funded by DBT, New Delhi became operational during June, 1999 and has filled the void for exchange of available information with and between intended users.
The Centre facilitates the research work of the department by providing bioinformatics softwares (PRISM, EXOME HORIZON, HYPERCHEM, GENEIOUS etc) and databases (Biotechnology Abstracts) in addition to the online bioinformatics tools and databases, email and online literature search facility. Research work being offered to Post graduate students in biotechnology using bioinformatics tools and applications like primer designing, phylogenetic/evolutionary studies, ligand receptor interactions and molecular characterization of viruses using various online and offline bioinformatics tools/softwares. 8 M.Sc and 3 Ph.D students have completed their degrees using bioinformatics tools/databases and softwares effectively. The following specific achievements in the area of bioinformatics have been made (i) The three genes of “Tomato leaf curl virus Himachal strain” ToLCHimV and a Bean yellow mosaic virus isolate Solan coat protein (CP) gene were sequenced, and submitted to the NCBI and phylogeny of the genes was traced using bioinformatics tools. (ii) Sequencing of coat protein gene of Bean yellow mosaic virus (BYMV) from gladiolus (Gladiolus sp.) was done.(iii) Phylogenetic analysis of Lily symptompless virus, cucumber mosaic virus (CMV) apple mosaic virus, apple chlorotic leaf spot virus has been done. (iv) Motif searches were performed in carlaviruses coding for coat protein gene sequences and cucumoviral coat protein of cucumoviruses. (v) Primer designing against Lily symptompless carlavirus (LSV) infecting Lilium spp. and apple chlorotic leaf spot virus infecting apples using bioinformatics tools has been completed.(vi) Studies on Molecular characterization of a potyvirus infecting radish (Raphanus sativus L.) in Himachal Pradesh have also been completed.(vii) Plant virus interaction studies with virus inhibiting principle from Asparagus adscendens Roxb.
Four patents on plant biotechnology work and another one (PCT) with help of the Centre have been granted.
Trainings on basics as well as on advanced topics in computer applications/ bioinformatics/IPR are also being offered to scientists, technical/ministerial staff and research scholars/students of the University and outside the University. Centre has organized 36 short term trainings/ workshops/ seminars till date and 881 persons have been trained/participated in them. 26 MSc / BTech Biotechnology students from different universities and institutes have completed their 4-6 months duration research project in bioinformatics during 2009-12.
The Centre provides complete technical support to the university in organizing International and National symposiums besides other facilities.
The Bioinformatics Centre has developed information systems viz, (i) Package of Practices of Fruit Crops in Himachal Pradesh ,(ii) Alternative Methods of Plant Disease Control (iii) Package of Practices of Vegetable Crops in Himachal Pradesh (Hindi version).
The Centre has developed a database on ‘Plant Species Germplasm’ available in the university.
The Centre has developed 5 video CDs on Temperate Horticulture in collaboration with the Directorate of Extension Education of the University.
The Bioinformatics Centre has also developed training manual on ‘Computer Basics’ for internal circulation.
The Centre has completed two adhoc research projects.
Website of the university was developed in Jan., 2000 and maintained till March 2004.
Major research activities in Biotechnology and its related fields:
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Micro propagation
Cell Mutagenesis & Genetic Transformation
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Gene Tagging/Gene Mining/Identification of isolation of novel genes
DNA fingerprinting/Molecular characterization/Genetic diversity
Isolation and characterization of industrially important microorganisms from HP.
Bioinformatics
Area of specialization: Crop Biotechnology/ Horticulture : Virus detection and elimination
Major achievements made during 2012: The Centre facilitated the research work of the department by providing bioinformatics support. i)
Research
In silico sequence analysis and docking studies of plant parasitic nematodes:(Xiphinema spp. : 28S ribosomalRNA and Meloidogyne incognita were carried out. ii)
Trainings/Workshops/Meetings organized
No short term training in bioinformatics could be organized due to non receipt of grants.
One M.Sc Bioinformatics student from Hans Raj Mahila Maha Vidyalaya (Jalandhar) completed her four months project/training wef 15-01-12 to 15-05-12. The title of her project was “In silico sequence analysis and docking studies of plant parasitic nematodes:(Xiphinema spp. : 28S ribosomalRNA and Meloidogyne incognita).”
One B.Tech. Bioinformatics student from J.P. University Waknaghat completed his one month training in Bioinformatics during June- July, 2012.
Infrastructure facilities in the Bioinformatics Centre: Two - Servers, 20 PCs, 4 - Printers (Mono / Colour/ DMP), Scanner and Xerox Machine.
Details about Staff members working in the Centre: Sl. No. Name 1. Dr. S V Bhardwaj 1.
Ms Anju Sharma
2.
Mr Kailash Sharma
3.
Ms Kamlesh Nagar
4.
Ms Taruna Sharma
Designation Prof. & Head & Coordinator Information Officer
Specialization Plant Virology / Biotechnology M.Sc. Statistics, MCA & PG Diploma in Bioinformatics Technical Assistant M.Sc. (Computer Science), PGDCA Data Entry B.Com, Operator Diploma in Computer Application Data Entry Diploma in Computer Operator Application
Working Since 1999
Status Coordinator
21st July, 1999
Salary of the staff has been adjusted in different scheme of the university w. e. f. 01-04-2012
16th June, 2000 19th June, 1999
1st Sept., 2006
Educational activities : Teaching and Research in Short and long term trainings.
Papers published or presented in the conferences (2012) : Papers published
Neha Sharma, Satya Vrat Bhardwaj, Anju Sharma, Manica Tomar, Rajinder Kaur, Pritam Dass Thakur and Anil Handa. 2012. Comparative Genomic and Proteomic Phylogenetic Analysis of Indian Isolate of Partial Coat Protein Gene Sequence of Zucchini Yellow Mosaic Virus (ZYMV) using Data Mining. Journal of Proteomics and Bioinformatics. 5(9): 196-203.
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Sharma Pratima, Amarjit K Nath, Reena Kumari, S. V Bhardwaj. 2012. Purification, characterization and evaluation of insecticidal activity of trypsin inhibitor from Albizia lebbeck seeds. Journal of Forestry Research 23: 131-137.
Genes Sequenced
Gupta R., Bhardwaj S.V., Sharma A., and Verma Y. (2012) Asparagus antiviral protein gene, partial cds. Accession No. JQ347294.
Gupta,M., Shirkot,P., Sharma,A. and Bhardhwaj,S.V.(2012) 16S ribosomal RNA partial sequence of thermophillic bacteria producing Taq DNA polymerase from the hot water springs of Himachal Pradesh, India.Accession No. JQ886455.
Papers presented
Molecular characterization and phylogenetic analysis of tomato leaf curl virus (ToLCV) in Himachal Pradesh.(2012). Paper presented in National Symposium on “ Emerging Issues in Plant Health Management & Annual Meeting of IPS(NZ) held at UHF, Nauni Solan on Sept 28-29, 2012.
Books
Rajinder kaur and Satya Vrat Bhardwaj 2012. “Biotechnology: A ready Reckoner”. In press
Initiation of R&D activities in Bioinformatics: Nil Details of Training/Workshop organized and total no. of users trained during 2012
One M.Sc Bioinformatics student from Hans Raj Mahila Maha Vidyalaya (Jalandhar) completed her four months project/training wef 15-01-12 to 15-05-12. The title of her project was “In silico sequence analysis and docking studies of plant parasitic nematodes:(Xiphinema spp. : 28S ribosomalRNA and Meloidogyne incognita).”
One B.Tech. Bioinformatics student from J.P. University Waknaghat completed his one month training in Bioinformatics during June- July, 2012.
Impact shown by the Centre: No. of peer review publication raised by the centre No. of peer review publication raised through the support of your centre No. of genes sequenced No. of Information systems created No. of Patent obtained No. of Patent filed No of short term trainings/workshops/seminars conducted in the fields of computer applications/bioinformatics/IPR No. of Personnel trained so far in short term trainings No. of MSc students who took help from bioinformatics centre for their research within the Department of Biotechnology, Dr YSPUHF No. of PhD students who took help from bioinformatics centre for their research within the Department of Biotechnology, Dr YSPUHF No. of MSc/PhD students from Microbiology/Plant Pathology/Forestry who took help from bioinformatics centre for their research No. of students from other institutions who completed their 1-6 months training projects in bioinformatics No. of training manual developed
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Proposed activities for 2013-14
Research work in different aspects of Bioinformatics to Ph.D/ M. Sc students in the department.
Short term trainings or workshops and long term training/project work on Bioinformatics.
Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
Dr S V Bhardwaj Professor and Head, Department of Biotechnology, and Coordinator, SubDIC, Dr Y S Parmar University of Horticulture and Forestry, Nauni, Solan HP. 173230 01792-252639 01792-252844
[email protected];
[email protected] www.yspuniversity.ac.in Dr S V Bhardwaj
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G. B. Pant University of Agriculture & Technology, Pantnagar Coordinator: Dr. AK Gupta Summary of the progress made by the centre from its inception Bioinformatics Sub-DIC was established in November 1998 in the College of Basic Sciences & Humanities, G. B. Pant University of agriculture & Technology, Pantnagar. This is one of the first Sub-DIC in Uttarakhand. Since inception, centre is actively involved in teaching and conducting research in bioinformatics. The bioinformatics education to the students is disseminated through theoretical and practical courses in Bioinformatics. Every year, the Bioinformatics courses- “Elements of Bioinformatics” and “Use of computers in molecular modeling” are being offered by the centre to the PG students of various disciplines including Biotechnology, Biochemistry, Biophysics, Plant Physiology, Plant Breeding and Genetics. Every year more than 60 students enthusiastically enroll and successfully complete these courses. Other than the teaching of university’s students, centre also actively disseminates bioinformatics knowledge to students, researchers and academicians of other universities by conducting on-hand training and organizing workshops both on wide and specific areas of Bioinformatics and System Biology with special reference to the applications in Agricultural Biotechnology. These workshops had always attracted numerous applicants for participation from various parts of the country.
Major activities of the centre during the year 2012-13. A.
Teaching: As per BMSA guidelines of ICAR, the bioinformatics course for PG students has been revised in the form of “Introduction to Bioinformatics” from the session 2010-11. Understanding the immense importance of bioinformatics in the post-genomic era, Two new courses entitled ”Bioinformatics and molecular modeling” and “Biocomputing and System Biology” have been included in the course curriculum of the newly started B-Tech biotech programme and being offered from the academic year 2010-2011 to the B-Tech Biotech students to scintillate the young students to the most challenging areas of bioinformatics and allow them to venture in the Bio-IT sectors.
B.
Research: Recently, to view deeper insights to understand MAPK signaling in plants newer techniques like Machine learning tool has been included in the ongoing study. The efforts here also been made to develop a ‘MAP Kinase analyzer’ tool for identification of phosphorylation sites in various interacting MAP kinase partners, In addition to develop ‘Phyto Diab Care’ database of antidiabetic plants and Phyto MAPK DB a Plant MAPK Interactome Database. Different in silico approaches have been performed to understand the molecular basis of high calcium in developing grains through in silico analysis of genome wide distribution and expression of calcium related genes involved in calcium signaling and transport and also investigate the role of plant specific transcription factors like Dof1, PBF-Dof in regulating the nitrogen use efficiency and stress responsiveness in finger millet. The focused attempts towards proving finger millet as nutraceutical crop through bioinformatics tools are also underway. Working on different aspects of bioinformatics, in 2012, a total of 5 research papers have been published in reputed international journals and many research papers are under preparation review.
C.
Hardware, Sofware and Data analysis support: Since, centre has been continuously expanding the activities in teaching, training and research in bioinformatics and hence there is continuous need of more infra-structure facilities. To meet the growing requirements of the centre, seven new high performance personnel computers, one Sony LCD TV, Online UPS along with commercial softwares like MOE (Molecular Operating Environment) one year licence, E-Scan antivirus, Wingate Proxy server for 50 users of one year licence were purchased. Beside, centre is striving to provide internet connectivity through Wi-Fi system to all the faculty members of college from this year. The centre has acquired state of the art bioinformatics packages such as DNA STAR, GCG Package, MOE, Hyperchem, Genocluster, Sigma Plot and Sigma Stat which provides data analysis facility for the on-going research in area of Biotechnology.
D.
Training/Workshops: The center in 2012 conducted a 4 day workshop on the topic “Functional Genomics & System Biology in Agriculture” from Sept 15th to 18th, 2012. The workshop attracted more than 80 participants from various universities/institutes of our country. For this workshop, on-hand practicals and lectures were organized by eminent scientists like Dr. G.P.S. Raghava from IMTECH Chandigarh, Dr. Vikrant Gupta from CIMAP, Lucknow, Dr. Naveen Bisht from NIPGR New Delhi, Dr. Sanjay Kapoor of Delhi University South Campus, of our country who have in-depth knowledge of theoretical concepts of bioinformatics and computational biology as well as wide knowledge of various bioinformatics and system biology tools, In addition to this Bioinformatics facility is also being utilized for the
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organization of 21 days “ National Training Workshop on Application of Genomics in Crop Improvement” from 27th Dec 2012-16th Jan 2013. Apart from teaching and organizing theme-specific workshops, centre is helping the students of other disciplines for successful conducting and analyzing their research experiments, the centre also imparts short duration training to students of other universities who applied for their project/thesis dissertations every year. In year 2012, one student each from Chhatrapati Shahu Ji Maharaj University, Kanpur and Banasthali University, Jaipur successfully completed their dissertation. Their work in the form research papers is under preparation for publication in reputed international journals.
Proposed Activities of the Centre in 2013-2014
Teaching: Development of advanced teaching modules on various areas of bioinformatics and are now under progress which is aimed to provide most recent and in depth knowledge to the students and academicians of the university.
Research: The centre has identified some frontier areas of applications of bioinformatics in agriculture which would be main focus of research in the future. These areas are, elucidation of molecular and regulatory networks of complex traits like nitrogen use efficiency, biofortification, mineral nutrition through system biology approaches beside the complexity of polygenic traits of biotic and abiotic stresses which would be explored and understood through in silico experiments.
Parallel to the research activities the centre has also planned to develop and expand its website where all the activities of the centre would be displayed.
In 2013, the centre plans to organize two event entitled “Brainstorming session on Prioritizing research area in Nano-Bio-Information Technology for the development Hill States” (April 2013), and National Training Workshop entitled “Molecular docking and simulation for identification of molecules for agricultural and veterinary applications” (14th -17th Sept 2013) in order to train the mid career faculty/scientists, research scholars and students to the emerging areas of bioinformatics and Molecular docking, simulation that has potential applications in improving agriculture.
Creation of tools and databases: The development of two novel databases named as “Seed Pro Nutra Care” database for providing functional attributes of seed specific proteins and “TRIPATH” database for providing the genetic and genomic resources of three important fungal pathogens (Rust, Smut and Bunt) of Wheat is under progress. A database named ‘Himalayan Agri Bioresource Informatics System’ would be developed that will contain and cover the bioresource potential of Uttarakhand like underutilized ethnic grains of Uttarakhand, microbial diversity resourse medicinal plants, mushrooms, fresh water fishes, cattles.
Organization of meeting of Coordinators of Bioinformatics Centres located in Himalayan states: In order to consolidate the efforts of Bioinformatics Centres running by the financial assistance of the DBT, there is need to organize a Coordinators meeting for defining the programmes pertaining to the development of Himalayan states and avoiding the duplicated efforts in documentation of Himalayan resources and harnessing their potential for generation of new knowledge, processes and products through both in silico and wet experimentation.
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Guru Nanak Dev University, Amritsar Coordinator : Prof. Gurcharan Kaur Summary of the Progress made by the centre from its inception: To cater to scientific information needs of the scientists and research fellows working in the University and other institutes of this region the department has established the Distributed Informatics Sub-Centre (DISC) in the year 1995 with the financial assistance from DBT, Govt. of India, New Delhi. 23 research papers have been published in the year 2011-12.The DISC is assisting students and faculty from neighbouring Departments and Colleges/Institutes in updating their knowledge through different databases/softwares available in the Centre. The Centre is also providing practical training in Bioinformatics as well as computer based application, software analysis, computational methods, etc. to M.Sc. and Doctoral students. Training workshops at regular intervals are also organized to apprise faculty and students of the latest developments in Bioinformatics.
Major research activities in Biotechnology and its related fields : The broader areas of research of the Department include : (i)
(ii)
Medical Biotechnology
Therapeutic potential applications of PSA mimetics in cell culture and mouse models of brain injury and disease:
Ashwagandha derived phytochemicals for development of differentiation-based therapy of brain cancers:
Cellular and molecular mechanisms of adverse effects of antiepileptic (AEDs) and mood stabilizing drugs:
Plant Biotechnology
Role of genes encoding peptidyl Prolyl Cis-Trans Isomerases in plants
Transgenic analysis for the role of genes involved in vesicle transport in abiotic stress tolerance of wheat
Study of leaf spot disease of Withania somnifera and development of a biotechnological approach for its resistance.
Molecular and biochemical approaches to study brassinosteroid mediated responses in rice using salt and pesticide stress:
Insight into secondary metabolite production and their accumulation in withania somnifera using in vitro propagation system
(iii) Microbial Biotechnology
Characterization of cellulolytic microorganism
Myxobacteria as a potential source of antimicrobial activity
Anti-cancer activity of the extracts of the isolated myxobacteria
(iv) Structural and Computational Biology
(v)
Sequence and structural analysis of ribonuclease genes present in genome of malaria parasites
Sequence and structural analysis of PfEMP1 family of proteins in Plasmodium falciparum
Analysis of homo-repeats present in the genome of Plasmodium falciparum
Database of non-coding RNA of malarial parasites
The evaluation of agronomical and quality traits of kidney bean and field pea germplasm
Area of specialization : Biotechnology
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Major achievements made during 2012-13: (i)
An offline server for bioinformatics tools has been developed in order to cater the needs of the students and researchers which will serve as a useful repository of information.
(ii)
Structured networking work of the department is being initiated and will be completed before 31st March, 2013.
(iii) A database of Library Books Catalogue with the Department have been developed and put on intranet for use by students and researchers. (iv) Tools are being developed for sequence analysis.
Infrastructure facilities in the Bioinformatics Centre: At present the hardware installed includes Computers Systems (62), Coloured Laser Printers (2), Laser Printers (6), Scanners (2), Xerox machine, Multimedia Projectors (4), two laptop computer and two podium system. These facilities are being extended to the students, research scholars, and faculty members of the University departments as well as neighbouring Institutes. DISC has facilitated faculty members/research scholars in strengthening their research publications. So far about 26000 users comprising of students, research fellows and teachers of Guru Nanak Dev University and neighbouring Institutes have availed the services since its inception in the year of 1995. Since its inception, the DISC has procured various scientific softwares like Microsoft Office 2000, SQL Server 2000, Borland Turbo c++ Suite, Visual Studio, Sigma Stat, Sigma Plot 2001, (V-7.1), Grafit version 4, Minitab 13.3, Lasergene-5 Sequence Analysis, Oracle 10g, Exome, Exome Blast, Exome Horizon and Hyperchem software.
Details about Staff members working in the centre: Sl. No. Name 1. Mr. Bhupesh Kumar 2.
Mr. Harbhajan Singh
3.
Mr. Kawaljeet Singh
Designation Programmer
Specialization Computer Science
Working Since 03.11.2009
Computer Operator Attendant
30.08.1995
Status Presently in the process of absorption by the University Absorbed by the University
25.05.2006
Fixed Salary
Educational activities : The Department of Biotechnology, Government of India is a constituent of National Network centers imparting job-oriented training to the students in Biotechnology. The Department is offering a two-year degree programme leading to M.Sc. in Biotechnology since 1991. About 20 researchers are presently pursuing their Ph.D. in different areas of Biotechnology. In order to educate researchers and young faculty about the latest technologies Workshops, seminars and Conferences are being organized regularly.
Papers/ published or presented in the conferences : 23 papers have been published in various journals during the year 2011-12 with an average impact factor of 2.89 (List attached - Annexure I).
Initiation of R&D activities in Bioinformatics: 1.
Development of database on cell adhesion molecules in neuronal plasticity.
2.
Analysis of plant NADPH oxidase in different plant species.
3.
Development of Sequence Analysis tools
Details of Training/Workshop organized and total no of users trained Since its inception in the year 1995, the Department has organized eleven workshops using DISC facility benefiting more than 165 young faculty and doctoral students of different Institutions/Universities. (List attached –Annexure – II).
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Impact shown by the Centre: 19 M.Sc. Biotechnology students of the Department successfully completed their project work using the DISC facilities during the session 2011-12. The DISC has organized eleven workshops benefiting more than 165 users.
Proposed activities for 2013-14 : 1.
Development and uploading of various databases/sequence analysis tools to meet the needs of the researchers in bioinformatics and biotechnology.
2.
A workshop will be organized in February, 2013 to train the students, research fellows and young faculty members of the University and neighbouring institutes.
3.
Procurement of Drug Discovery Software for research activities.
4.
Development of database on cell adhesion molecules in neuronal plasticity.
5.
Analysis of plant NADPH oxidase in different plant species.
Contact details:
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Name of the Coordinator
Prof. Gurcharan Kaur
Postal Address
Distributed Informatics Sub-Centre (DISC) Department of Biotechnology Guru Nanak Dev University Amritsar – 143 005
Phone No.
0183-2258431
Fax No.
0183 - 2258272
Email
[email protected] [email protected]
Website
http://www.gndu.ac.in/ http://department.gndu.ac.in/department/biotech/Website/index.html
Name of Contact Person
Mr. Bhupesh Kumar, Mr. Harbhajan Singh
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Annexure - I
List of Publications (2011-12) : S. No.
Publications
Impact Factor
1.
Hardeep Kataria, Sunil C. Kaul, Renu Wadhwa and Gurcharan Kaur (2012) Withania somnifera water extract as a potential candidate for differentiation based therapy of human neuroblastoma. PLoS ONE (Accepted)
4.41
2.
Hardeep Kataria, Sunil C. Kaul, Renu Wadhwa and Gurcharan Kaur (2012). Water Extract from the Leaves of Withania somnifera Protect RA Differentiated C6 and IMR-32 Cells Against Glutamate-Induced Excitotoxicity. PLoS ONE, 7(5): doi:10.1371/journal.pone.0037080
4.41
3.
Raman Kumar Kamboj, Sukhprit Singh, Avinash Bhadani, Hardeep Kataria, and Gurcharan Kaur (2012) Gemini Imidazolium Surfactants: Synthesis and their BioPhysiochemical Studies. Langmuir, 28(33):11969-78.
4.19
4.
Sushil Kumar and Gurcharan Kaur (2012) Intermittent Fasting Dietary Restriction Regimen Negatively Influences Reproduction in Young Rats: A Study of HypothalamoHypophysial-Gonadal Axis. PLoS ONE (Accepted)
4.41
5.
Rumani Singh, Dinesh Lakhanpal, Sushil Kumar, Sandeep Sharma, Hardeep Kataria, Manpreet Kaur, Gurcharan Kaur (2012) Late onset intermittent fasting dietary restriction as a potential intervention to retard age associated brain function impairments in male rats. AGE 34 (4):917-33
6.28
6.
Ashutosh Sharma, Varinder Singh, Gagandeep Singh and Pratap Kumar Pati (2012) First report of leaf spot disease in Withania coagulans caused by Alternaria alternata in India. Plant Disease (http://dx.doi.org/10.1094/PDIS-06-12-0559-PDN)
2.44
7.
Isha Sharma, Bhardwaj, R. and Pati, P. K. (2012) Mitigation of adverse effects of Chlorpyrifos by 24-epibrassinolide and analysis of stress markers in a rice variety Pusa Basmati-1. Ecotoxicology and Environmental Safety. 85: 72–81
2.29
8.
Ashutosh Sharma, P. K. Nagar and Pratap Kumar Pati (2012) ROS modulated responses during pathogen infestation in plants. In: Advances in Plant Physiol- An Int. Treatise Series Vol 14: Edited by A. Hemantaranjan, Scientific Pub., India.
---
9.
Ashutosh Sharma, Abhinay Thakur, Sanehdeep Kaur and Pratap Kumar Pati (2012) Effect of Alternaria alternata on the coccinellid pest Henosepilachna vigintioctopunctata and its implications for biological pest management. Journal of Pest Science (DOI 10.1007/s10340-012-0432-3).
1.50
10.
Sharma A and Pati P. K. (2012) First record of the carmine spider mite, Tetranychus urticae, infesting Indian genseng, Withania somnifera, in India. Journal of Insect Science. 12, 50
0.947
11.
Savita, Alka, Pati P. K., Virk GS and Nagpal A (2012) An efficient micropropagation protocol for Citrus jambhiri Lush. and assessment of clonal fidelity employing anatomical studies and RAPD markers. In vitro Cell Dev. Biol.-Plant. (DOI 10.1007/s11627-0129430-7)
1.497
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12.
Sushil Kumar, Jyoti Parkash, Hardeep Kataria, Gurcharan Kaur (2011) Enzymatic Removal of Polysialic Acid from Neural Cell Adhesion Molecule Interrupts GonadotropinReleasing Hormone (GnRH) Neuron-Glial Remodeling. Mol Cell Endocrinol., 348 (1): 95103.
4.12
13.
Dinesh Lakhanpal and Gurcharan Kaur (2011) Neuroendocrine plasticity in GnRH release is disrupted by valproic acid treatment of cycling rats. Acta Neurologica (In Press)
0.416
Virdi A.S., Pareek A. and Singh Prabhjeet (2011). Evidence for the possible involvement of calmodulin in regulation of steady state levels of Hsp90 family members (Hsp87 and Hsp85) in response to heat shock in sorghum. Plant Signaling and Behaviour , 6:1-7.
2.00
15.
Singh Prabhjeet and Virdi A.S. (2011). Calmodulin-binding proteins in plants: Implications in abiotic stress adaptation. J. Plant Biology (invited review).
0.85
16.
Dutta T., Kaur H., Singh S., Mishra A., Tripathy J.K., Singh N., Pareek A. and Singh Prabhjeet (2011). Developmental changes in storage proteins and peptidyl prolyl cis-trans isomerase activity in grains of different wheat cultivars. Food Chemistry 128(2), 450-457.
2.69
17.
Singh, N., and Singh Prabhjeet (2011). Amaranth: Potential source for flour enrichment. In V. R. Preedy, R. R. Watson, & V. B. Patel, (Eds.), Flour and breads and their fortification in health and disease prevention (pp.101- 111). London, Burlington, San Diego: Academic Press, Elsevier.
---
18.
Pati, P.K., Kaur Jaspreet and Singh Pritika (2011) A liquid culture system for shoot proliferation and analysis of pharmaceutically active constituents of Catharanthus roseus (L.) G. Don. Plant Cell Tiss. Org. Cult. 105:299–307
3.09
Sharma, A., Sharma, I. and Pati, P. K. (2011) Post-infectional changes associated with the progression of leaf spot disease in Withania somnifera (L.) Dunal. J Plant Pathology. 93 (2), 397-405
0.91
19.
Sharma, I. Pati, P.K. and Bhardwaj, R. (2011) Effect of 24-Epibrassinolide on oxidative stress markers induced by Nickel ion in Raphanus sativus L. Acta Physiologiae Plantarum 33:1723–1735
1.63
20. 21.
Sharma, I., Pati, P. K. and Bhardwaj, R. (2011) Effect of 28-homobrassinolide on antioxidant defence system in Raphanus sativus L. under Chromium toxicity. Ecotoxicology. 20:862–874
2.35
22.
Sharma A and Pati P. K. (2011) First report of Withania somnifera (L.) Dunal, as a New Host of Cowbug (Oxyrachis tarandus, Fab.) In Plains of Punjab, Northern India. World Applied Sciences Journal 14 (9), 1344-1346
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23.
Sharma A and Pati P. K. (2011) First Record of 28-Spotted Ladybird Beetle, Henosepilachna vigintioctopunctata (F.) Infesting Withania somnifera (L.) Dunal in Punjab Province of Northern India. Pest Technology 5 (1), 91-92
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14.
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Training/Workshops: S. No. Title of Workshop /Year 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11.
No. of Participants Workshop on “Latest Trends in Bioinformatics” March 4-6, 1998 16 Workshop on “ Use of Internet & Patenting in Biosciences Research” March 23-24, 1999 14 Workshop on “ Role of Networking in Scientific Information Processing” October 27- 28, 1999. 10 Workshop on “Internet and Web Designing” October 5-6, 2000 15 Workshop on “Tools for Data Mining” October 7- 8, 2003. 17 Workshop on “Tools of Bioinformatics” March 3-4, 2005 21 rd th Workshop on “Advances in Bioinformatics” February 23 & 24 , 2006 18 Workshop on “Bioinformatics : Conceptualizing Biology in terms of Molecules” February 22rd & 16 23rd , 2007 Workshop on “Structural Bioinformatics towards Drug Design” March 21st -22nd , 2008. Workshop on “Bioinformatics tools in Biological Research” March 19th -20th , 2010 Workshop on “Bioinformatics Applications in Genomics and Proteomics” November 5th -6th, 2011
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Himachal Pradesh University, Shimla Coordinator: Professor T. C. Bhalla Summary of the progress made by the centre from its inception The Bioinformatics Centre of Himachal Pradesh University was established in 1999 with financial support of Government of India, Ministry of Science and Technology, Department of Biotechnology (DBT), New Delhi. The Centre is housed in the Netaji Subhash Chandra Bose Bhawan of Himachal Pradesh University. The Centre has successfully organized sixteen training/workshops covering various aspects of the Bioinformatics and has trained around 265 participants through these trainings/workshops. Presently, Centre is emphasizing on genome wide studies which includes development of tools and techniques for search of novel sources of nitrile metabolizing enzymes. Beside this, Centre provides various facilities for M.Sc and B.Tech students belonging to different institute of northern India for completing their research project i.e.Insilico studies of different industrially important microbial and plant enzymes. Centre has recently installed sequence & molecular modeling software for detailed in-silicoanalysis of various bioinformatical problems.
Major research activities in biotechnology and its related fields: The research activities of the University in the area of Biotechnology have major focus on microbial diversity, microbial enzymes, traditional fermented food and stem cell.
Major activities of the centre during the year 2010-11
Organized practical classes in ‘Computer Applications and Bioinfor matics’ course for M.Sc. Biotechnology/ Microbiology students.
Infrastructure facilities in Bioinformatics Centre i)
Computer Hardware Beside earlier infrastructure following facilities have been added
ii)
ii)
Lap Top with icoreprocessor (hp make)
:
One
I core7 Desktop (hp make)
:
Four
HP Laser Jet printer
:
One
Multimedia Projector(Sharp)
:
One
Software
EXOME Software
:
One
MS Office 2010
:
One
Window 07 (Professional)
:
One
Communication: Two Telephone lines: 0177-2832153, 2832154 Internet Facility, Email: hpuniv.btisnet.nic.in
Details about staff members working in the centre Name
Designation
Area of Specialization
Prof. T.C. Bhalla
Coordinator
Mr. Nikhil Sharma Mr. Manoj Kumar
Information Officer Technical Assistant
Enzyme and Fermentation Technology Biochemistry MCA
Mrs. Leena Mishra
Data Entry Operator
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Period of working From the start of Centre (1999) till date 4th July, 2011till date 16th August, 2011 till date
Computer Applications 9th July, 2001 till date
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Types of services provided The Centre provided the following services to the students, research fellows, and faculty members of the University:
Derwent Biotechnology Abstracts ,Offline Database, Nucleotide and Protein Sequence Analysis, Bibliographic and Patents Search, E-Mail and Internet Access, Training in Bioinformatics.
Books 148 (covering diverse areas of bioinformatics), Journals 2
Papers/Abstract Published
The Centre has communicated/published following research papers. i)
Sharma N and Bhalla TC (2012) Motif design and validation.J Data Mining Genomics Proteomics.3:3.
ii)
Kapoor S, Sharma N,Savitri and Bhalla TC (2012)Comparative analysis of amino acid sequences from mesophiles and thermophiles inrespective of Carbon-Nitrogen Hydrolase family. 3 Biotech(Springer).DOI: 10.1007/s13205012-0111-3.
iii)
Kanwar R, Sharma N, Savitri and Bhalla TC (2012)Computational analysis of amino acid sequences in relation to thermostability ofinterspecific nitrile degrading enzyme (amidase) from various thermophiles/hyperthermophiles.J Data Mining Genomics Proteomics (accepted).
iv)
Sharma N and Bhalla TC (2012) Classification of nitrilases using support vector machine.3rd World Congress on Biotechnology.Hyderabad International Convention Centre. India.(abstract)
Other achievements Center has trained more than 32 undergraduate and postgraduate students from different colleges & universities under winter / summer training. They have studied the various physio-chemical and structural properties of many enzymes such as lipases, pectinases, asparginase, gultaminase, nitrilase, amidase, hydratase etc. They also performed the studies on evolutionary and phylogenetic relationship of these enzymes. Further designing and validation of motifs were also done by these students.
Details of training/workshops organized and users trained This Centre has organizedeighteenworkshops/ training programs.About two hundred sixty fiveparticipants (students, research scholars, scientists and teachers) from various institutions/ organizations have been trained through these workshops/ training programs.
Impact of the centre on growth of Biotechnology
Quality of project reports, dissertations and publications in the area of Biotechnology has been improved by the on-line and offline literature database search done at the Centre. With constant support of the center Department of Biotechnology and Biosciences have published several papers in their respected field.
Future activities
Organizing three day workshop on Networks, Pathways and System-Integrated Approaches. Study of extremophiles and gene mining for novel sources of nitrile metabolizing enzymes Development and upgradation of databases pertaining to Microbial Diversity and Fermented Foods of Himachal Pradesh.
Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
Professor T. C. Bhalla Bioinformatics Centre (Sub-DIC), H.P. University, Summer Hill, Shimla-171005. 0177 2832153, 0177 2832154
[email protected] hpuniv.btisnet.nic.in Professor T. C. Bhalla
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Indian Institute of Advanced Research, Gandhinagar Coordinator: Dr. Desh Deepak Singh Summary of the progress made by the center from its inception: The objectives of the center are compilation of information on plants and their pathogens and tropical pathogens in a user friendly manner. Tritryp portal and tools for genome analysis have been devloped. A database on plant pathogens has been developed. A database on plant lectins hasd been devloped alongwith tools. These are hosted as open resources on IIAR website.
Major research activities in biotechnology and its related fields : Various research groups in the Institute are working in the areas of Plant biotechnology for gene prospecting and enhanced functionalities, understanding the factors responsible for virulence in pathogens like Vibrio spp. in the human health, understanding the role of various factors in apoptosis in cell biology and genome analysis in bioinformatics.
Area of specialization: Leishmania Genome analysis, prospecting of therapeutically relevant biomolecules like lectins, microbila biofilms, development of databases and software tools, human resource training.
Major activities during the year 2012-13: a)
Tritryp portal which is an open resource on these pathogenic organisms and is compiled in a user friendly manner. (http://software.iiar.res.in/tritryp).
b)
Development of databases on plant lectin, adhesin and software tools based on machine learning techniques.
c)
Genome analysis of Leishmania for identification and structural characterization of important virulence factors especially those invovled in host-pathogen interactions.
Infrastructre facilities: The Department is well equipped in computational resources with state of the art equipments including Five node cluster system (Sun Microsystems), Desktops (Dell, HP) Workstations (IBM, Dell), Graphics work stations (SGI), servers (IBM), printers (HP).
Staff members: Dr. Desh Deepak Singh (Co-ordinator) Dr. Anju Pappachan (faculty) Mr. Vijay Singh (Information Officer), Mr. Dhaval Patel (Technical Assistant) and other members include ars, one DBT-post-Doc, one SRF, and two JRF one of whom is CSIR net qualified and project assistants.
PhD schol-
Services provided: Online databases, tools and bio-resources freely available online from the website, training and HRD.
Educational Activites: Two students in the center are registered for PhD with Pune University and two more are now registered with MS University, Baroda. The institute has been granted university status and educational courses are being planned which have a substantial bioinformatics interface.
Initiative to validate the outcome of Bioinformatic resources: Experimental work on plant lectins is being undertaken for their structural characteriztion. Strucutral studies through X-ray crystallography for the Leishmania putative virulence which is upported by DBT grant.
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Collaborative work: The institute has active collaboration with NCL Pune for lectin work and proposed work with RIKEN, Japan.
Databases/softwares developed: Tritryp portal, Plant pathology database, Protanno, GluD, Adhesin-Profiling, Alu-finder, plant lectin database, SVM based tool for annotating adhesins have been developed and hosted on IIAR website for open source use by the community.
Papers published: Nair, D, Singh, V, Yamaguchi, Y and Singh, DD (2012). Jatropha curcas haemagglutinin is similar to 2S albumin allergen from same source and has unique sugar affinities. Planta 236, 1499-1505.
Invited talks:
“The next gen genomics / proteomics techniques and natural products drug discovery” International conference on Drug Discovery from Natural Products at NIPER, SAS Nagar, November 22, 2012 (Invited lecture)
“Systems interactomics: Are the technologies there” International Symposium on Proteomics, NCL. Pune, November 24, 2012. (Invited lecture).
Initiation of R & D activates: a)
isolation and structural characterization of plant lectins based on bioinformatics analysis. b) cloning, expression and structural studies on Leishmanial proteins based on bioinformatics anlaysis.
Impact shown: Human resource development through training, Poster presentations, invited lectures by coordinator in nearby colleges, and interface with researchers for bioinformatics analysis are undertaken on regular basis.
Future activities: Training programs, development of resources. Starting a Post-graduate course in Bioinformatics and taking up the hits from bioinformatics analysis for experimental work.
Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
Dr. Desh Deepak Singh Bioinformatics Centre, Indian Institute of Advanced Research, Koba, Gandhinagar – 382007, Gujarat 079-30514150
[email protected] website: www.iiar.res.in Dr. Desh Deepak Singh
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Indian Institute of Integrative Medicine Coordinator: S. Koul Summary of the Progress made by the centre from its inception: The centre started as mainly the information source and support activities initially and has developed to a full-fledged research unit which is now actively involved in major research activities of the Institute.
Major activities of the centre during the year 2012-13: The research activities carried out at the Sub-DIC at IIIM Jammu are as under:
Molecular Modelling studies on bacterial efflux pump NorA.
In our efforts to identify potent bacterial efflux pump inhibitors from synthetic as well as natural source, piperine was earlier identified as NorA inhibitor. Further to this, Capsaicin (8-methyl-N-vanillyl-6-nonenamide), a major constituent of hot chilli, was identified as NorA inhibitor at IIIM. In order to understand the mechanism of action, we carried out molecular docking studies of capsaicin on the in silico modeled 3D structure of NorA (identified at IIIM). A strong H-bond interaction at a distance of 1.89A° with Ile23 of the protein NorA is observed in case of capsaicin. The aliphatic chain of capsaicin extends into the hydrophobic cleft involving residues Pro24, Phe140, Ile244, Gly248 and Phe303 of NorA (figure 1a). The location of key interactive residues in the case of capsaicin with respect to the orientation of the helices is shown in Figure 1b.
QSAR of parhtenin analogues for pro-apoptotic activities
In continuation of our studies towards the development of NCEs for anticancer targets, several parthenin analogs were identified as potent proapoptotic agents. These analogs were quantitatively related to their structures by carrying out Quantitative Structure Activity Relationship (QSAR) of 37 compounds possessing the activity. A highly statistical QSAR model was developed using the Genetic Function Approximation algorithm, which involved several descriptors viz., topological, spatial, thermodynamic, information content and E-state indices. The final model comprised of five descriptors viz., Superdelocalizability, Hosoya index, LUMO and one each of E-State index and Atom type descriptor. The statistical significance of the model was authenticated with a very good correlation and cross-validation correlation parameter (r2 = 0.9 and q2 = 0.839). The model was also validated for external prediction criteria and was found to be well within the acceptable range. The model would be very useful for designing and lead optimization of anti-cancer compounds and also for prediction of activity of new compounds in this series.
Insilico evaluation of compound library for identification of potent EGFR inhibitors
In another anticancer target, EGFR (epidermal growth factor receptor), a sub-structural based and similarity based search on the 20,000 compound library (procured form Chembridge Inc.) was carried out using erlotinib (known inhibitor) in order to identify the possible new hits as inhibitors of EGFR. Based on the search results, 17 molecules were submitted for in vitro evaluation of EGFR inhibitory activity and one molecule showed comparable IC50 values to the reported inhibitor. This molecule has been taken for further in silico modification for exploring the improvement in the affinity towards EGFR and subsequent synthesis.
Development and maintenance of Web-enabled database with sub-structural search feature
The web-enabled database of compound library has been enriched further with the Institutional natural products and synthetic compounds. The same is being updated regularly.
Coordinated the ERP implementation at IIIM
Coordinated the ERP implementation within the Institute for effective transition to paper-less office and hence contributed to the e-governance project of the Institute.
Human Resource Development. As a part of Human Resource Development, this year 28 students were trained in the Discovery Informatics Division towards the partial fulfillment of their course work (as specified):-
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5 students from M.Sc Bioinformatics (4-6 months); 5 students from M.Sc Bioinformatics/Biotechnology (2-3 months); 14 students from B.E. (Computer Science/IT)/MCA (4-6 months) and 4 students from B.E. (Computer Science/IT) (2-3 months).
Publications (2012): 1.
Pro-apoptotic properties of parthenin analogs: a quantitative structure–activity relationship study. Med Chem Res 10.1007/s00044-012-0225-5
2.
Capsaicin, a novel inhibitor of the NorA efflux pump, reduces the intracellular invasion of Staphylococcus aureus. J Antimicrob Chemother. 2012, 67:10, 2401-2408
3.
Novel thermostable lipase from Bacillus circulans IIIB153: comparison with the mesostable homologue at sequence and structure level. World J. Microbiol. Biotechnol. 2012, 28:1, 193-203
4.
Design and synthesis of novel N,N’-glycoside derivatives of 3,3'-diindolylmethanes as potential antiproliferative agents. Med. Chem. Commun., 2012,3, 1082-1091 DOI: 10.1039/C2MD20098H
Contact details:
Dr. S.Koul, / Sh. Amit Nargotra Ph: +91 191 2569000-010 xtn: 269
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Indian Institute of Technology (IIT) Delhi, New Delhi Coordinator: Prof. T.R. Sreekrishnan Summary of the progress made by the centre from its inception The Biochemical Engineering & Biotechnology department was established in 1969 at IIT Delhi to generate quality human resource & undertake research work particularly in the area of Biochemical Engineering & Industrial Biotechnology. The department is presently offering a unique five-year dual degree (B.Tech and M.Tech) program in Biochemical Engineering and Biotechnology. The department also has a two-year M.S. (by research) and very interdisciplinary Ph.D. program in the area of Biochemical Engineering and Biotechnology. The BTIS sub-centre at IIT Delhi was established in 1989 (equipped in 1991) by the support of the DBT, GOI, New Delhi, as a part of the nation wide networking of Biotechnology Institutions of National importance.
Major research activities in biotechnology and its related field: The department is very actively engaged in almost all emerging areas of biotechnological research e.g., Bioprocess Engineering, Down Stream Processing, Bioprocess control, Modeling and Simulation of Bioprocesses, Plant Cell technology, Animal Cell Technology, Genetic Engineering, Environmental Engineering, Bioinformatics, Molecular Machines and Nanotechnology etc. The BTIS-sub centre acts as an integrated information resource centre in the teaching and research in all the above areas of Biochemical Engineering and Biotechnology. The centre provides total computer support for extensive computations, information retrieval and dissemination for all the departmental courses and to the ongoing research projects (M.Tech., M.S., Ph.D. and sponsored projects) of the department and also to the neighboring educational centres. Recently the centre has graduated from an Information Resource Centre to an “Instruction facility” for quality teaching and research particularly in Bioinformatics, Genomics and Proteomics, Mathematical Modeling of Bioprocesses, and Artificial Neural Network based bioprocess control.
Area of specialization of the centre The main teaching and research focus of the Department is in Biochemical Engineering & Biotechnology. It has a very popular Dual Degree program (B.Tech & M.Tech) in Biochemical Engineering & Biotechnology. The above program has elective courses on Bioinformatics, Genomics & Proteomics data analysis for DNA Microarray apart from the courses in other emerging areas of Biotechnology listed above. The main research areas of the department are: Biochemical Engineering / Industrial Microbiology / Fermentation / Bioinformatics
Major activities of the centre during the year Research and Training Infrastructure facilities in the bioinformatics centre A.
Computer & Communication facilities
IBM Netfinity 5000 Server : 1, Dell Server with dual Processor : 1, Intel Xeon Server : 1, Desktops (Pentium IV/III/II) : 4/2/1, Workstations (Intel Core 2 duo/ Dual core): 10/5, Silicon Graphics Workstation : 1(From Institute grant), Color LaserJet Printer: 1(From Institute grant); LaserJet Printer: 3, Deskjet Printer : 2, Scanner: 2, Fax Machine: 1, Xerox Machine: 1, Networking speed through IIT, Delhi network : 2X5 Mbps. B.
Major Databases /Software packages:
Academic licensed : Accelyrs Gene 2.5, Matlab (R2008a) with Bioinformatics Tool Box (Access through Institute LAN), Discovery Studio 2.1 modules (Application areas – Sequence Analysis, Protein Modeling and Simulation) Vendor licensed : Chem Office 2005 (version 13.1), LaserGene (version 5.0), Endnote (version 7.0), Reference Manager 10, Design Expert (Statistical Optimization Software), Office XP professional, Java 1.1, Lotus Smartsuite (version 9.6), Operating System media : Windows XP professional, Windows 2000 NT server, Windows 2000 academic, Windows 98, Windows Vista Business.
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Other: Derwent Biotechnology Abstract (1982-Till date) (on CD), Medline(1982-1998) (on CD), Science Direct by Elsevier Science (On-line Access), Institute is the member of INDEST consortium initiated by MHRD, Institute has the provision for procurement of printed as well as electronics version of selected journals.(Details on www.iitd.ac.in). C.
Databases & other information resources: Bibliographic Database of research publications of the department Catalogue of Departmental Library Bibliographic Database of Departmental Theses Full Text Database of Departmental Theses
Details of staff members working in the Centre: S.No. 1. 2.
Name of the staff Khusboo Bafna Arpit Jain
Designation Project Associate Project Associate
Working since 2012 – present 2012 – present
Absorption status Contractual Contractual
In addition to the above positions, we also have two positions of Studentship/Traineeship each who are trained regularly.
Types of Services Provided: Literature Search: Information retrieval and storage facility from its rich In-house / on line database(s) & Journals to the faculty, student and researchers of IIT Delhi/ Neighboring Institutions. Bioinformatics Courses & Project work: For the elective courses on Bioinformatics, Genomics & Proteomics for the dual degree (B.Tech & M.Tech), students heavily use the infrastructure facilities of the center. Beside the final year M.Tech students of the department and students from the other universities also do their dedicated 6-12 months major project work using the Centre’s facility.
Educational activities with details of placement The courses on Bioinformatics (2-0-2, 3 credits), Genomics and Proteomics (3-0-0, 3 credits) and “Data Analysis for DNA Microarrays” (3-0-2, 4 credits) are offered for the B.Tech/M.Tech/M.S. students at IIT Delhi.
Ongoing student projects in Bioinformatics (A) Comparative study of the synergistic and modular modes of binding of zinc finger proteins to DNA (Harshit Malhotra - Supervisor D. Sundar, DBEB), 2012-2013 (B)
Finding the genes in eukaryotic genomic DNA (Armaan S. Sandhu – Supervisor: D. Sundar, DBEB), 2012-2013.
(C)
A computational study of DNA-protein interactions (Shayoni Dutta – Supervisor: D. Sundar, DBEB), 2011 - till date.
Initiative to validate the outcome of bioinformatics resources The Centre has been publishing papers in the area of Bioinformatics.
Collaborative works/initiatives: The Center has active collaboration with various departments within institute e.g Chemistry, Biological Sciences, Electrical Engineering and Computer Science & Engineering (CSE) of IIT Delhi. The department has also strong collaboration with Indian Institute of Technology (IIT) Guwahati, Alagappa University and Jawaharlal Nehru University (JNU), New Delhi. The Centre also has an active collaboration with National Institute of Advanced Industrial Science & Technology (AIST), Tsukuba, Ibaraki, Japan.
Databases/Softwares packages developed:
Zif-BASE
: a database of zinc finger proteins and associated resources
Zif-PREDICT
: a web tool for predicting DNA-binding specificity in zinc fingers
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Custom-made softwares for Bioprocess Modeling & Simulation
Catalogue of “Departmental Library” comprising about 2,000 records, searchable by author, title and keywords
Bibliographic database of Ph.D and M.Tech thesis of the department comprising about 572 records; about 150 full-text versions of the Ph.D. and M. Tech. theses of the department using “Greenstone Digital Library Software”
Institutional repositories of theses, dissertation and other biological information
Other In-house developed specialized databases like Plant Cell Culture (PCC), Animal Cell Culture (ACC) etc.
Papers presented in the conference with reference: Chatterjee, B., Katiyar, S.P., Dutta, S., Sundar, D. and Chaudhuri, T.K. (2012). Role of Celastrol in Hsp90/Cdc37 complex disruption and kinase binding of Cdc37. Proceedings of the International Conference on Bioinformatics (InCoB-2012), Bangkok, Thailand, October 2012, p-159.
Initiation of R & D activities in Bioinformatics The department faculty are involved in research projects (Extramural and Intramural) (i)
Funding Agency : Department of Health Research (DHR), Govt. of India Principal Investigator – Dr. D. Sundar Period of Support : 2012-13 Amount of Support : Rs. 30 Lakhs “Program support for Computational Genomics”
(ii)
Funding Agency : Lady Tata Memorial Trust Principal Investigator – Dr. D. Sundar Period of Support : 2011-14 Amount of Support : Rs. 31 Lakhs “Towards modifying nature’s DNA recognition system for highly specific genome editing”
(iii) Funding Agency : Department of Biotechnology (DBT), Govt. of India Principal Investigator – Dr. D. Sundar Period of Support : 2011-14 Amount of Support : Rs. 16.2 Lakhs “Betraying the parasite’s redox system: Studies on spermidine synthase of Leishmania donovani”
Details of the training/workshop organized and total no. of user trained.
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Mr. Akil Z. Surti, Lecturer in Gujrat Technological University, Ahmedabad, Gujrat and Ms. Akansha Gupta, Lecture in IMS Engineering College, Ghaziabad, UP were selected for the “Summer Faculty Research Fellow Program 2012” under the “Continuing Education Program” of IIT Delhi for doing research under the guidance of Dr. D. Sundar, the faculty mentor at IIT Delhi. The objective of this program was to facilitate and orient the faculty fellows to undertake research. The faculty fellow also got an opportunity to interact and work with the research students of Dr. Sundar’s lab group and got exposure to the equipment and lab facilities associated with bioinformatics research.
Organized a Indo-UK Workshop on ‘Next Generation Sequencing and Data Analysis for Microbial Applications’ along with Newcastle University, UK during March 29-30, 2012. The objective of this workshop was to foster an understanding of the concepts and application of next generation sequencing (NGS) to the biology of engi-
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neered systems. This workshop was supported in part by the Engineering and Physical Sciences Research Council (EPSRC), UK.
Organized a two-day Short term Training Course on Bioinformatics during October 22-23, 2012.
Impact shown by the centre on the growth of biotechnology and allied areas. i.
Patents & Technology Transfer
Bisaria V.S., Srivastava A.K., Baldi A, Jain A., Gupta N. (2007) A process for enhanced production of bio-active compounds, Indian Institute of Technology Delhi , India. Patent Application No. 1266/Del/2007. ii.
Research Papers published in peer reviewed journals by using BTIS Sub – Centre’s Support.
The Department has published more than 400 journal papers, 30 Books / Book Chapters, More than 150 conference publications since 1990 in different peer reviewed journals with the help of BTIS facilities of the centre. Details of the publication are available Faculty/Area wise on our website www.iitd.ac.in. ii.
Bioinformatics Research Papers Published, in peer Reviewed journal by the Centre. 01.
Roy, S., Dutta, S., Khanna, K., Singla, S. and Sundar, D. (2012). Prediction of DNA-binding specificity in zinc finger proteins. Journal of Biosciences 37(3): 483-491.
02.
Kumar, V., Punetha, A. and Sundar, D. and Chaudhuri, T.K. (2012). In silico engineering of aggregation-prone recombinant proteins for substrate recognition by the chaperonin GroEL. BMC Genomics 13(7): S22.
03.
Grover, A., Katiyar, S.P., Jeyakanthan, J., Dubey, V. and Sundar, D. (2012). Blocking Protein Kinase C signaling pathway: mechanistic insights into the anti-leishmanial activity of prospective herbal drugs from Withania somnifera. BMC Genomics 13(7): S20.
04.
Grover, A., Shakyawar, S.K., Saudagar, P., Dubey, V.K. and Sundar, D. (2012). Epitopic analysis of potential vaccine candidate in Leishmania infantum for development of human vaccine. Letters in Drug Design and Discovery 9(7): 698-705.
05.
Grover, A., Katiyar, S.P., Jeyakanthan, J., Dubey, V. and Sundar, D. (2012). Mechanistic insights into the dual inhibition strategy for checking Leishmaniasis. Journal of Biomolecular Structure and Dynamics 30(4): 474487.
06.
Grover, A., Katiyar, S.P., Singh, S.K., Dubey, V. and Sundar, D. (2012). A Leishnmaniasis study: structure-based screening and molecular dynamics mechanistic analysis for discovering potent inhibitors of spermidine synthase. Biochimica et Biophysica Acta - BBA: Proteins and Proteomics 1824(12): 1476-1483.
Future Activities Due to increased emphasis on Computational Biology, Bioinformatics, Genomics etc. in the present scenario attempts will be made to train more students for Bioinformatics related projects. The centre will focus on the development of user-friendly interactive software tools for Modelling & Simulation of Bioprocessing, Bioprocess control, Genomics, Proteomics, etc. which is the unique area of expertise of Biochemical Engineering and Biotechnology Department in the country. The centre has excellent expertise in strategic and emerging areas of biotechnology. Attempts will be made to develop Multimedia Course Materials for different key areas of Biochemical Engineering & Biotechnology and these can be eventually put on the BTIS centre Web Server for access by other BTISnet Centres of the country.
Contact details: Name of the Coordinator Postal Address Phone Number Email Website Name of Contact Person
Prof. T.R. Sreekrishnan Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT), Delhi, Hauz Khas, New Delhi - 110016 (011) 26591066, 26596316
[email protected] http://btis.iitd.ac.in Dr. D. Sundar (
[email protected])
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Indian Institute of Technology, Kharagpur Coordinator: Professor S. C. Kundu Section-A : Project Details A1. Project Title: Bioinformatics SUB-DIC A2. DBT Sanction Order No. & Date: BT/BI/02/016/98, dated 18.11.1998 A3. Name of Principal Investigator: Professor S. C. Kundu Co-PI/Co-Investigator: Professor S. Dey A4. Institute: Indian Institute of Technology, Kharagpur - 721302 A5. Address with contact nos. (Landline & Mobile) & e-mail: Department of Biotechnology, IIT Kharagpur, 03222-283764, 9434012848,
[email protected] A6. From January 1999 – March 2017 continuing A7. Approved objectives of the project: 1.
Creation of biological database (s)
2.
Interaction of macromolecules (protein-protein, protein-DNA, protein-RNA)
3.
Protein structure predication and homology modeling
4.
Training of personnel in bioinformatics
A8. Specific Recommendations made by the Task Force: Creation of biomaterials and tissue engineering database, Protein-RNA docking and affinity benchmark
Section-B : Scientific and Technical Progress Summary of the progress: SUB DIC Centre of IIT Kharagpur provides facilities to the B.Tech, M. Tech and Ph. D students to carry out their day to day computational work, project work and trainings in the field of bioinformatics. The Institute offers a separate 3 credit course in bioinformatics for the students. A laboratory credit course on Bioinformatics is being conducted for the B.Tech and dual degree M. Tech. students. A number of thesis, publications, oral and posters presentations are being made in national and international journals/conferences on the relevant areas of Bioinformatics and Biotechnology.
Major activities during the year 2012: Creation of PRince: a web server for structural and physicochemical analysis of Protein-RNA interface “for understanding the specificity of the protein–RNA recognition process and “Protein-RNA docking benchmark” for the development and comparison of the protein–RNA docking methods. A “Protein-RNA affinity benchmark” database is created for the prediction of protein-RNA binding affinity and a database for Biomaterial is created.
Infrastructure facilities: Computer hardware: Several Pentium Core2 Duo PCs, Silicon Graphics O2, Workstation, Sun Server with Thin Clients. HP Color Laser Printer, HP Scanner, Fax, Digital Xerox machine. Operating systems: MS Windows Vista-XP, RHEL4, Linux, and Solaris 9-10. Internet facility: 2*STM-1 link (300 mbps). Scientific software packages: Sequence analysis: OMIGA 2.0, Sequencer 4.1.4, EMBOSS. Molecular modeling: GCG Wisconsin Package, MSI Insight II (Perpetual licensed), Modeler, Swiss PDB viewer, Discovery Studio 1.5, Pymol, Rasmol, Chimera, VMD, Schrodinger, Naccess, Hbplus. Programming language: C, C++ PERL, JAVA and DBMS.
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Staff members at present: Names Ms. Subia Bano Ms. Rashmi Rekha Barua Mr. Sourabh Mukherjee
Designations SRF Project Technician Project Officer
Specializations Bioinformatics Bioinformatics Computer Sci. Bioinformatics
Work period 3.6 Yrs. 1 Yr 2 ½ months
Database: Biomat_dbase: A biomaterial database is developed by the use of CSS, Java Script, HTML, PHP, Adobe Photoshop and MySql in UNIX platform that is published in The Open Tissue Engineering and Regenerative Medicine Journal 5, 9-16.
Type of service provided: The centre offers a good collection of the electronic resources of a large number of journals full text and several abstracts through INDEST consortium through high-speed broadband Internet facility (Speed: 300Mbps) and other computational facilities.
Educational activities with the placement details: Institute offers separate 3-credit theory and Bioinformatics laboratory courses to the students. Both independently and through campus interview B.Tech, Duel degree, M. Tech. and Ph.D students get their desired jobs/research places abroad and in India.
R & D activities carried out during 2012-2013: UG/PG/ Ph. D students are provided different bioinformatics projects for their academic / project work, thesis and to develop a specialized databases on the relevant fields. The ongoing projects in Bioinformatics like Structure-function relationship of stress related protein, folding and binding of protein and energy minimization by the use of molecular dynamics and simulation, Insilico analysis of low molecular weight penicillin binding Proteins (PBP) of E-coli, Metagenomics and Molecular Phylogenetic analysis, antigen-antibody interactions and protein-RNA interactions, analysis of Inverted repeats in the promoter sequence for Two Component System in M. tuberculosis, Functional genomics of rice plant, Cancer peptide database, B-cell and T-cell epitope prediction and creation of EST database, biomaterials, biomedical device modification, tissue engineering.
Publications during 2012-2013: Several papers are published related on bioinformatics and biotechnology during the session of 2012 and 2013 in peerreviewed journals like Nucleic Acids Res., Proteins Struct. Funct. Bioinfor., Biochimie, Research in Microbiology , J Chem. Phys., Phys. Chem. Chem. Phys., Int. J of Signal Processing, Image Processing and Pattern Recognition, BMC Bioinformatics, Genomics, PLoS ONE, The Open Tissue Engg. Regenerative Medicine, J. Chem. Phys., Biochem. J., Knowledge-Based Systems, Expert Syst. Appl., Micron, Biochimie, Biochem. Biophys Res. Commun., FEMS Microbiology Letters, Biomaterials, Adv. Functional Materials, Adv. Drug Delivery Review, Acta Biomaterialia, Macromolecular Bioscience, Nanotechnology, Soft Matter, etc.
Proposed activities for the session 2013: Molecular modeling and structural analysis of RNA dependent RNA polymerase, development of macromolecular docking algorithm, development of biological database, structural bioinformatics analysis of macro molecular assembly and designing of their algorithms, deciphering the structure and function of SuhB analogue protein from S. aureus, Functional characterization of soluble penicillin-binding protein 6 of E. coli , gene analysis of protozoan parasites and identification and characterization of P. vulgaris micro RNAs differentially expressed in biotic and abiotic stress conditions, biomaterial design, tissue engineering and biomedical devices, etc. Contact details : Professor S. C. Kundu (email:
[email protected]), 09434012848, 03222-283764, Co-coordinator: Professor S. Dey (email:
[email protected]), 03222-283760
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Indian Veterinary Research Institute, Izatnagar Coordinator: Dr. Ashok K. Tiwari Area of Specialization of the Centre The Centre supports the Bioinformatics activity for all life science streams especially genomics of animals and animal pathogens.
Major activities of the centre during the year 2012-13 1.
Organized two National Workshop cum Training program on “In silico Approach for Genome Analysis” [March 31 to April 2, 2012] & “Use of Bioinformatics Tools in Biotechnology” [Nov. 29 to Dec. 1, 2012] wherein more than 50 students participated.
2.
Bioinformatics Reference database has been developed & being updated regularly.
3.
Online/Off-line information was collected and distributed to help the scientists / students of the institute.
4.
The Centre has provided the bioinformatics support over hundred students for their PhD and MVSc Thesis research work.
5.
Students and Scientists of IVRI and other organizations were trained as & when required in handling bioinformatics databases and tools for sequence analysis, primer designing, probe searching, microarray analysis and phylogenetic analysis etc.
6.
The Bioinformatics Centre has updated and maintained its own website (www.bicivri.in).
7.
Bioinformatics facilities were extended to post graduate students (both MVSc & Ph.D) of IVRI. Facilities were also extended for conducting practical of the course ‘Bioinformatics in Biotechnology’. More than 60 students of Biotechnology and other disciplines registered the course and doing their practicals.
8.
Molecular Docking study for Huntington disease and Protein Data mining.
Infrastructure facilities in the Bioinformatics Centre:
Computer & Communication Facility: Bioinformatics Centre has almost all modem facilities with 1 mbps VSAT connectivity, Wifi, Broadband, Fax, and 12 computer terminals.
Scientific Software Packages: Lasergene (DNASTAR), Genocluster Software (IGIB Jalaja), ClustalW, Rasmol, Gene designer, Emboss, Geneious, SeqTools, Oligos, Open bable, Chemsketch, Oligo Analyzer, Mega5.0, Autodock (MGL Tools), Sequin etc.
Details about staff members working in the Centre S. No 1. 2.
Name of the staff Dr. Ashok K.Tiwari Mr. K.N. Kandpal
Designation Project Coordinator Information Officer
Specialization Molecular Biology and Biotechnology Computer Application
Working 2011 2011
Types of services provided (i) Online/Off-line collection and dissemination of information. (ii) Bioinformatics data analysis. (iii) Organizing Training and Workshop etc. (iv) Bioinformatics Research (v) Internet, E-mail facilities.
Initiative to validate the outcome of bioinformatics resources Students and Scientists of the institute are using bioinformatics facilities available at the centre. The Tools available in the centre have been used by students in their thesis research. A number of diagnostics, differential diagnostics, vaccines etc. were developed and identifications of marker genes for characterization of species and breeds etc. were carried out, by applying Bioinformatics tools available in the Centre.
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Collaborative works/initiative
Institute has more than 90 National/International projects where bioinformatics tools are used. Centre is providing all possible supports in these research projects, as and when required.
Theory and Practical for the course entitled “Bioinformatics in Biotechnology” offered to MVSc. and PhD students of different disciplines of IVRI is being conducted at the Centre. This course is being attended by more than 60 students in each semester. The students are encouraged to use all available software.
Papers published or presented in the conferences with reference (2012-2013) 1.
Kandpal KN, Rawat S.S.(2012), Khan Mohd. Faheem Modern Library and Information sciences and its security., AAlDI. vol. 81, page 338-340.
2.
Kandpal KN, Rawat S.S.(2012), NARS Library moving towards the open source software, vol. 81, page 190-195.
3.
Kandpal KN, Rawat S.S.(2012), E-Resources on veterinary education and research An overview, vol. 81, page 190-195.
4.
Khan, Mohd. Faheem, Tiwari K. Ashok and Jaitly, A.K. (2012), Pipeline for retrotransposons analysis. , 100th Indian Science Congress, Kolkata.
Future Activities (2013-2014): The future plan can be delineated into following three major activities: 1.
Scientific Support: The centre will cater the need & expert’s support to different National, International projects and Post Graduate Research Projects of the Institute and will continue to exchange information.
2.
Training and P.G. Education: The centre will organize short term and long term training programmes & National workshop for the students and research workers in the fields of Biotechnology, Bioinformatics and other related disciplines.
3.
R & D Plan
In silico Drug designing for various veterinary pathogenic diseases.
New Bioinformatics tools/software development.
Details of Training and Workshops (2012-13) S. No.
Workshop Title
Sponsor
Date
1.
In silico Approach for Genome analysis
DBT
March 22 – 24, 2012
2.
Use of Bioinformatics Tools in Biotechnology
DBT
Nov. 29th – 1st Dec, 2012
Participants Participants Affiliation of Type participants Scientists, PhD NDRI Karnal, Scholars, MVSc SKUAST Jammu, students. Mangalayatan 25 University Aligarh, GADVASU, IVRI Scientists, PhD Integral University, Scholars, MVSc Lucknow, AMU 32 students. Aligarh, IVRI
Details of Studentship and Traineeship Two trainees and one student trainee (Under DBT Studentship and Traineeship program) are engaged for six months and working on In silico Drug Designing for Huntington disease, Protein Data mining for Paratuberculosis and Genome analysis of disease resistant genes in salmonellosis at the Bioinformatics Centre during 2012-13.
Impact shown by the Centre on the growth of biotechnology and allied areas: The information provided by Bioinformatics Centre helped in analysis of genes of various pathogens, identified primers for PCR, real time PCR and characterization of pathogens etc. by different divisions and centres of the institute.
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Contant details : Name of the Coordinator Postal Address Phone Number
Dr. Ashok K. Tiwari Distributed Information Sub-Centre, NLVS, Indian Veterinary Research Institute, Izatnagar (U.P.) - 243 122 0091-581-2300305
Fax No. Email
0091-581-2303284 , 0091-0581-2300305
[email protected]
Website Name of Contact Person
www.ivri.nic.in, www.bicivri.in Dr. Ashok K. Tiwari
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Institute of Life Sciences, Bhubaneswar Coordinator: Dr. Subrata K Das Summary of the progress made by the centre from its inception: Bioinformatics is an interdisciplinary research area that relies on computational and statistical methods to solve biological problems. With the advancement of high throughput technologies, biological experiments now generate huge amount of data, ranging from genomic sequences to gene expression profiles and to protein structures. Considering the importance, our centre is mainly involved in the functional genomics and proteomics study of important microorganisms, genes and proteins. Besides, our centre is working on the area of synonymous codon usages, amino acid usage and constraints selection studies in Prokaryotes and Eukaryotes using Multivariate Statistical techniques (MSA). In this regard, different data reduction techniques like Correspondence Analysis (COA), Principal Component Analysis (PCA), Factor Analysis (FA) were used for finding selection pressures for genomes having industrial importance. Our centre has future aim to carry out next generation sequence data analysis.
Major research activities in biotechnology and its related fields : The centre organized a National workshop on Functional Genomics and evolutionary Biology. Our centre is also working on the area of synonymous codon usages, and constraints selection studies in Prokaryotes and Eukaryotes using Multivariate Statistical techniques (MSA). In this regard, different data reduction and techniques like Correspondence Analysis (COA), Principal Component Analysis (PCA), Factor Analysis (FA) were used for finding hypothetical variables (components) that account for as much of the variance in multidimensional data (codon and amino acid usage) as possible. DISC personals delivered lectures at different institutes in the state for the awareness in the bioinformatics.
Area of specialization: Microbial Genomics, Proteomics and Evolutionary Biology Major achievements made during 2012-13:
Whole genome sequencing and prediction of different metabolic pathways and their role in gene function and regulation
Protein structure prediction, Protein modeling, protein-protein and Protein-ligand interactions
Computational Biology
To Support Scientists and students in their research by using Bioinformatics tools and techniques.
Infrastructure facilities in the Bioinformatics Centre: IBM x365 series Server: 1 Windows 2000 Server: 1 Proxy Server: 1 DNS Server: 2 Mail Server: 1 RAS and Print Server: 1 SQL server 2004, Corel Draw 12, Adobe Photoshop CS, Microsoft Front Page 2003, Flash MX, Adobe In Design CS, Windows XP Professional, Windows 2000 Pentium IV based computer: 8 Scanner: 1 Color Inkjet Printer: 1
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Details about Staff members working in the centre: Sl. No. Name 1. Sunil Kumar
Designation Information Officer
2. 3.
Lab technician Lab Technician
Satya Sidharth Mohanty Kinshuk Chandra Nayak
Specialization M.Sc. (Biotechnology) Advanced Diploma in Bioinformatics PGDCA MCA M.Sc in Statistics
Working Since 3rd Oct, 2002
Status Permanent
14th Sep, 2004 29th Sep, 2004
Permanent Permanent
Educational activities; Besides doing research in bioinformatics, we are also teaching the Pre-Ph.D course work for the students enroll for the Ph.D. degree under Utkal University.
Papers/published or presented in the conferences :
152
1.
Prabla Kumari, Saumya Bandyopadhyay and Subrata K Das*. 2012. Microbacterium oryzae sp. nov., isolated from rice field. Int. J. Syst. Evol. Microbiol. doi:10.1099/ijs.0.046870-0
2.
Jhasketan Badhai, Prabla Kumari, P. Krishnan, T. Ramamurthy and Subrata K Das*. 2012. Presence of SXT integrating conjugative element in marine bacteria isolated from the mucus of the coral Fungia echinata from Andaman Sea. FEMS Microbiology Letters. DOI: 10.1111/1574-6968.12033.
3.
Saumya Bandyopadhyay, Peter Schumann and Subrata K. Das*. 2012. Pannonibacter indica sp. nov., a highly arsenate-tolerant bacterium isolated from a hot spring in India. Archives of Microbiology. DOI : 10.1007/s00203012-0840-z.
4.
Subrata K. Das* and P.K.Chakrabortty. 2012. Characterization of a (pckA) mutant of the non-nodulating bacterium Rhizobium pusense NRCPB10 induced by transposon Tn5 mutagenesis. 3Biotech. 2: 311-318.
5.
Kinshuk Chandra Nayak* (2013) Comparative genome sequence analysis of Sulfolobus acidocaldarius and 9 other isolates of its genus for factors influencing codon and amino acid usage. Gene, 513, (1) 163-173.
6.
Kinshuk Chandra Nayak* (2012) Comparative study on factors influencing the codon and amino acid usage in Lactobacillus sakei 23K and 13 other lactobacilli. Mol. Biol. Rep. 39, (1) 535-545.
7.
Gaurav Sablok, Kinshuk Chandra Nayak, Franck Vazquez, Tatiana V.Tatarinova* (2011) Synonymous codon usage, GC3 and Evolutionary patterns across plastomes of three pooid model species - Emerging grass genome models for monocots. Molecular Biotechnology. 49(2), 116-28.
8.
Panda SK, Kumar S, Tupperwar NC, Vaidya T, George A, Rath S, Bal V, Ravindran B. 2012. Chitohexaose activates macrophages by alternate pathway through TLR4 and blocks endotoxemia. PLoS Pathog. 8(5)doi: 10.1371/journal.ppat.1002717.
9.
Fazil MH, Kumar S, Rao NS, Selvaraj C, Singh SK, Pandey HP, Singh DV. 2012. Comparative structural analysis of two proteins belonging to quorum sensing system in Vibrio cholerae. J Biomol Struct Dyn. 30(5): doi: 10.1080/07391102.2012.687523.
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10. Fazil MH, Kumar S, Farmer R, Pandey HP, Singh DV. 2012. Binding efficiencies of carbohydrate ligands with different genotypes of cholera toxin B: molecular modeling, dynamics and docking simulation studies. J Mol Model. 18(1): doi: 10.1007/s00894-010-0947-6.
Details of Training/Workshop organized and total no of user trained Center conducted National workshop on “Functional Genomics and Evolutionary Biology” from time to time. More than 50 students from different part of the country has been trained at our center.
Impact shown by the Centre: Institute of Life Sciences working on Genomics, Proteomics and phylogenetic analysis. Genome analysis were done by using comparative genomics. Work is going on in molecular modeling and simulation. Bioinformatics center has been providing Scientific support to scientists and Ph.D students by using Bioinformatics tools and Internet and Email facilities. Ph.D students and faculty members of the Institute using this facility for literature search as well as for research. Center is providing services like installing, implementing and maintaining software packages on computers, preventive maintenance of computer, networking, maintaining web site i.e. www.ils.res.in of the Institute.
Proposed activities for 2013-14 Comparative genomics The core of comparative genome analysis is the establishment of the correspondence between genes (orthology analysis) or other genomic features in different organisms. It is these intergenomic maps that make it possible to trace the evolutionary processes responsible for the divergence of two genomes. A multitude of evolutionary events acting at various organizational levels shape genome evolution. At the lowest level, point mutations affect individual nucleotides. At a higher level, large chromosomal segments undergo duplication, lateral transfer, inversion, transposition, deletion and insertion. Ultimately, whole genomes are involved in processes of hybridization, polyploidization and endosymbiosis, often leading to rapid speciation. The complexity of genome evolution poses many exciting challenges to developers of mathematical models and algorithms, who have recourse to a spectra of algorithmic, statistical and mathematical techniques, ranging from exact, heuristics, fixed parameter and approximation algorithms for problems based on parsimony models to Markov Chain Monte Carlo algorithms for Bayesian analysis of problems based on probabilistic models. These approaches will be followed to understand the phylogeny of the prokaryotic and eukaryotic organisms.
Computational biology Systems biology involves the use of computer simulations of cellular subsystems (such as the networks of metabolites and enzymes which comprise metabolism, signal transduction pathways and gene regulatory networks) to both analyze and visualize the complex connections of these cellular processes. Artificial life or virtual evolution attempts to understand evolutionary processes via the computer simulation of simple (artificial) life forms.
Contact details: Name of the Coordinator Postal Address
Dr. Subrata K Das Institute of Life Sciences, Nalco Square, Bhubaneswar- 751 023
Phone Number Fax No.
0674 -230 3342 0674- 230 0728
Email Website
[email protected] www.ils.res.in
Name of Contact Person
Dr. Subrata K Das
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Karnataka Veterinary, Animal & Fisheries Science University, Mangalore Coordinator: Dr. Indrani Karunasagar Summary of the progress made by the centre from its inception: The Bioinformatics Centre (Sub-DIC) at the College of Fisheries, Mangalore had her insception in 2000 and since then is actively involved in carrying out research, preparing databases and conducting training programmes in the area of aquatic bioinformatics. The Centre initiated research with genome analysis of the major shrimp pathogen- White spot syndrome virus (WSSV). Novel primers designed for detection of the virus enabled development of a commercial kit and the technology development award. Using bioinformatics tools, comparative analyses of the three complete genome sequences available in GenBank was done with respect to their repeat type and composition. This was further used in genotyping and characterization of the variable regions in the white spot syndrome virus (WSSV) for molecular epidemiology. Several immunogenic outer membrane proteins of fish pathogens such as Aeromonas, Vibrio and Edwardsiella species identified using bioinformatics tools were cloned and expressed. They show promise as potential vaccine candidates in affording protection to fish against infections by these warm water bacterial pathogens when experimentally challenged. A number of submissions to the Genbank have been assigned accession numbers. Our work included studies on the virulence genes in human pathogens such as Salmonella, Vibrio parahaemolyticus and V. vulnificus associated with fish and water. A number of sequences pertaining to the virulence genes of these organisms and also the sequences corresponding to the genomic regions of the fish borne trematodes, Opisthorchis viverrini and Clonorchis sinesis respectively have been deposited in GenBank and accession numbers assigned. >6000 EST sequences generated from Penaeus monodon in relation to White spot syndrome virus infection and putative genes associated with immune function have been identified and are available in the public domain. The centre is also actively involved in the study of defence genes of the tiger shrimp, P.monodon. The cloning and expression of several antimicrobial molecules (lysozyme, ferritin, crustin, antilipopolysaccharide factor, histone subunit 2A, glutathione peroxidase, superoxide dismutase, intracellular fatty acid, fortilin and cathepsin) has been successfully performed and their antimicrobial activity studied. All the molecules have been assigned Genbank accession numbers. Phylogenetic analysis of sequence data identified several non- culturable and culturable microbial community associated with sponges. The 16S rDNA data pertaining to each microbial community has been deposited in GenBank and accession numbers obtained for over 300 sequences of Brevibacteria, Actinobacteria, Proteobacteria, Firmicutes and Chlamydiae
Major research activities in biotechnology and its related field : -
154
Sequencing whole genomes of viruses associated with shrimp -
Development of rapid DNA based methods for the detection of pathogens and application of these methods for diagnosis of diseases
-
Study of archaea for the removal of ammonia to make water reusable.
-
Search for novel antimicrobial peptides participating in the defence response in shrimps.
-
Development of recombinant outer membrane protein vaccines for Aeromoniasis, edwardsiellosis and vibriosis
-
Development of recombinant proteins and ds RNA to combat viral diseases of shrimp.
-
Development of recombinant proteins and ds RNA to manage white muscle disease in MrNV( nodavirus) infection of Prawn.
-
Development of molecular diagnostics for fishborne trematodes
-
Study of marine toxins, harmful algal blooms and public health aspects of fish and fishery products.
-
Development of DNA based methods for rapid detection of harmful algae and cysts, blooms and their toxicity
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Development of monoclonal antibodies to shrimp and fish pathogens
-
Development of microsatellites as molecular markers to study disease resistance in Penaeus monodon (tiger prawn) and Macrobrachium rosenbergii (freshwater prawn)
-
Genotyping of viral and bacterial genomes
Area of specialization: Aquatic Biotechnology and public health microbiology
Major achievements during 2012-13: a.
Study on the protective efficacy of recombinant OMPs of Edwardsiella tarda and E. ictaluri Diseases due to the fish pathogens Aeromonas and Edwardsiella spp. are considered a major threat to the freshwater aquaculture industry. Although several attempts have been made on the development of effective vaccines against these pathogens, it has been not been successful due to the heterogenic (both biochemically and serologically) nature of these pathogens. As a part of developing recombinant vaccines, we studied the outer membrane proteins (OMPs) of Aeromonas hydrophila and found them to be potent vaccine candidate against infectious bacteria and many recombinant. The gene encoding for the OMP proteins OmpA, OmpW and OmpF2 protein were cloned from E. tarda and expressed. The high protective efficacy exhibited by these recombinant proteins further shows that these outer membrane proteins of E. tarda could be used as a promising potential vaccine candidate for common carps.
b.
Studies on nodavirus disease of Macrobrachium rosenbergii White tail disease (WTD) is a newly emerging disease of cultured M. rosenbergii caused by Macrobrachium rosenbergii nodavirus (MrNV) and extra small virus (XSV). The RNA1 (1175 bp) and complete sequence of RNA2 (3126 bp) of an Indian isolate MrNV was generated for the first time. The efficacy of bacterially expressed recombinant proteins (capsid proteins) of MrNV and XSV in protecting M. rosenbergii against WTD was investigated. A new RT-PCR developed & optimised for the detection of upto 24 copy numbers of shrimp nodavirus, which can be extended for regular health monitoring of prawns.
c.
Development of molecular based diagnostics for simultaneous detection of viruses of crustaceans Studies have shown that all the four DNA viruses (MBV, HPV, IHHNV, WSSV) occur simultaneously in shrimps and therefore it was found necessary to develop a multiplex PCR for the simultaneous detection of these viruses. We have developed 11different combinations of multiplex PCR for the detection of DNA viruses. The multiplex PCR combinations developed offers a more rapid, efficient and stringent screening of viruses based on severity of viral infection in both postlarvae as well as in adult shrimps. This is being validated on several samples and is ready for patent application.
d.
Serotyping and molecular characterization for study of genetic diversity among seafood associated non-typhoidal Salmonella serovars Infections due to seafood associated Salmonella serovars are great risk to public health. S. Weltevreden was observed to be the most predominant serovar. Typing of Salmonella serovars using RAPD and ERIC-PCR suggested the existence of a genetic diversity. Though both PCR based techniques were found to have a good discriminatory index, a better discriminatory ability was observed when the results obtained by the two techniques were combined and taken for composite analysis. Our study showed that use of protein profiling in combination with established typing methods such as RAPD and ERIC-PCR may provide useful information in typing of non-typhoidal Salmonella isolates associated with seafood and to develop strategies to protect public from Salmonella infections.
e.
Studies on genes responsible for biofilm formation by Salmonella Weltevreden In food-processing industries, microbial biofilms are undesirable since they are a persistent source of contamination and resistant to antibacterials and sanitizers. In S. Weltevreden, identified genes (csgD, adrA and gcpA) to be responsible for biofilm production and showed that gcpA activates cellulose production and biofilm formation in both high and low nutrient medium. The ssE gene found responsible for survival of S. Weltevreden in epithelial cells.
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Detection of class 1 integrons in Salmonella Weltevreden and silent antibiotic resistance genes in some seafood associated nontyphoidal isolates of Salmonella Seafood associated S. Weltevreden were subjected to antibiogram analysis. The multidrug-resistant isolates were analyzed for the presence of integron using integron-specific primers. The study demonstrated the presence of silent multidrug resistance genes and class I integrons in seafood-associated Salmonella strains. Prevalence of antibiotic resistance genes catA1 and tetA suggests that these could be reservoirs in the environment. Integrons present in representative isolates of S.Weltevreden and S. Newport were sequenced. While S.Weltevreden contained class 1 integron with a single gene dfrA7 in the integron cassette and an adjacent dihydropteroate synthetase gene along with the usual quaternary ammonium compound resistance gene, S. Newport contained class 1 integron with dhfrA1, OrfC, in the integron cassette and an adjacent dihydropteroate synthetase gene along with the usual quaternary ammonium compound resistance gene.
g.
Development of shrimp densovirus dsRNA as an immunoprotectant Two densoviruses, PmDNV and PstDNV affect shrimp aquaculture in India causing growth stunting. Due to the lack of information on complete genome of Indian strain of densoviruses, we have sequenced whole genome of these two viruses and based on these, nonstructural and structural protein genes were used for the synthesis of dsRNA using LITMUS 38 i vector (bidirectional T7 promoter vector) in Escherichia coli HT115. The used dsRNA drastically reduced the replication of densoviruses in challenged shrimps. Further, the mode of delivery of these dsRNAs will be studied, this could be used as an effective control measure against densoviral infection in shrimp.
h.
Study of Type-III secretion system in Vibrio parahaemolyticus associated with seafood Pathogenecity of Vibrio parahaemolyticus is associated with production of TDH and/or TRH but recent studies have shown the possible involvement of other virulence factors. The presence of T3SS gene cluster has been documented in clinical isolates of V. parahaemolyticus and known to play an essential role in pathogenesis mechanism. In this study, we have analyzed the distribution of T3SS2-beta variant in trh+ve V. parahaemolyticus isolates from seafood harvested along southwest coast of India. All of the trh+ve and tdh+ve/trh+ve isolates used, possessed T3SS2-beta gene cluster. The study of T3SS2 along with other virulence factors will help in better understanding of pathogenesis mechanisms of V. parahaemolyticus. This is the first report from India confirming the presence of T3SS2-beta in V. parahaemolyticus isolated from marine environments.
i.
Capture and removal of ammonia from fish processing waste water using Archaea Samples were collected from fish processing effluents and aquaculture ponds for isolation of ammonia oxidizing archaea (AOA) which can be used for downstream application of reducing ammonia in ammonia rich environment. Using bioinformatics tools, primers were designed for 16S rRNA, 23S rRNA and amoA gene for the detection of AOA. Using primers developed in our lab we were successful in the detection of AOA in the samples collected and the generated sequences are submitted to GeneBank. Presently we are attempting to isolate and culture AOA.
Infrastructure facilities in the Bioinformatics Centre: a.
156
Major Infrastructure Facility NT Server
-
1 no.
Computers (Desktop)
-
15 nos.
Laser printers (B/W)
-
1 no.
Laser printer (colour)
-
3 nos.
Inkjet printers
-
3 nos.
Epson Dot Matrix Printer
-
1 no
U.P.S.
-
2 nos.
Photocopier
-
1 no.
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b.
Scanner
-
2 nos.
Network Connectivity
-
Lease line connectivity of 2 Mbps
Software Procured - Gel Compare II software - Discover Studio Gene ver 1.5 - Systat Version 10.2 - Exhome BLAST - Genome cluster
Details about staff members working in the centre: Sl. No. Name 1 Dr. Malathi Shekar
Designation Information Officer
2
Mr. Madhukrishna M.
Technical Assistant
3
Mrs. Mohini M.
Data Entry Operator
Specialization Working since Status Ph.D in Food Science & Aug. 2001 – to date Not absorbed Technology Advance diploma in Computers and software programming Computer specialist Jan. 2007- todate Not absorbed (Hardware & Software) Accounts &Computation Dec. 2006- todate Not absorbed
Educational activities: a.
Use of computational softwares both online and stand alone - BLAST, FASTA, CLUSTAL W, EMBOSS, DSGene, SYSTAT, GELCOMPARE II, Exhome Blast, GenoCluster, SEQUENCE QUICKIE, Rasmol, TRF software etc. in routine research
b.
Web based data mining and prediction studies on available sequences in Genbank.
c.
Primer designing, uploading sequences to GenBank, e-submission of journal articles for publication etc.
d.
Providing e-journals such as Aquaculture journal to the university library for benefit of students and staff.
e.
Maintaining e-manuals such as FDA manual, FAO risk assessment documents, AAPQIS etc.
f.
Designing, updating and maintaining of website for university involving teaching campuses and research stations of Mangalore, Bangalore, Bidar, Shimoga and Hassan. Assisting researchers from neighbouring medical colleges in analysis of data
The Centre is collaborating with the following Centres and Universities
UNESCO Microbial Resources Centres
Wurzburg University, Germany
University of Goteborg, Sweden
Centre for Tropical Marine Ecology, Bremen, Germany
University of Kristianstad, Sweden
James Cook University, Townsville, Australia
Ghent University, Belgium
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Papers published/presented in conferences: Bhowmick P.P., Shabarinath, S., Devegowda, D., Shekar, M., Ruwandeepika, H.A.D., Karunasagar, I., Karunasagar, I. 2012. Serotyping and molecular characterization for study of genetic diversity among seafood associated nontyphoidal Salmonella serovars. Ind. J. Med Res. 135: 371-81. Deekshith, V.K., Kumar, B.K., Rai, P., Shabarinath, S., Karunasagar, I. and Karunasagar, I. 2012. Detection of class I integron in Salmonella Weltrvreden and silent antibiotic resistance genes in same seafood associated non-typhyodal isolates of Salmonella in south West coast of India. J. Appl. Microbiol. 112:1113-22. Hamod, M.A., Nithin, M.S., Yassamin, N.S., Karunasagar, I. and Karunasagar, I. 2012. Outer membrane protein K as a subunit vaccine against V. anguillarum. Aquaculture 354-355:107-110. Khushiramani, R., Maiti, B., Shekar, M., Grisha, S.K., Akash, N., Deepanjali, A., Karunasagar I. and Karunasagar I. 2012. Recombinant Aeromonas hydrophila outer membrane protein 48 (omp48) induces protective immune response against Aeromonas hydrophila and Edwardsiella tarda. Res. Microbiol. 163: 286-91. Maiti, B., Shetty, M., Shekar, M., Karunasagar, I., Karunasagar, I. 2012. Evaluation of two outer membrane proteins, Aha1 and OmpW of Aeromonas hydrophila as vaccine candidate for common carp. Vet. Immunol. Immunopathol. 149: 298-301. Singaiah NaveenKumar, Malathi Shekar, Indrani Karunasagar, Iddya Karunasagar. Genetic analysis of RNA1 and RNA2 of Macrobrachium rosenbergii Nodavirus (MrNV), India Strain. Virus Research (Article in press) Rai, P., Safeena, M.P., Krabsetsve, K., La Fauce K., Owens, L. and Karunasagar, I. 2012. Genomics, molecular epidemiology and diagnostics of infectious hypodermal and hematopoietic necrosis virus (IHHNV). Ind. J. Virol. 23:203-214. Rajendran K.V., Makesh, M. and Karunasagar, I. 2012. Monodon Baculovirus of shrimps. Ind. J. Virol. 23:149-160. Safeena, M.P., Rai, P., Karunasagar, I. and Karunasagar, I. 2012. Molecular biology and epidemiology of hepatopancreatic parvovirus of penaeid shrimp. Ind. J. Virol. 23:191-202. Shekar, M., Karunasagar, I. and Karunasagar, I. 2012. In silico identification and comparison of surface binding pockets of Vibrio parahaemolyticus thermostable direct hemolysin proteins. Int. J. Pharm. Bio. Sci. 3: B280-288. Shekar, M., Pradeep, B., Karunasagar, I. 2012. White spot syndrome virus: genotypes, epidemiology and evolutionary studies. Ind. J. Virol. 23:175-183. Shetty, M., Maiti, B., Santhosh, K.S., Venugopal, M.N. and Karunasagar, I. 2012. Betanodavirus of marine and freshwater fish. Distribution, genome organisation, diagnosis and control measures. Ind. J. Virol. 23:114-123. Shetty V.A., Kumar, S.H., Shetty, A.K., Karunasagar, I. and Karunasagar, I. 2012. Prevalence and characterization of diarrheagenic Escherichia coli isolated from adults and children in Mangalore, India. J. Lab Physicians.4: 24–29. Shetty, M., Maiti, B., Venugopal, M.N., Karunasagar, I. and Karunasagar, I. 2012. First isolation of Edwardsiella tarda from diseased striped catfish, Pangasianodon hypopthalamus (Sauvage). J. Fish. Dis. (in press). Pradeep B., Rai, P., Mohan, S.A., Shekhar, M.S., Karunasagar, I. 2012. Biology, host range, pathogenesis and diagnosis of white spot syndrome virus (WSSV). Ind. J. Virol. Ind. J. Virol. 23:161-174 Adiga, R., Karunasagar I. and Karunasagar I. 2011. Outer membrane protein secretin of Type III secretion system of Vibrio vulnificus: structure prediction and orientation. Open Access Bioinformatics, 3: 61-66. Adiga R., Karunasagar, I., and Karunasagar.I. 2011. Molecular Docking Studies of Type III Secretion System Effector SopB Homolog in Vibrio vulnificus J. Comput. Sci. Syst. Biol. 4:16-20. Bharathi, P., Bhowmick P.P., Shekar, M. and Karunasagar I. 2011. Biofilm formation by pure and mixed culture of Lactobacillus isolates on polysterene surface in varying nutrient conditions. Biotechnol. Bioinfo. Bioengg. 1: 93-98. Bharathi, P., Shekar, M. and Karunasagar, I. 2011. Evaluation of antimicrobial activity of Lactobacillus species associated with dentures. Biotechnol. Bioinfo. Bioengg. 2: 235-239.
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Bhowmick P.P., Devegowda, D., and Karunasagar, I. 2011. Virulotyping of seafood associated Salmonella enterica subsp. enterica isolated from Southwest coast of India. Biotechnol. Bioinfo. Bioengg. 1: 63-69. Neema, M. Karunasagar I. and Karunasagar I. 2011. Antigenic epitopes and MHC binders in OmpA of fish pathogen Edwardsiella tarda: a bioinformatics study. Biotechnol.Bioinfo.Bioengg. 1: 39-45. Neema, M., Karunasagar,I. and Karunasagar, I. 2011. Structural and functional characterization of outer membrane protein N in Edwardsiella ictaluri: A bioinformatics approach. Int. J. Pharma Sc. Res. 2: 13-26.
Details of Training/workshop organized and total no.of user trained The Centre has conducted 11 short term training programmes and trained >150 personnel on basic aspects of bioinformatics. The Centre conducted a National level symposium in 2006 with >200 participants The Centre also took initiative in training rural women in the operation of computers. Women were taught computer fundamentals and the basic softwares such as MS-word, MS-Excel, and word processing software in local language
Impact shown by the Centre: -
For the first time, the complete genome sequence for the Indian strain of two important emerging viruses in shrimp aquaculture, Hepatopancreatic parvovirus (HPV, acc.nos. NC_011545) and Infectious hypodermal and hematopoietic necrosis virus (IHHNV, acc. no. GQ411199) were generated.
-
19 DNA microsatellites in the genome of Macrobrachium rosenbergii were developed, sequenced and submitted to GenBank, which will be useful in breeding programme studies.
-
Probe based method - DNA dot blot, colony hybridization were standardized for rapid and sensitive detection and enumeration of the pathogen
-
Unique primers designed for amplification of specific genes of shrimp viruses and bacterial pathogens, show promise for diagnostics
-
Using the bioinformatics facility the centre has been able to publish
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>75 papers in peer reviewed journals in the area of Biotechnology and bioinformatics
-
Deposit 514 nucleotide sequences and ~ 6000 P.monodon EST sequences in GenBank
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30 Ph.D thesis with Bioinformatics support
-
The National Technology development award for developing a PCR based test kit to detect the White spot syndrome virus of shrimp was done in this centre.
-
Two patents are ready to be filed
Proposed activities for 2013-14 a.
Removal of ammonia from fish processing and aquaculture waste water by Archaea.
b.
Study of defense genes of tiger shrimp (Penaeus monodon) with respect to bacteria (Vibrio harveyi) and white spot virus (WSSV) infection
c.
dsRNA as an antiviral strategy to combat densovirus infections of shrimp and development of nanoparticles for delivery.
d.
Screening for ligands that bind in the thermostable hemolysin of .parahaemolyticus
e.
Conduct training programmes and human resource development
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Additional details : Research students & staff of the department of microbiology participated and presented papers in the Eighth International symposium on “Diseases in Asian Aquaculture”, during 21-25, November 2011, Mangalore, India. Three papers were selected for ‘Best Poster Award’ in the session “Molecular Biology, Genomics and Bioinformatics” A research scholar was bestowed with the ‘Young Scientist Award’ by the Association of Microbiologists of India, at the National conference held during 22-25, November, 2012 at Bhubhaneshwar, Odisha, India. Dr. Indrani Karunasagar was conferred the ‘Prof. J.V. Bhat Endowment Oration’ Award, for 2012-13 by Manipal University, Manipal.
Contact details: Name of the Coordinator
: Dr. Indrani Karunasagar
Postal Address
: Department of Fishery Microbiology, KVAFSU, College of Fisheries, Mangalore
160
Phone Number
: 0824-2246384; 2243755
Fax No.
: 0824 - 2246384
E-mail
:
[email protected];
[email protected]
Website
: www.mircenbiotech.com
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Mahatma Gandhi Institute of Medical Sciences, Wardha Coordinator: Dr. B. C. Harinath Summary of the progress made by the centre from its inception Bioinformatics Centre at JB Tropical Disease Research Centre, Mahatma Gandhi Institute of Medical Sciences was established in March 1999 with support from Department of Biotechnology, as part of National Bioinformatics Network. The Centre has thrust on Medical / Health Informatics since inception and is actively involved in infectious disease diagnostic research and training. In addition to providing academic bibliography service and in-house Training programme for staff involved in Hospital Information service, the Centre organizes yearly National level Workshop / Seminar / Symposium. So far 15 such events have been organized which were well received and appreciated. Further, this Centre also publishes SEVAMED a Quarterly Update on Infectious Disease Research and Traditional Medicine enters 14th year of its publication and has been well received by the medical teachers and scientists through out India. In addition to giving selected references and abstracts in hard copy ‘SEVAMED’ is now available online with complete bibliography and link to abstracts for easy retrieval with interactive web pages, beneficial to the researchers, medical practitioners and teachers. Centre has developed customized Database Software for patients’ information and launched a web portal MGIMS-JBTDRC Arogya on Holistic Healthcare and Research in Lifestyle diseases and MGIMS-JBTDRC Health Update for current awareness on Emerging Infectious Diseases and Lifestyle Health Problems. Further databases have been developed on Mycobacterial proteases (Mycoprotease-DB, http://www.bicjbtdrc-mgims.in/MycoProtease-DB/), Mycobacterium tuberculosis Proteome comparison (MTB-PCDB, http://www.bicjbtdrc-mgims.in/MTB-PCDB/) and Human Papillomavirus Proteome (HPV-PDB). The Centre has started online Health Informatics Certification Course from July 2010 with quarterly enrolment which is being well received.
Major research activities in Biotechnology and its related fields The main thrust has been to apply the latest and sophisticated techniques of immunology and molecular biology in developing tools for immunodiagnosis, monitoring, prophylaxis, surveillance and their application in better management of the diseases such as Filariasis, Tuberculosis etc.
Area of specialization: The Bioinformatics Centre has thrust on Medical / Health Informatics
Major achievements made during 2012-13
Online Certificate Course on Health Informatics (OHIC): OHIC, six months certification course is being conducted at Bioinformatics Centre, MGIMS, Sevagram since July 2010 which provides online training to Healthcare personnel and interested graduates in Science, Business Administration & Information Technology (http://www.bicjbtdrc-mgims.in/ohic) and 29 students from UK, Uganda, Mauritius, Ethiopia, Saudi Arabia and from different states of India have registered so far.
SEVAMED….goes online with complete bibliography and with link to abstracts SEVAMED, a quarterly bibliography journal has entered 14th year of its publication. This has been well received by the scientists & medical teachers in medical colleges. Centre has launched SEVAMED online as e-journal with complete bibliography and with link to abstracts for easy retrieval with interactive web pages (http://www.bicjbtdrcmgims.in/sevamed/).
Web Portal Developed Centre has launched MGIMS-JBTDRC Arogya Web Portal which presents progress being made in Holistic Healthcare and Research in Lifestyle diseases by Indian Institutions for better awareness, interaction and advancement in holistic therapy and research (http://bicjbtdrc-mgims.in/arogya-webportal/). This web portal basically provides healthcare information at reputed Holistic Healthcare and Research Centers in India on one platform for benefit of medical practitioners and general public.
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MGIMS-JBTDRC Health Update developed and quarterly updates are provided on emerging infectious diseases and lifestyle health problems (http://www.jbtdrc.org/Health-Update/).
Database Developed The Human papilloma Virus Proteome Database (HPV-PDB) developed at this centre, domiciles proteomic and genomic information on 150 HPV strains sequenced so far. Easy expandability & retrieval of the strain specific data at one place, facility for sequence analysis & exploration potential of predicted structures, easy access to curate and annotate data through various search options etc are few of its important features.
Workshop Organized 15th Workshop on Biomedical Informatics supported by DBT was held at Bioinformatics Centre, JBTDRC, Mahatma Gandhi Institute of Medical Sciences, Sevagram, on December 2, 2012.
Bioinformatics Studentship Ms. Supriya Gupta from Apaji Institute of Mathematics & Applied Computer technology, Banasthali University, Rajasthan carried out her dissertation work entitled ‘MGIMS-JBTDRC Arogya Web portal on Holistic Healthcare & Research in Lifestyle Diseases’ during 2nd January to 20th June, 2012.
Infrastructure facilities in the Bioinformatics Centre:
Computer & Communication facility: i.
Computer Hardware: (i) Server – 3, (ii) Dell Workstations - 4 (iii) PCs - 19; (iv) Laptop - 3; (v) Printers - 4, (vi) Photocopier, digital copier cum printer - 4 (vii) Cisco Router, (viii) Patton Modem, (ix) Wireless router-2, (x) Switches, (xi) LCD Projector (3), (xii) Scanner, (xiii) Digital Camera, (xiv) Sony Handy cam. (xv) Spiral Binder etc. Bioinformatics Centre, Immunology & Molecular Biology laboratories are networked through LAN.
ii.
Computer Software: Windows NT with service pack 6, Microsoft Windows NT 4.0 Service pack 4, Windows 98, 2000, XP, Office 2007, SQL Svr Standard Edtn 2005 Win 32, Visual Studio Pro 2008, Visio Std 2007, Developer Training Service Pack 3, Microsoft Visual Studio 6.0 Professional Edition with MSDN Library, Adobe Dreamweaver CS3 Win 9.0, Flash Pro CS3 Win 9.0, Adobe Photoshop Extended CS3 10.0, Win Adobe PageMaker 6.5, Wings 2000, Tally 7.2. MATLAB 7, Geneious Pro & freely available online Bioinformatics software for sequence analysis, 3D visualization tools etc. are also being used. Communication Facility: The Institute has got installed 1 Gbps Internet connectivity and campus is Wi-Fi with high bandwidth.
Details about Staff members working in the centre Sl. No. Name 1 Mr. Lingaraja Jena
Designation Info. Officer
Specialization Bioinformatics
Working Since 2007
Status Absorbed
2
Mr. Pramod Deshmukh
Tech. Asst.
Information Technology
2001
Absorbed
3 4
Ms. Vinita Hutke Ms. Mrunmayi S. Kakde
CO CO
Bioinformatics Bioinformatics
2011 2012
Under consideration
5
Ms. Mayuri Topale
DEO
Bioinformatics
2012
Information Officer and Technical Assistant posts have been absorbed by the host Institute while the posts of CO & DEO are under consideration.
Educational activities Centre provides training and research facilities to medical teachers, students and scientists pursuing their career in Medical, Bioinformatics & Biotechnology courses. BIC also support short Term & Dissertation Projects to students pursuing M.Sc. in the related disciplines under DBT’ traineeship and studentship programs.
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Centre has also started Online Health Informatics Certification (OHIC) Course of 6 months duration for Healthcare Professionals & Paramedical, to deliver basic concepts in Health Informatics in the form of online training.
Papers published/presented in the conferences
Lingaraja Jena, Satish Kumar, Bhaskar C Harinath. MycoProtease-DB: Useful resource for Mycobacterium tuberculosis complex and nontuberculous mycobacterial proteases. Bioinformation 8(24): 1240-1242 (2012)
Lingaraja Jena, Satish Kumar, Bhaskar C Harinath. Effect of Single Amino Acid Mutations on Mycobacterium tuberculosis H37Rv With Reference To H37Ra: Predicting A Structure-Function Relationship Using Computational Approaches, presented in International Symposium on Proteomics Beyond IDs at NCL, Pune during November 22-24, 2012.
Initiation of R & D activities in Bioinformatics
Exploring Genome/Proteome analysis of M. tuberculosis strains and databases development (MycoproteaseDB and MTB-PCDB).
Exploring collaboration with Dr. Varma Lab at Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Mumbai for structural & functional characterization of HPV strains.
Details of Training/Workshop organized and total no of user trained 15th Workshop on Biomedical Informatics supported by DBT was held at Bioinformatics Centre, JBTDRC, Mahatma Gandhi Institute of Medical Sciences, Sevagram, on December 2, 2012. Following the welcoming of the Guests & Speakers in an informal starting, ten presentations: Health Informatics & BIC’s Contributions – A Brief Review; Hospital Information System at MGIMS; Computing Biomedical And Healthcare Research; Pathogenicity of Mutations in BRCA1 Domains and Hydrophobic Interactions; Telemedicine, an Overview; Multi-Target Drugs – A Bioinformatics Approach For Screening of Compounds From Complementary and Alternative Medicine; Biomedical communication and Cloud Computing in Digital Era; HPV-PDB: Proteome database on Human Papillomavirus; Effect of Single Amino Acid Mutations on Mycobacterium tuberculosis H37Rv with reference to H37Ra: Predicting a Structure - Function Relationship Using Computational Approaches; PACS: Challenges in future were made by the Speakers: Dr. B. C. Harinath (Sevagram); Dr. S. P. Kalantri (Sevagram), Dr. G.D. Mogli (Hyderabad); Dr. A. K. Varma (Mumbai); Dr. Dileep Bhale (Hingoli); Dr. Prasad A. Wadegaonkar (Amravati); Dr. S. N. Singh (Pune), Dr. Satish Kumar (Sevagram), Ms. Mrunmayi S. Kakde, Mr. Lingaraja Jena & Dr. Vinit Gupta (Sevagram). Overall emphasis of the proceedings of the Workshop was on Medical / Health Care Informatics, Healthcare Research, Telemedicine, Genomics, Proteomics and Biomedical Communication. 8 Speakers and 33 Delegates amongst 37 registered, attended the workshop. Maximum representations were from Maharashtra while few from Gujarat & Andhra Pradesh. The Scientific content and deliberations were well appreciated.
Impact shown by the Centre
Online Health Informatics Certification (OHIC) Course has been well received and so far 29 students from UK, Uganda, Mauritius, Ethiopia, Saudi Arabia and from different states of India have registered for the course.
SEVAMED - Quarterly Update on Infectious Disease Research and Traditional Medicine has entered 14th year of its publication and has been well received by the scientists & medical teachers in medical colleges. SEVAMED is also available as E-Journal (http://www.bicjbtdrc-mgims.in/sevamed/).
The purpose of MGIMS-JBTDRC Arogya web Portal is to make the world aware of the richness of Ayurveda and our other Indian systems of Medicine. We are receiving inputs from institutions of excellence namely SVYASA, IRIIM, IPGT&RA, NIN, The Yoga Institute, ANHC etc. for inclusion in the web portal for sharing their research activities.
MGIMS-JBTDRC Health Update web portal has been well received by medical & paramedical professionals and public in general.
National level workshops in Biomedical Informatics and training courses in Infectious Diseases are organized every year. So far 15 such events have been organized which were well received and appreciated.
So far, 13 PG students have completed their projects under Bioinformatics traineeship and studentship programme.
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Proposed activities during the year 2013-2014
Updating of MGIMS-JBTDRC Arogya Web Portal by providing updates on healthcare and research information of reputed Holistic Healthcare and Research Centers in India
Updating of web portal MGIMS-JBTDRC Health Update related to Emerging Infectious Diseases and Lifestyle Health Problems.
Continuation of SEVAMED Quarterly an Update on Infectious Disease Research and Traditional Medicine to bring awareness and promote health research related to integrative medicine in particular.
Analysis of proteomic variations among one avirulent and four clinical strains of Mycobacterium tuberculosis based on the data available from MTB-PCDB database from time to time to explain drug resistance & virulence.
Structural and functional characterization of HPV strains, sequenced so far, to study host- pathogen interaction.
Organization of National Level Workshops on Biomedical Informatics.
Exploring transformation of OHIC to Diploma in Health Information Technology.
Contact details: Name of the Coordinator Postal Address
Dr. B. C. Harinath, PhD (USA), Director, JBTDRC & Coordinator, BIC Bioinformatics Centre, JBTDRC, Mahatma Gandhi Institute of Medical Sciences, Sevagram (Wardha) - 442 102
Phone Number Fax No.
07152 - 284038 07152 - 284038
Email Website
[email protected],
[email protected]
Name of Contact Person
Dr. Satish Kumar, MD, Professor, Biochemistry & Dy Coordinator, BIC (e-mail:
[email protected])
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www.bicjbtdrc-mgims.in, www.jbtdrc.org, www.mgims.ac.in www.arogyadham-seva.com, www.mindandbodyhealth.org
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National Botanical Research Institute, Lucknow Coordinator: Dr. Sudershan Kumar Background: CSIR-NBRI Bioinformatics SubDIC was established in 1999-2000 by orders of the then Hon’ble Minister of Science and Technology and VP CSIR, as a collaborative work in between DBT and CSIR with the following objectives: a)
to collect compile and curate Legume database of South Asia under the aegis of the International Legume Database and Information Service (ILDIS), U.K.
b)
to undertake bioinformatics research for providing stimulus to bioinformatics by initiating database standards, software production, digitization of plant diversity information, development of network and establish linkages so as to bring bioinformatics to many biotechnologists, traditional botanists and several Institutions at regional, national and international level.
c)
to maintain plant species diversity database i.e. comprehensive database of all Indian plants on web to facilitate the study and conservation of Indian biodiversity, and its relation in biotechnology and other areas.
d)
to develop a herbarium specimen database and network the herbaria of India so as to enhance specimen based biotechnological research.
e)
to strengthen the linkages with national (DBT’s BTIS network) and international databases like ILDIS, UK, and GBIF Denmark and other global programmes.
Salient Achievements Upto March 2012: 1.
Under the aegis of the International Legume Database and Information Service (ILDIS), a scientifically validated unique database of 2030 legumes of eight South Asian Countries viz. India, Nepal, Bhutan, Bangladesh, Sri Lanka, Maldives, Myanmar and Pakistan was developed and linked with ILDIS, UK and database is available on internet (www.ildis.org) & is in use worldwide.
2.
Plants of India database of 19000 taxa was initiated and it contains information on species nomenclature, including scientific names, common names, geographical distribution, descriptors, uses, etc. and is being updated.
3.
NBRI subDIC was also assigned nodal role in CSIR network project “TKDL” from 2004-05 onwards and it undertook development database on nomenclature and uses of 2600 species identified by CSIR TKDL Apex Centre situated at HRDC, Ghaziabad.
4.
NBRI subDIC also established the 1st ever NBRI-LAN and website for the use all R&D groups of NBRI for about years from 1999-2009. NBRI LAN is functional and still used in Bioinformatics Division and as a backup of whole institute.
5.
Coordinator participated as an expert in project review & steering group (PRSG) meetings held for the year 20092010, 2010-2011, 2011-2012 of DIT Govt. of India.
6.
Developed a new model “Indian Microbial Diversity Information System” which will enable to develop tools for developing a database on microbial diversity. Using this model compiled, curated database on 1100 fungi species of Uttar Pradesh containing information on species name, host name district of occurrences and genomic information.
Work Done During 2012-2013: I.
Continued the work on updation and upgradation of database of Legumes of South Asia as per International commitment.
II.
Development of database of 100000 herbarium specimens of National herbarium of CSIR-NBRI.
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Established DUS center for three crops viz. Canna, Bougainvillea, and Gladiolus for PPV & FRA, Govt. of India.
IV.
Developed new source code for digitization of 100000 herbarium specimens.
Proposed Activities For The Year 2013-2014: (i)
Continue with updation & upgradation of the maintenance of the International Legume Database and Information Service (ILDIS) which is an international commitment and centre will continue updation and upgradation of Legumes of South Asia.
(ii)
Development of Web server on legumes in India.
(iii) Continue upgradation of plants in India database and setup a Web server on plants of India. (iv) Complete editing for bringing out outputs books, proceedings, papers related to national and international projects. (v)
Develop database under the aegis of PPV & FRA Govt. of India DUS characters of Canna, Bougainvillea & Gladiolus.
(vi) Organize workshops, training programmes, to achieve the objectives of the relevant projects. (vii) Continuous maintenance of NBRI-LAN and websites for the use of all R&D groups. (viii) Establish an online herbarium specimen database of 100000 specimens of CSIR-NBRI national herbarium & establish linkage with other herbaria of India. (ix)
Establish a website CSIR-NBRI Sub DIC and establish linkage with other centres.
Details About Staff Members Working In The Centre: Name of the staff Dr. Sudershan Kumar
Designation Coordinator
Ms. Leena Wahi Gupta Ms. Uma Singh
TA Contr.
Ms. Avantika Priya
Specialization Bioinformatics
Period of working Since inception
Absorption status Permanent
Bioinformatics Bioinformatics
Since inception 2010
Permanent Temp.
PA-II
Bioinformatics
2012
Temp
Ms. Shruti Shree Ms. Harjeet Kaur
PA-II PA-II
Bioinformatics Bioinformatics
2012 2012
Temp Temp
Mr. Gaurav Srivatava
PA-II
Bioinformatics
2012
Temp
Note: Data processing work is being done on job contract basis through official contractor of NBRI.
Contact details : Dr. Sudershan Kumar Senior Scientist & Coordinator, Bioinformatics SubDIC CSIR-National Botanical Research Institute Rana Pratap Marg, Lucknow – 226001 (U.P.) Phone: (0)9415022174 Email:
[email protected]
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National Dairy Research Institute, Karnal Coordinator: Dr. J. K. Kaushik Summary of the progress made by the centre from its inception: The centre was established in the year 1988-89 but actually came into existence in January, 1990. The activities of database creation and data acquisition commenced in 1990 itself whereas literature scanning service was started in June 1991. Initially, institute staff was imparted training in computer orientation and CD-ROMs usage as a regular feature. In 1996, the dial-up connectivity was established. Subsequently, KU-band VSAT was installed in 1998; service of the Internet was made available to the institute scientists. Several workshops (about a dozen) on various emerging topics in the field of Bioinformatics with relevance to Animal Sciences have been successfully conducted by the centre. The centre is also conducting Executive Committee meetings from time to time and has participated in all the Coordinators’ meetings held by the Department of Biotechnology. Ultimately, the Sub-centre switched over to multifarious research activities including comparative genomics and proteomics data analysis, expression and promoter analysis; identification of SNP and their structural modelling; an evolutionary study on aspartic proteinase with implication in milk clotting; various soft computing/ machine learning predictive models in animal production and processing applications; strengthening of laboratory facilities through procuring new hardware and software, viz., Servers, and Workstations along with software packages like CLC Main Workbench for sequence analyses; Simulation and structure analysis packages, Gene expression analysis package and MATLAB with bioinformatics toolbox to name a few. In 2011, the BTIS sub-centre moved to a new dedicated space in Animal Biotechnology Centre.
Major research activities in biotechnology & its related fields The major areas of research include Embryo Biotechnology; Reproduction Augmentation; Livestock (Buffalo & Cattle) and Lactic Acid Bacteria (LAB) Genomics; Biological pathway analysis; Development of functional foods, Probiotics & recombinant dairy enzymes, Development of molecular methods for detection of food borne pathogens and adulterants; Structural Biology/Bioinformatics of biological macro-molecules; Gene expression analysis and proteomics of mammary gland and reproductive organs; and successful application of emerging soft computing and machine learning algorithms in modelling various animal production and processing aspects. The Institute offers degree programmes at Master and Doctoral levels in the fields of Animal Biotechnology and allied disciplines like Animal Genetics & Breeding, Animal Biochemistry, Animal Nutrition and Physiology and Dairy Microbiology. Basic and advanced courses in Bioinformatics are offered to these PG students.
Area of specialization: Animal Biotechnology, Animal Genomics and Proteomics, Lactic acid bacteria genomics, Soft Computing and Machine Learning Algorithms and Statistical Models.
Major achievements made during 2012-13: i.
Structural modelling and determination of energetic cost of non-synonymous single nucleotide polymorphism (nsSNP) in livestock animal proteins.
ii.
Comparative modelling and structural analysis of xanthine oxidoreductase.
iii.
Several stable reference genes were analysed for use in gene expression studies in mammary gland.
iv.
Predictive models based on connectionist paradigms, viz., error back propagation, radial basis function and generalised regression learning algorithms have been developed to predict 305-day milk yield in different lactations (up to first six calvings) as well as for overall data of Murrah buffaloes.
v.
The connectionist network was successfully used to predict the body weight from body measurements in Attappady black goats, mainly known for their valuable meat and skin. The study was made to compare the relative efficiency of regression models vis-à-vis neural network models for prediction of first lactation 305-day milk yield in Sahiwal cows.
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Several connectionist models vis-à-vis conventional empirical sorption models were developed for modelling sorption (adsorption and desorption) isotherms in dried acid casein prepared from buffalo skim milk, at various temperatures over a range of water activity (0.11–0.97).
vii.
A Learning Management System (LMS) for uploading various e-courses in Dairying including Bioinformatics developed in MOODLE software environment.
Providing e-mail and the Internet access to scientists and students of the Institute; strengthening Genome Analysis work in Livestock in terms of production, reproduction and disease diagnosis; conducting various training programs and workshops for scientists/faculty and Post-Graduate (PG) students belonging to various academic and R&D institutions; delivered several invited expert lectures/presentations by Institute Bioinformatics faculty at various forums, i.e., seminars, workshops, short-courses, etc., organised within/outside the Institute; subscribing to forty five online international journals as well as providing the Institute scientists with online access (IP address based) to as many as 1153 important journals through Consortium for e-Resources in Agriculture (CeRA, http://cera.jccc.in/); Wi-Fi connectivity is operational at the Institute Hostels; Online Examination Laboratory for the recruitment of scientists (through ASRB); and software development through studentships/traineeships, for MIS and data analysis requirements of Institute researchers.
Infrastructure facilities in the Bioinformatics Centre: The BTIS sub-centre at the Institute is equipped with the following computational and supporting facility A.
Computer and Communication facilities: Servers (2), workstations (6), Visual graphics workstation (SGI fuel workstation - 1), desktops (5), Printers (1), Scanner (1), UPS (1), NKN lease line.
B.
Scientific software packages: MATLAB – Bioinformatics Toolbox, SAS with JMP Genomics, CLC Bio-workbench, YASARA – Structure, SPDBV, MolIde, Scwrl4, VMD, FoldX, Clustal-X, UGENE, GeneSpring, Pathway Studio, WEKA, Programming languages’ compilers, etc.
C.
Databases and other information resources: JASPAR (TBS and promoter analysis), local copy of PDB and Swissprot, Derwent Biotechnological Abstracts &, CAB Abstracts.
Staff members at the Sub-centre Name of Staff Dr. J. K. Kaushik
Designation Senior Scientist & Coordinator
Specialisation Period of working Animal Bio-Technology Sept 2010 - continuing
Dr. A. K. Sharma
Senior Scientist & In-charge Computer Centre; and Co-Coordinator (Additional Charge)
Computer Applications May, 2007 - continuing
Educational Activities: The institute offers two courses in basic and advanced Bioinformatics at Master and Ph.D. degree level to students of various disciplines.
Publications
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i.
Varshney, N, Mohanty, A. K., Kumar, S., Kaushik, J. K., Dang, A.K., Mukesh, M., Mishra, B. P., Kataria, R., Kimothi, S. P., Mukhopadhyay, T. K., Malakar, D., Prakash, B. S., Grover, S. & Batish, V. K., 2012. Selection of suitable reference genes for gene expression studies in milk somatic cells of cow and buffalo. J Dairy Sci. 95: 2935-2945.
ii.
Dongre, V.B., Gandhi, R.S., Singh, A., Ruhil, A.P., 2012. Comparative efficiency of artificial neural networks and multiple linear regression analysis for prediction of first lactation 305-day milk yield in Sahiwal cattle. Livestock Science 147, 192–197.
iii.
Minz, P. S., Sharma, A. K., Raju, P. N., 2012. Automatic food quality evaluation using computer vision system – a framework. Beverage and Food World, 30(3), 23-26. Special Issue on “Instrumentation, Process Control & Automation Systems, Coding/Marking & Weighing Systems”.
iv.
Raja, T. V., Ruhil, A. P., Gandhi, R. S., 2012. Comparison of connectionist and multiple regression approaches for prediction of body weight of goats. Neural Computing and Applications 21, 119–124.
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v.
Ruhil, A. P., et al. (Editors), 2013. Data Mining Techniques for Farm Animal Management. Agrotech Publishing Academy, 11-A, Vinayak Complex-B, Durga Nursery Road, Udaipur-313001. In Press.
vi.
Sharma, A. K., 2012. Neural computing and applications to livestock research. In: Dixit, S. P., et al. (Editors) Genomic and Phenomic Tools for Livestock Genome Analysis, pp. 51-58. Published by NBAGR Karnal. Lambert Academic Publishing GmbH & Co. KG, Saarbrücken, Germany. ISBN 978-3-659-28418-2.
vii.
Sharma, A. K., 2012. Concepts and application of neural network models in animal management. In: Ruhil, A. P., et al. (Editors) Data Mining Techniques for Farm Animal Management, pp. 105-113. Agrotech Publishing Academy, 11-A, Vinayak Complex-B, Durga Nursery Road, Udaipur-313001. (Chapter 9). In Press.
viii. Sharma, A. K., 2012. SAS programming essentials for statistical computing in animal sciences. In: Ruhil A. P. et al. (Editors) Data Mining Techniques for Farm Animal Management, pp. 187-208. Agrotech Publishing Academy, 11-A, Vinayak Complex-B, Durga Nursery Road, Udaipur-313001. (Chapter 17). In Press. ix.
Sharma, A. K., Sawhney, I. K., 2012. Modelling moisture sorption isotherms in dried acid casein using bioinspired connectionist approach vis-à-vis empirical methods. In: Proceedings of the ISAS 66th Annual International Conference on Statistics and Informatics in Agricultural Research, December 18-20, New Delhi. (Paper ID: CP9.07)
x.
Sharma, S., Sharma, A. K., 2012. An in-silico Approach for Protein Secondary Structure Modeling – Prediction of Helical Transmembrane Region using Artificial Neural Network Approach through MATLAB. Lambert Academic Publishing GmbH & Co. KG, Saarbrücken, Germany. ISBN 978-3-8465-8268-8. Price: €49.
Initiation of R&D activities in Bioinformatics Several research studies were carried out in the fields of Animal Biotechnology, Animal Genomics and Proteomics, Lactic acid bacteria genomics, evolutionary study on aspartic proteinase and development of several Databases, MIS and Webenabled Interactive Decision Support Systems for monitoring Institute Livestock Farm management information as well as to disseminate experts’ advice to various end users such as farmers, students/researchers and industry; and application of emerging Soft Computing and Machine Learning Algorithms and Statistical Models in various animal bioinformatics studies.
Details of training/workshop organized and total no. of users trained (04) Four external students were provided summer training at NDRI BTIS sub-centre. i.
Mr. Jaikee Singh, M.Tech. (Bioinformatics) of Sam Higginbottom Institute of Agriculture Technology & Science (SHIATS), Allahabad, worked on topic entitled ‘Evaluating Risk of Death due to Hepatitis using ANN and SVM Classifiers under WEKA Environment – A Small Case Study’.
ii.
Mr. Sudhanshu Chaudhary, M.Sc.(Bioinformatics) of SHIATS worked on topic entitled ‘Diagnosis of Diabetes using ANN and SVM Classifiers under WEKA Environment – A Small Case Study’
iii.
Mr. Vishwas Uttam, M.Tech. (Bioinformatics) of SHIATS worked on topic entitled ‘Predicting Breast Cancer Recurrence using ANN and SVM Classifiers under WEKA Environment – A Small Case Study’.
iv.
Ms. Sonia Saini, M.Sc. (Bioinformatics), Kurukshetra University, worked on ‘Structure–Stability Relationship in Lactoferrin using in-silico Mutational Analysis’.
Conferences/Training/Workshop conducted (20 participants) One-week training programme on the topic entitled “Data Analysis using SAS” was conducted for PhD (Dairying) scholars of NDRI during July 16-21, 2012.
Impact shown by the centre The BTIS Sub-centre at NDRI Deemed University is well known for its contribution, expertise/excellence and facilities in Bioinformatics R&D throughout the northern region of the country by virtue of its academic programs, research publications, conferences/workshops/symposia/advanced faculty training programs, Research Lab, etc. The sub-centre is constantly getting several requests from various university departments of Bioinformatics/Computer Science & Engineering
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for training placements of their UG/PG students. Also, various research journals especially in the fields of Animal Bioinformatics/Biology and Computer Sciences have invited NDRI faculty to serve on their Editorial Boards as reviewers/ technical-editors. The faculty is also invited as experts in Bioinformatics/Computer Science to serve on academic panels/ advisory boards of various universities as well as for conferences/other events within the country as well as abroad. The faculty of the sub-centre has recently received research grant from DBT for developing buffalo genomic resources. The sub-centre’s faculty/students have bagged many awards in recognition of their research findings published as journal articles, books and theses.
Proposed activities for 2013-14
Identification and modelling of non-synonymous SNPs.
Comparative proteomic analysis for discovery of biomarkers.
Analysis of promoter regions and transcription binding sites for selected buffalo genes.
Modelling moisture sorption isotherms in dairy products using bio-inspired computing techniques vis-à-vis classical empirical methods.
Web-enabled Interactive Information Delivery System for Dairy stakeholders.
Contact details: Name of Contact Person(s)
:
Postal Address
:
Phones(Office)
:
Fax E-mail
: :
Website
:
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Dr. J. K. Kaushik, Coordinator Dr. A. K. Sharma, Co-Coordinator BTIS Sub-Centre, Animal Biotechnology Centre (ABTC), National Dairy Research Institute, Karnal – 132001 (Haryana) INDIA. +91 184 2259531 (JKK); +91 184 2259015 (AKS) +91 184 2250042.
[email protected],
[email protected];
[email protected],
[email protected] http://www.ndri.res.in/
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National Institute of Oceanography, Goa Coordinator: Dr. BabanIngole Summary of the progress made by the centre from its inception India is one among 12 mega-biodiversity countries and 25 hotspots of the richest and highly endangered eco-regions of the world. Among the Asian countries, India is perhaps the only one that has a long record of inventories of coastal and marine biodiversity dating back to at least two centuries. In terms of marine environment, India has a coastline of about 7500 km, and Exclusive Economic Zone (EEZ) of 2.02 million km2 adjoining the continental regions and the offshore islands and a very wide range of coastal ecosystems such as estuaries, lagoons, mangroves, backwaters, salt marshes, rocky coasts, sandy stretches and coral reefs, which are characterized by unique biotic and abiotic properties and processes . Indian seas and coastal belt has a vast wealth of biodiversity which needs to be explored sampled and identified using modern sampling and taxonomic tools. On other hand, over exploitation (especially the fish stocks) is eroding the stock leading to extinction threats. Therefore in order to conserve this natural wealth Govt. of India under the lead i.e. Ministry of Environment and Forests identified biodiversity conservation as a primary thrust area. Inventorization of the marine flora and fauna is one of main objective of this centre. The basic aim of the centre is to study and record the marine biodiversity of Indian waters, which is made available in the form of digital data. The centre have developed several database on different groups of marine organisms
Major research activities in biotechnology and its related field: The major research activities in biotechnology and related field at National Institute of Oceanography are bioactive molecules from marine environment, identification and preparation of extracts of pharmaceutical importance from marine organisms, identification of marine organisms for compounds with industrial application. Area of specialization of the centre Marine Biodiversity Informatics.
Major activities of the centre during the year 2012 – 13
Developed online database on Coastal birds (www.birds.biosearch.in )
Database on Seaweeds from Indian coasts (www.seaweeds.biosearch.in )
Database on Mammals and Reptiles (www.mammals.biosearch.in )
Developed database on Marine Microbes within biosearch from Indian coastal waters, which has organized morphological, molecular and taxonomic information of marine microbial diversity. (www.biosearch.in/microbes)
Further Development and refinement of online database on marine flora and fauna of Indian coastal waters, bioSearch which can be accessed on www.biosearch.in The data upgradation, validiation and curation is a continuous process and is in progress.
Participated in the “International next generation sequencing data analysis workshop” organized by Pune University during 10-13 December 2012
Participated in the “National Training cum workshop on DNA Barcoding of Fish and Marine Life – Molecular Analysis and Bioinformatics Approach” organized by Bharathidasan University, Tiruchirappalli, Tamil Nadu during 12 – 14 September 2012.
Participated in the training course “Marine GIS applications using ArcGIS” Organized by UNESCO/IODE Project Office, Oostend Belgium in collaboration with INCOIS, Hyderabad via OTA Global Classroom.
Training imparted to Post-graduate students in bioinformatics and facilities are provided to complete short term project work.
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Databases /Software packages developed
bioSearch online database on marine organisms from Indian waters. At present it has 19680 species records of marine biota and 1814 species records of microbial diversity.
Developed Database on Coastal Birds of India. At present it has 405 species records including synonyms. www.birds.biosearch.in
Developed Database on Seaweeds from Indian coasts. It has 1319 species records including synonyms and varieties. www.seaweeds.biosearch.in
Database on Mammals and Reptiles which includes 51 records of mammals 15 records turtle and 28 snakes records including synonyms and varieties. www.mammals.biosearch.in
Research Publications :
Krishnamurthi & Chakrabarti (2012): Diversity of Bacteria and Archaea from a landfill in Chandigarh, India as revealed by culture-dependent and culture-independent molecular approaches- Syst. Appl. Microbiol (In Press). http://dx.doi.org/10.1016/j.syapm.2012.08.0 09.
Krishnamurthi S, Bhattacharya A, Schumann P & Chakrabarti T (2012): Microbacterium immunditiarum sp. nov., a novel actinobacterium isolated from a landfill surface soil.- Int. J. Syst. Evol. Microbiol 62, 2187-2193.
Krishnamurthi S, Suresh K & Chakrabarti T (2012): Desulfotomaculum indicum sp. nov., a novel sulphate reducing bacterium isolated from a landfill s
Bhagat J, Ingole B.S., A. Sarkar & M. Gunjikar (2012). Measurement of DNA Damage in Planaxis sulcatus as a biomarker of genotoxicity. The Ecoscan (Spe. Issue) 1:219-223
Chatterjee, T.; Fernandez-Leborans, G.; Ramteke, D.; Ingole, B.S. (2013) New records of epibiont Ciliates (Ciliophora) from Indian coast with descriptions of six new species. Cah. Biol. Mar.: 54; 2013; 143-159.
Sivadas, S.; Ingole, B.S.; Sen, A. (2012) Some ecological aspects and potential threats to an intertidal gastropod, Umbonium vestiarium. J. Environ. Biol.: 33; 2012; 1039-1044
Chatterjee, T.; Marshall, D.J.; Guru, B.C.; Ingole, B.S.; Pesic, V. (2012) A new species of the genus Acarothrix (Acari: Halacaridae) from Brunei Darussalam and India. Cah. Biol. Mar.: 53; 2012; 541-546.
Pesic, V.; Chatterjee, T.; Ingole, B.S.; Velip, D.; Pavicevic, A. (2012) A new species of Litarachna Walter, 1925 (Acari: Hydrachnidia) from the West Indian Coast, with a discussion on the diversity of the family Pontarachnidae Koenike, 1910. Cah. Biol. Mar.: 53; 2012; 547-553.
Stohr, S.; Sautya, S.; Ingole, B.S. (2012) Brittle stars (Echinodermata: Ophiuroidea) from seamounts in the Andaman Sea (Indian Ocean): first account, with descriptions of new species. J. Mar. Biol. Assoc. UK: 92(5); 2012; 11951208
Proposed activities for 2013-14 The identification of a species based on morphological and anatomical description is the most powerful tool to authenticate species identification and building monophyletic taxa, and often used by all biologist including geneticists and molecular biologist. The last decade or so, Molecular technique notably DNA barcoding have increasingly be used for accurate identification of already known species and reveals a new horizon in biodiversity research in robust way. Therefore there is an urgent need to develop an inventory of the coastal biota based on a reliable tool such as DNA barcoding which is clearly lacking at the present moment. The Bioinformatics Centre at NIO is committed itself towards improving the understanding of the marine biotic resources in the Indian waters. The proposed future activities are as follows. 1.
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DNA Barcoding of known marine species from Indian waters and development of database to document the biotic resources in an organized manner and disseminate the information for effective management, conservation and utilization
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2.
Upgradation of database on Marine Microbes will continue, which in turn would facilitate production of (1) catalogue of all known diversity of single-cell organisms inclusive of the Bacteria, Archaea, Protista and associated viruses, a first of its kind initiative in our country (2) to explore and discover unknown microbial diversity, and (3) to place that knowledge into appropriate ecological and evolutionary contexts.
3.
Provide training and expertise to young researchers in the field of molecular phylogenetics through short term training/workshops with an aim to increase the pool of future academicians and research manpower in the areas of systematics and taxonomy of prokaryotes.
4.
Initiate collaborative programmes with other institutions for enriching biodiversity information resources and promoting human resource development in bioinformatics.
Contact details : Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
Dr. BabanIngole Bioinformatics Centre, National Institute of Oceanography, Dona Paula, Goa 403 004 (0)832- 2450281 (0)832-2450606
[email protected] www.niobioinformatics.in Shri Devanand Kavleka,
[email protected]
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National Institute of Plant Genome Research, New Delhi Coordinator: Dr. Gitanjali Yadav Summary of the progress made by the center from its inception The Distributed Information Sub Centre (DISC) at NIPGR was established in early 2007 and aims to serve as a support structure for all IT related issues at the institute, in addition to providing computational facilities, bioinformatics related services to the researchers in various laboratories at the Institute, catering to the needs of scientists in plant biology, physiology and agriculture.
Area of specialization of the center Plant Comparative Genomics and Plant Stress Biology
Objectives of the Center
To Serve as a National Plant Genome Information System
To Develop software, database and other tools required for creating infrastructure in the field of plant genomics, proteomics and plant molecular biology
To Conduct training programs to make users aware of available facilities in plant computational biology and its applications
To share and distribute the plant related databases and information
Major activities of the center during the year 2012-2013
Comparative analysis of chloroplast and nuclear genomes from various plants
Six-month Traineeship in the area of gene expression networks in Arabidopsis thaliana.
Bioinformatics based analyses of the Chickpea nuclear genome that has been sequenced at NIPGR
Databases/Software packages developed
A database of TPS genes and proteins in available plant genome and EST sequences
A program for identification and classification of Plant Terpene Synthases
NEXCADE: An online webserver for Perturbation analysis of complex networks
A Linux based Software Package (OSI) for Network Analysis in Batch mode
PLecDom: Plant lectin Domain Analysis (http://nipgr.res.in/plecdom.html)
ESSOILDB: The Essential Oil Database (http://nipgr.res.in/essoildb.html)
Proposed activities during the year 2013-2014 Research:
Construction of molecular interaction networks for plant developmental pathways.
Perturbation analysis of complex biological networks
Genome wide comparison of core histone subunits and histone-like proteins in Oryza sativa.
Training:
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A National Workshop on Advances in Plant Genomics will be conducted in March 2013.
Two students will be selected to undergo training for a period of six months at NIPGR starting from Jan 01, 2013 to June 30, 2013.
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Details about staff members working in the center Sl. No. Name of the Staff 1. 2. 3.
--Mr. P.C Aiyappa Mr. Subhasish Mondal
Designation
Specialization
Information Officer Technical Assistant Data Entry Operator
--Perl Programming Network Administration
Period of working --Two months 4 years
Papers published 1.
Yadav G* and Babu S (2012) NEXCADE: Perturbation Analysis for Complex Networks. PLoS ONE 7(8): e41827. doi:10.1371/journal.pone.0041827
2.
Yadav G, Anand S and Mohanty D (2012) Prediction of inter domain interactions in modular polyketide synthases by docking and correlated mutation analysis. Journal of Biomolecular Structure and Dynamics. doi:10.1080/ 07391102.2012.691342
3.
Kumari S, Shridhar S, Singh D, Priya P, Sharma P, Bhavishi K, Schrick K, and Yadav G*. (2012) The role of lectins and HD-ZIP transcription factors in Isoprenoid based plant stress responses Proc. Ind. Natl. Sci. Acad. (Accepted)
4.
Gaur R, Azam S, Jeena G, Khan AW, Chaudhary S, Jain M, Yadav G, Tyagi AK, Chattopadhyay D, Bhatia S (2012) High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.). DNA Research (In press).
Educational
activities with details of placement
All students who have undergone Traineeship or Studentship at NIPGR – Sub-DIC in the past six years are currently pursuing their PhDs abroad, or have been absorbed at project positions in different research laboratories across the country. All students are able to find placement with the help of the rigorous training program at the Sub-DIC.
Contact details : Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
Dr. Gitanjali Yadav National Institute of Plant Genome Research, Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi - 110 067 +91-11-26730103 +91-11-26741658
[email protected] www.nipgr.res.in/facilities/facility_disc.php Dr. Gitanjali Yadav
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National Institute of Technology, Raipur Coordinator: Dr. M. K. Verma Major activities of the centre during the year 2012-13: Development of Center to cater the needs for the researchers, students and teaching faculties related to biotechnology, biomedical, computer technology and Bioinformatics including other basic sciences. Initiated & enriched the research environment which resulted in: i.
No. of Publication
: 05 (International journal)
ii.
No. of Thesis guidance
: 02 (M.Sc./M. Tech)
iii.
Tool Design
: 03 (ANFIS, ANN, Fuzzy)
iv.
Ph. D guidance
: 01 (Inference system for asthma-submitted)
Major research activities in Bioinformatics and its related fields : a.
Research work in Bioinformatics was carried by students of M.Phill./M.Sc./B.Tech Bioinformatics, Biomedical, Biotechnology, and Computer Technology.
b.
Research work initiated and carried in the Bioinformatics especially in Homology Modeling, Vaccine and Drug Designing and Evolutionary Analysis.
c.
Data base generation and Data mining were initiated by center.
d.
Research work completed in the field of Fuzzy Logic/ANN and Medical Bioinformatics.
Detail about staff members working in the centre S. No. 1. 2.
Name Dr. M. K. Verma Ashish Patel
Designation Coordinator Information Officer
Working Since 2006 Since 01-05-08
Status Regular Working
3. 4.
Jyotsna Choubey Kunal Waldekar
Technical assistant Data Entry Operator
Since 18-07-12 Since 05-10-12
Working Working
Infrastructure facilities in the Bioinformatics Centre: e.
Computer & Communication facility with Internet.
f.
Scientific Software packages: MATLAB TOOL BOX, Genechek and Genowitch, IRNA.
g.
Databases & Library facilities.
Publications: (a)
International Journals: 1.
“Molecular Modeling and Docking Analysis of Novel Drug like Compounds for NDM-1 Accepted in International journal computer application” Accepted in proceedings of International journal of computer application. Amrit Jagyasi, Jyotsna Choubey, Ashish Patel, M. K. Verma.
2.
“Insilico Docking Analysis of Nitrogen Containing Bisphosphonate with Human Fernasyl Pyrophosphate Synthase” Accepted in proceedings of International journal computer application Accepted in International journal of computer application. Jyotsna Choubey, Ashish Patel , M. K. Verma.
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“ANFIS Approach for the Diagnosis of Asthma severity” Accepted in proceedings of International journal computer application. Ashish Patel, Swati Bhonsle, M. K. Verma, Qamar Rahman
4.
“Insilico Interaction Analysis of Single And Multi Wall Carbon Nanotube With Different Ion Channel”. Accepted in proceedings of International journal of computer application. Karishma Banchor, Jyotsna Choubey, Ashish Patel, M.K.Verma
5.
“Application of fuzzy logic in biomedical informatics.” Accepted in proceedings of International journal of computer application. Ashish Patel, Shailendra K. Gupta, M. K. Verma, Qamar Rahman
Future activities: 1.
One month summer/winter training in the field of bioinformatics.
2.
Developing user friendly e-Tutorials for different Bioinformatics Software’s.
3.
Center will continuously going to develop the basic infrastructure facilities to make benefiting the students/ Researchers/ Faculty members etc.
Contact details : Name of the Coordinator:
Dr. M. K. Verma
Address of communication:
Sub-DIC Bioinformatics, N. I. T. Raipur, G. E. Road, Raipur (C.G.) Mobile: +91-9425203472
Email:
[email protected]
Website: www.nitrr.ac.in
Name of Contact Person(s):
Dr. M. K. Verma Email:
[email protected]
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Rajiv Gandhi Centre for Biotechnology, Thriuvananthapuram Coordinator: Dr. Sathish Mundayoor The Bioinformatics Centre (DISC) at RGCB funded by Department of Biotechnology, Govt of India, under the National Bioinformatics Network program started functioning from May 2002 with a view to catering to the needs of the scientific community. The main function of the Centre is to act as a member of Bioinformatics Network System for providing information and technology inputs to the interested users on topics pertaining to the relevant areas of Biotechnology, especially genomics and proteomics.
Major activities Development of Centre to cater the needs for the researchers, students related to biotechnology, bioinformatics and computer technology. Initiated and enriched the research environment which resulted in:
Publications (peer reviewed): 04
Poster Presentations: 02
Training: B.Tech: 04, M.Sc: 07, M.Tech: 04,
Development of database archives and softwares.
R&D activities in Bioinformatics
Hypotheses generation and validation of possible outcomes
Infrastructure facilities Computer hardware/ Communication facilities To keep in pace with the developments in bioinformatics field, impetus is given to set up the necessary computational infrastructure and resources for the research community. The centre has upgraded its computational resources by setting up high performance computing facility. Twelve Intel Core-i7 processors (customized for cluster computing), three Dell PowerEgde T300 Workstations and five Dell Vostro 400 computers are available for computational research activities. The centre have 10 Mbps managed leased line connectivity and computers are well connected through LAN.
Scientific Software packages The molecular modeling package Accelrys Discovery Studio 2.5 was purchased on DBT grand, is used for molecular modeling, docking and simulation studies. Apart from commercial packages, the centre maintains latest version of free bioinformatics softwares such as: - EMBOSS, Autodock, WHATIF, MODELLER, ClustalW, Phylip, Cn3D, Rasmol, SOAP, Bowtie, HMMER, MEGA4, XMGRACE, GROMACS, FTDOCK, PyMOl, Z-dock etc.
Websites/Web servers The Centre is actively involved in creating softwares and integrated knowledgebases for those who are working in the areas of plant bioinformatics. Some of the databases and webservers developed at the centre are: PKSIIIexplorer[http://type3pks.in/ tsvm/pks3/], PKSIIIpred [http://type3pks.in/prediction/], TypeIII Polyketide Synthase Database [http://type3pks.in].
Services provided Data retrieval, Next-Generation Sequencing analysis, Molecular modeling, Drug design and Virtual screening services are offered. This facility provides project works to students undergoing B.Tech/M.Tech/M.Phil/M.Sc courses from a large number of universities/institutes.
Publications
178
1.
Deepa Rajan S, Rejimoan R, Sivakumar KC, Sathish Mundayoor.,An SVM based Tool for the Prediction of Nitrogen Fixing Proteins. IJCA., June 2012., 0975 – 8887.
2.
Anitha Jose, Rejimoan R, Sivakumar Kc,Sathish Mundayoor., Prediction of Extracellular Matrix Proteins using SVMhmm Classifier., IJCA., June 2012., 0975 – 8888.
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Thasni KA, Ratheeshkumar T, Rojini G, Sivakumar KC, Rakesh Sathish N, Srinivas G, Asoke B, Veena S, Priya S., Structure activity relationship of plumbagin in BRCA1 related cancer cells. Mol Carcinog. 2012 Jan 30. doi: 10.1002/mc.21877.
Presentations 1.
Mallika V, Aiswarya G, Sivakumar KC, Soniya EV.,” Structural analysis of chalcone synthase proteins from selected members of Zingeberabceae: An insilico approach.” In the International Conferences on Advances in Biological Sciences (ICABS 2012) held at Kannur, Kerala, March 15-17, 2012.
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T.M. Bhagalpur University, Bhagalpur Coordinator: Prof. (Dr.) A.K. Roy Summary of the progress made by the Centre from its inception: The Centre is an established unit of T.M. Bhagalpur University and it has been engaging regular classes on Computer application & Bioinformatics for the Post & Under graduate students of Science faculty and also providing information to the teachers & research scholars for Ph.D. works since its inception. As such it has been acting as integrated information resource on all aspects of research, Molecular biological data and Data Mining of Biological resource. The centre has developed adequate infrastructure with good dry lab which has been availed by the teachers, staffs & students of this University. An attendance register has been maintained daily for the users. Record clearly shows that about approx 100-150 users are taking benefit of it in a month. The centre has also its own research activities on different aspects of plant science & arranging workshop at local, regional & national level.
Major research activities in biotechnology and its related fields :
Cytogenetic studies of selected plant species.
Data Mining of Medicinal Plants & their diseases of Bhagalpur & Jharkhand region.
Data mining of endangered & endemic plants of Bihar & Jharkhand region.
Area of Specialization of the centre:
Dynamics of genes and proteins
Generation of database.
Major achievements of the centre during the year 2012-13:
Database developed on “Medicinal Plant of Bihar & Jharkhand region”. Anyone can see uses of particular plants, disease symptoms of medicinal plants and what fungi are responsible for its disease condition.
Regular theory and practical classes to the M.Sc. Biotechnology and other students of science faculty on Computer Applications & Bioinformatics.
Assisting research scholars of different department to collect the information from Internet.
Manage & updating of University website (www.tmbu.org) and assist University in computer related works.
Developed a database on “Katarni” a local race of Oryza sativa which is famous for its aroma and fineness.
Infrastructure facilities in the Bioinformatics Centre:
180
A.
Computer & Communication facility: 3 Servers (Web, Mail and Database), 22 clients workstation, One Laptop Intel P-M Processor 1.66 Hz., One Multimedia Projector (Sony). Networking Equipments: Modem: One External, Internet Connection: 512 kbps BSNL Broadband Connectivity, Sony Digital Camera
B.
Scientific Software Packages: Exome, Exome Blast, Exome – ED, Widows 2003 Server with xp clients, Red Hat Linux server ad. Std
C.
Databases and other Information resources: 100 books covering various fields of bioinformatics & Database of Medicinal Plants & dynamics.
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Details about staff members working in the Centre: Name Prof.(Dr.) A.K. Roy
Designation Coordinator
Area of Specialization Microbiology, Biotech.
Period of working since 08-12-2011
Dr. Rakesh Ranjan Mr. Saket Vinayak
Technical Assistant* Data Entry Operator*
Statistics & Comp. Appl. Comp. Appl.
since 22-06-2006* since 28-06-2006*
Ms. Archana Dixit
Traineeship
Bioinformatics
since 28-08-2012
*University has already taken suitable steps for the Manpower absorption issue in consultation with HRD, Govt. of Bihar (vide University Latter No. B/9835 dated 7/08/2012). It is expected that the issue will be settled within one year.
Educational activities:
Assisted faculties and students from neighboring science departments and college/Institutions in updating their knowledge through different databases / software available in the centre.
Regular theory and practical classes of Bioinformatics and computer papers of M.Sc. Students of DBT sponsored P.G. Dept. of Biotech and UG Students of college of this University.
P.G. Diploma in Bioinformatics will begin in the Centre from the coming academic session. Approval of syllabi and duration of the course is awaited for the assent of the Chancellor’s office of Bihar.
Papers published or presented in the conferences with reference (2012-13):
Database of unreported diseases of medicinal plants.
Initiation of R & D activities in Bioinformatics:
Near Bhagalpur, a primitive tribal community of Dravidian origin called “Paharias” residing in and around the Rajmahal Hills of Santhal Pargana. This isolated patch of human genome has been selected for investigation and with the objective to identify the genetic reasons for the gradual decrease in the population.
Details of Training /workshop organized and the total number of user trained:
Training Course on “Basics of Bioinformatics & Computer Application” for the UG Biotech students of regional colleges was organized on March 23 & 24, 2012. 31 participates were participated in Training Course Batch-I. (Report submitted to DBT office)
Training Course on “Basics of Bioinformatics & Computer Application” for the UG Biotech students was organized on April 9 & 10, 2012 at University level. 29 UG Biotech students were participated in Training Course Batch-II. (Report submitted to DBT office)
Training Course on “Basics of Bioinformatics & Computer Application” for the UG & PG Biotech students was organized on May 7 & 8, 2012 at University level. Twenty-seven (27) UG & PG Biotech students were participated in Training Course Batch-III. (Report submitted to DBT office)
National Training Course on “Basics of Bioinformatics & Computer Application” in collaboration with T.N.B. College, Bhagalpur on Dec.’ 13 & 14, 2012. Total no. of participants was 55 (fifty-five). (Report under progress)
National Training Course on “Bioinformatics Software-Database development & Applications” on February 21st -23rd, 2013 (proposed) for three days. 30 participates are expected to participate.
Impact shown by your centre on the growth of biotechnology and allied areas:
Bioinformatics awareness spread through the Institute web-site and by organizing workshop.
Proposed activities for 2013-14:
Bhagalpur is known as Silk City. Tasar Silk of this region is unique and has world over recognition. We intend to run a research project in association with animal scientist to generate genetic improvement in Tasar silk worm.
To develop databases on rare and endangered plant species & horticulture crops (Litchi & Mango) of this region.
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Contact details: Name of the Coordinator Postal Address Phone Number Email Website
Prof. (Dr.) A.K. Roy Coordinator Sub-DIC, University Centre of Bioinformatics, T. M. Bhagalpur University, Bhagalpur- 812007 0641-2501382, Mobile: +91(94312)04572
[email protected] www.bioinformatics-tmbu.org.in
Name of Contact Person
Prof. (Dr.) A.K. Roy
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Tamil Nadu Agricultural University, Coimbatore Coordinator: Dr. P. Nagarajan Summary of the progress made by the centre from its inception The Distributed Information Sub Centre (DISC) housed at the Centre for Plant Molecular Biology & Biotechnology, Department of Plant Molecular Biology & Bioinformatics, Tamil Nadu Agricultural University is functioning with the financial support of DBT since 1989. It is actively involved in educational and research activities of plant molecular biology, biotechnology and bioinformatics.
The centre has organized 31 bioinformatics training programmes since its inception. It also conducted various man power training programmes which includes workshops, educational programmes and seminars
The internet connectivity in the bioinformatics lab has been upgraded to 10 mbps for the benefit of scientists and students
Major research activities in biotechnology and its related fields
Marker assisted selection for genes conferring resistance against diseases and pests in economically important crops like rice for blast, bacterial leaf blight, gall midge, mung bean for yellow mosaic virus and quality traits like low phytase in maize and fibre quality in cotton.
Development of genetically modified plants in rice (drought, salinity tolerance), maize (low phytate), brinjal (shoot and fruit borer), cotton, banana, papaya, ground nut and soybean for both biotic and abiotic stresses
QTL mapping and marker aided selection for drought tolerance in rice and cotton
Characterization of root proteome of rice for water stress
Cloning and characterization of abiotic stress inducible promoters from rice
Development of agriculturally important databases
Development of sequence analysis tools
Area of specialization: Plant Molecular Biology and Bioinformatics
Major achievements made during 2012-13 1. Annotation of genes corresponding to drought QTL’s in rice Analysis of a drought tolerant QTL flanked by RM212-RM302-RM8085-RM3825 revealed the presence of 180 CDS falling in this earmarked region. Of the 80 hypothetical proteins, we could predict the possible functions for nearly twenty of them. They happened to be involved in functions associated with drought tolerance. The following are the summary of the predicted functions, hormone signaling (GA & ethylene), leaf senescence, redox homeostasis, selenium homeostasis, transport and storage of nitrogen, photosynthetic process and salt transport. 2. CDRPred – A tool to determine Complementary determining regions in Plant immunoglobins CDRPred is a tool for predicting complementarity determining regions (CDRs) in antibodies. These structures are complement to an antigen’s shape; consequently, CDRs can be used as a key to determine the protein’s affinity for specific antigens. The antigen receptors are characteristically composed of two variable domains which are located on two different polypeptide chains, heavy and light chain. For each antigen receptor, there are six CDRs that can collectively come into contact with the antigen. A single antibody molecule has two antigen receptors therefore it contains twelve CDRs. Finally, it is essential to predict the tertiary structure of CDRs in an antibody towards designing novel antibodies. This standalone tool works based on machine learning approach using support vector machine and designed using cgi-perl.
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“ProDisC” a standalone tool to predict the inter atomic distance of proteins “ProDisC was created using Perl to predict the inter atomic distance of known protein structures deposited in the Protein Data Bank or for protein structure modeled by computational method. ProDisC is designed in such a way that it is able to predict the inter atomic distances for all atoms of the protein or for user defined atoms of a protein. The output displays the information on first and second atom its atom number, atom name, residue name, residue number, chain and atomic coordinates followed by distance between two atoms in angstrom unit. The tool is freely available at http://code.google.com/p/tool-prodisc/. The tool is user friendly and requires input file in PDB format for its calculation
Infrastructure facilities in the Bioinformatics Centre
44 Intel Core 2 Duo computers used for bioinformatics teaching and training activities
Another ten Intel Core 2 CPU desktop computers are connected to LAN used for browsing
10 mbps internet connectivity has been established exclusively at 24/7 for the user centre routed through an IBM proxy server
Two Apple desktop computers used for molecular modeling and Docking studies
A Sun bio with 4+1nodes are used as server for Commercial softwares
Details about Staff members working in the centre Sl. No 1. 2.
Name K.Priyadharsini A.B.Dhivya
Designation Senior Research Fellow
Specialization Bioinformatics
Working Since 1.3.2012
Status Temporary
2.1.2013
Temporary
Senior Research Fellow Computer Science
Educational activities A four year undergraduate B. Tech (Bioinformatics) program is offered in this department from the academic year (2006-07). Besides, a one year PG Diploma program in Bioinformatics had been started as distance learning course.
Papers/ published or presented in the conferences Archana Prabahar, Srividhya Vellingiri, Sathishkumar Natarajan, Kalpana Raja, Renganathan Gandhimeyyan, Bharathi Nathan. 2012. “ Ajocin (Allicin+Ajoene) can inhibit the enzymatic activity of aflatoxin biosynthesis in peanuts and prevent human carcinogenic exposure”. International Journal of Agriculture and Food Science, 2(3): 81-89 Boobalan C and Bharathi N. 2012. “ProPCalc –A tool for calculating the protein properties”. International Journal of Advanced Computer and Mathematical Sciences,3(2): 205-208 Karthikeyan, A., M. Sudha, N. Senthil, M. Pandiyan, M. Raveendran and P. Nagarajan. 2012. Screening and identification of random amplified polymorphic DNA (RAPD) markers linked to mungbean yellow mosaic virus (MYMV) resistance in mungbean (Vigna radiata L Wilczek). Archives of Phytopathology and Plant Protection, 45 (6): 712-716 Senthil,N.,JMurukathick, M. Pandiyan,A.Larthikeyan, M. Sudha, M. Raveendran, P.Jayamani, S.Kalaiselvi and P. Nagarajan. 2012.Paithumbase-Biometrical traits based query system for studying mungbean ( Vigna radiata (L.) Wilczek) phenomics, International Journal of Applied Information Systems.4:36-39. Venkateswarlu Yadavalli , Gajendra P. Narwane, M.S.R. Krishna, Nagarajan Pothi, Bharathi Muthusamy. 2012. Tagging of brown planthopper resistance genes in F2s of IR50 × Ptb33 of Rice by using bulked segregant analysis. Rice Science., 19 (1): 70-74
Initiation of R&D activities in Bioinformatics Development of data bases of agriculturally important crops and tools for identification of transcription factors, NBS-LRR genes related to disease resistance and In silico analysis of plant proteins related to different stresses are carried out in this centre.
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Details of Training/Workshop organized and total no of user trained Fifteen participants from different State Agricultural Universities, Bharathiar University, ICAR, Arts and Science colleges etc. has attended the training programme on “In silico Methods for Plant Genome Analysis” organized on 27th February – 2nd March, 2012. They were given special lectures and hands on training in the relevant topics.
Impact shown by the Centre Three batches of 97 students were graduated with B.Tech (Bioinformatics) degree and qualified for higher education in national level institutes. Another 110 students are in various stages of their degree progamme. Bioinformatics R & D initiatives were made on data base development, genome annotation, tools development of genomics and proteomics study.
Proposed Activities (2013-14)
Differential expression analysis of genes corresponding to well characterized drought QTL’s in rice
ISSPred - Intron splice site prediction tool in plant DNA
To organize training programme on “Approaches to Plant Genomics”
Contact details: Name of the Coordinator Postal Address
Phone Number
Dr. P.Nagarajan Department of PMB and Bioinformatics Centre for Plant Molecular Biology & Biotechnology Tamil Nadu Agricultural University, Coimbatore - 641 003 91 - 422 - 6611304
Fax No. Email
91 - 422- 2431672
[email protected],
[email protected]
Website Name of Contact Person
http://btistnau.in Dr. P.Nagarajan, Professor and Head, DPMB&B
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Tamilnadu Veterinary and Animal Sciences University, Chennai Coordinator: Dr. P. Kumarasamy Summary of the progress made by the centre since its inception :
Information Dissemination Upto Dec 2012, a total no.of 56932 teaching faculties/scientists and research scholars were benefited.(Offline:17255 & Online:39677). Information dissemination facilities are used by 57 colleges from 22 Universities in 21 different disciplines.
Gene Bank Entries Following Gene sequences have been submitted to the Gene Bank
Mycobacterium tuberculosis strain CBE-6 gyrase B (gyrB) gene, partial cds[Accession No. EU835533]
Mycobacterium tuberculosis strain CBE-7 gyrase B (gyrB) gene, partial cds[Accession No. EU835534]
Mycobacterium tuberculosis strain CBE-8 gyrase A-like (gyrA) gene, partial sequence.[Accession No.EU835535]
Education M.Sc. Bioinformatics from 2011-2012 One student is undergoing P.G. Diploma in Bioinformatics from 2004-2005 18 students completed and one student is undergoing
Development of Software packages (i)
Information Retrieval Package (IRP)
(ii)
Student Relational Database Management System(SRDBMS)
Creation and updation of Databases a)
Abstracts of Research findings on Poultry by TANUVAS scientists
b)
Abstracts of PG theses (1996-2003) & (2004-2010)
c)
Abstracts of completed research schemes of TANUVAS
Creation of Databases in the field of Bioinformatics
Biofilm Databank § Database on H5N1 interaction
PROLYMPH : An online database on cancer biomarkers expressed in canine lymphoma and mast cell tumor
Primer database § Chickenpox database
Canine mammary tumour database
Studentship/Traineeship projects 16 studentship/traineeship projects have been completed
Research Projects by External Students: 71 Completed:64
186
Ongoing: 7
Conduct of Training Programmes/Summer Institutes
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Programme
No. of batches 1 6 12 2 1
No. Trained 17 79 225 23 18
11 20 2
213 491 15
1
21
1
34
1
12
Training on “Application of Bioinformatics with special focus on Genomics and proteomics” Training on “Introduction to Bioinformatics”
1
25
1
20
One day workshop on “Information retrieval system” National Workshop on “Bioinformatics”
5
93
1
34
66
1320
Computer Appreciation Programme Information Technology Bioinformatics and Information Technology Bioinformatics and its Applications Recent Trends in Genomics, Proteomics & Drug Discovery Information Retrieval System Information Retrieval System Information Retrieval System (With special reference to Bioinformatics) Summer school on Bioinformatics and its application in Animal Health and Veterinary research Workshop on Application of Bioinformatics in day to Day life Workshop on Bioinformatics tools
1 2 3 4 5 6 7 8 9
10 11 12 13 14 15 Total
Nature of Participants Teaching staff of TANUVAS Scientists and faculties Scientists and faculties Scientists and faculties Scientists and faculties Teaching staff of TANUVAS PG scholars of TANUVAS Scientists and research scholars Research scholars & scientists of SAUs Research scholars and teaching faculties Lecturers and research scholars Research scholars and Teaching faculties Research scholars and Teaching faculties PG scholars of MVC Scientists and Research scholars
Major research activities in Biotechnology and its related fields:
3.
Completed research schemes in Biotechnology
:
47
On-going research schemes in Biotechnology
:
12
Area of Specialization of the centre: Veterinary and Animal Sciences including Fisheries Sciences
Major activities of the centre during the year 2011-2012(Upto Dec 2012) Research Projects by External Students Completed : 5 Ongoing : 7 (Wetlab :5 & Drylab:2) Training programmes organized: (I)
Workshop on “Application of Bioinformatics in Day to day Life” during May 28-29, 2012 was conducted and 34 research scholars and lecturers from Tamilnadu, Puducherry and Maharastra participated and Rs.500/- was collected as registration fee from each participant
(II)
Workshop on “Bioinformatics Tools” was organized during June 21-22 2012 and 12 research scholars and scientists from Tamilnadu and Jammu participated and Rs.1000/- was collected as registration fee from each participant
(III) Training Programme on “Bioinformatics application with special reference to Genomics and Proteomics” was organized during 8-10 August 2012 and 25 research scholars and scientists from Tamilnadu and Karnataka participated. Rs.1500/- was collected as registration fee from each participant
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(IV) Training Programme on “Introduction to Bioinformatics” was organized during 26-28 September 2012 and 20 research scholars and scientists from Tamilnadu and Andra Pradesh, Maharastra, Utrapradesh participated and Rs.600/- was collected as registration fee from each participant (V)
One day workshop on “Information Retrieval System” for PG students of Madras Veterinary College was conducted in 5 batches on October 29, November 2, 5, 6, 7 November 2012 and 93 students participated
(VI) National workshop on “Bioinformatics” was conducted during November 20-21 2012 and 34 research scholars and scientists from Tamilnadu, Andrapradesh, Karnataka and Haryana participated and Rs.500/- was collected as registration fee from each participant Offline Information Retrieval
:
386 scientists and research scholars (TANUVAS:17, Other universities:356 and other states:13)
Online Information Retrieval
:
221 scientists and research scholars of TANUVAS
Infrastructure facilities available in the Bioinformatics Centre A.
Computer and Communication facility IBM server, LINUX server, IBM, HCL, Lenovo Desktops etc. Black and Colour Printers, Scanner, LCD projector and OHP projector etc
B.
Communication Facilities 1 GB ISDN connectivity and computer aided teaching technology at Seminar Hall
C.
Scientific Software Packages and application tools Discovery Studio, Genesis pro, Exome Version 1.1, Gene tool, MS SQL server 2000, Visual studio.net, etc.
D.
Databases & other information resources VETCD, BEASTCD, MEDLINE, ASFA, BIOSIS,FSTA, Derwent Biotechnology Abstracts, Current Contents (CCOD) on CDROM, ERIC,NUCSSI
Details about staff members working in the centre SL. No 1
Name and Qualification Dr.P.Dhanapalan M.V.Sc.,Ph.D
2.
Dr.P.Kumarasamy, M.V.Sc.,Ph.D
3
Dr.S.Suresh Kannan, M.V.Sc.,Ph.D Dr.P.L.Sujatha, Ph.D.
4 5. 6.
Ms.V.Malarvizhi D.E, D.I.T Ms.M.Seethalakshmi B.Sc, MCA, BLIS
Designation
Specialization
Professor and Head and Project Coordinator Professor and Head and Project Coordinator Assistant Professor
Veterinary Clinical Medicine
Assistant Librarian
Information science, IT, Bioinformatics
Technical Assistant(SG)
Electronics Engineering and IT
Computer Operator
Computer applications, Library Information Science
Animal genetics and breeding Veterinary Microbiology
* Fund provided by TANUVAS on loan basis
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Period of working
Remarks
30.4.2007 to 31.3.2012 4.4.2012 to till date
Retired on superannuatio n on 31.3.2012 TANUVAS staff
15.7.2010 to till date 3.11.1999 to till date 1991 – till date 1993-till date
TANUVAS staff -doAbsorbed* TANUVAS staff
XXIVnd All India BTISnet Coordinators’ Meeting
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Educational activities M.Sc Bioinformatics course is being offered from the year 2011-2012 and one student is undergoing the course. PG Diploma in Bioinformatics is being offered from the year 2004-2005 and 18 students have completed the course and one student is undergoing the course. Viva-Voce examination conducted in Tracking course on “Drug designing” for B.V.Sc & AH degree course students.
Papers published or presented in the conferences Book: (i)
Designing of an Information Retrieval System in Veterinary Science: Controlled vocabulary Supported. By Dr.P.L.Sujatha Published by Lambert Academic publishing, Germany. ISBN:978-3-659-22241-2
Paper published (i)
“Characterization and Lytic Activity of Endolysin Induced by bacteriophage SA4 against Mastitogenic Isolates of Staphylococcus of Bovine Origin” Anil Kumar Mishra, Mayank Rawat, Abhishek, and Sureshkannan Indian Veterinary Journal: Volume No. : 89 (2012) Page 24-25
Paper presented in III Annual conference of International Association of Medical and Pharmaceutical virologists and International symposium on “Challenges and strategies in the prevention and management of viral infections” during 0911 November 2012 at CLRI, Chennai (i)
A computational approach to study the combination therapy using HIV inhibitors against HIV-type 1 infection Sujatha Mohanakrishnan PL, Preetha SP, Kumarasamy P and Sureshkannan S
Following Papers presented in the XXVI Annual convention of IAVMI and international seminar on “Future of Livestock health: A paradigm change to maximize productivity for economic gains” during 6-8 Sep 2012 at Madras Veterinary College, Chennai (i)
Target validation of VP1 and VP2 antigenic protein of human & canine parvovirus with antiviral herbs: A Bioinformatics Approach Devipriya.P, Dhanapalan.P., Kumarasamy.P.,Sureshkannan.S and Sujatha.P.L
(ii)
Insilico screening and evaluation of herbal bio-active principles against “3DPOL” RNA polymerase enzyme of Foot and Mouth Disease Virus Kavika, Dhanapalan.P., Kumarasamy.P.,Sureshkannan.S and Sujatha.P.L
(iii) In-Vitro lytic efficacy of Staphylococcus phage crude lysine CL1 and CL3 against Staphylococcus isolates from mastitis cases Sureshkannan.S., Mayankrawat.,Anilkumarmishra and S.Arunkumar Following Papers presented in the national conference on “New trends in Bioinformatics” during 30-31 Jul 2012 conducted at Indian Institute of Technology, New Delhi (i)
A paradigm shift to predict peptide based vaccine candidates against four serotypes of Dengue virus targeting NS1 protein” Sujatha, P.L., Kumarasamy. P, Sureshkannan. S
(ii)
Epigenetic approach in multi target drug designing using turmeric as a lead compound by tragetting DNA methltransferase(DNMTs) Kumarasamy.P ,Sujatha,P.L.,Sureshkannan.S
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XXIVnd All India BTISnet Coordinators’ Meeting (iii) Personalized nutrition for the prevention of cancer: A future perspective Premchand.S, Kumarasamy.P ,Sujatha,P.L.,Sureshkannan.S
Initiation of R&D activities in Bioinformatics Guided (i)
Research work on “Vascular Endothelial Growth factors of canine”
(ii)
Selection of target molecule and active principles of Gymnema sylvestre plant
(iii) Research work on Bacterial count in saliva sample of the Periodontist patient (iv) Research works on bacterial count from saliva; samples and molecular diagnosis of Streptococcus mutant
Details of Training/Workshop organized and total no. of users trained Sl. Program No. 1. Workshop on Application of Bioinformatics in day to Day life 2. Workshop on Bioinformatics tools 3. Training on “Application of Bioinformatics with special focus on Genomics and proteomics” 4. Training on “Introduction to Bioinformatics” 5. One day workshop on “Information retrieval system” (5 batches) 6. National Workshop on “Bioinformatics”
Duration 28-29 May 2012
No. of Trainees 34
21-22nd June 2012 8-10 August 2012
12 25
26-28th Sep 2012
20
29th Oct, 2 , 5th, 6th and 7th November 2012 20-21st November 2012
93
Nature of participants Research scholars and teaching faculties Lecturers, research scholars Research scholars and Teaching faculties Research scholars and Teaching faculties PG scholars of MVC
nd
Total
34
scientists and research scholars
218
Impact shown by centre on the growth of biotechnology and allied areas: The primary impact of this centre is manpower training in Bioinformatics at various levels includes Professors, Lectures, Scientists, Post Graduates etc., from various institutes of India. 1320 participants were trained in 66 trainings/workshops conducted since 1999. The Sub-DIC is assisting research scholars and scientists from neighboring institutes in updating their knowledge in bioinformatics offering projects in Bioinformatics through Bioinformatics resources available in the centre. So far, 64 external student research projects have been completed and 7 projects are undergoing
Proposed activities for 2013-14:
.
190
a.
PG Diploma course in Bioinformatics
b.
M.Sc Bioinformatics course
c.
Training on “Bioinformatics and its applications”
d.
Training on “Information Retrieval System”
e.
Studentship and Research Projects to external students
f.
Literature retrieval service through offline and online
g.
Creation and Updation of database .
h.
Conduct of Summer school on Bioinformatics
i.
Research in Bioinformatics
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Contact details : Name of the coordinator Postal Address
Phone Number Fax no. Email
Website Name of Contact person
Dr. P. Kumarasamy, M.V.Sc., Ph.D. Professor and Head & Project Coordinator Bioinformatics Centre & ARIS Cell Madras Veterinary College Vepery, Chennai – 600 007 044-25360106/25365418/25381506 ext.2064,2094 044-25365418
[email protected] [email protected] [email protected] www.tanuvas.ac.in Dr. P. Kumarasamy, M.V.Sc., Ph.D
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Tropical Botanic Garden and Research Institute, Thiruvananthapuram Coordinator: Dr. P. N. Krishnan Summary of the progress made by the centre from its inception The Sub-DIC of JNTBGRI (formerly known as TBGRI) was started in 1998 with the mandate of establishing a National nodal centre for biodiversity informatics. As per the direction of DBT, JNTBGRI has absorbed the manpower positions as regular employees in 2004 and currently the research team consists of four Scientists, seven Ph.D. students and supporting staff. To fulfill the mandate institute has established an Extension Centre, at Puthenthope, near to Technopark, Thiruvananthapuram. The Centre has developed software application packages and organized 16 databases related to biodiversity. Also screened thousands of phytochemicals reported in medicinal plants and identified lead compounds with anti tuberculosis, hepato protective and anti snake venom activities. Major research activities in biotechnology and its related fields : (i) Conservation Biotechnology, (ii) Bioproduction of plant specific compounds, (iii) Bioprospecting and DNA-based technologies, (iv) Biodiversity Informatics and (v) Barcoding of life forms.
Area of Specialization of the centre: Biodiversity Informatics and virtual screening of plant derived molecules for drug discovery.
Major activities of the centre during the year 2012 – 2013
Phytochemicals from seven Indian medicinal plants were docked with HBx protein and found out lead compounds with hepato protective activity.
Phytochemicals from eight plants were docked with Lipoarabinomannan (LAM), which is the virulence factor in Mycobacterium tuberculosis and identified lead compounds with anti-tuberculosis activity.
Phytochemicals from 20 medicinal plants were docked with 12 major toxic proteins of Naja naja venom and identified potential lead compounds with neutralizing activity. Similarly phytochemicals reported from three plants were docked with viper venom protein molecules and identified the lead compounds.
Scanned images (600 x 600 dpi) and data of 3000 herbarium specimens were incorporated on the database, Virtual herbarium of JNTBGRI.
BTISNET web site re-designing and information updating.
Database package was developed for documenting plant diversity of Malabar Botanic Garden.
Updated information on 16 databases, three web sites and two web portal sites maintained by the Centre.
Maintained BTISNET publication and library resources web portal and developed new web site for JNTBGRI.
Provided M.Sc. Bioinformatics dissertation works to four students and initiated two Ph.D. programmes.
Infrastructure facilities in the Bioinformatics Centre Computer & Communication facility: Web server (IBM) Pentium IV- 2 units; PCs Pentium IV – 14 units; Laptop computers – 1 unit; Printers- 4 units; UPS 2KV - 2 and 5 KV – 1 units; LCD projector – 1 unit; LAN and WAN with 2 Mbps Internet connection.
Details about staff members working in the centre: (i) Dr. S. Sreekumar, Scientist C (ii) Dr. C. K. Biju, Scientist B, (iii) Mr. Raveendran, SSA, (iv) Mrs. Sawmiya Das, D.E.O. and six Ph.D Research fellows.
Types of services provided: Web server, Internet, M.Sc./M.Tech. Ph.D. research guidance, data analysis, library, training, development of database packages for biodiversity documentation.
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Educational activities with details of placement : Seventy five students were completed their M.Sc./M.C.A. dissertations, of these, 20-working as teachers, 25- doing research work, 22 – working in private entrepreneurs and 3 - doing Ph.D. in abroad. Information about others is not available.
Initiative to validate the outcome of bioinformatics resources An expert committee is functioning to evaluate the outcome of the centre.
Collaborative works/ initiatives The centre joins with apex centre and developed web portal site for BTISNet Publications and Library resources and BTISNET web site. Collaboration was made with Kerala Agriculture University for conducting integrated biotechnology course sponsored by DBT. Also made collaboration with Malabar Botanic Garden for the development of a comprehensive database on plant diversity of Malabar Botanic Garden, Ollavana, Kozhikkode.
Databases/ Software packages developed No 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
Name of database Plant Info Garden Info Seed Pack LitFriend Fungal database Meliolales Biolit Sacred groves of Kerala Wild Ornamental Plants BTISNet Publication & Library Endemic Plants of Western Ghats Virtual Herbarium of JNTBGRI Mushrooms of Wyanad Library resource of JNTBGRI Germplasm of JNTBGRI Foliicolous fungi of Sacred Groves Foliicolous fungi of JNTBGRI
URL http://www.tbgri.in/plantinfo http://www.tbgri.in/gardeninfo http://www.tbgri.in/seedpack http://www.jntbgri.in/jntbgri/LitFriend_register.asp http://www.jntbgri.in/fungi http://www.tbgri.in/biolit http://tbgri.in/SacredGroveonline http://www.tbgri.in/Ornamentalplants http://www.tbgri.in/bioinfopub http://www.tbgri.in/endemicplants http://www.tbgri.in/herbarium http://www.tbgri.in/mushroom http://www.tbgri.in/JntbLib http://www.tbgri.in/germplasm http://www.tbgri.in/sacredfungi/ http://www.tbgri.in/tbgrifungi
Papers published in seminar proceedings Neethu TS, Nisha NC, Sreekumar S, Biju CK and Krishnan PN (2012) “In silico screening of Snake Anti-Venom Compounds from Sida acuta (L.) and Mucuna pruriens (L.) DC” presented in the seminar ‘Bioinformatica Indica’ held at Centre for Bioinformatics, University of Kerala, Thiruvananthapuram on 12th to 14th January 2012. Prathibha V, Sreekumar S, Nisha NC, Biju CK and Krishnan PN (2012) “In silico screening and identification of lead compounds with Naja naja anti-venom activity from Vitex negundo (L.)” presented in the National conference on Computational Biology and Chemistry, on 2nd and 3rd April 2012 at VIT University, Velloor, Organized by Bioinformatics Division, VIT University, Velloor, TamilNadu. Nisha NC, Sreekumar S, Biju CK and Krishnan PN (2012) “In silico screening of Naja naja anti-venom activity in selected medicinal plants” presented in 3rd International Conference on Bioinformatics and Systems Biology, held at Dept. of Zoology, Annamalai University, Annamalai Nagar, Tamil Nadu on 16th to 18th February 2012. Nisheeda Basheer A, Sreekumar S, Biju CK and Krishnan PN (2012) “Identification of lead compounds with hepato protective activity from Punica granatum through docking method” presented in 3rd International Conference on Bioinformatics and Systems Biology, held at Dept. of Zoology, Annamalai University, Annamalai Nagar, and Tamil Nadu on 16th to 18th February 2012.
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Sony Thomas, Biju CK, Sreekumar S, and Krishnan PN (2012) “Biodiversity documentation and database organization of foliicolous fungi in the sacred groves of Kerala State” presented in the second Indian Biodiversity Congress held at Indian Institute of Science, Bangalore on 9-11 December, 2012. Deepa V, Sreekumar S, Biju CK and Krishnan PN (2012) “The concept of Omics science- An Overview” presented in International seminar on world bioheritage concerns over climate change with a special reference to ethnic vegetables – Botanica 2012 held at Department of Botany, SN College, Chempazhanthy, Thiruvananthapuram, from September 7 and 8, 2012. Nisha N.C., Sreekumar S, Biju C.K., and Krishnan P. N. (2012) “Identification of potential lead compounds with cobra toxic venom neutralizing activity in Acorus calamus L.” paper presented in International seminar on world bioheritage concerns over climate change with a special reference to ethnic vegetables – Botanica 2012 held at Department of Botany, SN College, Chempazhanthy, Thiruvananthapuram, from September 7 and 8, 2012.
Papers communicated in journal Nisha N.C., Sreekumar S, Biju C.K., and Krishnan P. N. In silico approach to prevent soft rot in vegetable crops (communicated to current science in August, 2012).
Initiation of R&D activities in Bioinformatics In silico screening and identification of lead compounds with anti-tuberculosis activity and hepato protective activity.
Details of Training/ Workshop organized A three day workshop on the topic “Biological database organization, molecular visualization and interaction “will be organized during the first week of February, 2013.
Impact shown by your centre on the growth of biotechnology and allied areas: Developed 16 databases related to biodiversity , published six papers in peer reviewed journals, 46 papers in seminar/ workshop proceedings, 4 training manuals, 3 chapters in books and one booklet, 4 brochures; guidance to 75 M.Sc./ M.Tech. /M.C.A dissertations, 6 Ph.D works are in progress and provided six months training to 24 students; organized 14 short term training and trained about 270 personnel and organized 7 national seminars; bioinformatics facility is regularly used by 350 staff of JNTBGRI and other institutions.
Future activities
To continue the ongoing database development and in silico screening of phytomolecules for drug discovery.
Contact details: Name of the Coordinator: Dr. P. N. Krishnan, Scientist F & Head Postal Address: Biotechnology and Bioinformatics Division, JNTBGRI, Palode, Thiruvananthapuram-695562 Phone: 04722869622, Fax No.:04722869246, Email:
[email protected] Websites: www.tbgri.in, www.bioinfotbgri.org Name of Co-coordinator: Dr. S. Sreekumar, Scientist C, STEC-JNTBGRI, Puthenthope, Thiruvananthapuram 695 586. Email:
[email protected]
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University of Kashmir, Kashmir Coordinator: Prof. K.I. Andrabi Summary of the progress made by the center from its inception
Developed a database on “Medicinal & Aromatic Plants” of J&K State. The database is available on our website www.bioinfoku.org
Successfully conducted eight national level workshops.
Has been providing services to various Institutes of the valley and Science departments of the University campus.
Has acquired several Software packages related to biosciences and the research scholars from Biosciences field are getting benefited from these packages.
Has started one-year (two semesters) PG diploma in Bioinformatics course.
Area of Specialization of the Centre:
Polymorphism studies in pure ethnic population [Kashmir].
Major activities of the center during the year 2012-13
Procured Accelrys Discovery Studio package
Web Based training by Accelrys for scholars/faculty.
Infrastructure facilities in the Bioinformatics Center A.
B.
Computer & Communication facility
SUN Bio-Cluster Grid
IBM Xeon Server Core Duo
VSAT (SCPC) with I Mbps bandwidth from Ernet.
2 Mbps Leased-Line Internet connectivity.
Databases & other information resources
Bio-Cluster Grid (Integrated Bioinformatics software & hardware solution)
CLC Combined Workbench.
Accelrys Discovery Studio
Details about staff members working in the center Name Prof. K.I. Andrabi
Designation Coordinator
Specialization Molecular Biology
Er. Mujtaba Shafi
Information Officer
J2EE, Linux, & Networking
Mohammad Hussain Ms. Arifat Ara
Tech.Asst Data Entry Operator
Period of working /Absorption 20 years 9 + years (absorbed) 3 Year (absorbed) 12 +years. (absorbed)
Papers published or presented in the conferences with reference i.
Bioinformatics Research Papers Published, in peer Reviewed journal by your centre. Masood & Mujtaba Shafi, Bioinformation 1(2): 56-57 (2005).
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Details of Training/ Workshop organized Topic
Year
No. of participants
PC Familiarization & applications
2000
13
Introduction to Bioinformatics & Biostatistics-I
2001
18
Computer fundamentals & Networking
2001
06
Introduction to Bioinformatics & Biostatistics-II
2002
14
Bioinformatics & Internet
2003
17
Internet Resources & Statistics for Biologists
2004
15
Bioinformatics: Computer Methods in Biology
2005
15
Introduction to Genomics and Proteomics
2007
21
Biocomputing
2009
20
Protein Modelling & Simulation
March 2013
Future activities
The center envisages starting a Postgraduate program in computational biology.
Contact details :
Name of the Coordinator: Prof. K.I. Andrabi Postal Address. Professor, Dean Research & Coordinator, Bioinformatics Center, The University of Kashmir, Hazratbal, Srinagar(J&K) -190 006. Email:
[email protected],
[email protected] Website: www.kashmiruniversity.net
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Acharya Nagarjuna University, Nagarjuna Nagar, Guntur Coordinator: Dr. A. Krishna Satya Summary of the progress made by the centre from its inception After the establishment of Bioinformatics Infrastructure Facility Centre at Department of biotechnology, Acharya Nagarjuna University, Nagarjuna Nagar in Guntur, it immediately initiated its activities by providing facilities to students and researchers to do work in the area of Bioinformatics. The establishment of this centre has facilitated to create a forum for interaction of students and teachers of various institutions to provide training in Computational biology to under graduate and post graduate students in the area by conducting Bioinformatics workshop and National seminar at University BIF centre. BIF had initiated multi –institutional consortium projects in bioinformatics to address various specific problems through Bioinformatics approaches. BIF promotes research in use of computational tools for molecular biology, genetics, protein chemistry, and biochemistry research at different level and centre offers work shop topics from DNA, RNA and protein sequence analysis to data base searching, genome prediction and molecular modelling.
Major activities of the centre during the year 2011-2012 Bioinformatics practical training has been given to PG, PhD students. A National Workshop on Bioinformatics Basics & Languages was conducted during March 27th to 29th 2012. In this workshop a number of candidates have got benefited.
Report of National Seminar and Workshop on Bioinformatics Basics & Languages 27th – 29th March, 2012 Bioinformatics Facility Centre, Department of Biotechnology, National Seminar was conducted in Department of Biotechnology for three days. In this seminar two technical sessions were done. Technical session-I was started on 27th march at 10 am. Delegates attended were Prof.G.Prasad (Registrar & Principal, ANU College of Arts, Commerce and Law) , Dr.Rathnagiri Polavarapu (Managing Director & CEO, Genomics Inc., USA) , Dr.Swami Mruthinti (Full Bright Nehru Scholar at ANU from University of West Georgia, USA) , Dr.M.Prashanth (Director & CEO, Bioclues), Dr.C.Ramachandra Prasad (IIIT, Hyderabad) , Dr.G.Rambabu ( Principal Scientist,GVK Bio, Hyderabad) , and guests and faculty , Research scholars and students have attended the seminar. Very wonderful topics were lectured by the Delegates and by faculty. The topics covered by them are new trends in Bio informatics, Biological Data bases, Languages, Tools, Pearl LINUX OS, Sequence alignment , Phylogenetic analysis, Sequence formats. In technical scission-II practical training was given on 29th march. Work to be done - For the research purpose after retrieving a sequence from genomic analysis, the sequence can be submitted to data bases to know the exact result. Study of gene sequence can be identified; data bases can run by tools, for protein prediction protein docking is needed.
Student projects carried out at newly established facility S. No 1
NAMES B.Suraghavi
2
K.Sudeesh
Project Title In silico studies and comparative docking studies pullulanase from different microbial sources. Homology Modelling and docking studies of metallo protease(sarratio peptidase).
Papers published1.
P. Suresh Kumar, KK.Pulicharla ,Mrinmoy gosh , KRS.Sambasiva rao.,Structural prediction and comparative docking studies of Psychrophillic â galactosidase with lactose ,ONPG and PNPG against to its counter parts of mesophillic and thermophillic enzmes.Bioinformation 6(8):311-314 (Impact factor-1.43)
Guidance for M.Tech desertations- BIF Centre was used for M.Tech students dissertation work. Manuscripts under preparation1.
B.Suraghavi, P.Suresh Kumar, A. Krishna satya, KRS Sambasiva rao., In silico studies and comparative docking studies pullulanase from different microbial sources.
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2.
K.Sudeesh, P.Suresh Kumar, A. Krishna satya, KRS Sambasiva rao., Homology Modelling and docking studies of metallo protease(sarratio peptidase).
3.
A. Krishna satya, K.Narendra, J .Swathi, K.M Sowjanya, A review on The Biopearl tool kit:open sources of Bioinformatics.
Abstracts submitted 1.
A. Krishna satya, K.Narendra, J.Swathi, K.M Sowjanya, The Biopearl tool kit:open sources of Bioinformatics submitted to AP Science congress on 14-16 november 2012 at Acharya Nagarjuna University.
Awards P.Suresh Kumar, KK.Pulicharla ,Mrinmoy gosh , KRS.Sambasiva rao., Structural & comparative docking studies psychrophillic â galactosidase ,presented a paper and awarded Junior Scientist award at National conference on Dec 12th 2012 at Coimbatore.
Proposed future activitiesModernization of the present infrastructure facility. 1.
To promote introductory Bioinformatics to under graduate students.
2.
To organise 2-6 months projects for PG students.
3.
To organise work shop and training for research scholars.
4.
For modelling of potent therapeutics molecules and drug designing.
5.
Stability studies by molecular designing.
Future Workshops cum seminars
A Three day national seminar on current trends in genomics & proteomics and hand training on protein 3D structural modelling limited for 12-15 students.
Three day workshop on Molecular modelling, Docking and Drug discovery limited for 12-15 students.
Initiation of R&D activities in Bioinformatics: Our Bioinformatics facility is engaged in R&D activity by helping PhD scholars, and they published the same.
Available Bioinformatics tools Modeller 9.v2 ,Auto Dock ,Phylip ,Mega 5, Tree view,Hex 4.0 , Muta primer, Fast PCR , Ludi , Primer Premier 5 , Bio Edit , MDL ISIS Draw, GENE DOC ,Amplifx 14, MISA ,Clustal W2 ,TREECON for windows ,CLC work bench 4, Gene designer ,Rasmol, UCSF Chimera ,Oligo Analyzer,Pdraw,SEQ Tools etc. Contact details :
Name of the Coordinator
:
Dr.A. Krishna Satya
Postal address
:
Coordinator (DBT-BIF Centre), Department of Biotechnology, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur, 522510.
200
Phone number
:
0863-2346358, 9490639577
Email
:
[email protected]
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Alagappa University, Karaikudi Coordinator: Prof. S. Karutha Pandian Summary of the progress made by the centre from its inception: Bioinformatics Infrastructure Facility (BIF) was established at Alagappa University during November 2006. This facility has been regularly used by students and faculty members of the Department of Biotechnology of Alagappa University (70 PG and Post PG students, 35 full time research scholars and 5 faculty members) and neighbouring institutions. The computational facility provided by the BIF since its creation paved the way for (i) publication of 90 research papers in SCI journals with an average impact factor of 2 in the area of bioinformatics and Biotechnology (ii) award of 10 PhDs from Alagappa University and (iii) submission about 150 M.Sc., project work dissertations and (iv) few hundred oral/poster presentations by the Faculty, Research Scholars and PG students in many national/international fora. A database called SPEIDS (Streptococcus pyogenes enzyme inhibitors using Docking Studies) has been developed which includes the annotation details of the inhibitors screened against novel targets of Streptococcus pyogenes. This national facility was instrumental for submission of 454 DNA sequences comprising 400 numbers of 16S rRNA gene sequences, 26 MLSTs, 20 ESBL gene sequences, 6 rpoB gene sequences, 2 metagenome derived gene sequences and complete sequence of a cryptic plasmid in GenBank NCBI Database.
Major research activities in biotechnology and its related fields: i) Unearthing Marine Microbial Diversity through culture Independent approaches such as DGGE, T-RFLP and Next Generation Sequencing Technologies (Illumina GAIIX)], ii) Exploration of industrially important enzymes and novel anti-infectives such as anti-biofilm agents and quorum quenchers from marine microbiota, seaweeds, seagrass and natural sources iii) Medical Biotechnology/ Molecular Characterization of Group A Streptococcus. iv) Biotechnology for Leather: Towards Cleaner Processing, v) Study on Gene Expression Technologies using C. elegans, vi) Plant Biotechnology and vii) Pharmacology of marine natural products and Antioxidant properties of Olive Oil.
Area of specialization: Medical Microbiology and Marine Microbial Biotechnology Major achievements made during 2012-13:
Published 23 papers in SCI journals with an average impact factor of 2.27.
Organized a three days training workshop for the teachers and research scholars from Universities/Colleges/ national Institutes during February 22nd – 24th, 2012.
Imparted theoretical and practical training to PG, Post M.Sc., Advanced Diploma in Molecular Diagnostics and doctoral students
Online and standalone packages were used to analyze the data for the research work and for M.Sc., project work desertions.
Infrastructure facilities in the Bioinformatics Centre: One GB NKN internet connectivity is being utilized for bioinformatic purposes by the PG students, Research Scholars and Faculty members of the host and neighboring Departments/Institutes. High end and Medium end Servers connected to Desktop Systems are loaded with advanced Operating Systems. The application softwares, Microsoft SQL server loaded 2005, Microsoft .Net framework 3.5, Microsoft Visual Studio 2005 are being used to create database in a virtual environment and also helps in storing large dataset in the High end server. Reprographic facility is also extended to PG and doctoral students.
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Details about Staff members working in the centre: Sl. No. 1. 2. 3.
Name R. Salini G. Ashwin Kumar Subramenium T. Ragupathi
Designation RA RA RA
Specialization Bioinformatics Biotech Biotech
Working Since Status 12.04.10 to date 29.09.10-31.10.12 01.12.12-to date
Educational activities The centre helps (i) M.Sc., Biotechnology (DBT-supported) (ii) DBT funded Post M.Sc., Advanced Diploma in Molecular Diagnostics and (iii) Ph.D. students in the preparation of their dissertations/theses and publication of their research findings in SCI journals and in various national/international fora. The students of the host and other institutions are provided theoretical and practical hands-on training using online and standalone tools for their course work and for preparing the competitive exams. The centre also offers Six months Bioinformatics projects for the M.Sc., students. Journals with online and printed versions are being subscribed in the areas of Biotechnology, Medical microbiology, Microbial Technology and Bioinformatics.
Papers published in SCI Journals during 2012-2013:
202
1.
Beema Shafreen R, Selvaraj C, Singh SK and Pandian SK (2013). Exploration of Fluoroquinolones resistance in Streptococcus pyogenes: comparative structure analysis of Wild-Type and mutant DNA gyrase. Journal of Molecular Recognition [Wiley] (Impact Factor: 3.31) (in press).
2.
Gowrishankar S, Thenmozhi R, Balaji K and Pandian SK (2013). Emergence of methycillin-resistant, vancomycinintermediate Staphylococcus aureus among patients associated with Group A Streptococcal pharyngitis infection in southern India. Infection, Genetics and Evolution [Elsevier] (Impact Factor: 3.128) (in press).
3.
Balaji K, Okanjo PA, Thenmozhi R and Pandian SK (2013) Virulence and multidrug resistance pattern of Vibrio cholerae O1 isolates from diarrheal outbreaks of south India during 2006-2009. Microbial Drug Resistance [Mary Ann Liebert, Inc. Publishers, USA] (Impact Factor:2.153) (in press).
4.
Gowrishankar S, Duncan MN and Pandian SK (2013). Coral associated bacteria as a promising antibiofilm agent against methicillin resistant and susceptible Staphylococcus aureus biofilms. Evidence-Based Complementary and Alternative Medicine [Hindawi Publishing Corp.] (Impact Factor: 4.774) (in press).
5.
Packiavathy IASV, Sasikumar P, Pandian SK and Ravi AV (2013) Prevention of quorum sensing mediated biofilm development and virulence factors production in Vibrio spp. by curcumin. Applied Microbiology and Biotechnology [Springer, Germany] (Impact Factor: 3.425) (in press).
6.
Bakkiyaraj D, Sivasankar C and Pandian SK (2012). Anti-pathogenic potential of Coral associated bacteria isolated from Gulf of Mannar against Pseudomonas aeruginosa. Indian Journal of Microbiology [Springer] (Impact Factor: 0.511) (in press).
7.
Bakkiyaraj D, Sivasankar C and Pandian SK (2012). Inhibition of quorum sensing regulated biofilm formation in Serratia marcescens causing nosocomial infections. Bioorganic & Medicinal Chemistry Letters 22:3089-3094 [Elsevier] (Impact Factor: 2.661).
8.
Balaji K, Thenmozhi R and Pandian SK (2012) Effect of subinhibitory concentrations of fluoroquinolones on biofilm production by clinical isolates of Streptococcus pyogenes. Indian Journal of Medical Research [ICMR] (Impact Factor: 1.826) (in press).
9.
Kalpana BJ, Aarthy S and Pandian SK (2012) Antibiofilm activity of alpha-amylase from Bacillus subtilis S8-18 against biofilm forming human bacterial pathogens. Applied Biochemistry and Biotechnology 167:1778-1794 [Humana Press, USA] (Impact Factor: 1.879).
10.
Balaji K, Thenmozhi R, Sundaravadivel M and Pandian SK (2012) Comparison of bacterial communities in the throat swabs from healthy subjects and pharyngitis patients by terminal restriction fragment length polymorphism. Applied Biochemistry and Biotechnology 167:1459-1773 [Humana Press, USA] (Impact Factor: 1.879).
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11.
Nithya C and Pandian SK (2012) Evaluation of bacterial diversity in Palk Bay sediments using terminal-restriction fragment length polymorphisms (T-RFLP). Applied Biochemistry and Biotechnology 167:1763-1777 [Humana Press, USA] (Impact Factor: 1.879).
12.
Annapoorani A, Parameswari R, Pandian SK and Ravi AV (2012) Methods to determine antipathogenic potential of phenolic and flavonoid compounds against urinary pathogen Serratia marcescens. Journal of Microbiological Methods 91:208-211 [Elsevier] (Impact factor: 2.018).
13.
Musthafa KS, Sivamaruthi BS, Pandian SK and Ravi AV (2012) Quorum sensing inhibition in Pseudomonas aeruginosa PAO1 by antagonistic compound phenyl acetic acid. Current Microbiology 65:475-480 [Springer], (Impact factor: 1.51).
14.
Annapoorani A, Jabbar AKKA, Musthafa KS, Pandian SK and Ravi AV. (2012). Inhibition of quorum sensing mediated virulence factors production in urinary pathogen Serratia marcescens PS1 by marine sponges. Indian Journal of Microbiology 52: 160-166 (Springer) (Impact factor: 0.511).
15.
Packiavathy IASV, Agilandeswari P, Musthafa KS, Pandian SK and Ravi AV (2012) Antibiofilm and quorum sensing inhibitory potential of Cuminum cyminum and its secondary metabolite methyl eugenol against Gram negative bacterial pathogens. Food Research International 45:85-92 [Elsevier, USA] (Impact Factor: 2.416).
16.
Musthafa KS, Pandian SK and Ravi AV (2012) Inhibition of quorum-sensing-dependent phenotypic expression in Serratia marcescens by marine sediment Bacillus spp. SS4. Annals of Microbiology 62:443–447 [Springer Verlag, Germany] (Impact factor: 0.350).
17.
Karthikeyan A, Kumar RR, Kumar NS, Amri ISA, Pandian SK and Ramseh M (2012). Antibiofilm activity of Dendrophthoe falcata against different bacterial pathogens. Planta Medica 78:1918-1926 (Georg Thieme Verlag KG, Germany) (Impact Factor: 2.153).
18.
Chandra Babu NK, Swarna Kumari B, Vimalarani SH, Shanthi C, Pandian SK and Sadulla S (2012) Microbiological aspects of hide and skin preservation by chilling. Journal of Society for Leather Technologists and Chemists (Impact factor: 0.561).
19.
Jayakumar K, Rajesh R, Dharuman V, Venkatasan R, Hahn JH and Pandian SK (2012) Gold nano particle decorated graphene core first generation PAMAM dendrimer for label free electrochemical DNA hybridization sensing. Biosensors and Bioelectronics 31: 406– 412 [Elsevier] (Impact factor: 5.397).
20.
Nisha SA, Pandian SK and Devi KP (2012). Assessment of anti-cholinesterase activity of Gelidiella acerosa: Implications for its therapeutic potential against Alzheimer’s disease. Evidence-Based Complementary and Alternative Medicine [Hindawi Publishing Corp.] (Impact Factor: 4.774) (in press).
21.
Kiruthiga PV, Mohanasundari V, Pravina M, Pandian SK and Devi KP (2012). p53 Exon 4 (codon 72) Polymorphism and Exon 7 (codon 249) Mutation in Breast Cancer Patients in Southern Region (Madurai) of Tamil Nadu. Asian Pacific Journal of Cancer Prevention 13: 511-516 [National Cancer Center of Korea] (Impact Factor: 1.240).
22.
Devi KP, Sakthivel R, Nish SA, Suganthy N and Pandian SK (2012). Eugenol alters the integrity of cell membrane and acts against the nosocomial pathogen Proteus mirabilis. Archives of Pharmacal Research [Springer, Seoul, South Korea] (Impact Factor:1.588) (in press).
23.
Kiruthiga PV, Shanmuganathan M, Manickavalli S, Pandian SK and Devi KP (2012). Silymarin attenuates Benzo(a)pyrene induced toxicity by mitigating ROS production, DNA damage and calcium mediated apoptosis in Peripheral Blood Mononuclear Cells (PBMC). Ecotoxicology and Environmental Safety 86:79-85 [Elsevier, USA] (Impact Factor: 2.294).
Initiation of R&D activities in Bioinformatics: Several educational, R & D and database organisation programmes are in progress. The major ongoing programes are (1) The Bioinformatics Centre has developed the database-SPEIDS (Streptococcus pyogenes enzyme inhibitors using Docking Studies) which includes the annotation details of the inhibitors screened against novel targets of S. pyogenes. (2) Virtual Screening of active compounds against various targets from bacterial pathogens and identification of novel leads are to be
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pursued. (3) Dissemination of biodiversity information – Biobank a 16S rDNA sequence repository for bacterial cultures from various resources. (4) Ph.D. programmes – 10 of them have been awarded and 39 more are pursuing. (5) Online resources- BankIT sequence submission tool used by the Ph.D. and PG students for depositing DNA/RNA/Protein sequences in the respective database of NCBI. Analysis of various spectral data as an outcome of research programmes carried out by the doctoral students. (6) Next Generation sequencing data analysis (6) Information updating and maintaining the web portal, BTISNet publication and library resources of DBT.
Details of Training/Workshop organized and total no of user trained Theoretical and practical training have been given in bioinformatics to the PG, Post M.Sc., M.E., and PhD students. A National Workshop on “Microbial Diversity: DNA to Database” conducted during February 22nd – 24th, 2012 and 120 candidates have got hands on training through this Workshop.
Impact shown by the Centre:
Developed following software packages/databases
Databases: 1.
Streptococcus pyogenes enzyme inhibitors using Docking Studies (SPEIDS) SPEIDS will include the annotation of the inhibitors screened against novel targets of S. pyogenes. These inhibitors screened against the appealing targets of Fatty acid pathway of S. pyogenes. www.speids.alagappabiotech.org
2.
Ribosomal database for the marine bacteria associated with coral reefs, sponges, marine sediment and sea water have been established which is expected to pave the way for sustainable tapping of marine microbial wealth for biotechnological prospects and protection of marine environment. The database also includes the information about bacterial isolates from stripped goat skin and the 16S rRNA sequences of Group A streptococcus. The data can be accessed from www.alagappabiotech.org/biobank.htm
Software Packages: 1.
Discovery Studio version 2.1 pacakage available from Accelrys. The module LigandFit was used for performing docking studies of active ligands against the targets of interest. The DS visualizer available is also used for preparing the proteins or ligand structure for publication in peer reviewed journal.
2.
Using online resources (software and database) for Identification and bioinformatics characterization of intein in DNA polymerase A gene of bacteriophage APSE (Acyrthosiphon pisum Secondary Endosymbiont bacteriophage) infecting the Aphid secondary endosymbionts of eukaryotic insects such as Acyrthosiphon pisum, Uroleucon rudbeckiae. reported intein in podoviridae family.
3.
Statistical packages available as standalone (SPSS 17.0, Unscramble etc.,) and online version are using for data analysis. Methods like Student T-test and one way ANOVA are applied to find the biological significance between the control and the treated samples. Principle component analysis for expression data (qPCR) to visualize the biological relevance and to filter noise. The high throughput data from Next Generation Sequencing (NGS) are analysed with the statistical packages to access good quality data, to cope with high dimensionality of the data and to extract significant biological information.
Development and maintenance of the website www.alagappabiotech.org.
Publication of 90 research papers in SCI journals and few hundred papers/posters in various National/International Seminars/Symposia/Workshops/Conferences and 4 chapters in books.
Organized 6 National Workshops providing theoretical and hands on training to young academicians, scientists, research scholars and PG students.
Proposed activities for 2013-14
204
a)
Next Generation sequencing data analysis pertaining to marine metagenomes.
b)
Organization of three days National Seminar cum Workshop on “Microbial Diversity and Infectomics” for the teachers and research scholars from Universities/Colleges/ national Institutes during February 27-March 01, 2013. Bio Informatics Infrastructure Facility (BIFs)
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Sustained development of ribosomal database for the marine bacteria associated with coral reefs, sponges, marine sediment and sea water for sustainable tapping of marine microbial wealth for biotechnological prospects and protection of marine environment.
Contact details:
Name of the Coordinator
: Prof. S. Karutha Pandian
Postal Address
: Coordinator Bioinformatics Infrastructure Facility Department of Biotechnology Alagappa University Karaikudi 630 003, Tamil Nadu : 04565 225215 : 04565 225202 :
[email protected] : www.alagappabiotech.org; www.alagappauniversity.ac.in : Prof. S. Karutha Pandian :
[email protected]
Phone Number Fax No. Email Website Name of Contact Person(s) Email
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Andhra University, Visakhapatnam Coordinator: Dr. K. Umadevi Summary of the progress made so for by the centre since its inception : Since its inception on 21st November, 2008, AU Bioinformatics Centre focused on its main objective of promotion of Biology teaching through Bioinformatics funded by the Department of Biotechnology, Government of India. Bioinformatics Centre (BIC) was inaugurated in Andhra University, Visakhapatnam on 15th August 2009.The centre became a focal point for providing various communication and computational facilities to the users from the university and also from other institutions. The Centre provides training to teachers and students of the university, affiliated colleges and other institutions through National level workshops, training programs by many eminent scientists working in the areas of bioinformatics and biotechnology and professionals from industry. The centre is open to the students, faculty and researchers of AU to retrieve literature and utilize the infrastructure available at BIF, AU. The infrastructure facility is being utilized by the Department of Marine Living Resources. The Center has been a catalyst for the growth of Bioinformatics in east coastal region of AP and has contributed significantly to manpower development.
Major activities of the centre during the year 2012–13: (a)
The centre provides online & off-line literature search facility from its rich information to the faculty, researchers and students of Andhra University.
(b)
A three days training programme was conducted for Biology teachers to familiar them in the area of Bioinformatics and also the BIF staffs participated in National workshops.
(c)
One Candidate appointed under Traineeship Programme and Two Candidates completed their Studentship.
(d)
The official website of AU Bioinformatics Centre (www.bifaumlr.com) has been renewed for further updating the activities of centre.
(e)
Based on the work carried out at the Centre, Two papers have been published in reputed international journals and two papers have already communicated.
(f)
The Antivirus Package “Kaspersky” is renewed and some advanced version of application software were installed for research work.
(g)
A new workstation with linux operating system procurement is under process for carrying computations in research areas related to protein modeling, ligand docking and simulation.
(h)
One MB meeting was scheduled and undertaken on 18th December 2012: Resolved to convert one Traineeship to Studentship programme.
Major Research activities in biotechnology and its related fields : Major Research activities in Biotechnology and its related fields are clustered around the fields of Protein Structure Prediction, Molecular Modeling, Protein-protein and Protein-ligand Interaction, Molecular Dynamics & Simulation, In silico Drug designing, Marine Bioinformatics, Application of computational tools and Techniques to analyze, visualize and interpret sequence, structure and gene expression data on a large scale.
Area of specialization of the centre:
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Structure Prediction, Molecular Modelling & Computer Aided Drug Designing
Marine Biodiversity and Molecular Phylogenetic Analysis,
Marine Bioinformatics
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Infrastructure facilities in the bioinformatics centre A. Computer & Communication Facility Computer Hardware: HP Smartstart (Set up and Installation for Proliant ML and DL 300,500 and 700 Series and Proliant BL Servers - 1 No HP Proliant ML110G5 Server - 1 No CLC Genomics Server Machine – 1 No HP v185e Computers with LCD Monitors - 12 Nos HP Laser jet M15222MFP Series PCL 6(Scanner cum Printer) -1 No Xerox Work centre 5020/B (Copier cum Printer) -1No HP DeskJet D4368 (Printer) -1 No 5.0 KVA online UPS system with 20 Nos. Batteries -1 No Communication facility: a. Centre was functioning with 250mbps BSNL Broadband connection. b. Telephone with STD & Fax facility. B.
Scientific software Packages: i.
Licensed Scientific Software: CLC Genomics Workbench & CLC Main Workbench
ii.
Licensed System Software: Windows 2008 server with License 10 user, Microsoft Windows Vista Business, Linux Operating System Licensed Application Software: MS OFFICE 2003 & 2007, Antivirus Package: Kaspersky Internet Security 2012
iii.
Application Software: Macromedia Dreamweaver 8, Macromedia Flash 8, Selteco (Menu Maker, Banner, Flash Design), Adobe Reader 8.0, Adobe Photoshop 7.0, Adobe Page Maker 7.x, Fine Reader OCR 7.0. Some software which are free for academicians have been installed for our research work – RASMOL, Cn3D, Pymol, SPDV, Clustal X, Python, MODELLER, MGL tool, Aurguslab, HEX, Autodock, Hyperchem, Vega ZZ, PHYLIP, FigTree etc......
Staff members associated with the Centre: NAME K. Umadevi
DESIGNATION Coordinator
Period of Working Since November, 2008
Ms. Subhalaxmi Nayak Shameer Pillarisetti
Research Assistant Traineeship
Since July, 2010 Since January, 2013
Databases/ Software packages developed One Database is under development process.
AquaInfoBase: Sequence relationship between the Aqua Living system and Human Diseases based on nucleotide/protein Sequences using BioJava, JSP and Oracle.
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Papers published or presented in the conferences with reference: 1.
Subhalaxmi Nayak, Umadevi K. and Reddy M. N. (2011) In silico retrieval of novel genes using SAGE Genie and comparative modeling of immunoglobulin lambda locus (IGL@) gene: a potent target of lung. International Journal of Bioinformatics Research. 3(1): 103-113.
2.
Jagannath M, Umadevi K, Subhalaxmi N (2011) Phylogenetic analysis of mitochondrial 16s rRNA and NADH Dehydrogenase genes of Takifugu (Pisces: Tetraodontiformes: Tetraodontidae). Online Journal of Bioinformatics. 12(2):255-273.
3.
Nayak S, K. Umadevi and M. Jagannath. (2012) A virtual PfkB Mycobacterium tuberculosis H37Rv protein. Online journal of Bioinformatics. 13(2):331-359.
4.
Subhalaxmi Nayak and K. Umadevi. (2012) In Silico Comparative Molecular Phylogeny of Mitochondrial 16s rRNA And COI genes of the spiny lobster Genus Panulirus (Decapoda: Palinuridae). Journal of Advanced Bioinformatics Applications and Research. 3(3): 364-373.
5.
S. Jeevan Amos, Subhalaxmi Nayak and K. Umadevi. Poster entitled “Computational studies on Ribonucleotide Reductase Large Subunit protein of White Spot Syndrome Virus of Penaeus monodon for novel antiviral drug discovery adopting Substractive Genomics Approach was presented in Indo-UK Conference on “Shrimp Aquaculture-Challenges & Innovative Solutions” 25th-27th January 2012, organized by Dept. of Bioinformatics, Bharathidasan University, Tiruchirappalli, Tamilnadu.
6.
In Silico Computational Subtractive Genome Analyses in White Spot Syndrome Virus for drug targets identification. (Communicated)
7.
Docking Studies towards Exploring Antiviral Compounds against Ribonucleotide Reductase Large Subunit Protein of White Spot Syndrome Virus of Penaeus monodon (Crustacean: Penaeidae). (Communicated)
Details of Training/ Workshop organized and total no. of user trained:
Three days 4th training programme on “Bioinformatics: A New Frontier for Biology Teaching” was conducted for Teachers of Higher Secondary Schools and PG Colleges of Andhra Pradesh during 20th to 22nd July 2012. Total no. of User trained: 20 (twenty).
Scheduled to organize the 2nd National Workshop on “Protein and Nucleotide sequencing: Application in Mapping the Marine Biodiversity” from 11th February to 14th February 2013 for Research Scholars of Marine Sciences. (In take of 25 Participant Research Scholars).
Scheduled to organize the 5th training programme on “Introduction to Molecular Modelling and Drug Designing in March 2013.
Types of service provided:
Six month Training for Studentship & Traineeship candidates.
Facility & guidance to Bioinformatics students for dissertations towards the partial fulfilment of the award of Master degree.
Training programmes for staffs & students of AU and staff & students of other nearby educational institutions.
Literature search by means of CD ROM and Internet.
Initiation of R & D activities in Bioinformatics: Current research activities focused on identification of drug targets for various human pathogens, computerized protein modelling, Docking Studies, Phylogenetic Analysis and Gene Analysis & Expression. The research activities were also extended towards developing databases and Pharmacophore Analysis of Marine Drugs basically who are having antibacterial and antiviral activity.
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Impact shown : The BIF is assisting research scholars and students of Life Science Departments of Andhra University in updating their knowledge in Bioinformatics by offering projects and hands-on training programme through bioinformatics resources available in the centre.
Proposed Future Activities: The Centre envisages— (a)
To Strengthen the R&D activities in the areas of Marine Drug Design using pharmaco-informatics and development of database on Marine drugs.
(b)
To initiate Research work in collaboration with researchers of different Departments
(c)
To organize workshops, Guest lectures, Training programs for familiarizing the application of Bioinformatics in Biology teaching and learning activities for teachers, Scientists, Research scholars and students to accomplish the tasks in Bioinformatics.
(d)
Further improvement of infrastructural facilities.
(e)
To publish ongoing research work related Marine diversity in reputed Bioinformatics Journals.
Contact details:
Name of the Coordinator
:
Dr. K. Umadevi
Postal Address
:
DBT – BIF Programme, Dept. of Marine Living Resources, Andhra University Visakhapatnam – 530 003, Andhra Pradesh.
Website
:
http://www.bifaumlr.com
Phone Number
:
0891- 2719121, (M): 09490794422
E-mail
:
[email protected],
:
[email protected]
:
Coordinator as above
Name of the Contact Person(s)
Bio Informatics Infrastructure Facility (BIFs)
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Assam Agricultural University, Jorhat Coordinator: Prof. Mahendra Kumar Modi Summary of the progress made by the centre from its inception: Since, its inception in 1990, the Sub-DIC at Assam Agricultural University, Jorhat has developed good infrastructure (including Hardware and software) for Bioinformatics research. In addition to supporting the core biotechnology research area the center has also started working on core bioinformatics research. Major research activities in biotechnology and its related fields at your institution: Agricultural Biotechnology
Area of specialization: Plant Transformation, Marker Assisted Breeding, Microbial Biotechnology, Medicinal and Aromatic Plants, Plant Molecular Biology
Major achievements made during 2012-13: A software pipeline for mining of Simple Sequence Repeats (Microsatellites) from raw EST data was developed published and made available to bioinformatics research community, which is freely available at http://bioinfo.aau.ac.in/ESMP.
Infrastructure facilities in the Bioinformatics Centre: Hardware: 1.
Sun High Performance Cluster -1
2.
Servers – 2
3.
Storage Server – 1
4.
Sun Workstation – 2
5.
Apple iMac – 3
6.
PCs – 30 (of various vintage)
7.
Printers, Scanners, Plotters, Switches, routers etc
Software: 1.
Discovery Studio3.5 (Molecular Modelling whole package for modelling and simulation)
2.
CodonCode Aligner (CodonCode Corp. USA) (For sequence assembly and alignment)
3.
DNASTAR Laser Core Suit and SeqMan NGen ( A Comprehensive package for DNA, RNA, and Protein sequence analysis and next generation sequence analysis)
4.
PAUP4.0 (SinaUer Assoc. Inc., Publ.) (Package for phylogeny analysis)
5.
MapQTL6.0 (A complete package for QTL analysis)
6.
Exome Horizon (25 user)
7.
Bio Linux 6.0 and 7.0
8.
SPSS 12.0
Internet Connectivity: The University is connected through National Knowledge Network (NKN) via a GBPS level fiber backbone, which the center also enjoys. On top of that the center also has access to a 5 MBPS Airtel leased line through a DeitY funded project
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Details about Staff members working in the centre: Sl. No. 1.
Name Dr. S. Singh
Designation Assoc Professor – cumInformation Officer
Specialization Genetic Engineering
Working Since 1990
Status
Educational activities : The Center imparts two 3(three) credit hour courses on for the Masters and PhD students of the university. The center also organizes workshop and hands-on training programmes for research scholars
Papers/ published or presented in the conferences : A.
B.
Core Bioinformatics area a.
B Dehury, K Sarma, R Sarmah, J Sahu, S Sahoo, M. Sahu, P Sen, M K Modi, G D Sharma, M D Choudhury, M Barooah (2012) “In silico analyses of superoxide dismutases (SODs) of rice (Oryza sativa L.)”. Journal of Plant Biochemistry and Biotechnology, DOI: 10.1007/s13562-012-0121-6
b.
Sarma K, Dehury B, Sahu J, Sarmah R, Sahoo S, Sahu M, Sen P, Modi MK and Barooah M. (2012) “A comparative Proteomic Approach to Analyse Structure, Function and Evolution of Rice Chitinases: A Step towards Increasing Plant Fungal Resistance”. Journal of Molecular Modeling, DOI 10.1007/s00894-012-1470-8.
c.
Sarmah R, Sahu J, Dehury B, Sarma K, Sahoo S, Sahu M, Barooah M, Sen P and Modi MK. (2012) “ESMP: A highthroughput computational pipeline for mining SSR markers from ESTs”. Bioinformation. 8(4): 181-184.
d.
Sahu M, Sahu J, Sahoo S, Dehury B, Sarma K, Sarmah R, Modi MK, Sen P and Barooah M. (2012). “An approach to delineate primers for a group of poorly conserved sequences incorporating the common motif region”. Bioinformation. 8(4): 206-208.
e.
Sahu J, Sarmah R, Dehury B, Sarma K, Sahoo S, Sahu M, Barooah M, Modi MK and Sen P. (2012). “In silico Mining for SSRs and FDMs from Expressed Sequence Tags of Camellia Sinensis”. Bioinformation. 8(6): 262-266.
f.
Sahu J, Sen P, Choudhury MD, Barooah M, Modi MK and Talukdar AD. “Towards an efficient computational mining approach to identify EST-SSR markers”. Bioinformation (2012) 8(4): 201-202.
g.
Phukon M, Namdev R, Deka D, Modi MK, Sen PPhukon M, Namdev R, Deka D, Modi MK, Sen P. Construction of cDNA library and preliminary analysis of expressed sequence tags from tea plant [Camellia sinensis (L) O. Kuntze]. Gene (2012) 506(1) 202-206
Other areas of Biotechnology: 15 (Fifteen) articles were published in other areas of Biotechnology.
Initiation of R&D activities in Bioinformatics: Currently we are working in the following R&D areas in the centrea.
Comparative Analysis of ADP-Glucose Pyrophosphorylase gene to understand the mechanism of enzyme regulation and design novel enzyme with enhanced features
b.
Computational Mining and Survey of Simple Sequence Repeats (SSR) and Single Nucleotide Sequence (SNP) in Expressed sequence tags of commercially important plants.
c.
Bioinformatics approaches for identification and characterization of resistant/ Avirulence gene in the crop genome with potential role in increasing their disease resistance
d.
Design and development of optimized computational tools for rational design of siRNA and prediction of miRNA along with their targets for development of RNAi mediated strategies in plants
Details of Training/Workshop organized and total no of user trained Organized a training on “Sequence Analysis and interpretation” and 30 no. of students were trained during November, 2012
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Impact shown by the Centre: The center has shown impacts in terms of research publication by the center as well as by the Biotechnology research group of the institution. software tools: The center has also developed a software pipeline named “EST-SSR-MARKER PIPELINE (ESMP)”. This pipeline integrates EST pre-processing, clustering, assembly and subsequently mining of SSRs from assembled EST sequences. The mining of SSRs from ESTs provides valuable information on the abundance of SSRs in ESTs and will facilitate the development of markers for genetic analysis and related applications such as marker-assisted breeding. The database is available for free at http://bioinfo.aau.ac.in/ESMP.
Proposed activities for 2013-14 1.
To provide services to the scientific community of NE India
2.
Organize National Workshop/Symposia on Bioinformatics for teachers, scientists and research scholars of this region.
3.
Databases on Avr/R gene and ESTs and other markers of plantation crops in progress and will be completed.
4.
The existing databases created earlier will be converted to web-accessible format so that these can be made available online.
Contact details:
212
Name of the Coordinator
Prof. M. K. Modi
Postal Address
Dept of Biotechnology, AAU, Jorhat - 785013
Phone Number
+91-376-2340095
Fax No.
+91-376-2340001
Email
[email protected],
[email protected]
Website
Bioinfo.aau.ac.in
Name of Contact Person
Prof. M.K. Modi
Bio Informatics Infrastructure Facility (BIFs)
February 03-04, 2011
XXIVnd All India BTISnet Coordinators’ Meeting
Assam University, Silchar Coordinator: Prof. M. Dutta Choudhury Summary of the Progress made by the centre from its inception: Bioinformatics Centre of Assam University, Silchar came into existence in the year 2008 with full financial assistance from Department of Biotechnology, Govt. of India under DBT-BIF scheme. Since its birth, the centre is actively engaged in teaching and research in the different fields of Bioinformatics. Realizing the need of incorporation of Bioinformatics tools in Life Sciences research, The Department of Life Science, Assam University took special initiative to establish this centre. In January 2009, the Bioinformatics Laboratory was inaugurated by Hon’ble Vice Chancellor Prof. Tapodhir Bhattacharjee. The centre organizes seminars, workshops and training programmes from time to time to popularize Bioinformatics in this region and the entire northeast as a whole. The main thrust area of research of the centre is Computer Aided Drug Designing. Teachers and researchers carry out intensive research in the field of drug designing from natural products with the help of Bioinformatics tools.
Major research activities in Biotechnology and its related fields at your institution: As Assam University, Silchar is located in one of the 25 biodiversity hotspots of the world, the major research activities focus on the rich biodiversity of the region. The main thrust area of research in Bioinformatics Centre is Natural Product based Computer Aided Drug Designing. In addition to these, Ethnobotany and Medicinal Plants, Natural Products, Cancer Genetics, Microbial Ecology, Stress tolerance in crop plants, antibiotic resistance etc. are different research fields in the university. Area of specialization: Natural Product based Computer Aided Drug Designing
Major achievements made during 2012-13: Organized a Training programme on “Statistical Tools in Biological Research” from 7th to 12th April 2012, where major focus was on QSAR studies. Several papers were published in impact factor journals during 2012. The total impact factor for eight (08) such papers is 11.3. Moreover, the centre is developing a database of ant diabetic phytochemicals.
Infrastructure facilities in the Bioinformatics Centre: Hardware Facilities IBM System x3650 High End Server IBM System x3650 Medium End Server Dell Precision T3500 Workstation SHARP 42” Professional Display Unit with smart PC Dell OptiPlex Desktop PCs SHARP Photocopier machine APC 3KVA online UPS with 1Hr. Backup Colour Printer/ Flatbed scanner HP Desktop PCs HP N6350 Network scanner HP CP1515n color network laser printer Sony NEX-5 Digital SLR camera Sony Video Camera HP 64 bit Desktop PC *
Bio Informatics Infrastructure Facility (BIFs)
01 no. 01 no. 01 no. 01 no. 10 nos. 01 no. 02 nos. 1 each 04 Nos. 01 no. 01 no. 01 no. 01 No. 01 No.
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Software Facilities Windows 2008 Server SE RedHat Enterprise Linux 5.0 SE MS SQL Server 2008 SE Visual Studio 2009 BioSolveIT FlexX MS Office QuicHeal Admin Console Antivirus 2011 AutoDock, Dock, Modeller, BioEdit, Clustal w, Clustal X, Chimera, Hex, PHYLIP, MEGA etc MATLAB Basic with Bioinformatics, SimBiology, Neural Network and Statistics Toolboxes * PAUP 4.0 * Statistica * Genious Pro 5.6.5 * ChemOffice 2010 *
01 no. 01 no. 01 no. 01 no. 01 no. 10 nos. 15 nos. Academic Licenses 02 nos. each 01 No. 01 No. 02 Nos. 01 No.
* New Hardware and Software procured in 2011-2012.
Details about Staff members working in the centre: Sl. No. Name 1. Dr. Pankaj Chetia
Designation Specialization Research Associate Computer Aided Drug Designing
Working Since Status Oct. 2009 Temporary
Educational activities The centre organizes training programmes and workshop on different aspects on Bioinformatics on regular basis. Moreover Assam University offers one PG Diploma in Bioinformatics and M.Sc. in Life Science & Bioinformatics where students regularly utilize the facilicities at BIF laboratory.
Papers/ published or presented in the conferences :
214
1.
Manabendra Dutta Choudhury, Pankaj Chetia, Karabi Dutta Choudhury, Anupam Das Talukdar and Mohan Datta-choudhari (2012). Atherogenic effect of Arecoline: A computational study. Bioinformation. 8(5):229-232. (Impact Factor: 1.15).
2.
Rupjyoti Saikia, Manabendra Dutta Choudhury, Anupam Das Talukdar and Pankaj Chetia (2012). An in silico insight into molecular mechanism of hypoglycemic rctivity Of Scoparic Acid D, a diterpenoid from Scoparia dulcis L. Asian Journal of Pharmaceutical and Clinical Research. 5(Suppl.2):153-158. (Impact factor: 0.7).
3.
Abhishek Chowdhury, Pradip Dey, Shantanu Sen, Pankaj Chetia, Manabendra Dutta Choudhury and Gauri Dutta Sharma (2012). An in silico appraisal of few bioactive compounds against kas-a for antitubercular drug efficacy. Asian Journal of Pharmaceutical and Clinical Research. 5(1):60-62. (Impact factor: 0.7).
4.
Sanjoy Singh Ningthoujam, Anupam Das Talukdar, Kumar Singh Potsangbam, Manabendra Dutta Choudhury (2012). Challenges in developing medicinal plant databases for sharing ethnopharmacological knowledge. Journal of Ethnopharmacology. 141(1):9-32. (Impact Factor: 3.014).
5.
Abhishek Chowdhury, Paulomi Paul, Pankaj Chetia and Manabendra Dutta Choudhury (2012). Screening of Few Epoxides as mt-MAPK Inhibitor Preventing Granuloma Formation to Serve as Tubercular Antidote. Letters in Drug Design & Discovery.10(2): 164-168. (Impact Factor: 0.872).
6.
Sanjoy Singh Ningthoujam, Anupam Das Talukdar, Kumar Singh Potsangbam, Manabendra Dutta Choudhury (2013). Traditional uses of herbal vapour therapy in Manipur, North East India: An Ethnobotanical Survey. Journal of Ethnopharmacology. 141(1):9-32. (Impact Factor: 3.014).
7.
Abhishek Chowdhury, Shantanu Sen, Pradip Dey, Pankaj Chetia, Anupam Das Talukdar, Amitabha Bhattacharjee and Manabendra Dutta Choudhury (2012). Computational validation of 3-ammonio-3-(4-oxido-1H-imidazol-1-
Bio Informatics Infrastructure Facility (BIFs)
February 03-04, 2011
XXIVnd All India BTISnet Coordinators’ Meeting
ium-5-yl) propane-1, 1-bis (olate) as a potent anti-tubercular drug against mt-MetAP. Bioinformation. 8(18):875880. (Impact Factor: 1.15). 8.
M. Dutta Choudhury, Monjur Ahmed Laskar, Shuvasish Choudhury and Pankaj Chetia (2013). Molecular mechanism of analgesic action of solanoglycosydane – An in silico study. Asian Journal of Pharmaceutical and Clinical Research. 6(1):80-82. (Impact factor: 0.7).
Initiation of R&D activities in Bioinformatics: The staff members of BIF are actively engaged in Bioinformatics researches. A good number of publications have already been made from BIF. Many Ph.D. sholars registered under Department of Life Science & Bioinformatics in Assam University are carrying out researches in the field of Bioinformatics from BIF. Moreover, the centre has taken initiative to apply for Major Research Project on Bioinformatics. PGDBI students of Assam University do one semester dissertation on Bioinformatics.
Details of Training/Workshop organized and total no of user trained Impact shown by the Centre: Title of the Workshop/ Training Organized Statistical Tools in Biological Research
Date of the Event 07-12 April 2012
Number of participants 48 Nos.
The Bioinformatics Centre has shown remarkable progress in last five years. A good numbers of pure Bioinformatics papers have been published from the centre. The centre is developing a database on anti-diabetic phytochemicals which will be made available online soon. The centre is creating its own identity in the region. Also the centre has produced a number of skilled manpower in the field of Bioinformatics by organizing Trainings and Workshops.
Proposed activities for 2013-14 1.
Training programme for BINC aspirants from 11th to 16th February 2013.
2.
Workshop on Artificial Neural Network in Drug Designing in February 2013.
3.
National Seminar on Contemporary Bioinformatics Research in India on 10th and 11th Nov 2013.
4.
DBT, Govt. of India entrusted BIF, Assam University to hold the 6th NEBINet Meet at Assam University.
Additional details: Name of Coordinator
:
Prof. M. Dutta Coudhury
Address
:
Bioinformatics Centre 1st Floor, Department of Life Science & Bioinformatics Assam University, Silchar-788011 Assam, India Phone/Fax: +91-3842-270920 Mobile: +91-94351-73637 email:
[email protected] [email protected] Website: www.bioinfoaus.ac.in
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Awadhesh Pratap Singh University, Rewa Coordinator: Dr. U.K. Chauhan Summary of the Progress made by the centre from its inception: The Department of Computer Science, the nodal department for BIF, was established in 1990 by the University Grants Commission (UGC) with the basic aim to serve students of Vindhya Region with job oriented courses & enable research in Computer/ IT related field by creating experimental laboratories & exploring frontiers areas in the IT related field. The Department offers M.Sc. in Information Technology & Computer Science, M.Phil & PhD programme in Computer Science. Bioinformatics is a newly emerging interdisciplinary research area which serves as link between biological and computational sciences. In view of the increasing demand and requirement of trained manpower in the area of Bioinformatics, Department of Computer Science, A.P.S. University Rewa, started M.Sc. Bioininformatics & Advanced Post Graduate Diploma in Bioinformatics (APGDBI) under self supporting program from the academic session 2004-2005 & 2005-2006 respectively, the later one under UGC innovative program. Apart from this M.Sc. In Biotechnology, Microbiology, Biochemistry courses are also being run under the canopy of faculty of life science & collaborative interdisciplinary academic activities (teaching & research) are encouraged within the Department. The Bioinformatics Centre, Department of Computer Science, A.P.S.U, has played pivotal role in creating research interest among the students on problems related to bioinformatics. Computational Biology (Artificial Intelligence, Machine Learning Techniques, and Data Mining Techniques in Biological domain) is one of the focus interdisciplinary research areas of this Centre. Many students from Computer Science/Biotech/biochemistry have completed their Ph. D. on problems related to bioinformatics. M.Phil students are also encouraged to pickup problems based on computational biology for their dissertation. More than 20 research papers have been published/ presented nationally / internationally by faculty/ research students/M.Sc. students of the Department of Computer science. Apart from this more than 50 papers have been published/ presented by the faculty/ researchers from the centre of biotechnology and biochemistry who work in collaboration with the Centre. Research work carried out was presented in international level conference held at Portugal 2005 & in USA 2007. (See Annexure). More than 100 major/minor projects has been completed by students of Centre for Bioinformatics, Dept. of Comp. Sc. , A.P.S. University, Rewa .To enhance the ICT support in education, a digital library consisting of e-books, ppts and pdfs of lectures of eminent professors from all over the word has been compiled based on the curriculum of the course. In order to expose student to the state of the art, collection of NPTEL video lectures of eminent professors/ scientists from IITs, IISc, and universities like MIT, Stanford, California, Berkley etc. is made available in a virtual classroom.
About DBT BIF program: The Department was funded under DBT BIF scheme in 2007 (Implementation for which could be initiated in Sep, 2011 only) to promote teaching & research in bioinformatics.
Major research activities in during 2012:
Ph.D. Thesis submitted during 2012 on relevant area Thesis Title
Submitted by
A novel bioinformatics based approach towards analysis of alternative splicing in chromosome i of the nematode caenorhabditis elegans Studies on oncolytic effect of vp3 gene/apoptin on malignant tumor of animal origin Studies on natural genetic diversity in indian major carp cirrhinus mrigala (hamilton) using mitochondrial and nuclear dna markers studies on natural genetic diversity pn indian major carp, labeo rohita (hamilton ) using mitochondrial dna and nuclear dna (microsatellite) makers
216
Date/ Year
Lav Kashyap
Submitted to (Under The Supervision of) Dr. U.K. Chauhan
Priyanka Pandey
Dr. U.K. Chauhan
2012
Prachi Masih
Center for Biotechnology Studies
2012
Rupesh Kumar Luharia
Center for Biotechnology Studies
2012
Bio Informatics Infrastructure Facility (BIFs)
2012
February 03-04, 2011
XXIVnd All India BTISnet Coordinators’ Meeting Preparation , purification and characterization of pegylated rhg-csf Development of molecular makers using aflp fingerprinting in mahseer species Modulating effect of hepcidin tfr and hfe gene mutation on the phenotype of iron deficiency anemia patients Association ofgenetic polymorphisms in slc11 al (nramp1 ), vdr and tnf-a genes with paediatric tuberculosis Exploring novel machine learning techniques for the study of biological networks Improved heuristic techniques for protein structure prediction A novel pentoid algorithm for the prediction of protein- protein interaction using svm classifier Development of predictive model for recurrent of breast cancer disease using weka Development of predictive model for diabities for pregnant women using data mining tecnique Towards development of web based erp of APS University Application of machine learning technique to develop predictive model for mallgnancy in breast cancer Invertigation of novel encoding strategy to construct future vectore for prediction of ppi using of neural networks. Evaluation of antidiabetic potential of aloe vera on streptozotocin induced diabetic rat Isolation and characterization of multi drug resistant patogens isolated from different hospital areas in Rewa district
Krishna Nand Tiwari
Dr. U.K. Chauhan
2012
Dhirendra Pratap Singh
Co Supervision ofDr. U.K. Chauhan
2012
Sanjay Kumar Pandey
Co Supervision of Dr. RM. Mishra Vice Chancellor DR. U.K. Chauhan
2012
Bpndi Das M.S.
2012
Garima Shrivastava
Dr. Navita Srivastava
2012
Sudhansu Shrivastava
Dr. Navita Srivastava
2012
Deepak Pandey
Dr. Navita Srivastava
2012
Vandana Singh
Dr. Navita Srivastava
2012
Reeta Dwivedi
Dr. Navita Srivastava
2012
Bheem Singh
Dr. Navita Srivastava
2012
Suneeta Singh
Dr. Navita Srivastava
2012
Pradeep Kumar Sharma
Dr. Navita Srivastava
2012
Shefali Paliwal
Dr. U.K. Chauhan
2012
Shalini Singh
Dr. U.K. Chauhan
2012
Area of specialization: Computational Biology (Artificial Intelligence, Machine Learning Techniques, and Data Mining Techniques in Biological domain) is one of the focus interdisciplinary research area of this Centre. Apart from this research work of international repute in the field of Medical & Molecular biotechnology/bioinformatics is also going on. Major achievements made during 2012-13: To strengthen the collaborative work A new team consisting of Coordinator: Prof U.K. Chauhan, from Biotech & Coordinators Dr. Navita Shrivastava from Computer Science & Dr. R.N. Patel from Biochemistry has been constituted. Procurement & Installation of the equipment purchased from BIF Grant. (Permission to carry forward for the balance amount is in process). 1.
Extension for XII plan is granted.
2.
Introduction of Bioinformatics as a paper in M.Sc. IT Course.
3.
Fifteen M.Phil Dissertation submissions on problems related to bioinformatics.
4.
Eight Ph.D. Thesis submission on problems related to the field.
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Five research papers published.
6.
Strengthening E-Library & Virtual Class Room Facility.
February 03-04, 2013
Infrastructure facilities in the Bioinformatics Centre: Computer & Communication facility:The Bioinformatics Centre is now fully equipped with 10 Intel core i3 system connected through network and BSNL 512 kbps broadband Connection,, 1 heavy duty Scanner( series HP Scanjet N9120), UPS ,photocopier (Canon image runner 2420L), LCD Projector, off line Video lectures.
Details about Staff members working in the centre: None so far. The centre is being run only with the assistance of regular staff of the associated Departments of the University.
Educational activities Ph.D. In the relevant area, one paper on Bioinformatics has been introduced in the M.Sc. (IT) course running in the Department of Computer Science in current session. M.Phil students are encouraged to do there dissertation work on problems related to computational Biology/Bioinformatics. So many Bioinformatics tools have been used in various research works in the Department of Biotechnology.
Papers/ published or presented in the conferences: Paper published:Garima Srivastava, Navita Srivastava. Gulshan Wadhvva. “Neural Network Model for Prediction of PPI using Domain Frequency & Association Score Base Classification of Protein Pairs”, International Journal of Advanced Research in Computer Science (1JARCS). Vol. 3. No. 3 (May-June 12), pp. 234-238, ISSN No. 0976-5697, 2012 1.
Rupesh K. Luhariya, Kuldeep K. Lai, Rajeev K. Singh, Vindhya Mohindra, Peyush Punia, U. K. Chauhan, Arti Gupta, W. S. Lakra. Genetic divergence in wild population of Labeo rohita (Hamilton, 1822) from nine Indian rivers, analyzed through MtDNA Cytochrome b region
2.
Tiwari P, DwivediR, Mansoori N, Alam R, Chauhan UK, Tripathi M, Mukhopadhyay AK. Do gene polymorphism in IL-ip, TNF-a and IL-6 influence therapeutic response in patients with drug refractory epilepsy? 2012 Epilepsy Research.101, 261—267
3.
Singh A, Sood N, Chauhan UK, Mohindra V. EST-based identification of immune-relevant genes from spleen of Indian catfish, Clarias batrachus (Linnaeus, 1758). Gene. 2012.502(1):53-
4.
Akanksha singh, Neeraj sood, U.K. Chauhan, Vindhya Mohindra (2012). EST- Based identification of immunerévèlent genes from spleen of Indian catfish, Claris batrachus (Linnaeus, 1754
Initiation of R&D activities in Bioinformatics: Though Research work is being done on problems related to computational Biology/Bioinformatics/Biotechnology, but the degree awarded is in computer Science/Life Science. An effort is being done to provide students Ph.D. In Bioinformatics from the BIF Centre of A.P.S.U. Rewa. As this University is running M.Sc. Bioinformatics course also which was suspended due to lack of resources in past few years but with the assistance of BIF infrastructure will commence from the coming session 2013-14.
Details of Training/Workshop organized and total no of user trained Following workshop & Short term training program was organized during 2012. 1.
“DBT Sponsored National Workshop on Machine Learning & Data Mining Techniques in Bioinformatics between lst-4th March 2012”.
2.
“Learning Bioinformatics Tools and Programming Techniques for Teaching and Research Purpose between 9th 21slJanuary 2012, Sponsored by DBT New Delhi*’
During this Training/Workshop 70 teachers/researchers/students were trained.
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Impact shown by the Centre: Center has organized workshop on Data Mining and Machine Learning Techniques in bioinformatics and also a workshop for teachers and researchers to make the aware of Tools and Programming Techniques for Teaching and Research Purpose. Two project works have been completed that was funded by DBT and MPCST and one project is running that will be completed in this current year under the supervision of Dr. U.K. Chauhan.
Proposed activities for 2013-14
Utilization of balance amount of XI Plan & implementation of XII Plan
Restart the M.Sc Bioinformatics course which was suspended in past two years due to lack of resources.
Proposal to start M.Phil In bioinformatics under SSP.
Commencement of Ph.D. In Bioinformatics.
Organizing workshops, training Programs & seminars on bioinformatics.
Generating resources to provide traineeship to students for their Project.
Submission of Research project to various funding agencies.
Contact details:
Name of the Coordinator
Dr. U.K. Chauhan
Postal Address
Dept. of Biotechnology, A.P.S.U. Rewa(M.P.)
Phone Number
+91-9893488375
Fax No.
+91-7662-233318
Email
chauhanuiiirediffmail.com
Website
http://apsurewa.ac.in/
Name of Contact Person
Dr. U.K. Chauhan,
Dept. of Biotechnology, A.P.S.U. Rewa (M.P.)
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Berhampur University, Berhampur Coordinator: Prof. (Mrs) U.R.Acharya Summary of the progress made by the centre from its inception: Berhampur University is the only University in Southern Odisha catering the demand of higher education in various fields’ right from its inception in the year 1967. It is not only catering the demands of higher education of Odisha, but the students from all neighboring states are equally benefited. The University is having various full time courses at Masters and Doctoral level. This University has started M.Sc in Biotechnology course in the year 2005.The major changes in the academics all over the globe opened new frontiers to understand life science in detail. Fulfilling the demand of this change, BIF Centre was sanctioned to Berhampur University by DBT, Govt. of India, New Delhi. Presently the Centre is established in the Dept. of Zoology, Berhampur University and is engaged in many academic activities leading to popularization and understanding of Bioinformatics and its importance in biological Science. The BIF Centre provides learning and training in Bioinformatics to the science students, scholars & teachers of the university and affiliated colleges. The main aim of our center is to create professionals, teachers and scholars in the field of Bioinformatics.
Major research activities in biotechnology and its related fields at your institution: Culture, isolation and screening of bacteria, Development of fish chromosome database. Area of specialization: Bioinformatics and Computational Biology
Major achievements made during 2012-13:
The Centre has its Webpage and online databases with url: www.bubif.ac.in .
Providing the Computational facility to the faculty members, scholars and students
Mr. S.K.Behera- Thesis submitted for the award of Doctor of Philosophy in Bioinformatics.
Infrastructure facilities in the bioinformatics centre: Hardwares and softwares for the BIF centre were procured as per DBT specifications.
Details about Staff members working in the centre: Sl. No. Name 1 Prof. (Mrs) U. R. Acharya 2 Mr. Santosh K. Behera
Designation Specialization Period of Working Absorption status Professor and Histo-Biochemistry Since 1985 Permanent Coordinator Research Associate Bioinformatics & Since Jan 2008 Temporary Computational Biology
Educational activities Students undergone their M.Sc project work (dissertation) in this Centre 1.
Mr. Saroja Kumar Pradhan- Comparative Proteomics of Blue-green algae and Green algae by using SDS-PAGE Analysis.
2.
Mr. Amar Ranjan Mistiri- Comparative proteomics of two different fishes by using SDS-PAGE Analysis.
3.
Mr. S.K. Tariquddin- Extraction of Agar from a red Seaweed Gracilaria verrucosa
Papers/ published or presented in the conferences :
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1.
*U.R.Acharya, S.K.Behera, M.K.Panda & S.K.Pradhan (2012). Proteomics of Blue - Green Algae & Green Algae through SDS-PAGE analysis. Emerging Science Journal.,4(11):14-18.
2.
*U.R.Acharya, S.K.Behera, M.K.Panda (2012).“Bioinformatics Analysis for Identification and Structure Prediction of Transmembrane Mucins” Emerging Science Journal., 4(11):1-4.
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Acharya U.R et al. (2012).“Cadmium Toxicity On Spermatogenesis And Its Amelioration By Vitamins” was presented in the “International Symposium on Environmental Impacts, Health Implications and Therapeutic Approaches” (ISEHT-2012) Organized by Dept. of Zoology, Vikrama Simhapuri University, Nellore (Andhra Pradesh), from 15th – 17th July, 2012.
Initiation of R&D activities in Bioinformatics: Structure prediction and homology modeling of proteins using bioinformatics tools and techniques.
Details of Training/Workshop organized and total no of user trained Date
Programme
21/03/12 and 22/03/12
A two days Workshop-Cum-Training programme On “Biotechnology and Bio-informatics Tools and Techniques”
Participants Teachers, research scholars & students
Impact shown by the Centre: Strengthening Biology Teaching using Bioinformatics Tool, organizing workshops on different aspects of Bioinformatics.
Proposed activities for 2013-14 i)
To organize hands on training, workshops and short term training programmes for utilizing the applications of Bioinformatics in biology teaching.
ii)
To establish collaboration with other institutions and BTISnet centres for information resources and expertise.
iii)
Development of on-line databases
Contact details:
Name of the Coordinator
Prof. (Mrs)U.R.Acharya
Postal Address
Coordinator, BIF Centre, Berhampur University, Berhampur, Dist-Ganjam (Odisha),PIN-760007
Phone Number
+91-9937615425/9437722099
Fax No. Email
[email protected] Website
www.bubif.ac.in
Name of Contact Person
Prof. (Mrs)U.R.Acharya/ Santosh Ku. Behera
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Bharathiar University, Coimbatore Coordinator: Dr. P. Shanmughavel Summary of the progress made by the centre from its inception: The post graduate course in bioinformatics was commenced in Bharathiar University during 2001 for the first time in India. In endorsement of the massive research activities performed by the Bioinformatics Division, it has become an independent department of the university during the academic year 2006. The department is engaged in various innovative projects in various disciplines supported by National and International agencies like DBT, UGC & ITTO, Japan. The department also conducts M.Phil and Ph.D courses. The Postgraduate students passed out from the department were easily absorbed in various research Institutions not only in India but also in Foreign Countries. Many of our students are pursuing their Doctoral programs in countries like France, UK, Germany and Singapore. The Department of Biotechnology (DBT), India has approved a Center for Bioinformatics for the establishment of Bioinformatics Infrastructure Facility (BIF) for the promotion of Biology Teaching through Bio-Informatics (BTBI) at our Department under the Biotechnology Information System Network (BTISnet). To its credit the Department also has collaboration with the Global Forest Information Service (GFIS), Vienna, Austria to exchange research information’s and Digital Biology laboratory USA. The centre providing various communication & computational facilities to users from the university and also from other institutions. Also arranged lectures by eminent scientist working in the area of bioinformatics. Introduced new PG. Diploma programme in Cheminformatics under UGC Innovative Programme
Major research activities in biotechnology and its related fields : Data mining, Nano Science and Drug delivery, Molecular modeling and Drug Design, Comparative Genomics, Computational Biology and Biodiversity Informatics and Phytomatics
Area of specialization: a.
Teaching and Research in Computational Biology
b.
Development of Drug Database and tools for Proteomics
c.
Screening and Development and Drug
d.
Reverse Technology for Drug Discovery
Major achievements made during 2012-13: Research Schemes Awarded S. No Title 1 2
Computational Identification of promoter regions in Fungal Genomes In-silico molecular design of anti-HIV microbicides and pre-clinical evaluation
Amount Sanctioned Funding Agency Status Rs. (Laks) 11.5 UGC (2012-15) Ongoing 27
ICMR (2012)
Approved
A – One
University Fund
2001
CISCO
University Fund
2001
VSNL
University Fund
———
Infrastructure facilities in the Bioinformatics Centre:
A.
Computer & Communication facility 5KVA online UPS with 10 Nos of batteries ISDN Router ISDN Connectivity
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Sun Netraj Server
Sun Solaris
University Fund
2001
Unix based student workstation
Sun Solaris
University Fund
2001
Unix based sun enterprise server
Sun Solaris
University Fund
2001
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Sun Solaris
University Fund
2001
Panasonic
University Fund
2001
HP
University Fund
2006
HP
DBT Fund
2007
HP model DX 2180 Intel Pentium (22 nos) HP model DX 2180 Intel Pentium (11 nos)
B.
Scientific Software packages -Important computational biology software’s. 1.
Schrodinger suite 2012
2.
Sybyl Flex X
3.
CLC Work Bench
Details about Staff members working in the centre: Sl. No. 1. 2. 3.
Name N. Jayakumar Sundra Balaji Jayam
Designation Reader Lecturer Lecturer
Specialization Data Mining Structural Biology Biochematics
Working Since 2008 2008 2008
Status Permanent Permanent Permanent
Educational activities Students have participated in various seminars, conferences and academic competitions in the emerging fields of Bioinformatics conducted at National and International institutes and won prizes and added laurels to the department. All the post graduate and diploma students were easily absorbed by the Bioinformatics company and research institutions.
Papers/ published or presented in the conferences : Papers Published in Bioinformatics: 2012 1.
Ramaswamy Sathish Kumar, Aathi Muthusankar and Piramanayagam Shanmughavel (2012) A structural insight towards identify specific epitopes of phytoplasma diseases. International Journal of Pharmacy and Biological Sciences (IJPBS). V2;99-109.
2.
Lisina K.V, Gopalakrishnan V.K, Muthusankar Aathi, Murugesh Easwaran and Shanmughavel Piramanayagam (2012). International Journal of Current Research. V4;p30-35.
1.
Ramaswamy Sathishkumar, Aathi Muthusankar and Piramanayagam Shanmughavel (2012) A structural insight towards identify specific epitopes of phytoplasma diseases. International Journal of Current Research (Communicated)
2.
Anandakumar Shanmugam and Piramanayagam Shanmughavel (2011) Comparative Genomics Efficacy in Annotating Non – Coding Regions. Journal of Genetics & Genomics (under review) (IF: 1.494)
3.
Sivashankari Selvarajan and Piramanayagam Shanmughavel (2011) A Web based Database for Hypothetical Genes in the Human Genome. International Journal of Computer Applications 14 (4):0975 – 8887
4.
Oviya Iyappan Ramalakshmi and Shanmughavel Piramanayagam (2010) Mining of SSR markers from Expressed Sequence Tags of bamboo species. Bioinformation. 5(6): 240-243
2011
2010
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5.
Radhika Ramachandran and Primanayagam Shanmughavel (2010) Preparation and characterization of biopolymeric nanoparticles used in drug delivery. Indian journal of Bioichemistry & Biophysics. Vol.47,Feb 2010, pp.56-59 (IF: 0.37)
6.
C.Nilavamuthan and P.Shanmughavel (2010) Linked Open Data (LOD) - Towards Making Online Biological and chemical Data Machine Understandable. Biobytes. Vol.6.
7.
Radhika Ramachandran and Primanayagam Shanmughavel (2010) HIV/AIDS - Innovative Therapies Biobytes Vol-6.
8.
Arunmeena and P.Shanmughavel (2010) Insilco identification of novel Coding Regions from Archeal GenomeAeropyrum pernix. International Journal of Bioinformatics Research, ISSN: 0975–3087, Volume 2, Issue 1, 2010, pp-53-55
9.
C.Nilavamuthan and P.Shanmughavel (2010) Application of Semantic Web Technology to Bioinformatics. International Journal of Bioinformatics Research, ISSN: 0975–3087, Volume 2, Issue 1, 2010, pp-67-71
10.
Muthu Sankar and P.Shanmughavel (2010) Insilco Docking Analysis for viral protein – Hemaggulutinin – Neuraminidase against the Syethetic Drugs for Human Parainfluenza Virus 3. International Journal of Pharma and Bio Sciences, Volume (2)
11.
Parthiban.M, P.Shanmughavel and R.Sowdhamini (2010) In silico Point Mutations and Evolutionary Trace Analysis of Nicotinic Acetylcholine Receptors in deciphering ligand-binding surfaces. J Mol Model (IF: 2.336)
Conferences 1.
R.Sathish Kumar, Murugesh Easwaran, C.Nilavamuthan and P.Shanmughavel (2011) Molecular interaction studies of toxic proteins and neurotransmitters towards development of novel drugs for Alzheimer disease. International Interdisciplinary Science Conference (Bioinformatics: An Interface between Computer Science and Biology), November 15-17, 2011, Centre for Interdisciplinary Research in Basic Sciences, New Delhi, India
2.
Shanmugam Anandakumar, Chandrasekaran Nilavamuthan and Piramanayagam Shanmughavel (2011) Comparative Identification of Novel genes from Non Coding Regions of Plasmodium MCBIOS Conference, Making Sense of the Omics Data Deluge, will be held February 17th and 18th in Oxford, MS on the campus of the University of Mississippi.
3.
P.Shanmughavel (2011) Secondary Structure Tools Overview The Ninth Asia Pacific Bioinformatics Conference, Jan 2011, Singapore
4.
C.Nilavamuthan and P.Shanmughavel (2010) Applications of Semantic Web Technology to Bioinformatics.Eight Asia-Pacific Bioinformatics Conference – February 2010. NCBS, Bangalore.
5.
R. Radhika and P. Shanmughavel (2010) Comparative studies of protein-ligand complexes of AMD3465 and its similar compounds against the modeled receptor CXCR4. Eight Asia-Pacific Bioinformatics Conference – February 2010. NCBS, Bangalore.
6.
Muthu Sankar and P. Shanmughavel (2010) Structural Studies on Human NDRG2 protein and their interaction with Natural & Synthetic compounds: a novel drug target for Alzheimer’s Disease.Eight Asia-Pacific Bioinformatics Conference – February 2010. NCBS, Bangalore
7.
E. Murugesh and P. Shanmughavel (2010) 4 Dimensional docking procedurals with Dystrophin by different changement in Receptor and Ligand docking algorithm. Eight Asia-Pacific Bioinformatics Conference – February 2010. NCBS, Bangalore.
8.
C. Gayathri Devi and P. Shanmughavel (2010) In silico interaction studies of Endothelin receptor with its antagonists. Eight Asia-Pacific Bioinformatics Conference – February 2010. NCBS, Bangalore.
Initiation of R&D activities in Bioinformatics: Semantic Web Technology - Local Database has been started to annotate to frame the Ligands from commercially available source. And this annotation could be a possible way to proceed to find out the novel drug strategies for our in-home
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identification of whatever we research with Disease mechanism. Simple Vector Machine was established in our server machine and this is aided to work with our training and test set of protein/ligand optimization. To run the E Pharmacophore for Quantitative study, Online database has been linked with FTP Server and all the systems has put up with higher rate of retrieval from their host machine. This serves the main features to find the Energy based Pharmacophore based on its group we are concentrating. More than 250 modeled protein deposited in Protein Modeled Database from University of California, San Francisco. Developing Tool for retrieval and analysis of Quaternary Protein Structure using Java Applet.
Details of Training/Workshop organized and total no of user trained Two Days National Workshop for College Teachers, March 13 to 14, 2010 One National Level Seminar on Cheminformatics, April 2011
Impact shown by the Centre: Produced
Ph.D
- 4
M.Phil
- 8
M.Sc
- 17
Cheminformatics Programme
- 13
Published one Tamil Bioinformatics book - Uyir Thagavaliyal
Proposed activities for 2013-14 Insilco Design and Studies of Novel Microbicides in Controlling HIV and Sexually Transmitted Diseases. Development of web directory of Software related Bioinformatics. To establish a state of art ‘Digital Library’ in the areas of Environmental studies, fully searchable by field codes such as the compound, structure, toxicity, pathology, gene, gene group, SNP metabolic pathway and network.
Contact details:
Name of the Coordinator
Piramanayagam Shanmughavel
Postal Address
Marudhamalai Road ,Bharathiar University, Coimbatore - 641046
Phone Number
+919486446101
Fax No.
+91-422-2422387
Email
[email protected],
[email protected]
Website
http://www.b-u.ac.in
Name of Contact Person
Dr. P. Shanmughavel, Ph.D, D.Sc.
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CCS Haryana Agricultural University, Hisar Coordinator: Prof. Sudhir Kumar Summary of the progress made by the centre from its inception: The Bioinformatics Section, CCS Haryana Agricultural University, Hisar is an independent Section in the College of Basic Sciences & Humanities. The Section has a PG programme in Bioinformatics since 2004. A total of 88 students have graduated till date and majority of them are placed in jobs. A revised curriculum for M.Sc. Bioinformatics has been implemented from academic session 2010-11 as per the recommendations of the Indian Council of Agricultural Research (ICAR), New Delhi which includes a Masters’ Dissertation as well along with Bioinformatics as Major, Biotechnology as Minor and statistics/ computer as supporting subjects.
Area of specialization: Teaching Bioinformatics Bioinformatics in Agricultural Sciences (rice - crop of interest) Sequence analysis Multimedia Databases Virtual High-throughput Screening
Major achievements made during 2011-12: Following research projects have been carried out:
Computational Prediction of codon Bias in rice (Oryza sativa) genes Subunit subunit interaction in heterotetrameric structure of rice ADP- Glucose pyrophosphorylase
Virtual High- throughput screening of peroxisome proliferator activated receptor inhibitors
In silico identification and analysis of simple sequence repeats (SSRs) in rice (Oryza sativa) ESTs
Infrastructure facilities in the bioinformatics centre: Computer & Communication facility PCs – 35 ; Servers – 2 ; 8-Node Linux Cluster – 1 Internet connectivity – 4 MBPS Scientific Software packages - GPL software, ChemOffice, PAUP, NTsys PC, Schrodinger Suite (one year)
Details about Staff members working in the centre: Sl.No. 1. 2. 3. 4.
Name Sudhir Kumar Sunita Jain Anil Panwar Neeru Redhu
Designation Professor & Head Associate Professor Assistant Professor Assistant Professor
Specialization vHTS, Structural proteomics Sequence analysis, Molecular Modeling, teaching Programming, Databases
Working Since 2004 in Bioinformatics 2004 in Bioinformatics 2010 2011
Status Permanent Permanent Permanent Permanent
Educational activities M.Sc. Bioinformatics – started in 2004, 88 students graduated till date. UGC/CSIR NET qualified by 8 students (2009-11).
Papers/ published or presented in the conferences : 1.
226
Kaushik R, Vashist M, Jain S, Sikka V K and Sudhir Kumar (2012) Subtle Structural Differences Crucial for Function in Similarly Engineered ADP-Glucose Pyrophosphorylase Larger Subunit in Rice and Maize. J. Pl. Biochem Biotechnol. 21(2), 275-278.
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Chandni Khyalia and Deepsikha. 2012. Comparison of Online Tools for Detection of Transposable Elements. International Conference on Biotechnology, Emerging Trends. September 18-20, 2012 pp 205
3.
Ritu, Aakanksha Jain, Sunita Jain and Sudhir Kumar. 2012. Multiple Sequence alignment : Comparison and evaluation. International Conference on Biotechnology, Emerging Trends. September 18-20, 2012 pp 206.
4.
Deepshikha and Chandni Khyalia. 2012. Online Resources for rice genome annotation. International Conference on Biotechnology, Emerging Trends. September 18-20, 2012 pp 207.
5.
Savita, Sunita Jain, Anil Panwar and Sudhir Kumar. 2012. GC3 Bias Prediction in the Rice (Oryza sativa L.) Genes. International Conference on Biotechnology, Emerging Trends. September 18-20, 2012 pp 209
6.
Drishta Sharma, Neeru Redhu, Sunita Jain and Sudhir Kumar. 2012. Virtual High- throughput screening of Peroxisome Proliferator- activated receptors inhibitors. International Conference on Biotechnology, Emerging Trends. September 18-20, 2012 pp 210.
7.
Mamta Rani, Neeru Redhu, Sunita Jain and Sudhir Kumar. 2012. In Silico Identification of miRNA in Rice (oryza sativa). International Conference on Biotechnology, Emerging Trends. September 18-20, 2012 pp 211.
Initiation of R&D activities in Bioinformatics:
The PG degree (since 2010-11) has a 20 credit research and priority is for crop protection and improvement.
Details of Training/Workshop organized and total no of user trained: Nil
Impact shown by the Centre: The Centre is engaged in teaching Bioinformatics since 2004 and offers M.Sc. Bioinformatics degree. Till date, a total of 88 students have earned Masters’ degree and most of them have found employment in teaching and research. some students are pursuing Ph.D. in India and abroad.
Proposed activities for 2013-14 The on-going teaching and research work would continue.
Contact details:
Name of the Coordinator
Prof. Sudhir Kumar
Postal Address
Bioinformatics Section College of Basic Sciences & Humanities CCS Haryana Agricultural University Hisar - 125 004
Phone Number
01662-289114
Fax No.
01662-234952
Email
[email protected] ;
[email protected]
Website
http://hau.ernet.in/bioinfo
Name of Contact Person
Prof. Sudhir Kumar
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Ch. Charan Singh University, Meerut Coordinator: Prof. H.S Balyan Summary of the progress made by the centre from its inception: Ever since the creation of the BIF, the facility is open to all the biology students. We organized a workshop entitled “Databases, data mining and retrieval of information” during March 2008. Subsequently, with the help of Professor KS Gill, Washington State University, Pullman, USA, a Hands on Training-cum-workshop on Virus Induced Gene Silencing (VIGS) that involved considerable amount of bioinformatics component was conducted during December 2011. As a follow up, the second phase of the Training-cum-Workshop on VIGS was conducted during 25 February to 24 March, 2012. The Department of Science & Technology, Government of India has been supporting the travel, boarding and lodging of Professor KS Gill under the CP-STIO project. In June 2012, we also organized a three day (June 14-16, 2012) workshop on Laboratory Information Management System (LIMS) with a view to monitor, retrieve and use the laboratory information stored with the help of LIMS. During these four training programme, number of users belonging to this university and elsewhere were trained.
Major research activities in biotechnology and its related fields : Since our specialization is in the area of Genetics and Plant Breeding, we focused our research efforts on the following aspects, which also involved the application of computers and bioinformatics. (i) Study of genome-wide syntenic relationship between wheat, Brachypodium and rice. (ii) In silico digital gene expression analysis using wheat ESTs and unigenes generated following leaf rust infection. (iii) In-silico analysis of wheat orthologs of rice genes for grain related traits. (iv) Insilico analysis of wheat orthologs of dwarf4, Aux1, Pin1 responsible for dwarfness in Arabidopdsis, CCD8 gene for tiller number and Roc5 for leaf rolling in rice. (v) In silico analysis of wheat orthologs of candidate genes for mutant phenotypes. (vii) Development of molecular markers such AFLP and SSRs in jute and wheat. (viii) Development of molecular maps in wheat and also the first molecular genetic map in jute. (ix) Linkage and association mapping analysis for various traits of economic importance such as pre-harvest sprouting tolerance, grain weight as well as yield and related traits in wheat. (x) QTL analysis for fibre yield and fibre quality traits in jute and cotton. (xi) Diversity analysis in wheat and jute germplasms. (xi) Marker assisted introgression of a QTL for pre-harvest sprouting tolerance and a major genes for protein content and leaf rust resistance in wheat. (xii) Undertaking genetic mapping of stem rot resistance in Jute. Area of specialization: Genetics, Plant Breeding (including Molecular Breeding) and Bioinformatics. Major achievements made during 2012-13: (a) One month Training-cum-Workshop on VIGS was conducted during February 25-March 24, 2012. (b) Three day (June 14-16, 2012) workshop was conducted on Laboratory Information Management System (LIMS) with a view to monitor, retrieve and use the laboratory information stored with the help of LIMS. (c) Eighteen (18) research papers were published in journals of international repute (see below under serial no.8).
Infrastructure facilities in the Bioinformatics Centre: A.
Computer & Communication facility: (i)
B.
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IBM THINK CENTRE: 10 Numbers; RAM 256 DDR-2 (Make IBM additional 256 MB DDR 2 Ram): 10 Numbers; IBM TFT 17” (in lieu of 17” monitor): 10 Numbers; (ii) IBM SERVER with 2 Dual Core Processor: One Number; IBM TFT 17” In lieu of 17” monitor): One Number; (iii) IBM SERVER Intel Xeon 3.00 Ghz Dual Core Processor EM 64 T: One Number; RAM 1 GB (Make IBM additional 1GB DDR2 RAM, 2×512 MB): One Number; IBM TFT 17” (in lieu of 17” monitor): One Number; (iv) 420 CP Multifunction Xerox Machine: One Number; (v) HP Laser Jet Printer (Model 5200 series): One Number; (vi) Scanner HP 2400C: One Number; (vii) Desk Jet HP 1360 Laser Jet Printer: One Number; (viii) DELL Laptop XPS L401X, Intel (R) Core (TM) i7CPU Q740 @1.73GHz, RAM 8.0GB, 64 Bit Operating System, 600 GB Disc. (viii) High speed internet facility
Scientific Software Packages: Windows 2003 Server 10 clients: One Number; Microsoft ISA Server 2005: One Number; Microsoft Visual Studio Standard 2005: One Number; MS SQUL Server 2005 Standard: One Number; MS Office 2003: One Number
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Details about Staff members working in the centre: Sl. No. Name 1. Anuj Kumar
Designation Specialization Working Since JRF Molecular Modeling & Simulation December 2012
Status Continuing
Educational activities: (a)
Following two courses have been introduced in our M.Sc. (Genetics and Plant Breeding) programme aimed at equipping students in various aspects of the application of computers and bioinformatics in the study of genetics: (i) Computers and Bioinformatics in Agriculture, and (ii) Genomics, Trascriptomics and Proteomics
(b)
In-silico analysis of wheat orthologs of dwarf4, Aux1, Pin1 responsible for dwarfness in Arabidopdsis, CCD8 gene for tiller number and Roc5 for leaf rolling in rice was carried out. (ii) In-silico analysis of wheat orthologs of genes for nitrogen use efficiency (NUE) in rice, Arabidopsis andmaize is continuing.
Papers/ published or presented in the conferences: (a)
Papers published in journals during 2012. 1.
Balyan HS, Gupta PK, Kumar S, Dhariwal R, Jaiswal V, Tyagi S, Agarwal P, Gahlaut V, Kumari S (2012) Genetic improvement of grain protein content and other health related constituents of wheat grain. Pl Breed (in press).2. Kumar S, Goyal A, Mohan A, Balyan HS, Gupta PK (2012) Further addition to physical maps of simple sequence repeats (SSRs) in bread wheat. Aust J Crop Sci. (in press)
3.
Kumar A, Chhuneja P, Jain S, Kaur S, Balyan HS, Gupta PK (2012) Mapping main effect QTL and epistatic interactions for leaf rust and yellow rust using high density ITMI linkage map. Aust J Crop Sci (in press).
4.
Agarwal P, Kumar S, Mir RR, Balyan HS and Gupta PK (2012) Some ENU induced mutation: a resource for functional genomics in bread wheat. Plant Mutation Reports (in press).
5.
Gupta, P.K., (2012) Professor Kameshwar Sahai Bhargava, A Memoir: Indian National Science Academy, New Delhi (in press).
6.
Jaiswal V, Mir RR, Mohan A, Balyan HS, Gupta PK (2012). Association mapping for pre-harvest sprouting tolerance in common wheat (Triticum aestivum L.). Euphytica 188: 89–102.
7.
Mir RR, Kumar N, Jaiswal V, Girdharwal N, Prasad M, Balyan HS, Gupta PK (2012) Genetic dissection of grain weight (GW) in bread wheat through QTL interval and association mapping. Mol Breed 29: 963–972.
8.
Das M, Banerjee S, Topdar N, Kundu A, Mir RR, Khurana JP, Tyagi A, Sarkar D, Sinha MK, Balyan HS, Gupta PK (2012). QTL identification for molecular breeding of fibre yield and fibre quality traits in jute. Euphytica 10.1007/s10681-011-0603-y.
9.
Banerjee S, Das M, Mir RR, Kundu A, Topdar N, Sarkar D, Sinha MK, Balyan HS, Gupta PK (2012). Assessment of genetic diversity and population structure in a selected germplasm collection of 292 jute genotypes by microsatellite (SSR) markers. Molecular Plant Breeding 2: 11-25.
10.
Das M, Banerjee S, Dhaliwal R, Mir RR, Topdar N, Kundu A, Khurana JP, Tyagi AK, Sarkar D, Sinha MK, Balyan HS, Gupta PK (2012). Development of SSR markers and construction of a first generation of linkage map in jute. J. Genetics 91: 21-31.
11.
Kumar S, Balyan HS and Gupta PK (2012) Comparative DNA sequence analysis involving wheat, Brachypodium and rice genomes using mapped wheat ESTs. Triticeae Genomics and Genetics 3:25-37.
12.
Kundu, A., Topdar N, Srakar D, Sinha MK, Ghosh A, Banerjee S, Das M, Balyan HS, Mahapatra BS, Gupta PK (2012). Origins of white (Corchorus capsularis L.) and dark (C. olitorius L.) jute: a reevaluation based on chloroplast microsatellites. J. Plant Biochem. Biotechnol.DOI 10.1007/s13562-012-0165-7.
13.
Shahryar FK, Kumar A, Bassi FM, Paux E, Al-Azzam O, de Jimenez MM, Denton AM, Gu YG, Huttner E, Kilian A, Kumar S, Goyal A, Iqbal MJ, Tiwari V, Dogramaci, M, Balyan HS, Dhaliwal, HS, Gupta PK, Randhawa GS, Feuillet C, Pawlowski WP (2012) DNA repair and crossing over favor similar chromosome regions as discovered in radiation hybrid of Triticum aestivum. BMC Genomics 13: 339-362. Bio Informatics Infrastructure Facility (BIFs)
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16.
17. 18. (b)
February 03-04, 2013
Mir RR, Kumar J, Balyan HS, Gupta PK (2012). A study of genetic diversity among Indian bread wheat cultivars released during last 100 years. Genetic Resour & Crop Evol 59:717-726. Gupta PK (2012). Angiosperm taxonomy in the age of genomics and information technology. In Maiti, G.G & Mukherjee, S.K. (eds.). Presidential Address, ‘Society for Angiosperm Taxonomy’, In Proc. Intern’l Seminar “Multidisciplinary Approaches in Angiosperm Systematics”, Univ. of Kalyani (11th–13th October, 2008). Pp. 284-296. Tyagi S, Gupta PK (2012) Meta-analysis of QTL for preharvest sprouting tolerance and dormancy in bread wheat. Triticeae Genomics and Genetics 3: 9-24. Gupta, PK, Balyan, HS, Kulwal PL, Gahlaut V (2012). Phenotyping, genetic dissection, and breeding for drought and heat tolerance in common wheat: status and prospects. Plant Breed Rev 36: 85-168. Gupta PK(2012). Molecular breeding for crop improvement: harnessing the genes. Biotech News 6: 135-137. Gupta PK (2012). Regulating the dual-use and dual-impact life science research: influenza virus versus biotech crops. Curr Sci 103: 995-1002.
Papers presented in international meetings/conferences during 2012 1.
Balyan, HS, Chhuneja P, Bansal KC (2012). Wheat research in India. In: BBSRC/DBT workshop at Norwich, UK, May 21-23, 2012
2.
Gupta PK, Balyan HS, Kumar S, Kumar R, Jaiswal V, Tyagi S, Agarwal P, Gahlaut V, Kumari S (2012) Markerassisted selection for crop improvement of some major crops in India. In: Plant & Animal Genomes XIX Conference, Town & Country Convention Center San Diego, CA, USA, January 12-16, 2012
Initiation of R&D activities in Bioinformatics: Undertaking the the following: (a) In silico analysis for wheat orthologs for dwarfness and abiotic tolerance. (b) In silico gene expression analysis using transcriptome data. (c) Detection of SNPs using Next-Generation transcriptome Sequencing data in wheat.
Details of Training/Workshop organized and total noumber of user trained: (a)
Second phase of one month Training-cum-Workshop on VIGS was conducted during February 25-March 24, 2012. (b) Three day (June 14-16, 2012) workshop on Laboratory Information Management System (LIMS) with a view to monitor, retrieve and use the laboratory information stored with the help of LIMS. (c) Trained around 20 users.
Impact shown by the Centre: (a) During the above workshops, we trained around 20 participants. (b) Some of the wheat orthologs for dwarfness identified in silico are nearing validation using Virus Induced Gene Silencing (VIGS) approach. (c) Trained 15 M.Sc. students in computer applications and bioinformatics in agriculture. (d) Published a number of papers involving substantial bioinformatics component and computer applications (see number 8 above). Proposed activities for 2013-14: (a) We would like to organize a workshop on “Application of Bioinformatics for Analysis of Next Generation Sequencing Data” along with our regular activities. (b) Plan to continue to identify wheat orthogolos of the genes for nitrogen use efficiency (NUE) and genes involved in providing tolerance to abiotic stresses such as water stress. (c) In silico gene expression analysis using transcriptome data of rust-wheat interaction. Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
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Prof.H.S Balyan Department of Genetics & Plant Breeding, CCS University, Meerut-25004 (U.P.) +91-9412515497 +91-121-2768195 (elefax)
[email protected] http://molbiolab.ccsu.webs.com Prof.H.S Balyan (Coordinator)/Sri Anuj Kumar JRF) Bio Informatics Infrastructure Facility (BIFs)
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College of Agricultural Biotechnology, Latur Coordinator: Prof. HB Patil Establishment of BIF support for the teaching activities of biology and its allied areas to the host institute: We have initiated following work towards establishment of Bioinformatics facility at this college.
Bioinformatics Laboratory set-Up We are going to set-up separate Bioinformatics laboratory, wherein 25 desktop computers have been arranged. Also we have made separate compartment for arrangement of training to the participants of Bioinformatics seminar/. All these computers have been connected by LAN with internet facility.
Server purchasing and Installation: We called tender for purchase of high end and medium end server two times but nobody has responded. Recently, we called this tender once again and process of their purchase is in progress.
E- Learning software: The software for learning of English and development of communication skill has been installed in this system.
Beneficitiary of the facility:
The facility is being used by Post graduate student for analysis of their Master research work.
This facility is being used by faculty from department of Plant Biotechnology, Biochemistry and molecular Biology, Food Biotechnology, Animal Biotechnology and Crop Science.
This facility is also being used by B.Sc and M.Sc. student for conduction of practicals of course Introduction to Bioinformatics.
Organization of Training/Workshop: Summer training entitled “Techniques and tools of Biotechnology and Bioinformatics” will be arranged in June 2013. Objectives: Integrated wet and dry lab training to B.Sc., M.Sc and M.tech students Contents: The training beginning with basics of Molecular biology tools and Bioinformatics would provide exposition to the following main area DNA/RNA Techniques: Basic techniques of DNA and RNA towards genomics and Proteomics. Molecular Biology tools and methods: Gene isolation, cloning and transformation Bioinformatics tools and Applications: Biological database and their annotations, Pairwise and multiple sequence alignment, Genome and Proteome analysis, Phylogenetic analysis, Gene and Protein structure Prediction, Methodology: Lectures, Demos and Hands on sessions Level of Participants: B.Sc., M.Sc and M.tech students No of Participants: 15 Expected date of Announcement: April, 2013. Boarding and Lodging Arrangement: Boarding and Lodging to be arranged by candidate themselves
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College of Veterinary Science, Assam Agricultural University, Guwahati Coordinator: Dr. Probodh Borah Summary of the progress made by the centre from its inception: (i)
Adequate infrastructure with required hardware and software has been developed at the centre and the facilities are being used by the faculty members and students of the institute as well as some other neighbouring institutions of higher education.
(ii)
So far 12 (twelve) training programmes have been conducted on different aspects of bioinformatics tools and their application in biological research and a total of 233 biology teachers/researchers of various institutes within and outside state participated in these programmes.
(iii) Additionally, so far 115 faculty members/subordinate staffs of the host institute have been trained in nine batches under a computer literacy programme conducted by the centre. (iv) A website (www.vetbifguwahati.ernet.in) has been developed and being maintained. (v)
An e-portal for the students of the college (e-Vet-Edu) has been developed, which is available in the internet through the website of the centre.
(vi) A total of 22 faculty members of the host faculty have been trained in three batches on creation of e-learning resources in collaboration with Education Technology Cell of the college. (vii) An e-Notice Board has been created and being maintained for publishing official circulars and notifications of the faculty. (viii) An online biodiversity database (ILRONE) and a globally accessible online SalTy Code server for Multiplex PCR-based Salmonella serotyping have been developed.
Major research activities in biotechnology and its related fields in the last two years: (i)
Molecular fingerprinting of six different species of domestic animals of north-eastern region, namely cattle, buffalo, pig, yak, sheep and goat was done by PCR-RFLP based on 12S rRNA and 16S rRNA genes of mitochondrial DNA.
(ii)
Relative expression of genes coding for the enzymes, Fatty Acid Synthase (FAS) and Stearoyl CoA Desaturase (SCD) and three major transcription factors, Sterol Regulatory Element Binding Protein (SREBP), Peroxisome Proliferator Activated Receptor ã (PPAR ã) and CCAAT-enhancer-binding proteins (CEBP) related to lipogenic processes were analyzed by real-time PCR to establish zinc-mediated hormonal regulation (Growth Hormone, Insulin and Leptin) of fatty acid synthesis and desaturation in adipose tissue.
(iii) A multiplex PCR was developed for rapid detection of pathogroups of E. coli isolates from man, animals and birds based on their virulence gene profile. (iv) A rapid, high throughput multiplex PCR assay based on 16 genes variably distributed in various Salmonella serovars was developed for identification of common clinical serovars of Salmonella within 2-3 hours. (v)
A globally accessible online server has been developed on “Serotyping of common clinical isolates of Salmonella by Multiplex PCR” in collaboration with Vaccine Research Institute of San Diego, California (URL: http:// 182.71.179.101/smart/ home.php)
(vi) RT-PCR method was standardized for detection of FMD virus serotype ‘O’ in clinical samples and its comparative efficacy was evaluated compared to sandwich ELISA and virus isolation. RT-PCR protocol for detection of Toll-Like Receptor-3 (TLR-3) in FMDV-infected tissue was also standardized. (vii) Incidence of polymorphism in fecundity related genes, GDF9 and BMPR1B in Assam Hill goat was studied by PCR-RFLP. The study revealed that the genetic factor responsible for prolificacy or multiple kidding rates is not related to the reported mutated alleles at GDF9 and BMPR1B major genes.
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XXIVnd All India BTISnet Coordinators’ Meeting Area of Specialization of the centre: Animal Biotechnology
Infrastructure facilities in the Bioinformatics Centre B.
Computer & Communication facilities: 17 computers, 5 servers, one colour Laserjet, one monocolor Laserjet and one Inkjet printer, one Digital Xerox Copier. The computers are connected to the faculty LAN with 24-hour 512 Mbps Internet connectivity with adequate power backup (20 KV UPS).
C.
Scientific Software packages: Visual Studio, My SQL, CLC Combined Workbench, Geneious Pro, Accelrys Discovery Studio, Exome Horizon, Bioedit, Phylip, ClustalW, Visual FoxPro, Adobe Photoshop, Pinnacle Video Capture and Editing Software, Macromedia Flash MX, etc.
D.
Membership to DeLCON Consortium.
Details about Staff members working in the centre: Name of the staff Dr. P. Borah
Designation Professor and Coordinator
Dr. N. Nahardeka
Prof. and Member, Ex. Ph.D. in Animal Committee Genetics & Breeding
Dr. B.K. Sarmah
Ph.D. in Veterinary Since inception Physiology M.Sc. (Bioinformatics) Since Feb. 2012
Permanent
Sri Nabajyoti Goswami
Assoc. Professor and Dy. Coordinator Research Associate
Ms. Minaskshi Das
Trainee
M.Sc. (Biotechnology) Since Dec., 2012
Temporary
Sri Pradip Sarmah
Typist
B.A.
Permanent
Sri Ranjit Kakati
Peon
Specialization Ph.D. Veterinary Microbiology
Read up to Class VIII
Period of working Since inception
Absorption status Permanent
Since 2008
Permanent
Since Nov., 2007
Temporary
rd
Since 23 May, 2008 Temporary
Types of services provided:Internet surfing, training and assistance on use of online databases and bioinformatics tools, statistical analysis of biological research data, guidance in genomic and proteomic research etc.
Educational activities with details of placement:DBT-funded Postgraduate programme in Animal Biotechnology (MVSc) was started from August, 2010. A separate compulsory course on Bioinformatics is offered by the BIF to all students registered under this programme.
Initiative to validate the outcome of bioinformatics resources:Being done through publication of research articles in reputed journals.
Collaborative works/ initiatives:Teachers/researchers of neighbouring institutions like Guwahati Medical College, Regional Dental College, NIPER, Guwahati, Gauhati University, Cotton College, B. Barooah College, Institute of Advanced Studies in Science & Technology, Guwahati etc. have been trained and offered facilities for use in their research works. Participants from within and outside the North Eastern Region have attended the training programmes organized from time to time. A special training was also provided to the technical staff of BIF, Mizoram University on Database Management, Web-hosting, PHP, etc.
Databases/ Software packages developed:i. A biodiversity database entitled “Indigenous Livestock and Poultry Resources of North East (ILRONE)” is under the process of development. The design and development has been completed and the date entry process is in progress. (URL: http://182.71.179.101/ilrone/project/index.htm) ii. A globally accessible online server has been developed on “Serotyping of common clinical isolates of Salmonella by Multiplex PCR” in collaboration with Vaccine Research Institute of San Diego, USA. The wet-lab
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component for development of the multiplex PCR was done by the Coordinator, BIF during his DBT Overseas Associateship under the University of California, Irvine from June 01 to November 30, 2010. (URL: http:// 182.71.179.101/smart/login.php)
R & D Projects: A project entitled ‘Creation of an online repository of biotechnology and bioinformatics resources of north-east India (BABRONE)’ sanctioned by DBT for Rs. 28.91 lakhs is being implemented since February 2012.
Papers/ published or presented in the conferences
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1.
Talukdar, A.; Hazarika, R.A.; Borah, P. and Barua, A.G. (2012). Survival of verocytotoxigenic Escherichia coli O157: H7 in simulating media for beef gravy. Indian Vet. J. 89 (2): 39-41.
2.
Barua, C.C.; Talukdar, A.; Begum, S.A.; Borah, P. and Lahkar, M. (2012). Anxiolytic activity of methanol leaf extract of Achyranthes aspera Linn in mice using experimental models of anxiety. Indian J. Pharmacol. 44: 6367.
3.
Barua, .C.; Roy, J.D.; Buragohain, B.; Talukdar, A.; Begum, S.A.; Barua, A.G. and Borah, P. (2012). Preliminary study on adaptogenic activity of Pantago erosa ex Roxb. In: Medicinal Plants: Phytochemistry, Pharmacology and Therapeutics, Vol. 2. pp. 183-194.
4.
Barua, .C.; Begum, S.A.; Talukdar, A.; Buragohain, B.; Roy, J.D.; Barua, A.G.; Borah, P. and Lahkar, M. (2012). Effect of Alternanthera brasiliana (L.) Kuntze on modified forced swimming test in rats. In: Medicinal Plants: Phytochemistry, Pharmacology and Therapeutics, Vol. 2. pp. 215-225.
5.
Mehtaz, S.; Borah, P., Sharma, R.K. and Chakraborty, A. (2012). Virulence characteristics and antibiogram of Clostridium perfringens isolated from animals and foods. Indian J. Comp. Microbiol. Immunol. Infect. Dis. 32 (1&2): 55-57.
6.
Borah, Partha Pratim, Borah, P. and Sharma, R.K. (2012). Antibiogram of Salmonella isolates recovered from various species sources of Guwahati area. The Blue Cross Book, 27: 26-29
7.
Borah, Partha Pratim, Borah, P. And Sharma, R.K. (2012). Biochemical magic of Salmonella. The Blue Cross Book, 27: 75-78
8.
Rahman, S. Mafruza, Sharma, R.K.; Borah, P.; Chakraborty, A.; Devi, Mandakini RK and Longjam, N. (2012). Characterization of Clostridium perfringens isolated from mammals and birds from Guwahati city, India. J. Venom. Anim. Toxins incl. Trop. Dis. 18 (1): 83-87.
9.
Sharma, P.J.; Sharma, R.K.; Borah, P.; George, S. and Devi, R.K. (2012). Immunological and Virulence Properties of Partially Purified Outer Membrane Protein of Porcine Strain of Pasterella multocida. Indian Vet. J. 89 (6): 1720.
10.
Dutta, R.; Laskar, S.; Das, B.; Borah, P.; Zaman, G.; Kalita, D.J. and Barman, N.N. (2012). Polymorphism of oocyte derived growth factor (GDF9) gene in Assam hill goat. National Symposium on Addressing Animal Reproductive Stresses through Biotechnological Tools and XXVIII Annual Convention of the Indian Society for study of Animal Reproduction held at Guwahati from November 21-23, 2012.
11.
Dutta, R.; Laskar, S.; Das, B.; Borah, P.; Zaman, G.; Kalita, D.J.; Tamuly, S. and Devi, M. (2012). Nucleotide sequencing and Polymorphism studies of BMPR1B gene in Assam hill goat. National Symposium on Addressing Animal Reproductive Stresses through Biotechnological Tools and XXVIII Annual Convention of the Indian Society for study of Animal Reproduction held at Guwahati from November 21-23, 2012.
12.
Kalita, P; Borah, Partha Pratim; Hussain, I and Borah, P. (2012). Virulence gene profilesSalmonella isolates from men and animals detected by PCR. Presented in National Seminar on Biotechnology Research in Sustainable Development held at Dibrugarh University from 27-28 February, 2012.
13.
Kar, S.K.; Naskar, S.; Sarmah, B.C. and Borah, P. (2012). Influence of micronutrient on growth, lipogenic hormones and adipose tissue gene expression in grower pigs. Presented in XII Annual Conference of the Indian
Bio Informatics Infrastructure Facility (BIFs)
XXIVnd All India BTISnet Coordinators’ Meeting
February 03-04, 2011
Society of Animal Genetics and Breeding (ISAGB), held on 22nd and 23rd November, 2012 at the College of Veterinary Science, Rajendranagar, Hyderabad. 14.
Kar, S.K.; Naskar, S.; Sarmah, B.C. and Borah, P. (2012). Interaction of micronutrient with growth, lipogenic hormones and adipose tissue gene expression in grower pigs. Presented in the National Symposium on “Addressing Animal Reproductive Stresses through Biotechnological Tools” and XXVIII Annual Convention of the Indian Society for Study of Animal Reproduction held at Guwahati from November 21-23, 2012.
Details of Training/Workshop organized and total no. of user trained: (i)
“Bioinformatics Tools and Their Application in Teaching Biological Sciences” from March 20-22, 2007. No. of participants = 12
(ii)
“Bioinformatics Tools and Their Application in Biological Research” from December 03-06, 2007. No. of participants = 20
(iii) “Molecular Techniques and Bioinformatics Tools and Their Application in Biological Research” from February 18-21, 2008. No. of participants = 21 (iv) “Bioinformatics: Current Approaches and Applications” from September 23-26, 2008. No. of participants = 20. (v)
“Molecular Techniques and Bioinformatics Tools in Biological Research” from December 02-05, 2008. No. of participants = 20.
(vi) “Creation and Management of e-Learning Module for Biological Sciences”, December 15-18, 2009, No. of participants = 20. (vii) “Introduction to Computational Biology and Bioinformatics”, February 22-25, 2010, No. of participants = 20. (viii) “Creation and Management of Biological Databases”, February 9-11, 2011. No. of participants = 20. (ix)
“Introductory Bioinformatics with Special reference to Sequence Alignment & Phylogenetic Analysis”, March 15-17, 2011. No. of participants = 20.
(x)
“Essentials of Data Management, Sequence alignment and Phylogenetic analysis” November 15-18, 2011. No. of participants = 20.
(xi)
“In-silico Characterization of Proteins from Sequences and Molecular Modelling Approaches”, November 0709, 2012. No. of participants = 20.
(xii) “Basic Concept of Molecular Modeling and Drug Designing” from January 08 – 10, 2013. No. of participants = 20.
Impact shown by the Centre: The centre is encouraging faculty members and students for using the facilities available at the centre for promoting their teaching and research activities. The Internet facility is being used extensively by the faculty members and PG students. Students and faculty members from a number of neighbouring institutions like Gauhati Medical College, Regional College of Nursing, Guwahati, NIPER, Guwahati etc. are also being provided the facilities as and when requested. A sizable number of participants from outside the NE Region have also participated in the training programmes conducted by the BIF. Consultancy and advisory services have been provided to a large number of institutions in the north eastern region for establishment of Bioinformatics Centres and Institutional Biotech Hubs.
Proposed activities for 2013-14: The future activities envisaged include continuation of training programmes to develop human resources in bioinformatics and molecular biology, introduction of a bioinformatics Degree/Diploma course in the university, taking up of more research works in bioinformatics, etc.
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Contact details:
Name of the Coordinator Postal Address
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Phone Number
Dr. Probodh Borah Professor, Department of Microbiology, College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati-22 0361-2334990 (O), Mobile: 094351-16191
Email
[email protected],
[email protected]
Website
www.vetbifguwahati.ernet.in
Name of Contact Person
Dr. Probodh Borah
Bio Informatics Infrastructure Facility (BIFs)
XXIVnd All India BTISnet Coordinators’ Meeting
February 03-04, 2011
Cotton College, Guwahati Coordinator: Dr. Rita Mahanta Progress made by the centre till date: The Bioinformatics Infrastructure Facility (BIF) Centre was established in Cotton College in June, 2008 and at present it is in its fifth successful functioning year. The centre is shifted from its earlier location to an independent building which is located in the Biotechnology Department of the Cotton college complex nearest to the Department of Zoology and Botany as a separate unit in September, 2011. It is equipped with two high capacity Broadband independent servers and connected simultaneously with BSNL high speed Broadband Internet connections to ten independent PC terminals accessible to individual users either independently or as batch activity. The set up is capable of functioning twenty four hours a day and is backed up with uninterrupted servo stabilized power supply system and the centre is equipped with Bioinformatics software ‘GENIOUS PRO’ in ten terminals. The objectives of the Centre are to provide infrastructural facility for utilization of Bioinformatics for understanding, study and development of Life Science and different branches of Biological Science. The target area for providing service is the inhouse as well as outside and guest students, faculty and research scholars of Biological and allied branches of science. The centre also holds periodical workshop and training programmes for sensitization and exposure to Bioinformatics tools and sites to interested newcomers in the field as well as holding and organizing advanced training schedules with interactive participation of National and Regional resource persons and practicing Bioinformatics under the target area.
Progress Report (2011 -2012)
The centre runs a Post Graduate Diploma Course in Bioinformatics, affiliated to Gauhati University.
The centre has completed the third batch of the post graduate diploma course.
Project work being carried out by the students of the Bioinformatics course are :
a)
Rupsmita Sharma – Study of some anti-oxidant compound of Mentha Mentha piperita to evaluate their functional Characteristics.
b)
Dimple Talukdar-Phylogenetic analysis of cytoplasmic Polyadenylation element binding protein 1 (CPEB1) of some organisms and construction of a protein model using different bioinformatics tools.
c)
Resume Boro - Prediction of 3D structure of Iodothyronine Deiodinase based on Homology Modeling and Comparative analysis of the target
d)
Nazia Islam – In Silico analysis of Mycolic Acid from Mycobacterium tuberculosis
e)
Smaranika Baishya – In Silico analysis of 3 hydroxy 3 methylglutaryl coenzyme A reductase from Panax quinquefolius (American ginseng)
The centre provides free access of resources to the students of the parent institute.
The servers present at the centre are regularly utilized during admission process of the parent institute.
The centre is regularly utilized for conducting regular Bioinformatics classes as per curriculum of Biotechnology and Life Sciences Courses of the parent institute.
Research Scholars of the institute avail all the resources of the centre, pertaining to their area of interest/research.
The centre with its existing Bioinformatics tools trying to meet the interests and need of the Faculty members and Research Scholars working in the field of Molecular Biology and Genetics , and is utilized for carrying out the Dry Lab Experiments of the Scholars.
The centre holds regular Computer classes for the PG students of the Department of Botany, Zoology and Biotechnology, Cotton College.
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The centre is regularly utilized by the Degree, Post graduate and Research Scholars of the parent institute for referring to and utilization of biomolecular and genetic information.
The centre is regularly engaged in generating resource materials accessible through the launched website on topics of Biological science, Molecular biology and allied subjects targeted to the teachers and student community with emphasis on Secondary Degree and Post Graduate Level Biology learning and teaching.
Continuation and expansion of resource generation and periodic updating of the materials accessible through the Centre website.
Research work on Nano Drug delivery is being carried out utilizing the resources of the centre.
Research Scholars working in the field of Molecular Biology and Genetics are carrying out their Genetic work by primer designing and sequence analysis.
The bioinformatics part of the one day summer camp on Biodiversity Studies for School students (Class XI and XII) of N.E. India, organized by The Energy Resource Institute (TERI) was carried out in this centre on April 27th, 2012.
Future Activities: -
Expansion of the existing facility by procuring more hardware and software.
-
Continuation and expansion of resource generation and periodic updating of the materials accessible through the Centre website.
-
to organise more training courses/ workshop for the Teachers/ Research scholars and in- house as well as outside and guest students, and faculty of Biological and allied branches of science.
-
to collaborate with other institutions for the development of database on animal genetic resources of NE Region.
Note: At present up gradation of the centre with modern techniques and software is not possible due to financial constrains. Further, workshop and training programme could not be organized due to nonavailibility of the recurring funds from the funding authority. Contact details: Coordinator
:
Dr. Rita Mahanta
Co-Coordinators
:
Manuranjan Borgohain Binoy Kumar Deka Bioinformatics Centre, Cotton College, Guwahati-781001
BSNL Landline
:
0361-2735647/09864274691 (M)
Email
:
[email protected] [email protected] [email protected] [email protected] [email protected]
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Dr. B. R. Ambedkar Center for Biomedical Research, Delhi Coordinator: Dr. Madhu Chopra Summary of the progress made by the centre from its inception ACBR is running courses M.Sc. and M.Sc.-Ph.D. in biomedical sciences covering almost all subjects of biotechnology and related fields. A list of publication in the year 2012-13 is being provided to show scientific progress during this period.
Major research activities in biotechnology and its related fields : Following are the fields of research in biotechnology at ACBR. The mandate is to perform and promote high quality research in Biomedical Sciences, in areas that touch human health, such as: Medicinal Chemistry; Bio-organic Chemistry; Protein Chemistry; Proteomics; Natural Product Chemistry; Bio-Inorganic Chemistry; Drug Metabolism and Toxicology; Pharmacology; Medical Biotechnology; Molecular Genetics; Developmental Biology
Infrastructure facilities in the bioinformatics centre A.
Computer & Communication facility
We have state of art computer and communication facility at the center with a number of workstations and computers. All the research labs have computers for Ph.D. students and M.Sc. Students and a well maintained computerized library and networking through Delhi University Computer Center.
B.
Scientific Software packages
ACBR BIF facility is equipped with softwares like Insight II, Discovery Studio 2.5, GCG, TSAR, and other softwares for statistical analysis. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status) Following is the list of faculty members who are regular users of the BIF Facility. S. N. 1. 2. 3.
Name of the Staff Dr. Madhu Chopra Prof. Vani Brahamchari Prof. Daman Saluja
Specialization Drug Design and Development Epigenetics Medical Biotechnology
Period of working Since 1996 Since 1998 Since 1998
Status Permanent permanent Permanent
4.
Dr. P. M. Luthra
Medicinal Chemistry
Since 1997
Permanent
5. 6
Dr. Neha Kasturia Ms. Neetu
Research Associate Traineeship
Dec 12 – till date Dec 12- till date
Temporary Temporary
7
Ms. Kalpana Sachdev
Studentship
Dec 12 – till date
Temporary
Types of services provided: Teaching and Research Papers published or presented in the conferences with reference (2012-13) S. N. (III) Tilte of the Paper Proximity of H2A.Z containing nucleosome to the transcription start site influences gene 1. expression levels in the mammalian liver and brain. Bargaje R, Alam P, Patowary A, Sarkar M, Ali T, Gupta S, Garg M, Singh M, Purkanti R, Scaria V, Sivasubbu S, Brahmachari V, Pillai B Modeling SNP mediated differential targeting of homologous 3'UTR by MicroRNA 2. Ahluwalia JK, Soni K, Sivasubbu S, Brahmachari V. 3
4. 5.
6.
(iv) Name of the Journal Nucleic Acids Res.(2012) doi: 10.1093/nar/gks665.
RNA Biol. 2012 Mar 1; 9(3).
Comparative modeling of human kappa opioid receptor and docking analysis with the peptide YFa. Mahesh C Patra, M. Krishan C Kumar, Santosh Pasha, Madhu Chopra*
Journal of Molecular Graphics and Modelling 2012, 33, 44–51 [Elsevier] Insilico Study of the A2AR-D2R Kinetics and Interfacial Contact Surface for AminoAcids. 2012 DOI Heteromeriza- tion. Prakash A, Pratibha Mehta Luthra, 10.1007/s00726-012-1218-x. 25 Strucutral analysis of Runx1 protein and its mutants in complex with RUNX3 promoter Under submission, 2012 shows altered conformations. Jyoti Zack, Madhu Chopra*, Laishram Rajinder Singh*, Gurumayum Suraj Sharma, Daman Saluja# Multiple mutations in the genome of Niesseria gonorrhoeae are associated with multi Under submission, 2012 drug resistant serovars. Divya Sachdev1, Indu kumari1 Manju Bala2, Madhu Chopra1, Vineet kumar1, Daman Saluja1# Bio Informatics Infrastructure Facility (BIFs)
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R & D activities in Bioinformatics Dr. Madhu Chopra 1.
Structure Based Design, Synthesis and Evaluation of Histone Deacetylase Inhibitors as Potent Antitumour Agents, Sanctioned by Department of Biotechnology (DBT Bioinformatics part).
2.
Computer-Aided Design of Novel NSAIDs as Selective Cyclooxygenase-2 (COX-2) inhibitors to target tumors: Pilot Study for Synthesis and Preliminary Activity for its Anti-tumor Potential. Investigators: Dr Madhu Chopra (PI) & Dr. Daman Saluja (CO-PI).
3.
Design and Synthesis of nonpeptidic Cholecystokinin receptor antagonists as potential tumour targeting agents, DST.
4.
Collaborative projects: (unfunded) a.
Computational Designing of an Inhibitor to control the progression of Osteoarthritis” in collaboration with Dr. Krishna Dalal, AIIMS
b.
Computational design and prediction of activity of novel opioid receptor antagonists and antitensin converting enzyme inhibitors with Dr. Santosh Pasha, IGIB.
Prof. Vani Brahmachari 1.
Role of homocysteine in coronary artery disease: Genetic and epigenetic studies Funded by: Department of Biotechnology (DBT) 2003- 2007. Collaboration with Functional Genomics Unit IGIB.
2.
Mining the Human Genome for Global Regulatory Genes: Identification, Characterization and Functional Analysis. Funded by DST: 2006-2009.
Dr. Pratibha M. Luthra 1.
Prediction of structure of Adenosine A2 receptor and design of A2 receptor specific antagonists.
2.
Study of interaction of BCl2 protein with natural compounds.
Prof. Daman Saluja 1.
In silico modeling of efflux pump protein mutants from Niesseria gonorrhea involved in antibiotic resistance.
2.
To understand the regulation of Gene Expression by RUNX-1 (AML) and its mutants
Details of Training/ Workshop organized and total no. of user trained :
Dr. Madhu Chopra as Convener and organizing secretary 4th Workshop on Bioinformatics and Molecular Modeling in Drug Design 18-20 February 2012. Total no. of Participants 30.
5th Workshop on Bioinformatics and Molecular Modeling in Drug Design March 2013. Course work taught by Dr. Madhu Chopra
Course Taught and Duration
M.Sc. Biomedical Sciences January – April every year M. Tech Process Development and Organic Synthesis July – December 2012
- Bioinformatics and Computer aided drug design as part of 4th semester course at ACBR - Bioinformatics and Drug Design 17 Lectures (2010), 15 lectures 2011, 15 lectures 2012
Invited Lectures (Dr. Madhu Chopra)
Computational Drug Design and Development, Symposium on Bioinformatics, DRDE, Gwalior. 22-24, August 2012.
Homology modeling and structure based drug design, Workshop on “Computational biology for Biology Teachers” at Miranda House January 9-10, 2012
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Impact shown by your centre on the growth of biotechnology and allied areas. Year of Course Commencement :
1998 (M.Sc.-Ph.D. Combined Programme in Biomedical Sciences)
Visiting/Guest Faculty: Research Publications (Last 9 years) : Patents & Technologies Transferred : Number of Projects: Ph. D. Students Students Qualified CSIR-UGC-NET Examination (1999-2010)
20 120 5 (i) Industrial : 3 (ii) Government Agencies : 65 Completed : 130, Ongoing : 40 160
Man Power trained Ph.D. Students : Completed
2
1.
Ruby Gupta, 2012, “Pharmacophore Modeling, Virtual Screening and Development of novel COX-2 Selective Inhibitors. Supervisor Dr. Madhu Chopra
2.
Amresh Prakash, 2012, “Insilico Approaches to Study the Role of adenosine A2A receptor (A2AR) in Parkinson’s Disease for Development of Novel Therapeutics” Supervisor Dr. P. M. Luthra.
Ph. D Students (In silico analysis carried out as a part of Ph.D., thesis work) under progress
8
1.
Manisha Sikka, “Analysis of genes involved in pathways: Targeting Cancer through cholecystokinin antagonists and cyclooxegenase – 2 Inhibitors.” Supervisor Dr. Madhu Chopra
2.
Monika Sharma, Computational Design and Development of HDAC inhibitors. Supervisor Dr. Madhu Chopra
3.
Lubna Wasim, Epigenetic regulation of cancer through HDAC inhibitors understanding the mechanism through networks. Supervisor Dr. Madhu Chopra
4.
Priyanka Verma, Joint Registration at AIIMS with Dr. Krishana Dalal, “Estimation of the level of Cartilage Oligomeric Matrix protein (COMP) in Osteoarthritis and Computational Designing of an Inhibitor to control the progression of Osteoarthritis” Co-Supervisor Dr. Madhu Chopra
5.
Nalini Yadav: Rational design and Development of anticancer compound taking lead from natural sources. Supervisor Dr. Madhu Chopra
6.
Shweta Mehndirata “Analysis of INO80 binding motif in the 5’ and 3’ flanking sequences of protein and regulatory RNA coding genes in the human genome” Supervisor Prof. Vani Brahmachari.
7.
Shruti Jain “Analysis of dINO80 binding motif in the 5’ flanking sequences of protein and coding genes in the Drosophila genome”. Supervisor Prof. Vani Brahmachari.
8.
Vishal Nimeysh Structure Prediction of Platelet Derived Epidermal Growth Factor Receptor (PDEGFR) to design novel PDEGFR antagonists for targeting tumor of brain. Supervisor Dr. P. M. Luthra.
M.Sc. Projects (In silico analysis carried out as a part of dissertation work)
10
Proposed Activities during 2013-14 We have several educational activities including teaching of various courses as special papers in four Semesters of M.Sc. Students, project/dissertation work by M.Sc. students as well as summer training programme involving the use of Bioinformatics facility. Moreover several R & D projects are in progress and to complete all the ongoing programmes, continued financial support from DBT is inevitable. The major ongoing programes which are to be extended for next plan period for completion are
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Teaching programme.
(2)
Training/dissertation, summer programme
(3)
On-going projects as mentioned above
February 03-04, 2013
New activities proposed
To initiate research projects involving modelling of GPCR, docking and virtual screening for development novel lead molecules and drug discovery.
Virtual screening of plant derived molecules, building databases for virtual screening for dug like compounds and drug discovery
Initiate collaborative programmes with other institutions for enriching biodiversity information resources and promoting human resource development in bioinformatics.
Contact details:
Name of the Coordinator
Dr. Madhu Chopra
Postal Address
Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007
242
Phone Number
011-27666272
Fax No.
011-27666248
Email
[email protected],
[email protected],
[email protected];
Website
www.acbrdu.edu
Name of Contact Person
Dr. Madhu Chopra
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Forest Research Institute, Dehradun Coordinator: Er. Neelesh Yadav Summary of the progress made by the centre from its inception: Forest Research Institute –Dehradun received the grant for BIF creation in year 2007-08.The centre has been established in the historical and magnificent main building of FRI. A core group has been created in the institute to take special research initiative for Bioinformatics. FRI is the premier and oldest institute of forestry research in the country. The Institute also administered training of forest officers and forest rangers in the country and after Independence it was aptly renamed as Forest Research Institute and Colleges. The separate Bioinformatics lab is under progress, hardware/ software is available but procurement of new tools is under process. The various training programs conducted in biodiversity informatics & related subject. The bioinformatics centre is working in close relation with the GIS cell to achieve spatial biodiversity informatics. This year the centre is working in planning commission funded projects also at national level coordination.
Major research activities in biotechnology and its related fields : The FRI has a well-established infrastructure of bioinformatics & GIS laboratory, library, herbarium, arboreta and experimental field areas for providing scientific and training services. The forest bioinformatics, GIS & RS, genetics & tree propagation, Forest pathology (Molecular plants pathological lab), tissue culture discipline, nanotechnology research in forestry, statistical modeling of trees & biodiversity and Climate Change with forest ecosystem are the main research domain those are working biotechnology aspect of forestry.
Area of specialization: Forestry Biodiversity Informatics, Bioinformatics, Database of DNA fingerprinting of important tress species like Sal, Deodar, Shisham, Eucalypts etc., medicinal plants of forests, Forest Products, Forest Soil and Land Reclamation, Genetics and Tree Propagation, Non-wood Forest Products, Pathology, Silviculture, Climate Change
Major achievements made during 2012-13:
Developed the database of forest pathology herbarium and DNA fingerprints database of Cedrus deodara species
The forest mycological herbarium database of nearly 9000 specimens has been developed in open source web technology.
Conducted three training programs on biodiversity informatics for the research scholars and scientists of the institute.
Developed the dedicated website of BIF centre ,FRI
Design & development, up gradation of DD herbarium, dehradun (collection of 3,30,000 plant specimens) .
Conducted in-house training programs on computer basics and internet technology to research staff of institute.
Database on Deodar and Kail Information System developed.
The BIF Centre developed a National Data portal for Planning Commission (NRAA funded) all India coordinated Projects “Identification of Extent of Forest Lands in Forest Fringe Villages” with its data analysis part.
Infrastructure facilities in the bioinformatics centre: I.
Computer & Communication facility : The BIF centre have the 20 Desktop computers (Core 2 duo based processor), 10 Desktop computers (Intel V Pro), Web server, database server, Internet leased line connection( 256 kbps) is available, Color Laser printer, photocopy machine, scanner.
II.
Scientific Software packages: SPSS, Windows server Standard 2003, Visual studio .NET (1 User), MS-Office 2007 , SQL Server 2000, MySQL server 5.0 , PHP 5, Apache server, (Open source soft wares) etc.
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Databases & other information resources : I.
Web based interactive database for Dehradun Herbarium (Approx 3,30,000 specimens) has been develop by the centre and the data entry work is going on.
II.
The database of Forest insects is developed.
III.
Forest pathology herbarium (mycology collection of 12000 specimens) database developed and completed in year 2011.
Details about Staff members working in the centre: Sl. No.
Name
Designation
Specialization
Working Since
Status
1.
Er. Neelesh Yadav
Scientist & Coordinator
Data Mining, Biodiversity Informatics
2003
Permanent
2.
Mukesh Bhatt
Technical Assistant
Web Technology, IT management
2011
Permanent
3.
Megha Sharma
Student under DBT Studentship
Web Technology
2012
Temporary
4.
Neeta Rana
Student under DBT Studentship
Web Technology
2012
Temporary
Educational activities : The Centre provides expertise and teaching inputs to the following courses at FRI Deemed University,
Two year Degree Courses:
M.Sc.(Forestry)
M.Sc. (Wood Science and Technology)
M.Sc. (Environment Management)
Doctoral Programme:
Under Doctoral Programme the BIF centre provides the computer application related support and guidance.
Papers/ published or presented in the conferences : I.
Exploring Patterns of plant diversity in India by plants herbarium of FRI, Indian Forester.
II.
Forestry Bioinformatics, Neelesh Yadav, a paper presented in Scientific Data and Knowledge within the Information Society ,20th CODATA International conference, Beijing, China.
III.
Role of Bioinformatics in Forestry Research, invited lecture delivered at State Biotechnology conference: Current Trends & Future Perspectives at Forest Research Institute University, by Neelesh Yadav and published in proceedings.
IV.
Dehradun herbarium Digitization published in the proceeding in “International Seminar on Plant Taxonomy in Biodiversity Management and Human Welfare” held at FRI Dehradun on 1-3 December.
Initiation of R&D activities in Bioinformatics: Since its inception the Centre has focused on R & D activities particularly in the area of biodiversity database development of computational tools for its storage, retrieval, analysis, interpretation and computer graphic modelling. The centre has also focused on the development of appropriate tools for integrating the information resources of BTIS Centres. The centre is tryng to become CoE for Bioinformatics forestry Research. Details of Training/Workshop organized and total no of user trained : One training on biodiversity informatics was conducted.
Impact shown by the Centre:
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The BIF Centre is working as a National Forest Biodiversity Informatics Centre under the ICFRE.
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The BIF Centre is working as nodal centre for Forest Bioinformatics and Biodiversity Informatics research & Development activities of the ICFRE Council.
BIF Centre is providing the training to the IFS and SFS trainees of the country.
BIF centre is working in collaboration with Mathematics Department, IIT Roorkee.
The center has published nearly 3 papers in international journals and 5 papers in national journals.
BIF centre is providing and supporting to FRI Deemed University in masters and research programme.
Proposed activities for 2013-14 :
To establish a national database repository for forestry biodiversity informatics with biodiversity data analytic tools and techniques.
Development of National Forests Web Portal is in pipeline for implementation.
To establish a comprehensive database including all information of plants growing in north India particularly and genetical data bank of imp. plants species.
To establish a web portal for establishing collaborative ventures with the institutions / researchers working on biodiversity matters and integrating the information resources.
To establish genetic sequence database of the intraspecific variants of the endemic plants of the Himalayan region.
Contact details:
Name of the Coordinator
Neelesh Yadav
Postal Address
37,Trevor Road, FRI Campus, Dehradun-248006
Phone Number
9411385495, 7579001926
Fax No.
0135-2756865
Email
[email protected]
Website
http://fri.icfre.gov.in
Name of Contact Person
Neelesh Yadav, Scientist, IT Cell,FRI Dehradun
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Gargi College, New Delhi Coordinator: Dr Shashi Tyagi The main focus of this year was bioinformatics teaching to the undergraduate students, students’ projects, supervision of Trainee and MSc student (studentship) and research by faculty.
Workshop A two-day workshop was conducted (27 Dec and 28 Dec, 2012) on Role of Bioinformatics in Genomics. On the first day lectures were organized and on the second day, practical session was conducted. The students as well as faculty participated in this workshop.
Research under traineeship A trainee (for 6 months) has been appointed (Sept 2012 onwards). Her research involves identification of S-nitrosylation sensitive motifs in plants. S-nitrosylation is a NO (nitric oxide) derived post translational modification which is known to regulate almost all processes in plants. More than 150 S-nitrosylated (SNO) proteins haven been reported in plants. Although a protein can have several cysteine residues which could undergo S-nitrosylation but only a few are sensitive to it. In animals, role of acid /base motifs in enhancing reactivity of cysteine towards S-nitrosylation are reported while such studies are not done with plant proteins. Therefore aim of the study is to find out the occurrence of such motifs in plants with S-nitrosylated proteins. Result of the study will help to define the features which will be useful in predicting the sensitivity of cysteine towards S-nitrosylation.
Research under studentship A student of MSc Biotechnology (Semester IV) has been appointed (Dec 2012 onwards). Her research problem involves analysis of functional as well as sequence diversity of rhamnosyltransferase enzyme in green plants.
Undergraduate students’ projects Students of BSc Life Science and Botany (Hons) implemented their bioinformatics projects at BIF, Gargi College. Their project involved in silico analysis of polymorphisms generated through restriction digestion of phylogenetically relevant genes of chloroplast genomes. They also analysed the maturase K sequence variations in tree, shrub and herb species of Euphorbiaceae members.
Other research/academic activities Faculty of all science departments have been using BIF to access public databases for research and online journals and to carry out and supplement their individual research.
Softwares installed/downloaded/used online DENDROUPGMA, HAPLODIV and HAPLONST programs have been downloaded and is being by faculty. PHYLIP Package is being used regularly for teaching BSc(H) Botany and Life Science students. Other softwares such as CLUSTALW and tools available at NCBI, EBI, DDBJ, SWISSPROT etc, are also used for biology teaching.
Paper presentations/Abstracts in Conferences Vidisha Minhas and Aparajita Mohanty (2012) “Plant Mitochondrial Genome Analysis for assessing its Importance in Phylogenetic Studies” at Silver Jubilee Bioinformatics Conference, December 6-8, 2012, Bioinformatics Centre, University of Pune. Surbhi Mittra and Jasmeet K Abat (2012) “Identification of S-nitrosylation sensitive motifs in plants” at Silver Jubilee Bioinformatics Conference, December 6-8, 2012, Bioinformatics Centre, University of Pune. Gayatri P, Disharika S, Aparajita M (2012) “In Silico Analysis of Maturase K-RFLP in Phyllanthus sp: A Step Towards Population Diversity Studies” at International Conference on Biotechnology: A Rendezvous With Basic Sciences For Global Prosperity (BTBS-2012), December 26-27, 2012, NASC Complex, Pusa, New Delhi.
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Future Activities (2013-14) 1.
Workshops and Seminars will be conducted for faculty and students
2.
Bioinformatics teaching along with project work by students will be carried out.
3.
Research focus will be: a)
Analysis of organelle genomes for their role in Cytoplasmic Male Sterile Lines (CMS) in plants.
b)
Protein Motif Comparison for analysis of motifs responsible for conferring sensitivity towards post translational modifications like phosphorylation, S-nitrosylation, glycosylation etc.
Contact details:
Name of the Coordinator
: Dr Shashi Tyagi
Address
: Dept. of Botany, Gargi College, Sirifort Road, N. Delhi-110049
Phone Number
: 9810381494
E-mail ID
:
[email protected]
Name of Co-coordinator
: Dr Aparajita Mohanty
Address
: Dept. Of Botany, Gargi College, Sirifort Road, N. Delhi-110049
Phone Number
: 9810567611
Email ID
:
[email protected]
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Gauhati University, Guwahati Coordinator: Dr. D.K. Sharma Summary of the progress made by the centre from its inception: The Department of Biotechnology, Ministry of Science & Technology, Govt. of India has sponsored the Bioinformatics Infrastructure Facility (BIF) of Gauhati University, Guwahati in 2008. During last four years, the centre has procured the necessary components prescribed by the DBT.
Major research activities in biotechnology and its related fields : The centre has been engaged in the R35 Intron gene of fresswater turtle species, since its inception. However, using bioinformatics tools RNA secondary structure of the said gene has been ascertained. Further, using bioinformatics tools two areas of research/investigation have been emphasized. (1)
Aging gene of turtle species-the long lived animal.
(2)
Detoxicating gene- Glutathime s-transferase gene-which is responsible in allowing the turtle species to survive even in the most polluted water.
(3)
Structure prediction of certain protein in varanus
Area of specialization: Molecular Genomics
Major achievements made during 2012-13: Intron gene has isolated and 237 sequences were submitted and obtained accession number.
Infrastructure facilities in the bioinformatics centre: The Bioinformatics Centre, Gauhati University has fully utilized the DBT sponsored BIF facility for providing online Bioinformatics lectures, tutorials, study materials and also by organizing awareness camps, invited lectures, popular talk etc. for P.G. students of Life Sciences. Over 2200 users have been benefited from this centre through the DBT sponsored ejournal access facility by the NER-DeLCON. BIF Library: The BIF library has a good collection of most of the latest books of modern Biology.
Details about Staff members working in the centre: SL. No Name 1 Dr. D.K. Sharma
Designation Prof. in Zoology & Coordinator BIFGU
2
Dr. D.K. Jha
Prof & Head, Department of Botany & Co-Coordinator BIFGU
3
Dr. P.J. Handique
4
Mr. Ankit Varma
Prof. & Head, Department of Biotechnology & Coordinator BIFGU Research Associate, BIFGU
5
Mr. Abinash Chutia Studentship, BIFGU
Specialization Ph.D; working on Molecular Biology, Bioinformatics and Conservation genetics Ph.D; working on Microbial Ecology
Status Permanent
Ph.D; working on Plant Biotechnology
Permanent
M.Sc. in Bioinformatics; Working on Protein Modelling
Temporary
MCA (pursuing), Working on Application designing using PERL Programming
Temporary
Permanent
Educational activities: The center is dedicated to train young biologist, Faculty members, researchers of Northeast India with the various tools and techniques in biotechnology, computational biology, programming languages and Biodiversity informatics.
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(A) Teaching and learning: Imparted lecture demonstration classes both in PG and UG level (certain colleges). (B)
Application of bioinformatics in the biological research.
Papers/ published or presented in the conferences : 1.
P Barman, PJ Handique and AK Handique (2012): In-silico determination of homolog of Melon R-gene R-FOM2 in chickpea (Cicer arietinum L.) giving resistance against Fusarium wilt caused by the fungal pathogen Fusarium oxysporum f. sp. Ciceris. Journal of research in Bioinformatics, Vol.1 (1): 016-022
2.
RK Sarma , R Debnath , R Saikia, PJ Handique, TC. Bora (2012): Phylogenetic analysis of alkaline proteinase producing fluorescent pseudomonads associated with green gram (Vigna radiata L.) rhizosphere, Folia Microbiol
3.
Baruah C., Goswami U.C. and Sharma D.K (2012) In Silico characterization of growth hormone from freshwater ornamental fishes: Sequence analysis, molecular modelling and phylogeny. African Journal of Biotechnology Vol. 11 (31), pp. 8005-8021; DOI: 10.5897/AJB11.3955
4.
Baruah C and Sharma DK.(2011). Structure and molecular evolution of Cytochrome-b among the freshwater turtle genera Pangshura and Batagur. NeBIO, 2(1): 5-12
5.
P.N.Bhattacharyya and D.K. Jha (2011) Antidermatiphytic and antioxidant Activity of Terminalia arjuna (roxb). Wight & Arn. Bark. International Journal of Pharmaceutical & Biological Archives 2(3):973-979.
6.
Bhattacharyy PN and D.K. Jha (2011): Plant Growth Promoting Rhizobacteria: Imergence in Agriculture. World Journal of Microbiology and Biotechnology. Doi: s11274-011-0979-9.
7.
Madhumita Talukdar, Aparajita Duarah, Shruti Talukdar, Manorama Bura Gohain, Rajat Debnath, Archana Yadav, Dhurva K. Jha and Tarun C, Bora.(2012) Bioprospecting Micromonospora from Kaziranga National Park of India and their anti-infective potential World Journal of Microbiology and Biotechnology, DOI 10.1007/s11274-0121080-8.
Initiation of R&D activities in Bioinformatics: Research Area: Protein modelling, RNA structure, Molecular Phylogeny & phylogeography, DNA & Protein Sequence analysis, Functional annotation and Biodiversity database development, Biological sequence conversion software development.
Bioinformatics Research:
Molecular phylogeny and Phylogeography of freshwater turtles of India.
Modelled important proteins from different organisms like Silk worm (Antheraea assamensis and Bombyx mori), Turtles, Fish, Bacterial and viral proteins from silk and HIV-2 pol-polyprotein.
National Freshwater Turtles & Tortoises Conservation Directory is progress.
Conservation genetics and Molecular markers of Indian freshwater turtles.
Developed Biological sequence conversion software Using PERL Programming.
Collaboration: 1.
The center has collaboration with CES-IISC Bangalore, NEILIT Society Guwahati, BIF centre- St Athony’s college, Assam University Silchar, Shillong, Turtle Survival Alliance and TCRP for biodiversity informatics and conservation genetics of freshwater turtles.
2.
The centre has collaboration with TCRP for conservation and Biodiversity Journals “Asian Journal of Conservation Biology”
3.
The Centre has collaboration with Birjhora Mahavidyalaya, Bongaigaon, in helding UGC Sponsored National seminar on “Recent research thrust in biodiversity conservation-northeast India: A hotspot of Biodiversity”.
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Details of Training/Workshop organized and total no of user trained Workshop/ Training to be conducted in the year 2012-13: Title of the Workshop/ Training Organized Bioinformatics Tools and techniques for gene and protein analysis Introduction to Bioinformatics and Biological Databases
Level of participants
Date of the Event
The researchers and college teachers Refresher courses for faculty members
1st -3rd March 2012
Application of Bioinformatics in teaching and research
The researchers and college teachers
26th - 27th December, 2012 25th Feb -4th March, 2013
Name of the Centre Bioinformatics Centre (BIF), Gauhati University, Guwahati-781014
Impact shown by the Centre: The centre has so far trained more than 400 Research scholars, students and Faculty member including practical classes (during the Refresher courses of Life science Faculties).
Proposed activities for 2013-14: (1)
Organized of Workshop/ Training.
(2)
Development of Biological sequence analysis software using PERL programming language.
(3)
Structure prediction of certain protein in varanus and structure determination.
(4)
Publication of a Bioinformatics newsletter on current bioinformatics education and research activities.
(5)
Establishment of Career guidance/information facility for Bioscience students.
Further links on the activities of the Researchers at the BIF Center
www.gauhati.ac.in/home/BIF
http://intergenerationalpartnership.wikispaces.com/Conservation+of+Turtle+Diversity+in+India
www.iucn.org/about/union/commissions/cec/?6105/Turtle-Conservation-Programme-Launched-by-CEC-YoungProfessional
http://turtleworld.nebio.in
Http://www.ajcb.in
Contact details:
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Name of the Coordinator
Dr. D.K. Sharma
Postal Address
Bioinformatics Centre, Department of Zoology, Gauhati University, Guwahati781014, Assam, India.
Phone Number
91-0361-2700470(0) ; +91-9435147412(M)
Fax No.
91-0361-2700294
Email
[email protected]
Website
http://www.gauhati.ac.in/home/BIF
Name of Contact Person
Dr. D.K. Sharma, Coordinator, BIFGU
Bio Informatics Infrastructure Facility (BIFs)
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Guru Jambheshwar University of Science & Technology, Hisar Coordinator: Professor Ashok Chaudhury Summary of progress made by the centre from its inception : The Department of Biotechnology, Ministry of Science & Technology, Government of India, New Delhi had sanctioned the “Establishment of Bioinformatics Infrastructure Facility (BIF) for the promotion of Biology Teaching through Bio-Informatics (BTBI) under the BTISnet program to the Department of Bio & Nano Technology, to Guru Jambheshwar University of Science & Technology, Hisar, Haryana and released the 1st installment of Rs. 10 Lakhs in September, 2006 The Department of Bio & Nano Technology was established in April 1998 with financial support under HRD Program from the Department of Biotechnology, Ministry of Science and Technology, Government of India, New Delhi. The department offers a two-year Master of Science program (Four Semesters) in Biotechnology, Microbiology, and a two-year M. Tech Program in Nano Science & Technology (Four Semesters) from Academic Session 2006-07 with major objectives of: Exposing students to the areas of Biotechnology, Molecular Biology, and Genetic Engineering, Industrial Microbiology and Nano Science & Technology. To train students for ability to work independently with technical skill, professional maturity and having adaptability to thrive under diverse pressures, for the innovative undertaking and to liaison with various industries.
Major activities in biotechnology and related fields : The Department also offers Ph.D. program in Biotechnology and Nano Science & Technology to conduct basic and applied research in the areas of Plant Cell Tissue Culture, Molecular Biology, Genetic Engineering, Biochemistry, Microbial Biotechnology, Bioinformatics and Nano Science & Technology. The courses offered are innovative in several respects with major thrust being on research areas pertinent to Plant Biotechnology, Microbial Biotechnology, Food Biotechnology and Bio & Nano Technology. Such courses will not only equip the students with sound knowledge and expertise in the area of Biotechnology and Nano Science & Technology but will also create avenues for research and job opportunities in future and for self-emplacement and in the Industries.
Infrastructure facilities in the centre : Well equipped and operational facilities have been created for the establishment of Bioinformatics Infrastructure Facility (BIF) for the promotion of Biology Teaching through Bio-Informatics (BTBI) under the BTISnet program of the DBT in the Department. A new four story building in the name of Bio & Nano Technology Centre has been constructed and the whole department including the BIF Lab will be shifting in the new premises shortly. Hard ware: The BIF center has Xeon server X 2.8GHz server/ 533/ 512 Mb 36X2 Gb, Hot plug SCSI Tower server, 42 number Pentium IV Processor dual core, 512 Mb RAM machines running on Window XP operating system. All computers connected with server through LAN. Internet connection is now available through Campus Wide Networking provided by dedicated 100 Mbps BSNL Line. Software : It has Win NT 2000 server, Win 98, Win XP. Educational Software Exomed from Mascon India Ltd; KaleidaGraph, Synergy Software USA and Amber 11, California University, USA. The centre has online access to public database, for information retrieval in the field of biotechnology and Bioinformatics and providing following services to the Scientist / Faculty / Research Students of the department and University
Bibliographic and patent search
E mail and internet access
Training in Bioinformatics
Course taught in the entire degree program run in the department i.e. M.Sc. Biotechnology, M.Sc. Microbiology, M. Tech Nano Science & Technology.
Course Contents
Computer Basics, and maintenance
Introduction to Bioinformatics
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Genomics and Bioinformatics
Tools & Software
Data mining Bioinformatics tools & techniques for gene and protein analysis 14th -15th March, 2013 02 Computational Biology
Title Date Duration (in number of days) Subject Area (As per list enclosed)
Data ware housing
Proposed Trainings in 2013 (Training code: [DBNT-01] OBJECTIVES: To create awareness among the participants regarding the use of Bioinformatics, genome and proteome analysis tools in their research work. CONTENTS : Bioinformatics and applications related to database retrieval, biological sequence analysis, genomics, proteomics and phylogenetic analysis. METHODOLOGY
: Lectures, Demonstrations, Hands on Session
LEVELOF PARTICIPANTS
: Scientists, Research scholars, students & staff Working in Biotechnology or Bioinformatics : Knowledge of basic computer operations and Biology
PRERIQUISITES REGISTRATION FEE India SAARC Other Countries
Without Accommodation Rs. 400
With Accommodation Rs. 500
US$ 50 US$ 100
US$ 100 US$ 200
NUMBER OF PARTICIPANTS
: 20
EXPECTED DATE OFANNOUNCEMENT
: February
Contact details :
Name of the Coordinator: Professor Ashok Chaudhury Postal Address: Chairman, Department of Bio & Nano Technology, Guru Jambheshwar University of Science & Technology, Hisar-125 001 Haryana Phone Number: 01662-263165; Fax No.: 01662-276240 Email:
[email protected] Website:http://www.gjust.ac.in
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Gurucharan College, Silchar Coordinator: Dr. Bibhas Deb Summary of the progress made by the centre from its inception: Bioinformatics Centre, Gurucharan College, Silchar was established in Feb, 2008 under the BIF financial assistance of Department of Biotechnology (DBT), Govt. of India. The centre has started its academic journey in July, 2009 with two days training programme on Application of Bioinformatics in Biological Studies. The mandate of the centre is to provide infrastructural facility for utilization of Bioinformatics tools for understanding, study and development in Biological sciences. Since its inception, the centre has marched forward steadily and has created adequate facility for study and exchange of biological information through communication system network among the Bioinformatics Centres.
Major research activities in biotechnology and its related fields : 1)
Software development in Bioinformatics.
2)
Role of heavy metal tolerant rhizobacteria in sustainable cultivation of rice and their in-silico studies.
3)
Fish Database development.
Area of specialization: Molecular Phylogeny, DNA and Protein Sequence analysis, Sequence analysis Software and Fish Database development
Major achievements made during 2012-13: As a part of Bioinformatics Research, our Centre has developed a standalone fish database “MATSYA” which holds a good collection of fresh water fishes found in Barak valley region of Assam. Two papers were presented in 3rd World Congress on Biotechnology held in Hyderabad in Sept, 2012. The project work carried out by the student of Bioinformatics Centre was presented in 100th Indian Science Congress, Kolkata in the form of Poster Presentation.
Infrastructure facilities in the bioinformatics centre: The Bioinformatics Centre, Gurucharan College, Silchar has utilized the DBT sponsored BIF facility and provide online journal search, database search and retrieval and other basic facilities for undergraduate students, research scholars and teachers. This year centre has enriched itself by owing some softwares and hardwares like HP-Desktop intel core i5 and i3, Windows 7 ultimate, SHARP Projector, LG-Split AC, Sony-HD-Handycam, LASER Printer etc. Internet Connections: The centre is having BBG super speed combo 6999 scheme of BSNL with a maximum speed of 24 mbps; this enables the user to easy and fast surfing. BIF Library: The centre holds a good collection of latest books in the field of Bioinformatics, Genomics and Proteomics, Evolution, Microbiology, Programming languages and others. A total of 60 books are there in BIF-library. The students, research scholars and faculty members are utilizing the library in its maximum extent. Bioinformatics softwares: AutoDock, Phylip, MEGA4.1,TreeView,Treecon, Hex 5.0, Bio-Edit, GENEDOC, clustalX2, clustalW2, Rasmol, pDRAW, SEQ Tools, Cn3D, acua, perl primer etc. e-journal access: The centre is using DBT’s e-library Consortium (DelCON) facility for journal search. Around 900 high impact and peer reviewed journals are retrieved and reviewed from the centre.
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Details about Staff members working in the centre: Sl. No. 1.
Name
Designation
Specialization
Dr. Bibhas Deb
Principal, G C College & Ph.D, Specialization in Coordinator, BIF agricultural microbiology, GC College, Silchar Biological Nitrogen fixation, Currently working on molecular characterization and in silico study of Soil diazotrophs and biofertilizer technology development. Dr. Nilendu Dhar Associate Professor, M.Sc in Zoology, Ph.D in Fish Department of Zoology & Biology and Limnology Deputy Coordinator, BIF G C College, Silchar Mr. Soumitra Nath Research Scholar M.Sc. in Biotechnology, PGDBI, ADBT; Working on Bacterial stress response, biodiversity and software development.
2.
3.
Working Since
Status
Feb, 2008 Permanent (since inception)
March, 2012
Permanent
October, 2010
Temporary
Educational activities
Certificate Course in Bioinformatics
Diploma Course in Bioinformatics
Papers/ published or presented in the conferences:
Status of Tuberculosis in Cachar District of Assam, India”, a paper published in Assam University Journal of Science and Technology, 2011(An international journal).
“From Bacteria to Electricity Using Microbial Fuel Cell Technology”, a paper presented in a national seminar organized by Department of Physics, G.C College, Silchar (2011).
“Copper tolerant Rhizobacteria for sustainable cultivation of rice” a paper accepted in International Conference on Biodiversity & Sustainable Energy Development in Hyderabad HICC, India (2012).
“Determination of heavy metal stress on bacterial diversity” a abstract published in 3rd World congress on Biotechnology in Hyderabad HICC, India (2012).
“MATSYA: A Fish Database of Barak Valley Region of Assam, India” a paper presented in a symposium WETLAND-2012 in Assam University, Silchar (2012).
“Phylogenetic analysis of some mammals based on cytochrome P450 gene” a paper presented in 100th Indian Science Congress, Kolkata, 2013.
Initiation of R&D activities in Bioinformatics: 1)
Software development in Bioinformatics.
2)
Role of heavy metal tolerant rhizobacteria in sustainable cultivation of rice and their in-silico studies.
3)
Fish Database development.
Researchers of Assam University are utilizing the BIF facility for their research purpose. Apart from this, faculty members of Gurucharan College are also availing the DELCON e-journal facility present in our centre.
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Details of Training/Workshop organized and total no of user trained The centre has so far trained more than 300 Research scholars, senior secondary & under graduate students and teachers by seminars, workshops and hands on practical classes. Title of the workshop Two days workshop on “Basics in Bioinformatics” One day Lecture Programme on “Recent Advances on Biotechnology” by Dr. Arpita Roychoydhury, Scientist in Centre for Molecular Microscopy, Institute for Physical Biology of Heinrich Heine University, Germany
Date of the event 11th – 12th Aug, 2012 23rd December, 2012 (in collaboration with Institutional Biotech Hub of G C College, Silchar)
Impact shown by the Centre: The centre is continuously spreading the essence of Bioinformatics in the grassroot level specially to the undergraduate and school students in the form of lectures and workshops. The centre has collaboration with Assam University, Silchar; North Bengal University, Siliguri; Himachal Institute of Life Science, Ponta Sahib; St. Edmund’s College, Shillong and others.
Proposed activities for 2013-14
Incorporation of more data in fish database“MATSYA”.
In-silico studies of the genes responsible for heavy metal tolerance in bacteria found in rice rhizosphere.
To organize a workshops/ seminars for the teachers/students/scholars etc in the month of March, 2013.
Some of the projects works done in the centre having future prospects are taken consideration for publication
Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
Dr. Bibhas Deb Gurucharan College, Silchar-788004, Assam 03842-264504, 09435173728 03842-267042
[email protected],
[email protected] www.gccbioinfo.org.in Dr. Bibhas Deb Principal, G C College and Coordinator, Bioinformatics Centre
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Holy Cross College for Women, Tiruchirappalli Coordinator: Dr. P. Daisy Progress made by the centre since its inception: Biology in the 21st century is being transformed from purely lab-based science to an information science as-well, called Bioinformatics, the field of science in which biology, computer science, and information technology merge to form a single discipline. In this connection, India was the first country to establish in 1987 a Biotechnology Information System (BTIS) network to create an infrastructure that enables it to harness, biotechnology through the application of Bioinformatics. The Department of Biotechnology (DBT) has taken up this infrastructure development project and created a distributed network at a very low cost. Holy Cross College(Autonomous), Tiruchirappalli, is one such Institution where a Bioinformatics Infrastructure Facility(BIF) was established in 2006 with the financial support of DBT, New Delhi. This BIF Centre has successfully stepped into its second level in the 12th five year plan. The Centre offers M.Sc Bioinformatics & PG Diploma in Bioinformatics Courses from its inception in addition to M.Sc, M.Phil and Ph.D Programs in Biotechnology. Since its inception, the main attention of the Centre is on higher research along with manpower development in the area of Bioinformatics. The Centre also persistently extends its services in the areas of Computer Aided Drug Designing, Structural Bioinformatics, Database Development, Systems Biology and Molecular Modeling. The Centre offers these computational facilities to the users from the nearing Institutions and Universities. The Centre is highly accessible round the clock with a separate 10 Mbps internet facility with Optical Fibre Cabling to the faculty, research scholars and students. The staff of the Centre in co-ordination with the staff of the Research Department of Biotechnology performs research as well as teaching. The Centre has so far organized 21 National level workshops and have taken an initiative in organizing the “Annual Symposium” in the emerging fields of Life Sciences. The College is extending the Life Sciences Laboratory facilities for wet lab research in regards to Phytotherapeutics and also its full support for the progression of the Centre. The Centre will become an outstanding Bioinformatics centre in this region and will contribute significantly in the development of manpower.
Major Research Activities Computer Aided Drug Designing, Structural Bioinformatics, Database Development, Systems Biology, Molecular Docking, Molecular Dynamics, Data Mining, Molecular Modeling, Simulation of Biomolecules, X-ray crystallography of micro molecules and software development.
Area of Specialization Phytochemistry and drug designing.
Major Activities (2012-2013)
256
9 Ph.D scholars are utilizing the facility for their in-silico work, which is a part of their Ph.D work.
XVIII National Workshop on, “Systems Biology & Network Pathways” was conducted by the Centre for the Assistant professors and research scholars during 22nd -24th of August 2012. Nearly 25 participants from various Universities and Institutions including Bharathiyar University, Coimbatore, Annai College, Bangalore, VIT Vellore, Bharathidasan University, Anna University, Trichy, Biodiscovery Solutions Bangalore and CECRI Karaikudi were participated and benefitted through this workshop. Dr.S.Parthasarathy, from Bharathidasan University, Trichy, Dr.Jeyakumar from Bharathiyar University, Coimbatore and Dr.Basant Kumar Tiwary from Pondicherry University were the Resource persons.
The Centre and the Star College Scheme of the College funded by the DBT, Government of India, jointly organized 3 one day workshops on “Bioinformatics” for the UG students.
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Bioinformatics for Chemistry Date 11.12.12 No of Beneficiaries 81(host Institution) Databases covered Pubchem, Drugbank, and molecules Software/ tools Chemsketch and ISIS Draw trained
Bioinformatics for Life Sciences
Bioinformatics for Physics 12.12.12 13.12.12 25(Shrimad Andavan College, Trichy) 20(Host Institution) Genbank, Swissprot and PDB PDB and Massbank Blast, ClustalW and Rasmol
Expasy tools for MS Data and Rampage
II M.Sc & III B.Sc (15 & 24) Zoology Students are regularly made use of the facility for their Major Practical Course in Bioinformatics. II B.Sc Zoology (25) students are also utilizing the facility to do their Evolutionary Biology Practical which is a Part of their Major Practical.
The facility is utilized by the III year B.Sc Chemistry (95) and Physics (54) students for their Skill Based Elective Course entitled, “Basics of Bioinformatics” offered by the Zoology Department.
The Centre organized short-time training program including on-line practical exposures for its M.Sc Biotechnology & Bioinformatics Students.
The Centre is offering a Major Core paper on, “Basics of Bioinformatics” and a Major Core Practical on, “Tools for Bioinformatics” for the B.Sc Biochemistry Course in the VI Semester.
Courses on Bioinformatics, genomics and proteomics for M.Sc Biotechnology and units on these Chapters for M.Phil Biotechnology are offered by the Centre.
The Major Core Courses for the Ph.D Scholars on genomics and proteomics are also offered by the Centre.
Staff Members
Dr. P. Daisy, Head & Associate Professor in Zoology and Co-ordinator
Dr. M. Rajalakshmi, Assistant Professor in Biotechnology and Part-Time Research Asssistant.
Ms. P. Vijayalakshmi, Research Assistant, Bioinformatics
Ms. R. Pon Nivedha, Studentship of the Centre
Ms. K. Saipriya, Assistant Professor in Zoology & Part-time Trainee of Centre
Services Provided Round the clock usage of all the facilities of the Centre is provided. Guidance for utilizing the software tools is also provided. Furthermore, the centre helps for the Life Science Ph.D Scholars of the host Institution and Universities and Institutions in and around Trichy (PG IBMS, Taramani Campus, Chennai, Bharathidasan University, Anna University & PRIST University, Trichy) in the Bioinformatics area. The Centre also offers research services to students (M.Sc-Biotechnology(04), Bioinformatics(04) and Zoology(07) and B.Sc(08) Zoology) to complete their project dissertations and conducts training programs for both the teachers and students.
Patents Patents granted
Patent No.:244666-(2010)
Patent No.:246537-(2011)
Patents filed
2879/CHE/2012- a process for preparation of a novel compound 17-[(E)-4-ethyl-1',5'-dimethyl-2'-hexenyl]-11hydroxy-5-(hydroxymethyl)-13,14-dimethyl-5,6,7,11, 12,13,14,15,16,17-decahydro-3H-cyclopenta[a]phenanthren3-one from Cassia fistula stem bark with anti-diabetic property.
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2880/CHE/2012- a process for preparation of a novel compound 17-[(e)-1',5' - dimethyl-2'-hexenyl]-11-hydroxy5-(hydroxymethyl)-13,14-dimethyl-5,6,7,11,12,13,14,15,16,17-decahydro-3H-cyclopenta[a]phenanthren-3-one from Cassia fistula stem bark with anti-diabetic property.
2881/CHE/2012- a process for preparation of a novel compound 17-[(2E,5E)-4', 7'- diethyl-1',8'-dimethyl-2',5'nonadienyl]-11-hydroxy-5-(hydroxymethyl)-13,14-dimethyl-5,6,7,11,12,13,14,15,16,17-decahydro-3Hcyclopenta[a]phenanthren-3-one from Cassia fistula stem bark with anti- diabetic property.
Current Research
A new crystal has been isolated from ethyl acetate extract of Andrographis paniculata (Nila vembu) leaf. Work is on progress to identify the structure by crystallography.
Collaborations The Centre already has research and academic collaboration with scientists from NUS- Singapore, The University of Camerino- Italy, The Western University of Australia, Indian institute of Horticultural Research, Bangalore, Solai Ayurvedics, Vellore, Centre for Research in Entomology, Loyola College, Chennai. In addition to these, the centre has signed MoU for the promotion of Research and Advancement with,
Dr. Shakila. K. Banu, Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A& M University, TX, USA and
Dr. G. Agaramoorthy, Professor, College of Environmental & Health Sciences, Tajen University, Taiwan
Papers Published- 07 Papers undere review-05 Contact Details: Postal Address: Dr.P. Daisy, Co-ordinator Head & Associate Professor of Zoology, Biotechnology & Bioinformatics Bioinformatics Infrastructure Facility, Holy Cross College (Autonomous), Tiruchirappalli-02 Annexure-1
Proposed activities of 2012-2013
The center has planned to organize a 3 day National Workshop on, “Computer Aided Drug Designing” during 21-23rd August, 2013.
A three day International Symposium on, “Recent Trend in Life Sciences” is intended to organize by the centre during November, 2013.
The center has planned to organize a 3 day National Workshop on, “In-silico approach of Molecular Evolution” during 11-13th December, 2013.
Annexure-1 1.
Periyasamy Vijayalakshmi, Chandrabose Selvaraj, Sanjeev Kumar Singh, Jaganathan Nisha, Kandasamy Saipriya & Pitchai Daisy.,2012. Exploration of the binding of DNA binding ligands to Staphylococcal DNA through QM/MM docking and molecular dynamics simulation. Journal of Biomolecular Structure and Dynamics. DOI:10.1080/ 07391102.2012.706080. Impact Factor-4.99.
2.
Arunkumar.R, Sharmila.G, Elumalai.P, Senthilkumar.K, Banudevi.S, Gunadharini. D.N, BensonC.S, Daisy.P, Arunakaran.J., (2012). Effect of diallyl disulfide on insulin-like growth factor signaling molecules involved in cell survival and proliferation of human prostate cancer cells in vitro and in silico approach through docking analysis. Phytomedicine. http:/ /dx.doi.org/10.1016/j.phymed.2012.04.009. Impact factor-3.268
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3.
SreeVishupriya K, Chandrsekaran P, Senthilkumar A, Sethumadhavan R, Shanthi V, Daisy P, Nisha J, Ramanathan K & Rajasekaran R. Computational analysis of deleterious missense mutations in aspartoacylase that cause Canavan’s disease. Journal of Science China Life Sciences . 2012, 55:1109-1119. (Impact Factor : 2.02).
4.
Pitchai Daisy, Periyasamy Vijayalakshmi, Chandrabose Selvaraj, Sanjeev Kumar Singh And Kandasamy Saipriya. Targeting Multidrug Resistant Mycobacterium tuberculosis HtrA2 with Identical Chemical Entities of Fluoroquinolones. Indian Journal Of Pharmaceutical Sciences (Article in Press). (Impact Factor: 0.626).
5.
Daisy Pitchai, Vijayalakshmi Gopalakrishnan, Vijayalakshmi Periyasamy and Rajalakshmi Manikkam.,2012. In-Silico Modeling And Docking Studies Of AA2BR with Catechin to explore the anti diabetic activity. International journal of pharmacy and pharmaceutical sciences 4(3), 328-333. Impact: 0.38.
6.
Daisy Pitchai, Lizzy Jaculine, Rajalakshmi Manikkam., 2012. Identification of dual agonistic novel ligands for insulin receptor and PPARã through molecular docking. International Journal of Pharmacy and Pharmaceutical Sciences. 4(4), 142-147. Impact Factor-0.38.
7.
P. Daisy ., Feril G. Jeeva Kani., 2012. Evaluation of antidiabetic activity of various extracts of Cassia auriculata linn. Bark on streptozotocin- induced diabetic Wistar rats. International Journal of Pharmacy and Pharmaceutical Sciences. 4(4), 312-318. Impact Factor-0.38.
Papers under Review: 1.
Pitchai Daisy*, Periyasamy Vijayalakshmi, Chandrabose Selvaraj, Sanjeev Kumar Singh, SaravanaKumar Kavitha, Jaganathan Nisha. Virtual Screening of potential inhibitor against FtsZ protein from Staphylococcus aureus. Journal of Inter disci?plinary Sciences: Computatio?nal Life Sciences.
2.
Pitchai Daisy*, Periyasamy Vijayalakshmi, Chandrabose Selvaraj, Sanjeev Kumar Singh, Eugenepachelli Queen Naveena, Jaganathan Nisha, Gopalakrishnan Vijayalakshmi. In-silco structure prediction, molecular dynamics, virtual screening and ADME prediction studies on LukS subunit protein from Staphylococcus aureus. Journal of Medicinal Chemistry Research.
3.
Pitchai Daisy*, Periyasamy Vijayalakshmi, Chandrabose Selvaraj, Sanjeev Kumar Singh,Jaganathan Nisha. Identification of potential herbal inhibitor against Exfoliative toxin of Staphylococcus aureus infection through in-silico Approach. Indian Journal of Microbiology.
4.
Pitchai Daisy, Rajamanickam Pon Nivedha, Rajamanickam Helen Bakiya. In Silico Drug Designing Approach For Biotin Protein Ligase Of Mycobacterium tuberculosis. Asian Journal of Pharmaceutical and Clinical Research.
5.
P.Daisy , K.Saipriya. R.Gomathi, R.Salini. Green Synthesis of Gold Nanoparticles Using Indigenous Medicinal Plants Tinospora Cordifolia And Gymnema Sylvestre. Digest Journal of Nanomaterials and Biostructures.
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Indian Institute of Technology, Guwahati Coordinator: Prof. Arun Goyal Summary of the progress made by the centre from its inception: During the past few months, the department of Biotechnology at IIT Guwahati has initiated the establishment of BIF. A suitable space to set up the facility was identified and after necessary approval was obtained, the basic infrastructure was set up. Sub-committees for the purchase of the proposed equipments were constituted and relevant purchases were made.
Purchase of equipment for BIF
Following equipment were purchased for BIF during February2011 to December 2011 i.
Photocopier – 01 No.
ii.
Scanner – 01 No.
iii.
Laser Printer (Network) – 01 No.
iv.
Desk-Jet Printer – 01 No.
v.
5 KVA On-line UPS System with Batteries – 01 No.
vi.
Server (High-end) – 01 No.
vii.
Server (Medium) – 01 No.
viii. Desktop PCs with accessories Webcamera and Microphone – 10 Nos. ix.
Internet connection items such as Patch Panel, Switch, Patch-cords, etc.
Following furniture were purchased for BIF
i.
Storwel – 02 Nos.
ii.
Glass Door Storwel – 02 Nos.
iii.
Computer chair – 15 Nos.
iv.
Four Door Book-case – 03 Nos.
12 User Perpetual License Sigma Plot 12.0 Software was purchased in July 2011
3 day workshop on “Basic Techniques in Bioinformatics” was conducted during 12-14th October 2011
Utilization Certificates and Statement of Expenditure upto 31st March 2012 and Cumulative Asset Certificate upto March 2012 were submitted to DBT in July 2012.
Major research activities in biotechnology and its related fields : The research and development activities in the Department of Biotechnology covers the diverse areas as biochemical engineering, plant biotechnology, environmental biotechnology, nanobiotechnology, protein and peptide chemistry, molecular biology, structural and computational biology, bioinformatics, parasite biology, tissue engineering, stem cell biology and gene therapy, enzymology, and proteomics. Faculty members from this Department are also actively involved in Centre for Energy, Centre for the Environment, and Centre for Nanotechnology, thereby participating in multidisciplinary research activities. Research activities in the Department of Biotechnology result in a good number of publications in both international journals and national journals and in various conferences (both national and international). New projects of worth Rs. 725.94 lakhs have been sanctioned to various Principle Investigators in the Department. Besides, a number of projects of about Rs. 2555.442 lakhs are ongoing, and a few projects of worth Rs. 199.9844 lakhs have been completed. Area of specialization: Biochemical engineering, Plant biotechnology, Environmental biotechnology, Nanobiotechnology, Protein and peptide chemistry, Molecular biology, Structural and computational biology, Bioinformatics, Parasite biology, Tissue engineering, Stem cell biology and gene therapy, Enzymology and Proteomics.
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Major achievements made during 2012-13:
Dr. Latha Rangan received “Prof Hira Lal Chakravarty Memorial Award” in area of Plant Sciences instituted by Indian Science Congress Association (ISCA) in the 99th session of ISC 2011-2012.
Mr. Pojul Loying, Ph.D. Student under supervision of Dr. Biplab Bose, participated in the European Molecular Biology Organization Practical Course on “Single Cell Gene Expression Analysis” at the European Molecular Biology Laboratory, Heidelberg, Germany from 19th to 23rd March 2012 among 16 other international participants. He received the Boehringer Ingelheim Fonds travel grant from Boehringer Ingelheim Fonds, Foundation for Basic Research in Medicine, Germany for participating in the course.
Dr. Latha Rangan received Young Scientist Award of “Indian Society of Chemists and Biologists (ISCB)” in the area of Biological Sciences for the year 2012.
Mr. Sudipta Ghosh, doctoral student under joint supervision of Dr.Latha Rangan and Dr. Utpal Bora, participated in the Training Course on “Extraction and modification of bioactive components and specialty chemicals from plants” held from 23 to 27 April 2012, at Anadolu University,in Eskisehir-Turkey, Organized by ICS-UNIDO. He received full travel support and assistance from ICS-UNIDO to participate in this training program.
Mr. Anil Chandra, M.Tech Student under Dr. R. Swaminathan has been awarded the First Prize in poster presentation for presenting the work entitled (“Perturbation in the Activity of hydrolytic Enzymes post Biotinylation and post Quantum dot conjugation and their stability” by Aditya Iyer, Anil Chandra and R. Swaminathan) in the International Conference on Microbial, Plant and Animal Research 2012 (March 29-31) held at MITS, Laxmangarh Rajasthan.
Mr. Mitun Chakraborty, PhD student of the department has received best poster presentation award for the following paper: Mitun Chakraborty, Manish Goel, Siddhartha Sankar Ghosh*, Pranab Goswami* Molecular Characterization and Structure Function Relationship Studies of a Novel Alcohol Oxidase from Aspergillus terreus MTCC 6324. “WORLD CONGRESS ON BIOTECHNOLOGY” held at Hyderabad, India; 4th-6th May, 2012, Book of Proceedings, Abstract no: P-88, Pg No: 76.
Infrastructure facilities in the Bioinformatics Centre: i.
Photocopier – 01 No.
ii.
Scanner – 01 No.
iii.
Laser Printer (Network) – 01 No.
iv.
Desk-Jet Printer – 01 No.
v.
5 KVA On-line UPS System with Batteries – 01 No.
vi.
Server (High-end) – 01 No.
vii.
Server (Medium) – 01 No.
viii. Desktop PCs with accessories Webcamera and Microphone – 10 Nos. ix.
Internet connection items such as Patch Panel, Switch, Patch-cords, etc.
x.
Furniture such as Computer chairs, Steel almirahs and Book-cases for storage have also been procured.
Details about Staff members working in the centre: Sl. No.
Name
1.
None
Designation
Specialization
Working Since
Bio Informatics Infrastructure Facility (BIFs)
Status
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Educational activities: The facilities available at the BIF, IIT Guwahati, have been extensively used for teaching computational biology to both undergraduate and graduate students. Papers/ published or presented in the conferences: None at the moment Initiation of R&D activities in Bioinformatics: Molecular modeling, DNA/RNA and protein sequence analysis are currently performed with the available free bioinformatics software.
Details of Training/Workshop organized and total no of user trained: 3 day Training course on “Basic Techniques in Bioinformatics” was conducted during 12th-14th Oct 2011 The topics covered were: * Introduction to bioinformatics, genomics and proteomics * Introduction to various Biological databases * Information search and data retrieval * Tools for similarity search and sequence analysis * Gene identification and prediction * Phylogenetic tree analysis * Protein structure-function relationships * Protein structure prediction and visualization Impact shown by the Centre: The major impacts shown by the Centre has been listed above as major achievements. (Sl. 4 above). Besides, it also impacts in providing quality education in the area of bioinformatics/computational biology to both undergraduate and postgraduate level students. In addition, the Centre also provided training to the short term trainees during summer vacation period and others during the training session that was conducted in 2011.
Proposed activities for 2013-14: a.
Recruitment of staff
b.
Training for young scientists, students by organizing a Bioinformatics Training Course.
c.
Creating databases and publications using the facilities.
Contact details: Name of the Coordinator Postal Address
Phone Number Fax No. Email Website Name of Contact Person
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Dr. Arun Goyal Department of Biotechnology Indian Institute of Technology Guwahati Guwahati 781039 +91 361 258 2250 (Biotechnology Office) +91 361 258 2249
[email protected] http://www.iitg.ernet.in/biotech/ Mr. Dhrubajyoti Sarma
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Indian Institute of Technology, Madras Coordinator – N. Manoj Summary of the progress made by the centre from its inception: The Bioinformatics Infrastructure Facility (BIF) is housed at the Department of Biotechnology, IIT Madras. The facility primarily provides educational and training facilities by supporting the bioinformatics and computational needs of the various academic programs conducted in the areas of biotechnology.
Major research activities in biotechnology and its related fields Research areas of biotechnology include: Vascular Biology; Systems Biology; Structure function of ion channels, Molecular enzymology; Biocatalysis; Mechanisms of signal transduction pathways; Design and synthesis of siRNAs; QSAR and Drug design; Bioreactor design; Computational Neuroscience; Molecular dynamics of biological molecules; Cancer biology; Virology; Human genetics; Computational biophysics
Area of Specialization of the centre: Biotechnology Major activities of the centre during the year 2012-13 The BIF has provided support for undergraduate and postgraduate teaching programs for courses, namely Bioinformatics, Biomechanics, Structural Biology, Computer Applications in Biology, Biostatistics, Computational Neuroscience, Bioprocess Modeling etc that utilize the computational facilities of the BIF. The facility also provides research students with support for retrieval of material for seminar presentations, literature survey, data analysis, bioinformatics analysis, use of specialized molecular modeling and drug design software. One workshop on Next-generation genomics was conducted with about 50 participants.
Infrastructure facilities in the bioinformatics centre A.
Computer & Communication facility:
12 iMacs running Mac OSX; 1 High end multi processor Mac PRO; 6 HP Graphics workstations; 6 HP Xeon 3D-Graphics workstations; 16 HCL Core2Duo PCs; 2 SGI Octane workstations; 2 HP printer/scanner/copier. All the computers are connected to the internet on a 33 mbps LAN. B. Scientific Software packages: InsightII, Cerius2, Autodock, SigmaPlot 11.0, SuperPro Designer, EndNote bibliography software, Molecular visualization software, other commonly used Bioinformatics programs. C. Databases & other information resources: The BIF is extensively used for online literature access through the IIT Madras library e-Gateway.
Details about non-faculty staff members working in the centre: 1. Mr. R.Satish
Technical Assistant (Temporary)
B.Tech, Information Technology
Jan’ 09
Types of services provided: The internet facility of BIF is extensively used to access online literature. All major web resources like web servers and sequence and structure databases are used. The graphics workstations are extensively used for molecular modeling studies. Other workstations are used for computationally intensive tasks. Additionally the BIF is used by students who come for short term projects at IIT Madras from institutions around the country. It also supports the research needs of several PhD students working in the areas of computational biology
Educational activities: The BIF supports the academic programs of B.Tech, M.Tech, MS and PhD students (numbering a total of about 450 members) for their research projects and course work.
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Databases/ Software packages developed: Faculty of the department have developed databases
Some recent publications from the department relating to bioinformatics/computational biology 1)
Priyadarzini TR, Selvin JF, Gromiha MM, Fukui K, Veluraja K. (2012). Theoretical investigation on the binding specificity of sialyldisaccharides with Hemagglutinins of Influenza A virus by MD simulations. J Biol Chem. (in press).
2)
Gromiha MM, Huang DS. (2012) Introduction: advanced intelligent computing theories and their applications in bioinformatics. BMC Bioinformatics. 13 (Suppl 7): I1.
3)
Gromiha MM, Harini K, Sowdhamini R, Fukui K. (2012) Relationship between amino acid properties and functional parameters in olfactory receptors and discrimination of mutants with enhanced specificity. BMC Bioinformatics.13 (Suppl 7): S1.
4)
A.M. Thangakani, S. Kumar, D. Velmurugan and M.M. Gromiha (2012) How do thermophilic proteins resist aggregation? PROTEINS: Struc, Func and Bioinf, 80:1003-15.
5)
Singh H, Chauhan JS, Gromiha MM. Open Source Drug Discovery Consortium, Raghava GP. (2012) ccPDB: compilation and creation of data sets from Protein Data Bank. Nucleic Acids Res. 40(Database issue):D486-9
6)
PM Sivakumar, Naga V S, G. Ramesh, J. Mohanapriya, V Prabhawathi, M Doble. Computational Approaches To Improve Aggrecanase-1 Inhibitory Activity of (4-Keto) Phenoxy) Methyl biphenyl-4-Sulfonamide: Group Based QSAR and Docking Studies. Medicinal Chemistry, Vol 8, 4, 2012, 673-682.
7)
Ayarivan P, Ramalakshmi N, M Doble, S Hema Iswarya and Raj Vijayabharathi, Synthesis, Leptospirocidal Activity and QSAR Analysis of Novel Quinoxaline Derivatives. Medicinal Chemistry, 2013, (in press)
8)
A Puratchikody, R Natarajan, M Jayapal and M Doble Synthesis In Vitro Antitubercular Activity and 3D-QSAR of Novel Quinoxaline Derivatives. Chem Biol Drug Des 2011; 78(6):988-98,
9)
P M Sivakumar, S. Vignesh, G. R Kumar and M. Doble Computational approaches to enhance activity of Taxanes as antimitotic agent. Medicinal Chemistry Research, DOI: 10.1007/s00044-011-9779-x.
10)
Anand RS, Somasundaram S, Doble M, Paramasivan CN. Docking studies on novel analogues of 8 methoxy fluoroquinolones against GyrA mutants of Mycobacterium tuberculosis. BMC Struct Biol. 2011 Dec 12;11:47.
11)
Murugan R, Kreiman G. Theory on the coupled stochastic dynamics of transcription and splice-site recognition. PLoS Comput Biol. 2012 Nov;8(11):e1002747.
12)
Murugan R. Theory on the dynamics of feedforward loops in the transcription factor networks. PLoS One. 2012;7(7):e41027.
13)
Chandran A, Ghoshdastidar D, Senapati S Groove binding mechanism of ionic liquids: a key factor in long-term stability of DNA in hydrated ionic liquids? J Am Chem Soc. 2012;134(50):20330-9.
14)
Natarajan K, Senapati S. Understanding the basis of drug resistance of the mutants of áâ-tubulin dimer via molecular dynamics simulations. PLoS One. 2012;7(8):e42351.
15)
BS Chander and V.S. Chakravarthy. A computational model of neuro-glio-vascular loop interactions. PLoS One (Accepted).
16)
D Sukumar, M. Rengaswamy, VS Chakravarthy. Modeling the contributions of Basal Ganglia and Hippocampus to Spatial Navigation using Reinforcement Learning, PLoS One (Accepted).
17)
Maya M., VS Chakravarthy, Ravindran B. An Oscillatory neural network model for birdsong learning and generation: Implications for the role of Dopamine in Song Learning, International Journal of Mind, Brain and Cognition, 2012. (Accepted)
18)
Sanjeeva KK, Maithreye R, VS Chakravarthy, N Gupte. On the neural substrates for exploratory dynamics in basal ganglia: A model, Neural Networks, pp. 65-73, 2012.
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19)
Athi NN. Coarse-Grained Models of Protein Folding as Detailed Tools to Connect with Experiments. WIREs: Computational Molecular Science, DOI: 10.1002/wcms.1133.
20)
Athi NN (2012). Predictions from an Ising-Like Statistical Mechanical Model on the Dynamic and Thermodynamic Effects of Protein Surface Electrostatics. Journal of Chemical Theory and Computation, 8, 4646-4656.
21)
Rajashekar Reddy, Smita S, A. K. Srivastava (2012) Development of a mathematical model for growth and oxygen transfer in in vitro plant hairy root cultivations. Applied Biochemistry and Biotechnology (DOI: 10.1007/s12010-0119515-5.
22)
Pitti T, Manoj N. Molecular evolution of the neuropeptide S receptor. PLoS One. 2012;7(3):e34046.
Initiation of R&D activities in Bioinformatics: Research activities are carried out by several individual research groups working in the area of bioinformatics and computational biology and who use the facilities in the BIF. Details of workshop & total no. of user trained: Workshop on “Next-Generation Sequencing for Genomics and Healthcare”, 1-3rd Nov 2012. About 60 participants were trained using facilities in the BIF. Impact shown by your centre on the growth of biotechnology: The primary impact of this centre is in manpower training at levels that includes a large number of undergraduates, postgraduates and research scholars of the Biotechnology Dept, IIT Madras. Several papers that utilized the BIF were published in high impact journals. Future activities: The BIF grant will be used for upgrade existing software/hardware facilities.
Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
Dr. N. Manoj Department of Biotechnology, IIT Madras, Chennai - 600036 044-22574113 Mobile:9940149208
[email protected] http://biotech.iitm.ac.in/bif/bif.html Dr. N.Manoj
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Institute of Bioresources and Sustainable Development (IBSD), Imphal Coordinator: N.C. Talukdar Major activities of the centre
Bioresources Database of North-east India comprising flora and fauna is developed with more than 5500 records.
Bamboo database of Manipur is developed and made available online comprising 87 bamboo species data.
Documentation of Medicinal and Edible Insects of Manipur has been done with 51 species data and published on online at institute’s website.
Molecular characterization of bamboo species of Manipur using AFLP is done in collaboration with BOSE Institute, Kolkata
The centre has prepared Orchid Database of Manipur with addition of 300 records from primary and secondary sources; this database is made online on Institute’s website.
In combo screening using molecular modeling, molecular dynamic simulation, molecular docking and in-vitro ADMET screening was done for bamboo species of Manipur for drug discovery and drug development.
At present Bioinformatics unit has developed three bioinformatics tools. 1. SSRIST-Simple Sequence Repeats Identification Search Tool for genomic DNA analysis, 2. REcutter- Restriction enzyme cutter and 3. Glogo- Genome sequence logo representations.
Centre is maintaining websites of the Institute.
Centre has provided enough space and computers for the usage of DBT’s electronic Library Consortium (DeLCON) to the researchers of the Institute.
Infrastructure facilities Computers: Two new computers from DISC fund and ten from the core fund has added to the existing infrastructural facilities of the Centre. Uninterrupted Power Supply: 24x7 uninterrupted power supply from the 10KVa UPS purchased from BTISNet fund is provided to the newly established bioinformatics laboratory of the centre. Communication facility: Internet bandwidth of 1 Gbps from NKN is separately provided to the bioinformatics laboratory of the centre. Scientific Software packages: Software’s for Molecular modeling, Drug designing and Protein docking can be access from the bioinformatics laboratory of the Centre. Trainings / Workshop The Bioinformatics Centre is engaged in organizing trainings for the bioinformatics and IT related course work of UGC for the IBSD-PhD-JRF program and PhD registered scholars of the region. DeLCON facilities at IBSD, Imphal and RCIBSD, Sikkim The DISC of IBSD is also engaged in various extending the DBTs e-Library Consortia (DeLCON) to IBSD headquarter at Imphal and Regional Centre of IBSD (RCIBSD) at Sikkim.
Future activities
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Comprehensive Orchid biodiversity database of Manipur and Sikkim region using advance web-enabled GIS technologies.
Collaboration with NEBINet partners for preparation of comprehensive database and conservation strategies of Orchid resources of North East India.
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Development of Database and Software on Biodiversity Documentation and Conservation for NE India with special reference to Manipur.
To conduct awareness programme on biodiversity and bioresources conservation for school children of the region.
Development of a Database on Medicinal plants and formulations used by the Maiba-Maibi (traditional male & female health practitioner) of Manipur.
Contact details: Coordinator: N.C. Talukdar, Director (i/c), IBSD, Imphal Institute of Bioresources and Sustainable Development (IBSD), DBT, Govt. of India, Imphal,Manipur- 795001 Phone: (91) 385-2446122 Fax: (91) 385-2446120 E-mail:
[email protected]
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CSIR- Institute of Himalayan Bioresource Technology P.0. Box-6, Palampur (H.P)-176061 The Bioinformatics Infrastructure Facility (BIF) of CSIR-IHBT started functioning from 2011. The centre aims at:
Modelling biological complex system to identify essential molecules, processes and regulatory motifs that are key to expression of complex systems. In this regard Protein interactome of asthma has been constructed to identify the mechanisms central to its molecular architecture. In future protein-protein interactions and machine learning algorithms will be focussed for development of anti-cancer drugs.
Evolutionary study of disease resistance in plants. Studies are underway to elucidate how plant disease resistance originated and evolved, and how this evolutionary innovation helped plants to survive and thrive in diverse and harsh conditions, especially in the Himalayas.
In future the centre would also focus on the understanding of abiotic/biotic stress with the development of gene coexpression network.
Contact details:
Dr. Aparna Maitra Pati Head Planning Project Monitoring and Evaluation Cell CSIR-Institute of Himalayan Bioresource Technology P.O. Box-6, Palampur,Dist. Kangra Himachal Pradesh-176061 (India) Ph: 91-1894-230741 Fax: 91-1894-230433
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International Centre for Genetic Engineering and Biotechnology, New Delhi Coordinator: Dr. Dinesh Gupta Summary of the progress made by the centre from its inception: Bioinformatics Facility at ICGEB was setup in early 2000 with the help of World Health Organization (WHO), to establish a regional Training Centre for Bioinformatics research and training. Since then, the centre, under structural and Computational Biology group, has held several training workshops in Bioinformatics for tropical disease researchers for the whole of South-East Asia. Simultaneously the centre has been involved in development of several bioinformatics tools and analysis results of which have been published and cited in reputed journals. The centre is granted support by DBT in 2009 to promote the activities of the centre further.
Major research activities in biotechnology and its related fields : The main research areas at ICGEB, New Delhi Labs focus on mammalian and plant biology. Biomedical projects are pursued in virology (hepatitis B and E viruses, human immunodeficiency virus and SARS virus), immunology (biology of the immune response and tuberculosis), development of diagnostics and vaccine candidates for dengue viral infection, structural biology (development of synthetic antibiotics, crystal structure determination of proteins and polypeptides) and in the field of malaria both in basic research and vaccine and drug development, as well as development of technologies for biopharmaceuticals and for diagnosis of infectious diseases. In the plant biology area, research projects address the study of insect resistance and biopesticidals, abiotic and biotic plant stresses and crop improvement through biotransformation.
Area of specialization: Comparative genomics, Structural Proteomics, Molecular Simulation, Machine Learning, Genome Analysis, Microarray studies, Development of highly specialized databases and Software packages.
Major achievements made during 2012-13: Development of new web servers: for details see http://bioinfo.icgeb.res.in One of our students qualified BINC 2012.
Infrastructure facilities in the Bioinformatics Centre: A. Computer & Communication Facility:
B.
1.
Servers:
1.1
IBM X3650 M2 (quad-core Intel Xeon X5500 series, 2.93 GHz and 1333 MHz front-side bus)
1.2
IBM X3650 M3 (3.46 GHz four-core Intel Xeon 5600 series processors, 1333 MHz memory access speed.)
2.
10 Sun Microsystem – Ultra 27 Workstations (2.93GHz, 4.8 GT/s QPI, DDR3-1066, 8M cache, SMT On, Turbo On, 130W),
3.
Printers, Scanners & Communication Facility.
Scientific Software Packages: CLC Workbench, AMBER 10, Modeller 9v6, Rasmol, SPDBV, PyMOL, AutoDock, VMD, Open Babel, RNA-hybrid, SVM, Vienna RNA package, SnoReport, Artemis, ACT, DNA plotter, Abacas, DS gene, GCG package.
Details about Staff members working in the centre: Sl. No. 1.
Name Achal Rastogi
Designation
Specialization
Working Since
Status
Junior Research Fellow (JRF)
Bioinformatics
2011
working
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Educational activities Regular bioinformatics seminars are held.
Papers/ published or presented in the conferences:
Joshi, P. K., Gupta, D., Nandal, U. K., Khan, Y., Mukherjee, S. K., & Sanan-Mishra, N. (2012). Identification of mirtrons in rice using MirtronPred: a tool for predicting plant mirtrons. Genomics.
Subramaniam, Sangeetha, Monica Mehrotra, and Dinesh Gupta. “Development of target focused library against drug target of P. falciparum using SVM and Molecular docking.” Journal of Cheminformatics 4 (2012): 1-1.
Gupta, D., Gupta, Y., Kumar, K., Gabrani, R., Sharma, S. K., Gupta, A., ... & Mohan Babu Appaiahgari, K. B. (2012). Molecular cloning and characterization of chikungunya virus genes from indian isolate of 2006 Outbreak. Journal of Pharmacy Research, 5(7).
Nanni, L., Lumini, A., Gupta, D., & Garg, A. (2012). Identifying bacterial virulent proteins by fusing a set of classifiers based on variants of Chou’s pseudo amino acid composition and on evolutionary information. IEEE/ ACM Transactions on Computational Biology and Bioinformatics (TCBB), 9(2), 467-475.
Gupta, Dinesh, and Narendra Tuteja. “Chaperones and foldases in endoplasmic reticulum stress signaling in plants.” Plant Signaling & Behavior 6.2 (2011): 232-236.
Subramaniam, Sangeetha, Monica Mehrotra, and Dinesh Gupta. “Support Vector Machine based prediction of P. falciparum proteasome inhibitors and development of focused library by molecular docking.” Combinatorial chemistry & high throughput screening 14.10 (2011): 898-907.
Initiation of R&D activities in Bioinformatics: Initiated projects to investigate protein methylation and role of phosphatases in malarial parasites. A project to develop tools for viral suppressors initiated.
Details of Training/Workshop organized and total no of user trained Workshop on High-throughput data analysis using R package (September 2012): Biological experiments are constantly churning out mountains of data. Current methods of high-throughput biological assays supply thousands of measurements per sample, and the sheer amount of related data increases the need for better models to enhance inference. Without an understanding of statistics and knowledge of the techniques required to analyze, summarize and interpret these data, we are very limited in what we can learn from our observations. Even with experiments that generate very little data, there is a need to simulate phenomena by modeling the behavior of systems and their parameters, which again often needs to be done statistically. It is therefore imperative that we understand the basics of probability, statistical distributions, descriptive statistics, and some simple parametric hypothesis tests. The workshop aimed to take the opportunity to give a preview of fundamental statistical methods from perspective of a biologist. We tried to address the challenges faced by researchers in High-throughput data analysis, along with the new insights to its current progress addressed by our distinguished speakers well-established in this field.
Impact shown by the Centre: Established inter and intra institutional collaborations. Tools developed by us are heavily used and accessed.
Proposed activities for 2013-14 The Group is also interested in using artificial intelligence based methods to solve bioinformatics problems. The Group has also performed large scale molecular modeling of Plasmodium falciparum proteins. Other research interests of the laboratory include comparative genomics to predict regulatory elements like miRNAs and their target mRNAs in genomes using Next Generation Sequencing (NGS) Technology. To organize hands on training, workshops and short term training programs for familiarizing the applications of Bioinformatics.
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Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
Dr. Dinesh Gupta PB 10504, ICGEB, Aruna Asaf Ali Marg, New Delhi 91-11-26742184 91-11-26742316
[email protected],
[email protected] http://bioinfo.icgeb.res.in www.icgeb.res.in Mr. Achal Rastogi
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Jamia Hamdard University, New Delhi Coordinator: Prof. Shakir Ali Summary of the progress made by the centre from its inception: This facility was created at Jamia Hamdard in 2008-09 under the BTBI program of DBT, Ministry of Science and Technology, Govt. of India with an objective of supporting bioinformatics training and research in the University in pharmaceutical and medical sciences. Since then the training and research activities at BIF JH are focused on the application of computational techniques in the development of new drugs in communicable and non-communicable diseases. The center is also involved in tertiary structure prediction of novel peptides. Major research projects involve studies on target based drug designing, target-drug interaction mapping, 3D QSAR, pharmacophore design, and drug target validation and prioritization. Studies are also in progress on the designing and development of new anti-malarial agents by generating robust QSAR model of novel synthetic molecules. Earlier, the center has also carried out and published a study on prokaryotic and eukaryotic nonmembrane proteins. Recently, we have published some of our results in good impact factor journals of international repute such as the Medicinal Chemistry Research and journal of computer science and systems biology. The faculty associated with BIF is actively involved in providing training and extends its infrastructure to the students and staff involved in research on bioinformatics and computational biology. We have been consistently providing training by virtue of short-term projects to M. Tech. Bioinformatics students of Jamia Hamdard as well as to the students from other universities/institutes. In 2012, students successfully completed their projects on anti-malarial drug designing using dihydroorotate dehydrogenase, and also lactate dehydrogenase as target for designing novel anti-malarial agents. The center, since it started functioning in 2009, has been consistently organizing seminars and workshops on different themes in the area of bioinformatics and computational research. The first seminar in the series, organized in 2009 on ‘Bioinformatics: Applications in Computer Aided Drug Design’, was intended to familiarize and sensitize the participants in practical applications of computational chemistry in drug discovery. In 2010, the BIF seminar focused on ‘Chemo-bioinformatics and Computational Biology’ and provided a good exposure to the participants to recent trends in the field of e-pharmacophore and super-drug database. This seminar was organized in collaboration with URDIP (CSIR), Pune, with whom JH has signed MoU. The seminar, organized in the third consecutive year (2011), was primarily aimed at training the students and faculty in the area of ‘Computational protein structure prediction’ to introduce methods to predict the protein tertiary structure from the sequence of amino acids in the polypeptide. Hands-on training was also provided by the experts on modeling GPCR. This year (2012) the seminar (Application of bioinformatics in drug discovery and development) was organized to provide deeper insight into current scenario of the methods available for drug discovery and development, and understanding the science underlying these challenges. Hands-on training is always an advantage, and like previous years, hands-on training was also provided, besides the invited lectures by eminent speakers, and posters by the delegates.
Major research activities in Biotechnology and its related fields :
Drug design and development,
Protein structure prediction,
Computational biochemistry, and
Systems biology.
Area of specialization: Drug Design and Protein Modeling
Major achievements made during 2012-13:
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1.
Project supported by DBT “computational design of some novel, non-pteridine analogs as selective Mycobacterium tuberculosis dihydrofolate reductase inhibitors”
2.
Organized a conference-cum-workshop on Drug Design and Bioinformatics
3.
Provided six month project training to 3 students
4.
Published 2 research papers
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Infrastructure facilities in the Bioinformatics Centre:
Database/Application Server and a medium end (Proxy & File) server,
Desktops with OS, and licensed software for molecular modeling and drug design (vLife MDS 3.5).
The lab is equipped with an overhead projector and interactive board.
Details about Staff members working in the centre: Sl.No. Name 1. Prof. Shakir Ali
Designation Professor
Specialization Biochemistry
Working Since 1994
Status Coordinator
2.
Asst. Professor
Pharm. Chemistry
2000
Dy. Coordinator
Dr. Mymoona Akhter
Educational activities Training to M.Tech (Bioinformatics Students) of Jamia Hamdard and students from other institutions.
Papers/ published or presented in the conferences:
Rajneesh Kumar Gaur, Prokaryotic and Eukaryotic Non-membrane Proteins have Biased Amino Acid Distribution, J Comput Sci Syst Biol 2009:2: 298-299
Omprakash Tanwar, Rikta Saha, M. Mumtaz Alam, Mymoona Akhtar 3D-QSAR of amino-substituted pyrido[3,2B]pyrazinones as PDE-5 inhibitors Med Chem Res (2012) 21:202–211
Akranth Marella, Omprakash Tanwar, Rikta Saha, M. M. Alam, M. S. Zaman, Mymoona Akhter, 3D Quantitative Structure-activity relationship for quinoline, benzimidazole and benzofuran based analogs as Phosphodiesterases IV (PDE-IV) inhibitors Med. Chem Res Accepted
Initiation of R&D activities in Bioinformatics: Project Supported by DBT “computational design of some novel, non-pteridine analogs as selective Mycobacterium tuberculosis dihydrofolate reductase inhibitors”
Details of Training/Workshop organized and total no of user trained 1.
Training to M.Tech (Bioinformatics) Students
2.
Organized four conference-cum-workshops on Drug Design and Bioinformatics
Impact shown by the Centre: The center is slowly getting recognition in the area of drug design and tertiary structure prediction
Proposed activities for 2013-14 Proposed to organize 5th Bioinformatics conference-cum-workshop in the area related to drug design and development.
Contact details: Name of the Coordinator/Dy. Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
Prof. Shakir Ali/Dr. Mymoona Akhter Bioinformatics Infrastructure Facility, Jamia Hamdard, New Delhi 110062 +911126059688
[email protected] [email protected] www.jamiahamdard.ac.in Prof. Shakir Ali/Dr. Mymoona Akhter
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Bioinformatics Centre, Jiwaji University, Gwalior Summary of the progress made by the centre from its inception: Desired computational and information technology facilities are being extended to the faculty and researchers in the University. The one-time grant for establishing the Centre was sanctioned in September 2006. The Facility has been established. Prepared teaching aids in Biotechnology for colleges affiliated to this University. We have established a MoU to work together in areas of Neuroinformatics with High Hopes Biotech, Agra. Extending bioinformatics and computational facilities to most teaching departments in the University.
Major research activities in Biotechnology and its related fields: The ongoing research of interests are: a)
Role of microglia and inflammatory changes in neuronal apoptosis and neurodegeneration.
b)
Studies on effects of presence of resting and reactive microglia on endogenous neurogenesis and gliogenesis from neural stem cells.
c)
Aging changes in microglia per se. Does age related deterioration of microglia and microglial cellular senescence cause increasing disability of microglia to provide neuroprotection following injury?
d)
Studies on immunophilin ligands as novel modulators of glial activity and mediators of neuroprotection.
e)
Role of glia in neurogenesis and histogenesis of neurons following exposure to the toxicity of deltamethrin in postnatal rats.
f)
Gram-negative Bacterial Endotoxin-induced Infertility.
g)
Genetic polymorphism in the tribal populations of North Madhya Pradesh in relation to genomic diversity and susceptibility to tuberculosis.
h)
Genetics of susceptibility to gall stone and gall cancer.
i)
Genetic diagnosis and counseling for (pre-natal) abnormalities in spontaneous abortions.
j)
Genetics of thalassemia and population screening.
k)
Conservation genetics of gharial and turtles.
l)
Genetic diversity of HLA in the two tribal groups of North Madhya Pradesh: Association with pulmonary tuberculosis.
Major activities of the centre during the year 2012:
The Centre provided support to a DBT sponsored Hands-on Workshop on “Molecular Analysis of Complex Diseases” during 20th February to 10thMarch, 2012. (Conducted by the Centre for Genomics)
A National Seminar was organized on “Current Trends in Neuroscience” during 18th-19th March, 2012.
The Centre was supported to organize a National Seminar on “Tribal Health and Genomics” during 19th -21stMarch, 2012. (Conducted by the Centre for Genomics)
The Centre supported the teaching of Bioinformatics to the students of M.Sc. Neuroscience and M.Sc. Molecular Human Genetics (DBT sponsored programmes).
Many researchers have been using the facility for their research activity leading to publications.
Infrastructure facilities in the Bioinformatics Centre: As sanctioned. Details about staff members working in the Centre: The position of RA has been advertised. Types of services provided:Information, Computational and Internet. Educational activities with details of placement: Not applicable.
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Initiative to validate the outcome of Bioinformatics resources: Nil. Collaborative works/ initiatives: Collaborative work with several Institutes including AIIMS, DRDO, Manipal Institute, NIMHANS, ITRC, CDRI, etc are under progress and several others are being planned. 10. Papers publishedor presented in the conferences with reference: The researchers at this University have contributed towards publications in the following manner:
Sharma, Shashi, Joshi, G., Dash, P.K., Thomas, M., Athmaram, T.N., Kumar, J.S., Desai, A., Ravi, A., Patro, I.K., Rao, P.V., Parida, M.M. (2013) Molecular epidemiology and complete genome characterization of H1N1pdm virus from India. PLOS ONE (In press)
Mishra, B, Leishangthem, G.D., Gill, K., Singh, A.K., Das, S., Singh, K., Xess, I., Dinda, A., Kapil, A., Patro, I.K., Dey, Sharmistha (2013)A novel antimicrobial peptide derived from modified N-terminal domain of bovine lactoferrin: Design, synthesis, activity against multidrug-resistant bacteria and Candida. BiochimicaetBiophysicaActa 1828 (2013) 677–686.
Swarnkar, S., Goswami, P., Kamat, P.K., Patro, I.K., Singh, Sarika, Nath, C. (2013) Rotenone induced neurotoxicity in rat brain areas: A study on neuronal and neuronal supportiveCells. Neuroscience 230,172–183
SupriyaSwarnkar, Sarika Singh, PoonamGoswami, Ramesh Mathur, Ishan K. Patro, ChandishwarNath (2012) Astrocyte activation: A key step in rotenoneinduced cytotoxicity and DNA damage. Neurochem. Res 10:2178-89
Swarnkar, Supriya, Goswami, P., Kamat, P.K., Gupta, S., Patro, I.K., Singh, S., Nath, C. (2012) Rotenone-induced apoptosis and role of calcium: a study on Neuro-2a cells. Arch Toxicol?86(9):1387-97.
Dhanwani, Rekha, Khan, M., Bhaskar, A.S.B., Singh, Rajpriya, Patro, Ishan, Rao, P.V.L. and Parida, M. (2012) Charecterization of Chikugunya virus infection in human neuroblastoma SH-SY5Y cells: Role of apoptosis in neuronal cell death. Virus Res., 163: 417- 686.
Marimuthu A, Sahasrabuddhe NA, Barbhuiya MA, Goel R, Murthy KR, Muthusamy B, Subbannayya T, Nanjappa V, Kumar P, Kelkar DS, Pinto SM, Sharma R, Renuse S, Jalaj V, Gupta S, Shrivastav BR, Tiwari PK, Chaerkady R, Harsha HC, Sirdeshmukh R, Pandey A (2012). Body Fluids-a rich resource of cancer biomarkers. J Cancer Res Ther,8(5) Supplement 1:S33.
Sahasrabuddhe NA, Barbhuiya MA, Pawar H, Singh TD, Subbannayya T, Harsha HC, Shrivastav BR, Chaerkady R, Tiwari PK, Pandey A (2012). Identification of potential biomarkers for gallbladder cancer using a quantitative proteomics approach. J Cancer Res Ther,8(5) Supplement 1:S37.
Singh TD, Sharma P, Gupta R, Barbhuiya MA, Poojari S, Shrivastav BR, Gupta S, Tiwari PK (2012). Methylation patterns of MASPIN and STRATIFIN genes in gallbladder cancer and gallstone diseases. J Cancer Res Ther,8(5) Supplement 1: S45.
Sharma PR, Prakash R, Mishra G, Singh TD, Poojary S, Mehra NK, Tiwari PK (2012). Prevalence of smear positive pulmonary tuberculosis in different ethnic groups in India: Evaluation of public health. Public Health,126(4): 295-9.
Mishra G, Poojary SS, Raj P, Tiwari PK (2012). Genetic polymorphisms of CCL2, CCL5, CCR2 and CCR5 genes in Sahariya tribe of North Central India: An association study with pulmonary tuberculosis. Infect Genet Evolv, 12(5):1120-7.
Singh TD, Barbhuiya MA, Poojary SS, Shrivastav BR, Tiwari PK (2012). The liver function test enzymes and glucose level are positively correlated in gallbladder cancer: A CAncer Registry Data (CARD) Analysis from North Central India. Indian J Cancer49(1): 125-36.
Barbhuiya MA, Singh TD, Poojary S, Gupta S, Kakkar M, Shrivastav BR, Tiwari PK (2013). Gallbladder cancer incidence in Gwalior district of India: five year trend based on the registry of a Regional Cancer Centre. Indian J Cancer (in press).
Sharma SK, Rohilla MS, Singh TD, Poojary S, Singh A, Lowalekar KB, Tiwari PK (2013). Analysis of Autosomal dominant spinocerebellar ataxia type I in an extended family of central India. Indian J Hum Genet (in press).
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Impact shown by your centre on the growth of Biotechnology and allied areas: The Centre is helping in research and publication in various areas of biology.
Future activities:
We wish to develop facilities for video conferencing based teaching in Neuroscience, Molecular and Human Genetics, etc.
We are willing to establish a strong Neuroinformatics base here of course with support from NBRC, Manesar.
We are planning to develop important databases on Genomic profiles of tribes in MP; Ageing population and prevalent age-related problems in MP; Neurological disorders and disabilities in Indian population, Aquatic resource of MP, Endangered species and wild-life resource of MP, Microbial wealth of MP, etc.
The basic Bioinformatics Facility shall be extended for teaching and research to the faculty and students of this University.
Contact details: Name of the Coordinator: Prof. Ishan Patro Postal Address: Coordinator, Bioinformatics Centre, Jiwaji University, Gwalior 474011. Phone Number: 0751-2442789, 2231816, 2231616 Fax No.:2231816 Email:
[email protected], Website: www.jiwaji.edu, www.neuroscienceju.com
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Karnatak University, Dharwad Coordinator: Prof. B. B. Kaliwal Summary of the progress made by the center from its inception:
Bioinformatics centre established
Organized a three day National Workshop on Bioinformatics and its applications.
About 30 candidates participated in the workshop from various institutes
Hands on training for M.Sc Biotechnology and microbiology students in Bioinformatics
Research in Bioinformatics along with Biotechnology and Microbiology
Publications in Bioinformatics, Biotechnology and Microbiology
Major research activities in biotechnology and its related fields : Toxicology, Medical Microbiology and Epidemiology of microbes
Area of specialization of the center: The details of Research areas undertaken in next five years is as fallows :
Phytochemical and pharmacological studies investigation of selected medicinal plants.
Studies on Biochemical, Molecular and Histopathological changes in mastitis infected mice.
Studies on isolation, molecular Characterization of bacteria and their effect on milk biochemical parameters in bovine mastitis
Studies on molecular characterization of bacteriocin producing bacteria isolated from bovine mastitis
Major activities of the center during the year 2011-12:
Full pledged teaching of bioinformatics to the students.
M.Sc biotechnology and Microbiology students trained in bioinformatics with theory as well as hands on training
Research in Bioinformatics in progress
Publications in Bioinformatics/Biotechnology /Microbiology
Facilitated 20 M. Sc Projects with the support of BIF centre
Details about staff members working in the center: Tranieship-1, Studentship-1 & Project Asst-02 Types of services Provided: Teaching and Research and data mining. Educational activities with details of placements: M. Sc Biotechnology and Microbiology, almost all students are well placed in various MNCs and National and International research and Educational Institutes. Initiative to validate the out come of Bioinformatics resource : Being planned. Collaborative works/ Initiatives-Nil Databases/Software packages developed: Nil Papers published or presented in the conferences with reference: 14 papers published in International Journals.
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Initiation of R & D activities in Bioinformatics:
Identification and analysis of putative promoter motifs in bovine herpes virus. Bioinformation, (2012) ISSN 0973-2036 & 0973-8894 8(23), 1167-1170.
Evaluation of anticarcinogenic activity of clerodendrum serratum leaf extract on liver and kidney of 7, 12dimethylbenz[a] anthracene (DMBA) induced skin carcinogenesis in mice. Euro. J. Exp. Bio., 1(4), pp130-141.
Application of arginine, histidine and their mixture on economic traits of the silkworm, B. MORI L. DAV Int. J. of Sci., ISSN 2277-5536 1(2), 107-111.
Imidacloprid induced intoxication in soil isolate Brevundimonas SP. MJ. 15. Int. J. Life sci & Pharam Res., ISSN 2250-0480 2, 3.
Antidiabetic effect of ethonalic leaf extract Phyllanthus amarus in alloxan induced diabetic mice. Asian Journal of Plant Science and Research, 2 (1): 11-15.
Phenotypic characterization and risk factors of nosocomial Staphylococcus aureus from health care centers. Advances in Microbiology. 2, pp 1-7.
Effect of clerodendrum serratum leaf extract on biochemical and oxidative stress parameters of testis in 7, 12dimethyle benz [a] anthracene induced skin carcinogenesis in swiss albino mice. Recent res.in sci and tech.
Antidiabetic efficacy of ethanolic leaf extract of Nymphaea odorata in alloxan induced diabetic mice. Int. J. of Pharamacy and Pharmaceutical Sci. 4(2), 338-341.
Production of a- amylase using banana waste by Bacillus subtilis under solid state fermentation. European. J. Expt. Biol., 2(4):1044-1052.
Antihelmintic activity of stem bark extract of Bridelia retusa spreng. International. J. Appl. Biol. Pharmaceutical Tech., 3(4), 20-25.
Influence of imidaclopride on biochemical parameters in E.coli Int. J. Pharma. Biol. Sci., ISSN-0975-6299 3(4), B1155-1163.
Isolation and characterization of nitrogen fixing Bacillus subtilis strain as-4 from agricultural soil. International. J. of Recent Sci. Res., 3 (9), 762-765.
Biodegradation of imidaclopride by soil isolate Brevundimonas SP. MJ. 15. Int. J. Current Research ISSN 0975833X 4(10), 100-106.
Characterization of toxin genes in staphylococcus aureus isolated from milk of cows with mastitis. Int. J. Recent Scientific Research ISSN 0976-3031 3(10),841-846.
Immobilization of Bacillus SP.JB-99 for the production of Alkaline protease. Int. J.Recent Scientific Research ISSN 0976-3031 3(10), 847-852.
Details of training / Workshop organized and total no. of user trained:
A total of 74-Microbiology and Biotechnology PG students trained in Bioinformatics
One studentship and traineeship fellow trained
Two project assistant working on projects
Impact shown by your center on the growth of biotechnology and allied areas: In this you may highlight the details like number of the paper published/ number of paper published with the help of your center, how your center is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents & copyrights acquired and other services offered etc: Sensitization and awareness in the scientific and student community about the Biotechnology and Bioinformatics in particular. The centre is engaged in teaching bioinformatics to the graduate, Post-Graduate students and research students.
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Facilitate PG/Ph.D students for their teaching and research in life science subjects. Future activities: To provide training for Students, teachers and Research personnel in Bioinformatics and Creation of the databases.
Proposed Activity for the year 2013-14
To organized 2-3 days National workshop on Bioinformatics.
To provide Training for UG/PG Students from other Departments.
To further enhance the Infrastructure of the centre.
Facilitate the Research in Microbiology and Biotechnology with Bioinformatics perspective.
Proposed budget for 2013-14 Sl. No. I (i) (ii) II (i) (ii) (iii) (iv) (a) (b) (c) (d)
(Rs. in Lakhs)
Head
2013– 2014 (Rs. in Lakhs)
Non- Recurring Equipments (Any) Software (Any) Recurring Manpower (Project asst etc) 02 Asst Professors Other Expenses: (Contingencies, Stationary, AMC of Equipments, Consumables Communication Charges, Other Services and Rental Charges etc.) Travel Other Costs: Database/Journal etc. Training on Bioinformatics Studentship / Traineeship in Bioinformatics Minor equipments for vet lab Total
-5.00 9.6 5.00 0.9 2.00 2.50 2.00 5.0 32.0
*Allocation applicable for the entire year
Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
Prof. B. B. Kaliwal Postgraduate Department of Studies in Biotechnology, Karnatak University, Dharwad 91-0836-2779533(O) Mobile: 9449278648
[email protected] www.kud.ernet.in Prof. B. B. Kaliwal
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Karnataka State Women’s University, Bijapur Coordinator: Dr. S B Madagi A brief report of the work done by the Department of Bioinformatics, Karnataka State Women’s University, Bijapur in the year 2012-2013 is as under : 1.
The Centre has organized three day workshop cum hands on training on “Bioinformatics tools for genome analysis” .This was scheduled during 16th to 18th march 2012. The college lecturers from zoology and botany depts. of local degree colleges were invited for the training and five PG students of microbiology dept. of BLDE medical college and five PG students of general medicine dept. of Al Ameen medical college students were also invited for the training. Further, fifteen PG students of Biotechnology of our university were also the participants.
2.
Two students namely Geeta Hosmani and Mangala Hiremath of 4th semester of MSc. Bioinformatics were given studentship for completion of their project work.
3.
Miss Vipra Savadatti is working as Research Associate in the dept. of Bioinformatics since September 2012.
4.
Four Research scholars have registered for PhD programme in Bioinformatics
5.
As of now, using the facility of BIF centre we have published four research papers and they are as follows: i)
Shivakumar Madagi et al,. Identification of membrane associated drug targets in Borreia burgdorfer: 257 substractive genomics approach, Bioinformatics 2011, 6 (9) : 356-359
ii)
Vijayakumari Malipatil & Shivakumar Madagi : Substractive genomics approach for insilico identification and characterization of Novel membrane associated drug targets treponemapallidium subspecies palladium SS14, International journal of Pharmaceutical Sciences and research 2011, vol 2 (7) : 1855-1860
iii)
S. B. Madagi (2011) searching most likely DNA sequence using HMM, proceedings of IAENG, WCE 2012, London UK 4-6 July 2012 page 244-246.
iv)
Savita Deshmukh & Shivakumar Madagi (2012): “ A Chemogenomics based approach for deorphanization teticular receptor 4: An orphan receptor of nuclear receptor super family” Journal of natural science, biology and medicine, (Accepted for publication)
6.
A One day hands on training on “Homology modeling” was organized for Bioscience teachers of BLDEA’s first grade college on 2-6-2012.
7.
Similar kind of one training on “Access to Bio-data banks and the utility of BLAST & FASTA was arranged to the Biology teachers of SECAB first grade college on 06-10-2012
8.
Two day workshop cum hands on training is schedule during 8 to 9 Jan 2013. Dr. Sameer Chaudary CSO & cofounder of RASA life science informatics, pune and Dr. N. Rathankar of Apsara innovations Bangalore are attending the workshop as resource persons. The workshop will be inaugurated by scientist Prof. S. K. Saidapur, Vice president Indian National Science Academy (INSA) and former Vice Chancellor of Karnatak University Dharwad, on 08th January 2013 at 10:00 Am at Science Block of this University.
Proposed Activities: Four training programmes for on different areas for Biosciences teachers and research scholars of nearby institutions. Research Publications: Planned to publish at least five research articles Contact details: Dr. S B Madagi, Coordinator of BIF centre, Karnataka State Women’s University, Science Block, Jnana Shakti Campus Torvi Bijapur – 586 109 Email Id: madagisb @gmail.com ; Ph No: 09448897522
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Kumaun University, Bhimtal Coordinator: Dr. Veena Pande Summary of the progress made by the centre from its inception Programme was sanctioned on 22nd September 2006 with the support of Department of Biotechnology Ministry of Science and Technology Government of India. Infrastructure and other facilities have been established in a new campus of 2467 sq meters, costing Rs 3,15,46000 at Bhimtal inaugurated on 08th January 2010 by our honorable Chief minister comprising of 9 labs,3 lecture theatres, 1 library, 1 auditorium, 1 conference room including one Bioinformatics lab with 35 desktops, two high end servers along with 24 hours Wi-Fi broadband internet, printing and photostat facility and Scientific Software packages. We are exploring different available Proteomics and Genomics softwares for purchase. Centre has Organized various three days trainings for faculty and research scholars of different Universities & institutes. The facility is used exhaustively by all M.Sc. and PhD Life Sciences students & faculty of the University for carrying out their research smoothly. Subscribed print and online versions of few journals are available for the students and faculty members.
Major research activities in biotechnology and its related fields:i.
A systematic characterization of local flora and fauna at molecular level and to develop strategy for its conservation.
ii.
To develop methods for sustainable exploitation of the aromatic and medicinal plants.
iii.
To study the microbial biodiversity of the region with special emphasis on cold tolerant microbes.
iv.
Biodiversity and Biotechnological applications of mycorrhizal fungi of Uttarakhand.
v.
To study the Genetic diversity of casts and tribes of Uttarakhand.
vi.
To develop protocols for in vitro micropropagation of rare, endangered and important forest species of this central Himalayan region
Activities of the centre for the year 2012-2013:
Department has organized a three days hands on training on the topic ” “Structure and Sequence Bioinformatics “ ” from 22-23 march 2011 for faculty, research scholars and students from different universities to get maximum benefit.
Has initiated collaboration for quality research & trying to published good quality papers viz:
1.
Pande, V. Pandey, M. Sharma, N.K. Lohani, Y.C and Midhha, S.K. 2012 Ectomychorrizal DB: A Symbiotic Association database Bioinformation. 8(2): 104-106.
2.
Bhattacharjee, B, Talambedu, U., Sadegh, S., Goyal, A.K.PandeV., Nagaveni, M.B., Patil, V.M,Joshi, J.and Middha, S.K. 2011 Computer aided screening of inhibitors to 5-á. reductase type 2 for prostate cancer Bioinformation 6(7) 262-265
Conference Proceedings:
Pande,V. ,Middha,S.K., Talambedu,U., Sharma,N.K. Nagaveni,M.B. ,Bhattacharjee,B.,2011 “Identification of Natural Inhibitors of 5-a Reductase type 2 for prostate cancer.”In Indo-US Workshop on Biocomputing(ISB2011) NITCalicut,Kerela
Pande,V., Middha,S.K., Talambedu,U., Bhattacharjee,B., Sharma N.K., Pandey,M.,Nagaveni, MB.“Screening Of natural inhibitors of Neuraminidase type 1 in H1N1 for treatment of swine flu- An Insilco approach”. Paper Accepted for APBC 2012 in Melbourne Australia on the
Proposed activities of the centre for the year 2013-2014: 1.
Department is going to organize a two days workshop on Bioinformatics in March for faculty, research scholars and students from different Universities/Research Institutes.
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To develop more collaborations for better research quality which is having more practical implications.
3.
Communicate research papers for quality journals.
Infrastructure facilities in the Bioinformatics Centre a. Computer & Communication facility High end server – 1
Proxy Server – 1
Desktop Computers – 35
Laptops – 3
Multimedia projector – 2
Scanner – 1
Printers (high end) – 2 (Laserjet), 1 (inkjet) UPS – 5 KV (2), 2 KV (1)
Xerox Machine – 1
The computers are connected through LAN and 24 hrs very high speed Broadband internet facility is available. Scientific Software Packages- Windows Office 2007, Windows XP, Red Hat Linux, Accelrys, Gene, Rasmol ,SQL, Visual Studio etc b. Databases & other information resources1.
DATABASE ON ECTOMYCORRHIZAL DIVERSITY OF KUMAUN REGION
2.
DATABASE ON DIVERSITY AND STATUS OF MEDICINAL PLANTS OF INDIAN HIMALAYA REGIONAbout to complete.
Types of services provided The center provides the following services to the students, research fellows and faculty members of the university: (a)
E-mail & internet access
(b)
Trainings in bioinformatics
(c)
Online access to public domain databases
(d)
The center offers a good collection of various journals (online and print version) to all researchers &faculty memberwsof the university
Contact details Name of the Coordinator: Postal address:
Phone Number: Fax Number: Email: Website:
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Dr. Veena Pande Depatment of Biotechnology Kumaun University Bhimtal Campus, Bhimtal Uttrakhand- 263136 (05942) 248042 (05942) 248042
[email protected] [email protected] www.kubic.nic.in
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Lady Doak College, Madurai Coordinator: Dr. R. Shenbagarathai Program made by the Centre since its inception : The Bioinformatics infrastructure Facility was established at Lady Doak College, Madurai in Nov 2006 with the grants from DBT to enhance Biology teaching through Bioinformatics. It is currently catering to the needs of teachers and students (UG/PG/M.Phil/PhD) belonging to the various departments such as Biotechnology, Zoology, Botany, Chemistry, Physics and PG Diploma in Bioinformatics to carry out their regular practical lab exercise, project and research work. It also extends this facility to students from nearby colleges. The centre is also actively conducting research in the field of parasporin, biopolymer and Dengue virus-host interaction.
Major Research activities (2012-2013) Research Activities
Prediction of sequence and structural motifs involved in Dengue virus-host interaction.
Homology modeling and comparative structural analysis of wild and mutant human tyrosinase.
Development of Database on Dengue virus (DENVirDB).
In silico virtual screening of phytochemicals for effective inhbition of Dengue virus-host interaction.
Workshop/Training Conducted:
Five days National level workshop on “Bioinformatics: Tools and Applications” conducted from 24th to 28th September, 2012 for faculty, research scholars and Post graduate students (No of participants: 25).
Two days training on “BioLuminate software suite” for the science faculty on 4th and 5th December, 2012.
Papers published/Presented:
Ayyasamy Mahalakshmi, Kabilan Sujatha, Poornima Kani, Rajaiah Shenbagarathai (2012) Distribution of cry and cyt Genes among Indigenous Bacillus thuringiensis Isolates with Mosquitocidal Activity. Advances in Microbiology, 2, 216-226.
Kkani Poornima, Viswanathan Saranya, Periyasamy Abirami, Chandrasekaran Binuramesh, Ponnusamy Suguna, Peter Selvanayagam, Rajaiah Shenbagarathai (2012) Phenotypic and genotypic characterization of B.t.LDC391 strain that produce cytocidal proteins against human cancer cells. Bioinformation. 8(10): 461-465.
Saranya.V., Poornimakkani., Krishnakumari.M.S., Suguna.P., Binuramesh.C., Abirami.P., Rajeswari.V., Ramachandran.K.B. & Shenbagarathai.R (2012) Quantification of intracellular Polyhydroxyalkanoates by virtue of personalized flow cytometry protocol. Current Microbiology.DOI:10.1007/s00284-012-0198-0.
Asnet Mary J., Paramasivan R., Tyagi B.K., Surender Mohan, and Shenbagarathai R (2012). Identification of structural motifs in the E2 glycoprotein of Chikungunya involved in virus - host interaction. Journal of Biomolecular structure and Dynamics. iFirst, 1–9.
Shree T, Asnet JM, Kumar R, Mohan T, Shenbagarathai R. (2012) Pharmacophore modeling and Identification of Dengue virus RNA dependent RNA polymerase, Online J Bioinform., 13(1):130-144.
John Asnet Mary, Karuppiah Chandran Priyadharshini, Gurusamy Prabakaran Rubia Amal,Gunasekaran Ramya, Radhakrishnan Nithya, Morkondam Balasubramanian Ambika & Rajaiah Shenbagarathai. (2012) MEDDB: A medicinal plant database developed with the information gathered from tribal people in and around Madurai, Tamil Nadu. Bioinformation 8(8): 389-391.
Asnet Mary J, Kavitha S, VictoriaV, Paramasivan R, Shenbagarathai R, Selvanayagam P, Madhanmohan T.(2012) In Silico Prediction of putative epitopes in structural polyprotein of Chikungunya virus. Online Journal of Immunology 12(1) 1:1-7.
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Ramakrishnan K, Shenbagarathai R, Kavitha K, Thirumalaikolundusubramanian P and Rathinasabapati R. (2012) Selenium levels in person with HIV/Tuberculosis in India, Madurai city. Clinical Laboratory, 58.
J.Asnet Mary and R.Shenbagarathai presented paper on “Identification of sequence motifs of envelope glycoprotein involved in Dengue virus-vector interactions” 6th Conference of Medical Entomology 2012, organized by Centre for Research Medical Entomology (CRME, ICMR), Madurai during October 18-19, 2012.
T.Mowna Sundari, J.Asnet Mary and R.Shenbagarathai presented paper on “In silico prediction of highly interacting peptides of Ganodermin with the Envelope protein of Dengue virus serotype 2” 6th Conference of Medical Entomology 2012, organized by Centre for Research Medical Entomology (CRME, ICMR), Madurai during October 18-19, 2012.
G.Suganya, J.Asnet Mary, and R.Shenbagarathai presented a paper on Detection of polymorphism of mtDNA COI in Culex quinquefasciatus by Single Strand Conformation Polymorphism (SSCP) in 6th Conference of Medical Entomology 2012, organized by Centre for Research Medical Entomology (CRME, ICMR), Madurai during October 18-19, 2012.
Bioinformatics infrastructure facility usage:
Bioinformatics lab is being used for regular bioinformatics lab classes by the UG, PG, M.Phil, Diploma and research students of Biotechnology, Zoology and Botany Department (No of beneficiaries per day ~70).
No of projects completed using this facility – 12
Proposed activities in 2013-2014.
Conducting trainings/workshop in bioinformatics
In silico virtual screening and docking of small molecules at the site of Dengue virus-host interaction.
Exploring more collaboration with neighbour institutes.
Contact details Name of the Coordinator
: Dr. R. Shenbagarathai
Postal Address
: Bioinformatics centre Department of Biotechnology Lady Doak College, Narimedu, Madurai – 625002, Tamil Nadu.
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Phone No
:
91-452-2535575
Fax. No
:
91-452-2535575
Email
:
[email protected]
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Lucknow University, Lucknow Coordinator: Prof. U.N. Dwivedi Summary of the progress made by the center from its inception: Since its inception the BIF centre has conducted a total of 14 short term training programmes / workshops and a total of 8 long term training/project work, of 3-4 months duration each, during which a total of 310 persons belonging to students, teachers and researchers were trained in the area of bioinformatics. Centre is also actively involved in conducting research pertaining to the area of lignin metabolism, screening of plant secondary metabolites for their potential therapeutic applications as anti-inflammatory, anticancerous and anticholinergic molecules. In addition, a database for secondary metabolites is also being developed. Centre has been upgraded /enriched with regards to the softwares as well as hardwares.
Major research activities
In silico analysis of lignin metabolizing enzymes and genes.
Screening, identification, molecular docking of secondary metabolites for their therapeutic applications as antiinflammatory, anticancerous and anticholinergic molecules.
Area of Specialization of the center: Area of Specialization of the center is as follows:
Computational genomics, proteomics and metabolomics of lignin.
Secondary metabolites as anti-inflammatory, anti-cancerous and anticholinergic substances.
Major activities of the center during the year 2012-13:
Training of students, researchers and faculties. 104 persons were trained through short term and long term workshops/training programmes.
Molecular modelling studies on COMT and CCoAOMT with reference to alternate methylation of intermediates of monolignol biosynthesis pathway.
Molecular modelling studies with reference to substrate-inhibitor specificity and active site comparison of bacterial, fungal and plant peroxidases.
Molecular modeling studies on selected terpenes for their therapeutic potentials as anticancerous and antiinflammatory molecules, with reference to cyclooxygenases (COX).
Molecular modeling studies on selected Alkaloids for their therapeutic potentials as anticholinergic molecules with reference to Alzheimer’s disease.
Infrastructure Facilities in the bioinformatics center
Computer & Communication facility:
Windows server (2 in numbers); HP desktop system (16 in numbers, 500 GB hard disk, 4GB RAM); scanner, inkjet & laser printer (color & B/W); photocopier; power backup UPS; High speed 24 Hr internet connectivity.
Scientific software packages:
Discovery studio, Bio-suite, Exome Horizon, DNA Star, MATLAB, Genecheck, CLC workbench, MEGA, Ligand scout, Autodock, Chem sketch, Visual studio, SQL server.
Statistical Software for data analysis (Sigma Plot-12)
Details about staff members working in the center: Ms. Manika Awasthi, RA, M.Sc. Bioinformatics, working since December 3, 2012.
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Types of services provided:
Development of human resource by way of organizing workshop, hands on training in the area of bioinformatics
Conducting long term project work (3-6 months duration) for students of M.Sc. Bioinformatics and Biotechnology as part of their curriculum.
Conducting research in the area of lignin metabolism, screening of plant secondary metabolites for their potential therapeutic applications as anti-inflammatory, anticancerous and anticholinergic molecules.
Ph.D. programme in Bioinformatics has been initiated.
Educational activities with details of placement: Not applicable (NA) Initiative to validate the outcome of bioinformatics resources: — Collaborative work/ initiative: NA
Database/ software package developed:
Database of Secondary Metabolites (under preparation)
Paper published or presented in the conference proceedings with reference:
Papers published/communicated/ presented in the Conferences/Symposia/Seminars/Proceedings during the year 2012-13:
Paper Published: I.
Phylogenetic analysis, molecular modeling, substrate - inhibitor specificity and active site comparison of bacterial, fungal, and plant heme peroxidases. Swati Singh, Veda P. Pandey, Huma Naaz and Upendra N. Dwivedi. Biotechnology and Applied Biochemistry. 2012, 59, 283–294.
II.
Structure-function analyses and molecular modeling of caffeoyl–O- methyl transferase (COMT) and caffeoyl– CoA-O- methyltransferase (CCoAOMT): Revisiting the basis of alternate methylation pathways during monolignol biosynthesis. Huma Naaz, Veda P. Pandey, Swati Singh and Upendra N. Dwivedi. Biotechnology and Applied Biochemistry, 2012 (Accepted).
III.
Identification of Acetylcolinesterase Targeted Novel Alkaloids as Potential Therapeutic Agent for Alzheimer’s disease: An in Silico Approaches. Huma Naaz, Swati Singh, Veda P. Pandey, Priyanka Singh, and Upendra N. Dwivedi. Indian Journal of Biochemistry & Biophysics, 2012 (Accepted).
IV.
Purification and Characterization of Peroxidase from Papaya (Carica papaya) Fruit. Veda P. Pandey, Swati Singh, Rupinder Singh and Upendra N. Dwivedi. Applied Biochemistry and Biotechnology. 2012, 167, 367–376.
Paper Communicated: V.
Structural modeling and simulation studies of human cycloxigenase (COX) isozymes with selected terpenes: Implications in drug designing and development. Swati Singh, Veda P. Pandey, Huma Naaz, Priyanka Singh, and Upendra N. Dwivedi. Computers in Biology and Medicine, (2012).
National Conferences: VI.
Temporal Expression, Cloning and In-Silico Studies on Peroxidase during Carica Papaya Fruit Ripening. Veda P. Pandey, Swati Singh, Huma Naaz and Upendra N. Dwivedi, Proceedings of the National symposium on Bioinformatics challenges in the Postgenomic era, organized by Jammu University, February 1, 2012 (Poster presentation).
International Conferences: VII. Identification of Acetylcholinesterase Targeted Novel Alkaloids as Potential Therapeutic Agents for Alzheimer’s Disease: An in silico Approach. Huma Naaz, Swati Singh, Veda P. Pandey, Priyanka Singh, and Upendra N. Dwivedi. Abstract published in proceeding of 2nd International Conference on Pharmaceutics & Novel Drug Delivery Systems, San Francisco, USA. Pharm Anal Acta 3:1 (2012). DOI: 10.4172/2153-2435.S1.09.
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VIII. Structural Modeling and Simulation Studies of Human Cyclooxygenase1 (HsCOX1) with Anti-inflammatory Terpenoids: Implications in Drug Targeting and Designing. Swati Singh. Abstract published in proceeding of 2nd International Conference on Pharmaceutics & Novel Drug Delivery Systems, San Francisco, USA. Pharmaceutica Analytica Acta 3:1 (2012). DOI: 10.4172/2153-2435.S1.09. IX.
Reactive Oxygen Species (ROS) metabolism during Carica papaya fruit ripening and temporal expression, cloning and in-silico studies on peroxidase .V.P. Pandey, S. Singh, H. Naaz, U.N. Dwivedi , presented in the 4th EMBO Meeting 2012, at NICE, France from September 22-25, 2012.
Initiation of the R&D activities in Bioinformatics:
In silico analysis of lignin metabolizing enzymes and genes
Development of database for secondary metabolites
Screening, identification, molecular interactions of secondary metabolites for their therapeutic applications as anti-inflammatory, anticancerous and anticholinergic molecules.
Details of training & workshop organized and total number of user trained (March 2012-February 2013) S. No. 1.
Type
Title
2.
Workshop
Duration
Short term training Bioinformatics: Tools, programme Techniques and Applications Bioinformatical Approaches for Sequence Analyses and Protein Structure Predictions Workshop Recent trends in structural bioinformatics and drug designing Short term training Bioinformatical approaches for programme protein sequence analysis and structure prediction
3.
4.
No. of Level of Participants Trainee March 22-23, 20 Students of M.Sc. Biochemistry & 2012 Biotechnology July 13-14, 26 Faculties, research scholar 2012 and students October 1213, 2012
26
Faculties, research scholar and students
February 8-9, 2013
30
Faculties, researchers and students
Impact shown by your center on the growth of biotechnology and allied areas.: In this you may highlight the details like number of paper published/ number of paper published with the help of your center, how your center is promoting various activities of your organization and neighboring institutions, manpower trained, tools developed, patents and copyright acquired and other services offered etc.
Since the establishment of BIF center, about 302 persons, belonging to student, researcher and faculty were trained.
8 project works of 3-4 months duration each were carried out.
6 original research papers published in International journals.
1 original research paper published in National journal.
5 papers presented in international while that of 6 in national conference/symposia.
Proposed activities for 2013-14
Organizing short term/long term trainings/ workshops.
Conducting research in areas of
Computational genomics, proteomics, metabolomics pertaining to lignin and diseases.
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Screening of secondary molecules as potential therapeutic molecules against cancer with topoisomerases, caspases, cyclooxygenases etc. as targets.
Exploring drug like properties of Indian spices using QSAR analysis.
Development of biological databases and tools.
Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
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Prof. U.N. Dwivedi Department of Biochemistry, Lucknow University, Lucknow-226007 0522-2740132 Mobile: 09415022445
[email protected]:
[email protected] www.lkouniv.ac.in Prof. U.N. Dwivedi
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Madras Christian College, Chennai Coordinator: Dr. (Mrs.) C. Joyce Priyakumari Major activities of the centre during the 2012- 2013 1.
Staff members
S.No. 1. 2. 3.
2.
Name Aparna.K Aparna. K Sagaya Jansi. R
Designation Traineeship Research Assistant Research Assistant
Date of Joining 02.09.2011 01.12.2011 01.06.2012
Date of Relieving 30.11.2011 date date
Number of students trained in Bioinformatics Plant Biology & Biotechnology and Zoology Major students of UG – 90 PG – 45
Publication
Aparna K, Sagaya Jansi R, Arul Samraj D, Joyce Priyakumari C. 2012. Homology Modelling and Docking Studies of Phospholipase A2 enzyme of Apis mellifera. (Accepted in Journal of Current Pharmaceutical Research, 2013, Volume:10, Issue 1)
Received PDB entry validation report for the 3D structure of phospholipase A2 from Apis mellifera.
Papers published or presented in the conferences Aparna K., Sagaya Jansi R., Arul Samraj D and Joyce Priya Kumari C (2012) Interaction of â-amyrin, a bioactive compound from Euphorbia hirta with phospholipase A2, a toxin from Rhopilema nomadica. National Conference on “Highthroughput Technologies in Bioinformatics” organized by Department of Bioinformatics, Karunya University, Coimbatore on August 23-24, 2012
Workshops attended
Dr. Arul Samraj D, and Dr. Ebenezer.G.A.I., one day National Symposium on “Bioinformatics: Challenges in the post-genomic area” on February 2nd, 2012 at University of Jammu.
Dr. Arul Samraj D. 23nd Coordinators of BTISnet and BIF meeting, organised by BIF Centre, School of Biotechnology, University of Jammu and BIF Centre, School of Biotechnology, Mata Vaishno devi University, Katra held in February 3rd and 4th, 2012.
Aparna K. 3rd National Seminar on Computer aided Drug design held on December 29-30, 2011 organized by Bioinformatics Infrastructure Facility, Department of Bioinformatics, SVIMS University, Tirupati.
M Sc dissertations
Docking studies on the binding of ovipostion stimulant(s) binding protein (OSBP) of the butterfly Atrophanura alcinous with an oviposition binding stimulant Artistolochic acid from Aristolochia debilis. Sivakumar S. 2012.
Homology modelling of Pierisin and Putative inhibition of apoptosis in Pieris brassicae and Danaus plexippus. Swathi P.S. 2012.
Homology modelling of the proteins hm00021, hm00023 and hm00024 responsible for wing coloration of the butterfly Heliconius melpomene
Projects on progress
Aparna K, Sagaya Jansi R. 2012. In vitro Anti microbial activity and sequence dertermination of Hydnocarpus wightiana.
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Projects Completed
3.
Aparna K. 2012. Interaction of Wedelolactone, a bioactive compound from Eclipta alba with Phospholipase A2, a toxin from Rhopilema nomadica.
Aparna K, Sagaya Jansi R. 2012.Interaction of â-amyrin, a bioactive compound from Euphorbia hirta with phospholipase A2, a toxin from Rhopilema nomadica.
Aparna K, Sagaya Jansi R. 2012.Homology Modelling and Docking Studies of Phospholipase A2 enzyme of Apis mellifera.
Sagaya Jansi R, Aparna K. 2012. Docking study of Biflavonoids from Selaginella bryopteris and Bcl-2, regulating Anti-apoptosis in UV Induced and Oxidative Stressed cells.
New activities intend to carry out during the 12th Five Year Plan
Introduction of Allied Bioinformatics to all UG-Science course
Collaboration with Liverpool Hope University UK in the following areas:a.
M.Sc. Computer Science degree by Hope University incorporating the credits earned in MCC on Bioinformatics theory, practical and project as Applied Computer Science.
b.
Undertake training of Biology Teachers of UK on Bioinformatics
Minor projects in Bioinformatics to all PG students of Zoology, Botany, Physics, Chemistry, Mathematics, Computer Science
Undertake training of Young Lecturers of Colleges in Bioinformatics
E-content on simulated Bioinformatics practical to be made online
Periodical workshops to train the Biology Teachers of Higher Secondary Schools so as to enable them teach Bioinformatics to the students effectively and thereby good and talented human resources are drawn to basic science particularly to Life Sciences
Adoption of 10 Higher Secondary Schools (5 Government and 5 Aided) for conducting programs to promote basic science with particular reference to Bioinformatics
Continue to offer Foundation Course to the overseas students who are visiting MCC under Semester in India program.
Contact details: Contact person : Dr. (Mrs.) C. Joyce Priyakumari, Co-coordinator,
[email protected], Bioinformatics Centre of BTISnet, Madras Christian College, Chennai 600 059, Email:
[email protected] Phone No. : 044 – 22398895; +917708107447
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Maharani Lakshmi Ammanni College for Women, Bangalore Coordinator: Prof. M.B. Nagaveni Summary of the progress made by the centre during 2012-13
Research publications
Two national level workshops and one national level conference
Training programs for students of UG and PG course
Specialized training programs for Biotechnology Finishing School students (Govt. of Karnataka initiative and supported by ABLE) to undertake internship and placement in biotechnology industry.
A.
BIF has conducted workshops for pre university students to create an awareness about bioinformatics and its wide use in making biology learning more interesting and exciting
B.
Dr. M.B. Nagaveni and Ms. Usha T. have presented poster at India Bio 2012
Major research activities in biotechnology and its related fields : Area of specialization of the center : Database creation, training programme, Major activities of the centre during the year 2012-13 A.
BIF centre has successfully conducted :
Two national level workshops
One national level conference
B.
Publications as listed in question number 12
C.
Lecture workshops for UG, PG & Biotechnology Finishing School students
Infrastructure facilities in the bioinformatics centre
Computer and communication facility: 25 computers, A dedicated BSNL line for internet access, High end Server for internet.
Scientific software packages: Accelrys GCG package, Discovery studio, Quantum software, Discovery studio 2 (all are commercial packages and free ware Hex, RasMol, Qmol etc.)
Databases and other information resources: PFam (Protein database)
Details about staff members working in the centre : Ms. Usha T. : Research Associate
Collaborative works/initiatives (a)
Dr. Veena Pande, Co-ordinator of DBT-BIF centre at Kumaun University, Nainital (UK)
(b)
Dr. Arnab Sen, Co-ordinator of DBT-BIF centre at North Bengal University, Siliguri (WB) for Bamboo database creation.
(c)
With Apsara Innovations for conducting training workshops for software Packages
Types of services provided: Faculty members and students have used BIF for carrying out their various research activities. Facility was used to conduct interactive classes for school children of neighbourhood to promote the objective of popularizing biology.
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Educational activities with details of placement
Training program (bioinformatics diploma course) for students for placements in companies like Jubilant Biosys, Accenture, Molecular Connections, Quintiles, Empower, Clinigene (Biocon group), Biowares, Apsara Innovation center- etc. as bioinformatics professionals
Specialized training programs for students of Biotechnology Finishing School to prepare them for internship (to make them industry ready for the purpose of placement). Students are placed in Apsara Innovations, Quintiles, GSK
Initiative to validate the outcome of bioinformatics resources: a.
Phytomellitus database was prepared and is available at www.bicmlacw.org/bt/
b.
Bamboo database is published and is available at http://www.bamboodb.ind.in/
c.
Publications in international journals
d.
Placement of I batch of Biotechnology Finishing school students
Databases/software packages developed : As mentioned in question no. 10. Other database creation is in pipeline Papers published or presented in the conferences with reference:
Paper publications: Veena Pande, Sushil Kumar Middha, Nitin Kumar Sharma, Yogesh Lohani, Mayank Panday “Ectomychorrhizal DB: A Database for symbiotic Association” Bioinformation 8(2): 104-106 (2012) Madagi S, Patil VM, Sadegh S, Singh AK, Garwal B, Banerjee A, Talambedu U, Bhattacharjee B. “Identification of membrane associated drug targets in Borrelia burgdorferi ZS7- subtractive genomics approach. Bioinformation. 2011;6(9):356-9. Bhattacharjee B, Usha T, Goyal AK, Pande V, Joshi J, Middha SK. Screening of Natural Inhibition of 5-Alpha Reductase type 2 for treatment of Prostate cancer- An Insilico Approach Bioinformation 2011;6(7): 262–265 (PMC3124690
Paper/Poster presentation: Dr. M.B. Nagaveni & Ms. Usha T. presented poster titled “Diabetes in Relation to the Risk of Alzheimer disease- A Graph theoretical approach” at Bangalore INDIA Bio from Feb 6-8, 2012.
Initiation of R&D activities in Bioinformatics:
Completed Phytomellitus database
Completed BambooDb in collobration with NBU-DBT-BIF, Siliguri
Completed Ectomychorizal Database with KU-BIF, Nainital
Details of Training/workshop organized and total no. of users trained : 250
National level workshop on “An in silico and in vivo approach to prokaryotic gene expression” from March 1417, 2012
National level conference on computational biology, pharmaceuticals and life sciences from 23-24 November, 2012
15 days National level workshop on “Proteomics and Genomics leading to Drug Target” from 25th November to 9th December 2012
(a)
Free training to Pre-univ. students to create interest towards life sciences
(b)
Conducting Diloma and certificate courses in Bioinforamtics for students comprising both UG and PG courses.
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Future activities for 2013-14
Training program on commercial software packages (Accelrys Software-Discovery studio and CLC Bio NGS software)
Database preparation: Apetite regulating compound database and Phototoxic compound database.
Conducting national level conference and workshop
Creating human resource in bioinformatics catering to the industrial needs through conducting workshops and industry internship programs.
Contact details : Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
Prof. M.B. Nagaveni Maharani Lakshmi Ammanni College for Women, Malleswaram, Bangalore- 560 012 26692137, Mobile: 9886205533
[email protected] Prof. M.B. Nagaveni
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Maharani’s Science College for Women, Bangalore Coordinator: Dr. Kavitha B Summary of the progress made by the centre from its inception: The Bioinformatics Infrastructure Facility in the college was set up the in Dec 2006. The facility now has 2 servers, 10 PC’s, a network printer, scanner and copier. A dedicated internet connection has been provided to the facility. New Software procured this year is MATLAB. Training programs have been conducted frequently. Last year saw Basic Bioinformatics Course and an Advanced two Months Bioinformatics Course to our college and neighboring college post graduate students. Training programs for Bioinformatics Software were also conducted. Access for browsing for research material is being providedfor M.Phil, Ph. D & Post doc Students. The facility is being used by the faculty of our college and neighboring colleges. One paper entitled “Phylogenetic Analysis of Airborne Fungal Allergens using Bioinformatics Tools” has been published in the Journal of Computational Intelligence in Bioinformatics and one paper is accepted and two papers were communicated. Two students were taken for Traineeship project and were engaged in a part of research projects of BIF center.
Major research activities in biotechnology and its related fields :
Tool to analyze Drug likeness and pharmacokinetic properties of the ligand compound is being developed.
Tool to find the FAB sites in allergic proteins is being developed.
Molecular Dynamics and Simulated study on allergic proteins and their docked complexes.
Area of specialization: Microbiology, Structural Bioinformatics, proteomics and Computational Biology, docking, and Phylogenetic studies
Major achievements made during 2012-13:
Database on Antifungal plant compounds is completed
Identification of potent Antifungal plant compound against alkaline serine protease of A. fumigatus by screening and docking was completed and accepted for publication
Database on Indian Earthworms with Genome and DNA barcoding aspects and available in web.
Two trainees have completed their tenure with the following projects
Name Sankarasubramanian J Ithayaraja M
Project title Identification of potent Inhibitor for RNA dependent RNA polymerase (RDRP) of Dengue Virus serotype-3- A Molecular docking study. Virtual screening of plant inhibitors for thioredoxin-like protein (TLP) of Fusarium culmorum using FlexX
Infrastructure facilities in the Bioinformatics Centre: A.
Computer & Communication facility- 2 servers (one windows server 2000 and one redhat Linux server), 10 desktops with internet connection.
B.
Scientific Software packages- Genious Pro Ver.3.5.6, SYSTAT-12, FlexX-4, Corina, FlexPharm, Amber11, Dock6.0, Modeller v9.0, and Matlab.
C.
Databases & other information resources- Pfam Database for Geneious Pro Ver.3.5.6, My SQL server. Database on Airborne fungal allergens has been developed and available for public access in the url www.mscwbif.org/afad. Database on Indian Earthworms (http://www.mscwbif.org/earthworm/home.html).
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Details about staff members working in the centre: The faculties of the Microbiology Department are involved in the activities of the facility apart from one RA and two trainees Sl. No. Name 1. Dr. Kavitha B
Designation Associate Professor and Head (Coordinator) Dr. Arun Jyothi Associate Professor Mathias (Co- Cordinator) Ms. K.B.Pavithra Research Associate
2. 3.
Specialization Environmental Microbiology Environmental and Medical Microbiology Structural Bioinformatics and Proteomics
Working Since Since 1992
Status Permanent
Since 1996
Permanent
Since August 2009
Temporary
Educational activities
Training Programme for B.Sc., and M.Sc., Students and faculty.
Access for browsing for research material is being provided for M.Phil and Ph.D Students.
The Software usage (BIF) is provided to our college and neighbouring college students and staff members for their research.
Papers/ published or presented in the conferences: Publications:
Arun jyothi Mathias, PavithraK.B., Manjunatha K., 2011. “Phylogenetic Analysis of Airborne Fungal Allergens using Bioinformatics Tools”, Journal of Computational Intelligence in Bioinformatics, vol. 5(1) pp1-11.
Pavithra.K.B*., Kavitha.B., Prabha.R, Rajasekaran.G., “Identi?cation of potent an- tifungal plant compound against alkaline proteinase of Aspergillus fumigatus” accepted in International Journal of Fundamental and Applied Sciences.
Papers/posters
A poster entitled “Promoter prediction and genome comparison of six strains of salmonella enterica” has been presented in one day national seminar ‘Motif’ conducted in Bharathiar Univeristy on 19thOctober 2012.
A paper entitled “Identification of potent antifungal plant compound against alkaline proteinase of Aspergillus fumigatus by Molecular docking” has been presented in Two days National conference conducted by Maharani lakshmi Ammanni College for Women, Bangalore on 23rd and 24th November 2012.
A poster entitled “Phylogenetic analysis on metalloproteinases of Aspergillus fumigatus with various fungal species- An Insilico study” has been presented in Two days National conference conducted by Maharani lakshmi Ammanni College for Women, Bangalore on 23rd and 24th November 2012.
Papers communicated:
Pavithra K.B., Amirthagowri.A., Kavitha.B., “A comparative docking study for identification of potent plant inhibitor for two fungal proteins of Aspergillus fumigatus” communicated to Journal of Computational Intelligence in Bioinformatics.
Pavithra K.B., Kavitha.B., Niranjan Babu.N., “Database on Antifungal plant compounds” communicated to Bioinformation journal.
Initiation of R&D activities in Bioinformatics:
Phylogenic analysis of fungal proteins and airborne fungal allergens.
Molecular Modeling of Fungal allergen proteins and Insilco Inhibition study of the same with the IgE.
Screening and docking studies of potent plant inhibitors against fungal pathogenic proteins
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Promoter prediction and comparison of eight strains of Salmonella enterica.
Phylogenetic Analysis on Metalloproteinases of Aspergillus fumigatus with various fungal Species- An Insilico Study.
Identification of potent Inhibitor for RNA dependent RNA polymerase (RDRP) of Dengue Virus serotype-3- A Molecular docking study.
Details of Training/Workshop organized and total no of user trained Date
April-May 2012
June-July 2012
December 2012
Training programme
Two months advanced Bioinformatics certificate course Two months advanced Bioinformatics Certificate Course Basic Bioinformatics
Participants
Organized by
No. of users trained 29
M.Sc., Students
BIF and Department of Microbiology, Maharani’s college
M.Sc. Students
BIF and Department of Microbiology, Maharani’s college
16
M.Sc., students
BIF and Department of Microbiology, Maharani’s college
14
Impact shown by the Centre: Have been able to create awareness of Bioinformatics to undergraduate and post graduate students. Make internet facilities more accessible to government college students, girls in particular
Proposed activities for 2013-14
Training for students and staff will be continued
Database of Ribosome inactivating proteins from plant origin
Training program for Govt. College teachers in collaboration with Dept. of Collegiate Education in Karnataka.
Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
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Dr. Kavitha B Coordinator, Bioinformatics Infrastructure Facility, Maharani’s Science College for Wn omen, Palace Road, Bangalore- 560001 080-22371416
[email protected] www.mscwbif.org/ Dr. Kavitha B
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Maharshi Dayanand University, Rohtak Coordinator: Dr. S.K. Gakhar Program made by the centre since its inception : Bioinformatics Infrastructure Facility was established at Maharshi Dayanand University Rohtak in the year 2009. The post graduate course in bioinformatics was commenced in year 2010. It has become an independent department in the year 2012. Adequate infrastructure with hardware and software has been developed at the centre and the facilities are being used by the faculty members and students of various departments under the Faculty of Life Sciences as well as some other neighbouring institutions of higher education. Department has also started conducting Pre- Ph.D./Ph. D. courses. In addition, the centre is also supporting the teaching of course of Bioinformatics in various departments under the faculty of life sciences at Maharshi Dayanand University, Rohtak. The details of activities are given below1.
Courses supported: M.Sc. (Bioinformatics) and Pre-Ph.D (Bioinformatics)
2.
HR-training imparted by BIF:
3.
a)
Workshop organization
b)
Summer training to undergraduate students
c)
M.Sc. Dissertation training to M.Sc. students
d)
Traineeship
e)
Studentship
f)
Faculty member participation as resource persons.
Achievements: a)
Workshop organized: A 3-days national workshop was organized during 21st – 23rd October, 2011, on “Molecular Evolution and Phylogenetics”, with 20 participants.
b)
Summer training: 1-month summer training was imparted to 6 students of B.Sc. (Bioinformatics)- IV semester, during 1st – 31st July, 2012, as listed below:
c) Sl. No
i)
Ms. Manisha, GVM Girls college, Sonepat, Haryana.
ii)
Ms. Ritu, GVM Girls college, Sonepat, Haryana
iii)
Ms. Anita, GVM Girls college, Sonepat, Haryana
iv)
Ms. Jyoti, GVM Girls college, Sonepat, Haryana
v)
Ms. Shweta, GVM Girls college, Sonepat, Haryana
vi)
Ms. Cheenu, GVM Girls college, Sonepat, Haryana
M.Sc. dissertation: Training was imparted to 09 students of M.Sc. (Bioinformatics)-IV semester, during JuneJuly, 2012, as detailed below: Name of student
1. 2. 3.
Ms. Monika Kumari Ms. Rajani Ms. Sween
4. 5.
Ms. Preeti Ms. Rekha
Name of training Topic supervisor Dr. M. Kulharia Study of structural transitions between PKM1 and PKM2. Dr. M. Kulharia Study of druggable targets of coagulation factor II (thrombin) Dr. M. Kulharia Comparative assessment of the homology modelling tools with respect to Factor V-B domain. Dr. M. Kulharia Study of druggable targets of coagulation protein factor IX. Dr. M. Kulharia Study of various binding sites on the surface of Gladomain in coagulation protein factor APC.
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Ms. Neeraj Saroha Ms. Sheenu
Dr. M. Kulharia Dr. Ajit Kumar
8. 9.
Ms. Shikha Mukhija Ms. Nisha Yadav
Dr. Ajit Kumar Dr. Ajit Kumar
10.
Ms. Sakshi Piplani
Dr. Ajit Kumar
11.
Ms. Sonia Saini
Dr. Ajit Kumar
Study of putative druggable binding sites of Factor XII 2D- and 3D- QSAR analysis of para (p, p’) substituent of DDT analogues. Phylogenetic analysis of some orphan nuclear receptors. 2D- and 3D- QSAR analysis of alkyl substituent of DDT analogues. Virtual screening of PPAR-Y modulator analogues and pharmacophore modelling. Phylogenetic analysis of some orphan nuclear receptors.
Traineeship: 3 candidates (Post M.Sc.) were imparted paid traineeship of 6 months as detailed below:
d)
Sl. No
e)
Name of student
1. 2.
Mr. Arunaditya Ms. Shikha Agrawal
Name of training supervisor Dr. S.K. Gakhar Dr. Ajit Kumar
3.
Ms. Tamanna Sharma
Dr. Ajit Kumar
Topic
Design & development of Indian malaria vector database-MALVEC Design & development of Indian malaria vector database-MALVEC
Studentship: 07 students were provided studentship during their M.Sc. (Bioinformatics), as listed below: i)
Mr. Piyush Agrawal
ii)
Mr. Vishwajeet Mishra
iii)
Ms. Radhika Khanna
iv)
Ms. Preeti Rana
v)
Ms. Bhawna
vi)
Mr. Amit Sharma
vii)
Ms. Priyanka Walia
f)
Faculty member participation as resource person in bioinformatics at external events:
i)
Dr. Ajit Kumar
S.No. 1
Date 18th Feb, 2012
Event National seminar on “Frontiers in Environment Research”
2
20th Oct, 2011
National Workshop on “Mol. Evolution & Phylogenetics”
3
11th May, 2011
Short term training course on Mol. Biology
ii)
Dr. M. Kulharia
S.No. 1
2
Event National seminar on “Molecular Techniques – The Face of Modern Sciences 14th -15th March 2012 Biosparks
3 4.
28th February 2012 2nd-4th Nov 2011
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Date 24th Oct 2012
Bioinformatics workshop National Conference on Thermodynamics of Chemical and Biological Systems
Venue SLP College, Jiwaji Univ, Gwalior MD University
Topic of Lecture Integrating QSAR methods: A new paradigm in pesticide design Mol. Evolution & Phylogenetic tree: Tools & Techniques MD University An overview of Bioinformatics tools
Venue MD University
JNU
Topic of Lecture Insight on Membrane protein interaction
Coarse grained md simulation Amity University HMM and ANN MD University FVIII activation by lipid interaction
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Publication details of faculty member (2011-12):
Chiara Mencarelli, Gerard H. Bode, Mario Losen, Mahesh Kulharia, Peter C. Molenaar, Robert Veerhuis, Harry W. M. Steinbusch, Marc H. De Baets Gerry A. F. Nicolaes and Pilar Martinez-Martinez (2012) “Goodpasture antigen-binding protein/ceramide transporter binds to human serum amyloid P-component and is present in brain amyloid plaques”, J Biol Chem 287(18):14897-911.
Vandana Saini and Ajit Kumar (2012) “QSAR Analysis of Saquinavir Analogues (Peptidomimetics) as Potent HIV-Protease Inhibitors”, S. A. J. Exp. Biol., 2(3):118-127.
Ajit Kumar, P.J. John and I. Soni (2012) “Enrichment and isolation of endosulfan degrading microorganism from natural resources”, J Biod. Env. Sc. 2(60): 41-53.
Parihar SS, Kumar Ajit, Kumar Ajay, Gupta R.N., Pathak manoj, Shrivastava Archana and Pandey A.C. (2012) “Physico-chemical and Microbiological analysis of underground water in and around Gwalior city, MP, India”, Res. J Rec. Sc. 1(6): 62-65.
Ajit Kumar and Rita Sharma (2012) “Production of alkaline pectinase by bacteria (Cocci sps.) isolated from decomposing fruit materials”, J Phytology 4(1): 01-05.
The Future Activities:
To develop data base on Malaria Vector in Indian perspective.
To organize hand on training, workshop and short term training programmes.
To establish collaboration with other institutes and BTITS, NET centres for information resources and expertise
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Manipur University, Canchipur Coordinator: Prof. N. Irabanta Singh Summary of the progress made by the centre from its inception: Comprehensive databases for medicinal fungi, Blue Green Algae, wild edible fungi and pollen grains found in Manipur and database for aerobiological Data for Manipur have been started at the BIF centre. Bioinformatics related four papers were presented at various national conferences. Some softwares for bioinformatics including one unit of Geneious Pro Ver. 5.3 has been procured. More than 290 persons from different professions had gained knowledge about various bioinformatics related works and tools which they have applied in their research works. So far 8 postgraduate students had received training on in-silico sequence analysis and phylogenetic analysis, 3 postgraduate students have been undergoing training on aerobiological database constructions.
Major research activities in biotechnology and its related fields : i.
DBT sponsored project on “Developing a Digital Database on Bio-resources of North East India - Through a Network Approach among North Eastern States.” Eight institutes from North East India are involved in this project. Prof. N. Irabanta Singh as coordinator for period of three years (2012 -2015).
ii.
Database construction for Aerobiological Data for Manipur, medicinal fungi found in Manipur, wild edible fungi found in North-Eastern States, etc.
Area of specialization: Aerobiological Database development and Bio-resources Database development
Major achievements made during 2012-13: i.
Various training programmes were organized for M.Sc. students (Life Sciences, Biotechnology and Biochemistry) and research scholars.
ii.
Continuation of development of comparative database for Blue Green Algae found in the rice field soil of Manipur and other North- Eastern States.
iii.
Continuation of development of a digital database networks in Aerobiology (Aerobiological Data) for Manipur state, India and then for whole North- East India has been.
iv.
Continuation of development of comprehensive databases for wild edible fungi including medicinal fungi found in North-Eastern States of India is initiated.
v.
Continuation of development of comprehensive databases for pollen grains found in Manipur States.
Infrastructure facilities in the bioinformatics centre: A.
Installed a Leased line Internet connection through BSNL, Telecom Department, Manipur.
B.
Available Hardware: i)
Two (2) Red Hat Linux Servers (High and Medium end, one for proxy).
ii)
Ten (10) Desktop Computers with Windows-XP Operating system.
iii) Two (2) Printers (one colour Printers and one black and white Printer). iv)
Two (2) Scanners (HP Model), A Digital Copier (Model-Canon)
v)
UPS-APC/Emerson online UPS System Capacity (6KVA, 230VAC).
vi)
Solar Cell for uninterrupted power supply during emergency.
vii) A Router & A Sony LCD Projector viii) Desk & bench
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Available Software: i)
MS Office 2007 and MS Visual studio 2008.
ii)
One unit of Geneious Pro Ver. 5.3 (Single User Academic Licenses)
iii) BioDiversity Pro-32, MEGA5.03, BioEdit, ClustalW2, pDRAW32 iv) D.
Rasmol and other online Bioinformatics tools.
The centre is providing Information Retrieval Facility to the students, research scholars and faculty members under School of Life Sciences (Life Sciences, Biochemistry and Biotechnology) by providing internet and e-journal accessibility through the DeLCON Core Library.
Details about Staff members working in the centre: Sl. No. 1.
2.
Name
Designation
Specialization
Dr. N. Irabanta Singh
Prof. of Life Sciences & Coordinator
Aerobiology, Plant Pathology & Bioinformatics
Huidrom Beebineeta Devi
3.
Brahmacharimayum Bipinkumar Sharma
4. 5. 6.
Bioinformatics, Working on database Project Fellow construction for Aerobiological data of Manipur. Bioinformatics, Working on Secondary Project Fellow data compilation for Airborne pollen grains.
Working Since 29th April, 2009
Status Permanent
June, 2010 till now Temporary June, 2010 till now Temporary March, 2012 till now
Sunibala Waikhom
Traineeship
M.Sc. Bioinformatics
Temporary
Vacant but advertised
studentship
M.Sc. Life Sciences/Bioinformatics/Biotechnology
-
-
Vacant
Laboratory Attendant
Undergraduate
-
-
Educational activities i.
The centre has been giving training to the students of M.Sc. Life Sciences and training will be extending to research scholars also for Manipur University.
ii.
M.Sc. students, Research scholars and faculty members of the Institute are availed of the uninterrupted internet facility and others E-Resources available at BIF centre.
iii.
One B.Tech. (Genetic Engineering) student from Sam Higginbotton Institute of Agriculture, Tech. & Sc., Allahabad is being trained at the centre on basic tools of Bioinfornatics.
Papers/ published or presented in the conferences: i.
Singh N.I. (2012). Bioinformatics in Aerobiology- An Indian Perspective. 17th National Conference of Indian Aerobiology Society on Impact of Airborne Microbes, Pune (13th to 15th Dec. 2012).
ii.
Devi H. B., Shrivastava Karuna and Singh N. I. (2012). Aerobiolocal Database Construction For Manipur (Adman Database) - A Priliminary Study, 17th National Conference of Indian Aerobiology Society on Impact of Airborne Microbes, Pune (13th to 15th Dec. 2012).
iii.
H. Beebineeta Devi and N. Irabanta Singh. (2011). QSAR: In Silico Study on Amantadine Hydrochloride Analogous Molecules for the Development of possible New Lead Molecules against Dengue Virus. National Conference, Manipur University.
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N. Irabanta Singh. (2011). Bioinformatics, computational and system biology- future perspective for North-East India. National Symposium on Biodiversity Status and Conservation Strategies with special reference to North-east India held at Manipur University, Manipur.
Initiation of R&D activities in Bioinformatics: DBT sponsored project on “Developing a Digital Database on Bio-resources of North East India - Through a Network Approach among North Eastern States.” Manipur University is main institute. Other collaborating institutes include i.
D.M. College of Sciences, Manipur
ii.
Gauhati University, Gauhati, Assam
iii.
Nagaland University, Makokchung, Nagaland
iv.
Mizoram University, Aizawl, Mizoram
v.
The Mountain Institute of India, Sikkim
vi.
North Eastern Regional Institute of Sciences & Technology, Nirjuli, Itanagar
vii.
Tripura University, Agratala Prof. N.Irabanta Singh acts as coordinator for period of three years (2012 -2015).
Details of Training/Workshop organized and total no of user trained: Seminars and Training (organized by the BIF Centre): Title of the Seminars/ Training Organized
Date of the Event
1. Copus and ScienceDirect Usage 2. Google Map Maker: Its Application and Prospects 3. Bioinformatics Approach for Sequence Analysis using online Bioinformatics Tools and Database. 4. Bioinformatics Approach for Sequence Analysis using online Bioinformatics Tools and Database. 5. One day workshop cum hand on training on “Google Map Maker – Mapping Manipur”.
24th Sept. 2010 16th Dec. 2010 4th-5th Nov. 2011 17th-18th Nov. 2011 22nd October, 2012
Total Number of User Trained 20 30 20 20 200 delicates from different professions.
National Workshop (Sponsored by DBT/GOI and organized by the BIF Centre): Title of the National Workshop Organized Computational and System Biology
Date of the Event 30th-31st March, 2011
Total Number of User Trained 30 Research scholars, Scientists and Lecturers from different Institutes.
Impact shown by the Centre:
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i.
A number of students have gained knowledge about the basic and software of bioinformatics and its related areas from the various training and workshop organized by the centre.
ii.
Research scholars from different university show interested in incorporating bioinformatics tools in their research works.
iii.
The BIF library has a good collection of the latest computer books and bound hard copies of journals.
iv.
The centre has e- journal access facility through NER-DeLCON sponsored by the DBT. A total of more than 600 (six hundred) issues for different scientific journals have been downloaded and complied so far. Further, compilations of more accessible journals are in progress.
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Proposed activities for 2013-14: 1.
To continue the development of a digital database networks in Aerobiology (Aerobiological Data) for Manipur state, India and then for whole North- East India.
2.
To continue the development of comparative database for Blue Green Algae found in the rice field soil of Manipur and other North- Eastern states is in progress.
3.
To continue the development of comprehensive databases for medicinal fungi found in Manipur, India is just initiated.
4.
To continue the development of comprehensive databases for wild edible fungi found in North-Eastern States of India is initiated.
5.
Continuation of development of comprehensive databases for pollen grains found in Manipur States.
6.
To organize National Workshop on “Current trends in Molecular Phylogenetics & Bioinformatics” to be held at the centre during 2013 and the same type will be organized annually.
7.
To provide short term trainings/workshops that are related to Bioinformatics and various research fields.
8.
To collaborate in research activities with other North-East Bioinformatics Centres.
Contact details: Name of the Coordinator Postal Address
Phone Number Fax No. Email Website Name of Contact Person
Prof. N. Irabanta Singh BIF Centre, Department of Life Sciences, Manipur University, Manipur – 795003. 0385 - 2435064 (0385) 2435965
[email protected] [email protected] http://en.manipuruniv.ac.in/ Prof. N. Irabanta Singh
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Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu Coordinator: Prof. K. Veluraja Summary of the progress made by the centre from its inception: The Bioinformatics Infrastructure Facility is centre was established at the Department of Physics in the year 2007. From its inception, the centre has progressed remarkably and contributed to the scientific community through its research facilities and developed human resources to work in the field of Bioinformatics and Molecular Biology. High level scientific softwares are purchased that includes AMBER12 towards increasing the computational efficiency. Research works have been published in journals acclaiming wide readership. Apart from the scientific contribution, the centre is focusing at the development of human resource in the emerging fields of Bioinformatics. After having started as a Bioinformatics Infrastructure Facility, the centre continues to use its expertise and specializes in the carbohydrate conformational study and proteincarbohydrate interactions.
Major research activities in biotechnology and its related fields : The structural specificity of protein-carbohydrate interactions are exploited through molecular dynamics simulations and molecular modeling of biologically important sialylglycans which includes human milk sialyloligosaccharides are carried out. The conformational models of human milk sialyloligosaccharides are deposited in the 3DSDSCAR database. The interactions of sialylglycans especially sialyldisaccharides with influenza Hemagglutinin is investigated using molecular dynamics simulations of 10ns duration. An atomistic level analysis of binding specificity is carried out and our results agree well with the experimental results. The research collaboration with AIST, Japan has reduced our computer time. This work has been published in the Journal of Biological Chemistry. The atomic level investigation on the interactions between proteins and carbohydrates has been an interest of the centre from its inception. The interactions of gangliosides with Botulinum neurotoxin had been studied using molecular dynamics simulations. Papers are published in Journal of Biomolecular Structure and Dynamics and Journal of Structural Biology. Genome analysis on Glycosylation is also being carried out at the centre. Extensive bioinformatics analysis is being done in this regards.
Area of specialization: 1.
Carbohydrate conformational analysis
2.
Protein-carbohydrate interactions through molecular dynamics simulations
3.
Software development for Genome and Proteome analysis
Major achievements made during 2012-13: 1.
Published two papers in highly cited journals
2.
More than 10 conference papers
Infrastructure facilities in the Bioinformatics Centre: 1.
High Power Computational Facility with UPS
2.
Dedicated internet, phone line and Books for Bioinformatics
3.
3DSDSCAR database and CCSD database for carbohydrate structures
Educational activities Students and Scholars of the physics department and other departments of the University are using this centre for their research and academic work. M.Sc and M.Phil students are carrying out projects in Bioinformatics. The students from M.Sc Biotechnology are given hands on training about vmd (visual molecular dynamics) and Protein Data Bank.
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Papers published or presented in the conferences: Journals: 2 (four more manuscripts under preparation) Conferences : more than 10
Publications: 1.
Molecular Modelling and Molecular Dynamics Studies of GD1A, GD1B and their complexes with BoNT/B-Perspectives in interaction and specificity S. Venkateshwari and K. Veluraja Journal of Structural Biology (2012) 180 ; 497-508.
2.
Theoretical investigation on the binding specificity of sialyldisaccharides with Hemagglutinins of Influenza A virus by MD simulations Thanu R. K. Priyadarzini, Jeyasigamani F. A. Selvin, M. Michael Gromiha, Kazuhiko Fukui and K. Veluraja, Journal of Biological Chemistry (2012) 287, 34547-34557.
Initiation of R&D activities in Bioinformatics: A Research collaboration with National Institute for Advanced Industrial Science and Technology, Japan has been initiated during 2009.
Details of Training/Workshop organized and total no of user trained To facilitate the exchange of scientific ideas and research interests, the centre has planned to conduct a two days national level seminar on structural Bioinformatics during the second week of March for the benefit of about 100 participants.
Impact shown by the Centre: The centre has impacted the research quality in the University level by its publications and by offering a value added certificate course.
Proposed activities for 2013-14
To promote the centre as a “Dedicated centre for carbohydrate conformational study” and nodal centre of “three dimensional structural databases for carbohydrates”
Accelerating the research on protein-carbohydrate interactions using theoretical methods
Exploring the molecular basis of diseases.
Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
Prof. K. Veluraja Coordinator – Bioinformatics Infrastructure Facility, Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu +919486133130, +91-462-2336768 +91-462-2334363
[email protected],
[email protected] www.msuniv.ac.in, www.3dsdscar.org Prof. K. Veluraja
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Maulana Azad National Institute of Technology, Bhopal Coordinator: Dr. K.R. Pardasani Summary of the progress made by the centre from its inception: MANIT is running M.Tech. Program in Bioinformatics since July 2006 and B. Tech. Program from July 2007.Three batches of M.Tech Bioinformatics and two batches of BTech Bioinformatics have passed out and all the students are well placed in India and abroad.More than twenty scholars have completed their PhD in the areas of Mathematical and Computational Biology,Bioinformatics and related disciplines under the faculty of MANIT, Bhopal.MANIT has organized about twenty training programs and conferences in bioinformatics. Department of Mathematics has also launched MTech Program on Computational and Systems Biology in July 2012. Also a Special Group on Bioinformatics have been launched in October 2009 under Technical committee 5 of International Federation of Information Processessing (IFIP) which has been upgraded to Work Group on Bioinformatics since April 2010. Further special Interest Group on Bioinformatics has been launched under Computer Society of India since April 2010 and all its activities are coordinated by this centre.
Major research activities in Biotechnology and its related fields : The institute plans to develop a versatile research team in the following areas of computational biology1.
Soft, Fuzzy,Vague and Rough Set Based Soft Data Mining in Bioinformatics and Computational Biology.
2.
Thermal Modeling of Cancer
4.
Modeling and Analysis of Biological sequences & Gene Expression
5.
High Performance Computing for Bioinformatics & Computational Biology.
6.
Computational Phylogenetics
7.
Neuroinformatics , Computational Neuroscience and Computational Cell Biology
8.
Machine Learning Models in Bioinformatics & Computational Biology.
Area of Specialization of the Centre: Mathematical & Computational Biology.
Major activities of the centre during the year 2012-2013: An Indo-Austrian project on Thermal Modelling of Cancer is in progress Guiding PhDs and MTech Dissertations in the fields of Bioinformatics, Mathematical, Computational and Systems Biology. Teaching in above areas in BTech , MTech and PhD Programs in Bioinformatics Research and Development in above areas
Infrastructure facility in the Bioinformatics Centre A.
Computer & Communication facility: 30 PIV computers along with one Quad core (high end) server, one Dual core medium) server. 5 laser printer’s Desk-jet printer, 1 photocopier and scanner one server high end (Procurement under process)
B.
Scentific Software Packages: At present we use online and free software‘s like BLAST, CLUSTAL - W , PHYLIP, RASMOL, PRIMER 3, EMBOSS, Autodoc, Hex,, Chemsketch, Hyperchem, VMD, , Pymol,Modeller,SPDBV, BIOEDIT, PHYLIP, GCG ACCELYRS, WEBCUTTERS ,Flex X etc.
C.
Database and other information resources: The online databases like NCBI, EMBL, PDB, CATH, SCOP, EXPASY, UNIPROT, GENBANK etc
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Details about staff members working in the centre: (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status): There are 10 Research Fellows working in the area of Bioinformatics. Mathematical and Computational Biology: Name of staff Dr. K.R.Pardasani Dr. Namita Shrivastava Dr. Madhvi Shakya Dr Neeru Adlakha
Designation Professor Professor Associate Professor Associate Professor
Dr. Usha Chouhan Dr. Chandan k. Verma Dr R.S. Thakur
Assistant professor Assistant professor Associate Professor
Research Assistants:
Specialization Computational Biology,Datamining Computational Genomics, Biomathematics, Biocomputing Mathematical & computational Biology Computational Phylogenetics Modelling, Gene expression Data Mining
Period of working 28 years 24years 23 years 21 years 11 years 13 years 10 years
Priyanka Solanki, Amita Jain
Types of services provided: I)
Training programmes/ workshops in the area of bioinformatics to provide exposure to basic skills of bioinformatics to the students of biotechnology/lifesciences, physical sciences and IT, from other institutes of our region and country. II) Guiding research for Ph.D degree and educational Programmes like B-Tech & M.Tech in the area of Bioinformatics.
III)
Consultancy.
IV)
Development of software and databases.
Educational activities with details of placement: Three candidates have been awarded PhD degree in the during the sessionand all of them are well placed. Initiative to validate the outcome of bioinformatics resources: I)
Feedback of participants in training / workshops.
II)
Feedback of students and research scholars of educational programme.
Collaborative works/ Initiatives: We have TBNET Project of DBT in collaboration with the institutes :JALMA, Agra,IISc Bangalore,TRC Chennai,TRI Banglore,JNU New Delhi,IOB Banglore Databases / Softwares packages developed: We have developed software packages for: 1 Haplotyping 2. Molecular Cutter 3. Ribo-pred server 4. ProCos 5.PSSMCalculator 6. Soft association rule mining in peptide sequences
Papers published or presented in the conferences with reference: Paper published- 15
Presented in conferences –16
Initiation of R& D activities in Bioinformatics: Since the faculty and students of MANIT are strong in the computational skills therefore we have focus on research and software development in the areas of bioinformatics. We have Ph. D Scholars with background of mathematics, biotechnology, computer science, IT and statistics. We have a very good interdisciplinary group to carry out teaching , research and software development in the areas of bioinformatics. We are developing computational techniques and softwares for soft set, rough set, fuzzy set and Vague set based approaches for soft data mining in Bioinformatics and Computational biology.We are also developing models in the areas of Computational neuroscience,computational Cell biology, Riboswitches based drug design and thermobiomechanics.
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Details of Training / Working organized and total no. Of user trained: Seven students of various institutes of India were trained under Project training. Impact shown by your centre on the growth of biotechnology and allied areas.: In this you may highlight the details like number of paper published / number of paper published with the help of your centre, how your centre is promoting activities of your organization and neighboring institutions , manpower trained , tool developed , copyrights acquired and other services offered etc Among all the NIT’S, MANIT, Bhopal has taken lead by starting B.Tech, M. Tech and PhD programmes in the area of bioinformatics. Also MANIT has taken lead among all NIT’S in organizing training programmes and conferences in the areas of bioinformatics since July 2004.. Three candidates have been awarded PhD degree during the session; A good number of candidates from different institutes come to our institute for Project/ Training. About 15 papers have been published in journals of international repute.A women scientist project has been awarded by DST in the department in the area of mathematical and computational biology. One Phd Scholar was selected selected for Split site Common wealth fellowship in the field of computational cell biology
Future activities 1.
Third IFIP International Conference on Bioinformatics during September23-26,2013
2.
Third International Conference of GAMS on Computational & Integrative Sciences during September 22-26,2013
Contact details:
Name of the Coordinator: Dr. K.R.Pardasani, Postal Address : Professor, Department of Mathematics, MANIT, Bhopal Phone Number: 0755-2671633 , Mobile: + 91 – 9425358308 Email:
[email protected] ,
[email protected] Website: www.manit.ac.in Name of contact person (s) : Dr. K. R. Pardasani
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Mizoram University, Aizawal Coordinator: Dr. Thangjam Robert Singh Summary of the progress made by the centre from its inception: The Bioinformatics Infrastructure Facility (BIF) centre was established in the Department of Biotechnology, Mizoram University, Aizawl in the year 2008. It was sponsored by DBT, New Delhi with the aim of promoting Biology Teaching through Bioinformatics (BTBI), (Order No. BT/BI/12/042/2007 dt. 11th Feb. 2008 of DBT, New Delhi). Since 2008 the BIF centre has organized numerous training and workshop sessions for both school students and Research Scholars. Besides these sessions the centre has also organized seminars on cutting edge scientific topics like RNAi, DNA barcoding, Phylogenetic analysis, Structural Biology, etc which were presented by eminent scientists from these respective fields. So far more than 18 training/workshop programs have been conducted by the centre covering the various aspects of bioinformatics for the benefit of students at the higher secondary, undergraduate, post graduate and research levels. The bioinformatics facility has been well served in the purpose of teaching and research activities not only in the Department of Biotechnology but also in different departments of the University. The flora and fauna databases such as in snakes, butterflies, banana and medicinal plants are some of the ongoing activities.
Major research activities in biotechnology and its related fields :
Molecular characterization, genetic improvement and in vitro regeneration studies of important plant genetic resources of the region
Molecular phylogenetics of floral and faunal resources found in the region
Molecular characterization of the fungal and bacterial resources found in the region
Studies on the abiotic stress using cyanobacteria as a model
Studies on the genetic basis of the incidence of various types of cancer in the region
Area of specialization:
Plant Biotechnology
Molecular phylogeny
Stress biology
Microbial Biotechnology
Cancer biology
Major achievements made during 2012-13:
More than 15 publications related to bioinformatics
5 Trainings & Workshops conducted
More than 200 participants benefited
Successfully conducted 5th NEBInet Coordinators meeting during 11-12 October, 2012
Infrastructure facilities in the bioinformatics centre: Internet Connection - Tulip (2 Mbps)
Hardwares:
Hp server - 2 nos.
Hp Desktop with Windows O.S - 10 nos.
Laser Printer - 1 no.
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Desk Jet Printer - 1 no.
6 KVA Online-UPS with battery – 1 no.
HP ProBook 4320s Notebook, Intel Core i5 – 1 no.
HP 3000 series Desktop Intel core2 Duo - 10 nos.
Apple iMac desktop – 2 nos.
Air Conditioner Haier 1.5 ton split AC – 1 No.
Software:
Windows Server 2008
Sigma Plot 11.0
Geneious Pro Ver. 4.5
Norton Antivirus
Symantec End-point Protection 11.5
NORTON 360
SQL Svr Std. 2008 SNGL OLP D
VS Pro 2008 SNGL OLP D
VSPro 2008 ENG DisKit MLV DVD
Biosuite Software
Firewall Server / Domain Controller server
Computer tables and chairs – 20 sets
Details about Staff members working in the centre: Sl. No. Name Designation 1. Dr. N. Senthil Kumar Professor 2. Dr. Satpal Singh Bisht Professor
Working Since 2007 2012
Status -
2007 2008
Assistant Professor Assistant Professor
Specialization Molecular Phylogeny Animal biotechnology Stress biology Microbial biotechnology Cancer Biology Plant Biotechnology
2012 2007
Cocoordinator Coordinator
Project Fellow Trainee
Plant Biotechnology Plant Biotechnology
September, 2012 November, 2012
Temporary Temporary
3. 4.
Dr. J. Bhattacharya Associate Professor Dr. Bhim Pratap Singh Assistant Professor
5. 6.
Dr. H. Lalhruaitluanga Dr. Thangjam Robert Singh Dr. PC. Lalrinfela Miss Atom Annupama Devi
7. 8.
Educational activities:
Bioinformatics is taken up at the M.Sc, M. Phil and Ph.D level in the School of Life Sciences in the University and also the facility is extended to other departments and Colleges as well as Schools.
Papers/ published or presented in the conferences : (selected ones during 2011-12) 1.
310
Lalrotluanga, Lalchawimawii Ngente, Senthil Kumar N, Gurusubramanian G. Insecticidal and repellent activity of Hiptage benghalensis against mosquito vectors. Parasitology Res. 2012; 111: 1007-1111.
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2.
Pranjal K, Brindha S, Soundararajan K, Senthil Kumar N. Analysis of aminoacids pattern in receptor tyrosine kinase using Boolean Association Rule. Bioinformation 2012; 8(8): 342-345.
3.
Anitha, D., Deepu Vijayan, Ajithkumar, Gurusubramanian, G. and Senthilkumar, N. 2011. Characterization of Bacillus thuringiensis isolates and their differential toxicity against Helicoverpa armigera populations. Journal of Basic Microbiology 51: 107-114.. ISSN 0233-111 X
4.
Zothansanga, Senthil Kumar, N. and Gurusubramanian,G. 2011. PCR pathotyping of native Bacillus thuringiensis from Mizoram. Science Vision 11 (3): 165-168
5.
Lalrotluanga, Senthil Kumar, N. and Gurusubramanian,G. 2011. Evaluation of the Random Amplified Polymorphic DNA assay for the detection of DNA damage in mosquito larvae treated with plant extracts. Science Vision 11 (3): 155-158
6.
Laltanpuii,R., Rita Zomuanpuii, Tejmala Hijam, Gurusubramanian,G. and Senthil Kumar,N. 2011. RAPD- PCR characterization of insecticide resistant and susceptible Anopheles species. Science Vision 11 (3): 159-164.
7.
Catherine, V., Zothansangi, Gurusubramanian, G. and Senthil Kumar, N. (2011) Morphological and molecular studies of six Junonia species of butterflies using RAPD-PCR technique. Science Vision, 11(3):141-146.
8.
Zothansangi, Catherine, V., Senthil Kumar, N. and Gurusubramanian, G. (2011) Genetic variation within two cryptic species of Cirrochroa by RAPD-PCR technique. Science Vision, 11(3):141-146.
9.
Brindha, S., Sangzuala Sailo, Liansangmawii Chhakchhuak, Pranjal Kalita, Gurusubramanian,G. and Senthil Kumar, N. 2011. Protein 3D structure determination using homology modeling and structure analysis. Science Vision, 11(3):125-133.
10.
Tejmala, H., Brindha,S., Gurusubramanian, G. and Senthil Kumar, N. 2011. In-silico comparison of distal-less protein variation in insects. Science Vision, 11(4):189-197.
11.
Zothansangi1, Catherine Ruati, V. L., Isaac Laldikbera, Gurusubramanian, G. and Senthil Kumar, N. (2011) Butterfly Diversity in Mizoram University Campus, Aizawl, India and Their Global Distributions. Advances in Environmental Chemistry, 11 (3), 249-252. ISBN: 93-81361-53-3
12.
Laltanpuii, Manu Thomas Mathai, Gurusubramanian, G. and Senthil Kumar, N. (2011) Diversity and Molecular Phylogeny of Odonata: A Case Study in Mizoram University Campus, Mizoram, India. Advances in Environmental Chemistry, 11 (3), 253-255. ISBN: 93-81361-53-3
13.
Lalrotluanga, Senthil Kumar, N. and Gurusubramanian, G. (2011) Mosquito Larvicidal Activities of Syzygium aromaticum Leaf extract against Culex quinquefasciatus Say. Advances in Environmental Chemistry, 11 (3), 269271. ISBN: 93-81361-53-3
14.
Esther Lalhmingliani, Gurusubramanian, G. and Senthil Kumar, N. (2011) Diversity of Wild Silk Moths in Mizoram, Northeast India. Advances in Environmental Chemistry, 11 (3), 301-302. ISBN: 93-81361-53-3
15.
Lalrinfela PC, Thangjam R (2012). Genome characterization of banana genetic resources of Mizoram, India. Science Vision, 2012; 12(1): 32-36
16.
Robert Thangjam and Lingaaraj Sahoo (2012). In vitro regeneration and Agrobacterium tumefaciens-mediated genetic transformation of Parkia timoriana (DC.) Merr.: a multipurpose tree legume. Acta Physiologiae Plantarum. Online first DOI 10.1007/s11738-011-0917-3
17.
Robert Thangjam and Damayanti Devi Maibam (2012). Sulphur free-radical reactivity of thioproline and crude extracts of Parkia timoriana (DC.) Merr. In: Advances in Environmental Chemistry, Tiwari D (ed), Excel India Publ, New Delhi, 2011 ISBN: 978-93-81361-53-5
18.
Thangjam Premabati, Lalrinfela PC and Robert Thangjam (2012). Randomly amplified polymorphic DNA (RAPD) analysis among edible non-seeded banana varieties (Musa spp.) of Mizoran, India. In: Advances in Environmental Chemistry, Tiwari D (ed), Excel India Publ, New Delhi, 2011ISBN: 978-93-81361-53-5
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Atom Annupama and Robert Thangjam (2012). Biotechnological Methods for Sustainable Utilization of Banana Genetic resources of Manipur, India. 135 -140. In: Biodiversity status and conservation strategy with special reference to Northeast India, R. Vartharajan (ed), CAS in Life Sciences, Manipur University, Imphal, 2012 ISBN: 978-81-923343-1-8
20.
Ajit Kumar Passari, Surajit De Mandal, Souvik Ghatak ,Nuii and Bhim Pratap Singh. Isolation and molecular characterization of endophytic fungi isolated from some medicinal plants of Mizoram (2012). in National Seminar on Environment, Biodiversity, Veda and Traditional Systems oraganised by Mizoram University, from 10th - 12th April, 2012.PP 18
21.
Surajit De Mandal, Souvik Ghatak, Ajit Kumar Passari, N Senthil Kumar and Bhim Pratap Singh. Antimicrobial and pharmacological activity of some traditional medicinal plant of Mizoram (2012). in National Seminar on Environment, Biodiversity,Veda and Traditional Systems oraganised by Mizoram University, from 10th - 12th April, 2012.PP 18.
22.
L. H. Rebecca, Zothansanga, B. P. Singh, G. Gurusubramanian and N. Senthil Kumar. DNA fingerprinting of Bacillus thuringiensis based on repetitive DNA sequence using ERIC-PCR. Science Vision (2011) 3 : 147-154
23.
Bhim Pratap Singh. Evaluation of Phosphate Solubilizing Fungi from Different Agro- climatic Zones of Mizoram and their Biodiversity Analysis. International conference on Advances in Environmental Chemistry (AEC-2011). pp.52-55
24.
Bhim Pratap Singh and Ajit Kumar Passari. Isolation and Characterization of Marine actinomycetes from water sediments of Mizoram, North East India. Presented a poster on National Conference on Mangrove Wetland and Near Shore Marine Ecosystems-From Sustainability to Management & Restoration at School of Environmental sciences, Jawaharlal Nehru University (JNU) during 5th-6th March 2012.pp 54.
25.
H. Lalhruaitluanga, M.N.V. Prasad, K. Radha, Potential of chemically activated and raw charcoals of Melocanna baccifera for removal of Ni(II) and Zn(II) from aqueous solutions. Desalination 271 (2011) 301-308. ISSN : 00119164;
Initiation of R&D activities in Bioinformatics:
Development of softwares and databases related to bioinformatics
Development of Flora and Faunal databases
Use of in silico approaches in sequence analysis and structural analysis
Details of Training/Workshop organized and total no of user trained: During 2011-12 Sl. No. Title 1. Training Course on Bioinformatics – An Introduction 2. Workshop on Bioinformatics – Structure and Determination of Macromolecules 3. Workshop on Random Amplified Polymorphic DNA (RAPD) Marker & its applications 4. Training course on Bioinformatics - An Introduction 5. Training course on Bioinformatics – An Introduction 6. Training Course on Bioinformatics – Proteins and their structure and prediction 7. One-day Outreach program for College students on Bioinformatics 8. Workshop on Molecular Phylogenetics and Evolution 9. Workshop on Structural Bioinformatics
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Duration 12 March 2011 28-29 th March 2011.
No. of participants 15 100
May 19-23th 2011
75
02 April 2011 03 August 2011 November 23-24, 2011
15 30 25
4th August, 2012
25
26-28, November, 2012 March 2013
36 To be conducted
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Impact shown by the Centre:
13 worshops/Trainings conducted since 2008 - more than 500 participants benefited
Increase awareness & use of bioinformatics and biotechnological tools at the teaching and research activities both at the school and University levels
Increase use of e-resources and improvement in publication
A Database on Butterflies of Mizoram developed using VB 2008 and SQL server 2005 (Client-Server technology).
PROT-PROP: A Java- application to predict the subcellular location of a protein based on physiochemical properties developed.
GC Graphing – A JAVA application to draw Graph of ORFs and Non-ORFs GC Contents developed.
A Database on Snakes of Mizoram was developed using PHP, Apache and MySql Server (Web -Server technology).
Banana Genetic Resource database (under construction)
Medicinal Plant database of Mizoram (under construction
Sequence submitted to NCBI
24 Internal transcribed spacer-2 (ITS2) from 24 fungal isolates from Mizoram soils (NCBI Accession No. HQ59690225)
8 ITS2 of Anopheles species (JN643725-28 and JN710012 - 15).
14 COI gene of butterfly species (NCBI Accession No. JN609220-23 and JN797782-91)
10 COI gene of Anopheles species (NCBI Accession No.’s JN596970-74, JN832671-75)
6 COI gene of dragon fly (NCBI Accession No.’s JN817424-29)
13 NBS-LRR resistance protein gene from banana (NCBI Accession No. HQ722029-41)
2 Bt crystal protein (NCBI Accession No. JN596969 and JN215465)
Proposed activities for 2013-14 Training/workshop Training on Basic Bioinformatics Workshop on Structural Bioinformatics Training on Basic Bioinformatics Workshop on Computional Biology & Bioinformatics Training on Basic Bioinformatics Workshop on sequence analysis
Schedule 21-22, February, 2013 28-29, March 2013 01-02, August 2013 28-29, November 2013 21-22, February 2014 28-29, March 2014
Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
Dr. Thangjam Robert Singh Department of Biotechnology, Mizoram University +91 389 2330859/861; 9436352386 (M) +91 389 2330834
[email protected] www.mzu.edu.in/schools/biotechnology.html Dr. Thangjam Robert Singh
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Nagaland University, Kohima Coordinator: Prof. S. U. Ahmed Summary of the progress made by the centre from its inception: Nagaland University BIF Centre was sanction on March 26, 2007 vide DBT sanction order No. BT/BI/25/001/2006-138 and was operating from the School of Engineering and Technology and Management’ (SETAM), Nagaland University, Dimapur with Prof. K. Kannan, former Vice Chancellor as Coordinator. In 2012, the BIF Centre is shifted to the Head Quarter at Lumami and Prof. Sharif. U. Ahmed and Dr. Chitta Ranjan Deb are appointed as Coordinator and Co-Coordinator respectively. The infrastructures created have been used by Scholars, Master and under-graduate students as well as trainees regularly under the ‘Teaching and Learning Curriculum’. Faculty members across the schools and departments have been using the facility for their academic and research purposes. Besides the University students, trainings are also imparted to the local youths, college students and teachers from the adjoining areas at regular interval. During March 26 - 29, 2012 the centre conducted a training program for the Research Scholars entitled ‘Application of Computer Science in Scientific Research’. Altogether 18 participants participated in the program. The external resource persons were invited for the program. The participants expressed their satisfaction and also requested for more such trainings at regular interval and one on advanced aspects. A month long short term training on ‘Computer Basics’ was organized for the youth of the nearby villages from 11th June to 11th July 2012 at HQ: Lumami. A total of 19 girls and boys were imparted training along with issuance of Certificate.
Major research activities in biotechnology and its related fields: Department of Botany is associated with in vitro propagation and conservation of rare and threatened economically important orchids and other some other species. Department is also involved in research on fermented food products, mushroom research, molecular biology research. Department of Zoology is involved molecular genetics research.
Area of specialization: Plant Tissue Culture, Fermented foods, Population Genetics. Major achievements made during 2012-13: The BIF Centre, Nagaland University imparted two trainings and two trainings are scheduled in the months of February-March, 2013. Some research activities like digitization of bioresources of Nagaland, orchid database of Nagaland, medicinal plants are initiated.
Infrastructure facilities in the bioinformatics centre: From the fund released by DBT in 2007, University has procured Desktop (10 nos.); Server (High end) (1 no.); Server (Medium) (1 no.); Lesser Printer and Desk-jet Printer (1 each); Photocopier and Scanner (1 no.); Window 2003 Server with License and Red Hat (1 each); Microsoft ISA Server 2005 for proxy server (1 no.); Microsoft Visual Studio, NET, MA SQL (1 each). University has not received any further grant from DBT. The sanction is awaited. Details about Staff members working in the centre: No Manpower is sanctioned to BIF Centre, Nagaland University. The Faculty members are involved in the present activities.
Educational activities Papers/ published or presented in the conferences: Nil Initiation of R&D activities in Bioinformatics: Some research activities like digitization of bioresources of Nagaland, orchid database of Nagaland, medicinal plants are being initiated. Details of Training/Workshop organized and total no of user trained: In the year 2012-13 two trainings have been conducted and two trainings are scheduled. Altogether 37 students / research scholars are trained. Impact shown by the Centre: The BIF Centre created some kind of awareness among the schools and colleges about the DBT activities in the North East India. We have received some request from the school to extend the training facilities to some of the adjoining schools and colleges. The research scholars of the University are regularly using the facilities created in the centre for their research.
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Proposed activities for 2013-14 The BIF centre in Nagaland University will extend the facilities for ‘Promotion of Biology Teaching and Learning through Bioinformatics’ to all the colleges affiliated to Nagaland University. Centre will conduct two short term training courses (710 days) for Research Scholars and faculty members of colleges and Universities. Two training programmes for the post graduate science students and two for social science students. Training to School students (Class IX to XII) and local youth on basic computing will be imparted during the year. Some research activities like creation of databases of ornamental fishes, tribal medicine, orchids, bamboo, medicinal plants etc. will be taken up.
Contact details: Name of the Coordinator & Co-Coordinator Postal Address
Phone Number Fax No. Email Website Name of Contact Person
Prof. S. U. Ahmed & Dr. Chitta Ranjan Deb Coordinator: Department of Zoology, Nagaland University, Lumami 798627, Nagaland Co-Coordinator: Department of Botany, Nagaland University, Lumami 798627, Nagaland 9436006808
[email protected] and
[email protected] www.nagauniv.org Dr. Chitta Ranjan Deb
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Narendra Deva University of Agriculture & Technology, Faizabad Coordinator: Dr. K.N. Singh Summary made by the centre since its inception: The centre was established with one time grant sanctioned in Semptember 2007. From 208-9, expenditure started and facility has been established. Computaional and information facilities are being extended to the faculties, researchers and students of the university.
Major activities during the year 2012-13 a.
BLAST, dendrogram generation, primer designing, EST sequence retrival apart of regular literature survey.
b.
Agricultural data analysis through SAS program.
c.
Training under BIF to Asst. Professor and Ph.D. students on application of bioinformatics in Agriculture for two days(18th and 19th October, 2012).
Details of staff members working in the BIF: K.N.Singh
: Coordinator
RA
: At present vacant to be filled soon
Papers published or presented in the conference 1.
D.K.Dwivedi, Anil Kumar, V.K. Misra and S. Dwivedi (2012)Phenotypic correlation and path coefficient analysis in rice (Oryza sativa L.) introgression lines under drought and controlled conditions. International J.Current Research4(7): 7-12
2.
Yadav Prasant, Khan N.A. , Shamim MD, Srivastava D. and Singh K.N. (2012) Efficacy of jackfruit protease inhibitor and Bt protein against yellow and pink stem borers of rice. Current Advances in Agricultural Sciences 4(2) 152-155
3.
Amita Singh, Md.. Shamim and K.N.Singh (2012) Genotypic variation in root anatomy, starch accumulation and its association with protein induction in upland rice (Oryza sativa) varieties under water stress. Agricultural research DOI 10.1007/S40003-012-0043-5
4.
D.K.Dwivedi, Pramila Pandey and Ram Krishna (2102) Genetic analysis of some quantitative traits in wheat (Triticum aestivum L.) Current advances in Agricultural Sciences 4(2) 159-162.
5.
Sunil Kumar, Satish Kumar, N Pratap and D.K. Dwivedi (2012) Estimation of hetrosis for grain yield and yield attributing traits in rice (Oryza sativa L.) Plant archive 12(1); 159-164
Initiation of R&D activities in Bioinformatics In silico si RNA construction and incorporating it in RNAi vector to control viral disease in plant.
Details of training/workshop organised and total no. of user trained Two days training (18th to 19th October 2012) was organised for Asst. Professors and Ph.D. students from various departments of the university . Total fifteen candidates were trained.
Proposed activities of 2013-2014
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a.
Continue various facilities’ under bioinformatics to students and faculties and organised training as regular activities.
b.
DNA bar coding studies in vegetable and horticultural crops especially Aonla and Laginaria species of poorvanchal.
c.
In silico work as si RNA construction and other dry lab projects.
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Contact details Name of coordinator: Dr. K.N.Singh Postal Address: Department of Plant Molecular Biology & Genetic Engineering NDUAT, Kumarganj, Faizabd 224229, UP Phone Number: 9450767369 E mail:
[email protected]
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National Research Centre on Equines, Hisar Coordinators: Dr. R K Vaid Report on bioinformaticsiInfrastructure facility (BIF) at NRCE, Hisar: The formal approval of The Bioinformatics Infrastructure Facility (BIF) in NRCE, Hisar was received on 22nd November; 2012. The release of the first installment of the total grant of Rs. 20.00 lakhs sanctioned by the Department of Biotechnology, New Delhi towards the promotion of Biology Teaching through Bioinformatics (BTBI) in NRCE Hisar is awaited after submission of MoA, as per rules.
The Center The National Research Centre on Equines at Hisar is headed by Dr. R. K. Singh,. NRCE is a leading research centre under the aegis of Indian Council of Agricultural Research (ICAR) with a mandate to undertake research in health and production aspects of Indian equines. Veterinary Type Culture Collection (VTCC) is a new upcoming microbial repository of veterinary, rumen and dairy microbes.
Present status and progress so far Although the bioinformatics intervention research as an adjunct to molecular research started about a decade ago by individual efforts of research scientists at the Centre, the BIF-infrastructural space as a separate unit in the institute complex is under planning. NRCE, as such is connected with Consortium for e-Resources in Agriculture (CeRA) facility and scientists are regularly browsing the resource scientific database. The centre is also having dedicated internet connectivity and all the laboratories/scientists are well connected through LAN network system.
Major research activities in biotechnology and its related fields at your institution At NRCE: Equine virus/bacterial/protozoan: Equine herpes Virus-1, 4; Equine Influenza indigenous isolate (A/equi-2/Ludhiana/87), A/eq/Katra-Jammu/06/08(H3N8); Japanese encephalitis isolate; Rhodococcus equi; Burkholderia mallei; Theileria equi and Trypanosoma evansi isolates from Indian horses, donkeys and mules; Equine Disease Immunologicals based Diagnostics: Equine herpes virus-1 (EHV-1) neutralizing monoclonal antibodies-based diagnostic kit; Equine herpes virus-4 (EHV4): A type-specific ELISA and immunostick assay Equine Rotavirus: A Mab based sandwich enzyme-linked immunosorbent assay (s-ELISA): Equine influenza virus (EIV) by haemagglutination inhibition assay; Theileria equi: A recombinant antigen based-ELISA diagnostic kit; Trypanosomosis: An indirect ELISA; Japanese encephalitis virus (JEV): Serum neutralization test (SNT) and haemagglutination inhibition (HAI) standardized; mAb-based ELISA for Japanese encephalitis underway; Equine infectious anemia: Coggins test for EIA; Equine viral arteritis: Virus neutralization for equine viral arteritis Molecular disease diagnosis using PCR/rtPCR/qPCR: Multiplex PCR for differentiation of EHV-1 and EHV-4. A RT-PCR using VP gene primers; RT-PCR for equine influenza diagnosis and typing; PCR based diagnostic for detection ofTheileria equi and Trypanosoma evansi specific DNA in bio-samples; Japanese encephalitis for RT-PCR diagnosis employing against E-gene and 3’NTR standardized, developed qPCR for assessing Theileira equi parasitic load in latently infected equids Monoclonal antibodies development: Monoclonal antibodies have been developed for diagnosis and characterization of equine herpes virus-1, equine rotavirus and Japanese encephalitis. Animal genomics: The NRCE has initiated a research project on genetic characterization of indigenous horse breeds and Indian donkeys. We have genetically characterized indigenous horse breeds and now Indian donkeys’ characterization is underway.
At VTCC: Whole genome sequencing and genome annotation and analysis: Pasteurella multocida buffalo isolate whole genome sequence under Pyrosequencing platform.
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Cloning and Sequencing of 16S rRNA gene for bacterial identification and phylogeny inferences: Rhodococcus equi, Bordetella bronchiseptica, Pseudomonas aeruginosa, Exiguobacterium spp, Paenibacillus spp, Staphylococcus spp, Bacillus cereus, Aeromonas spp., Streptococcus spp., Corynebacterium, Pseudomonas spp, Proteus spp., á-hemolysine positive Staphylococcus spp. were identified by sequence analysis of 16S rRNA gene. First isolation of and gene level molecular characterization of Rhodococcus equi from double-humped camels from Leh region. Atypical R. equi isolated and identified virulence plasmids and antigens by amplification of the vap gene family viz., vapA, -B, -C, -D, -E, -F, -G and -H of R. equi isolates by multiplex-PCR. Isolation and characterization of zoonotic camelpox viruses – Delhi, Jaisalmer, Barmer. Three full-length envelope protein genes (A27L, H3L and D8L) and one partial gene (C18L) of the isolated viruses from camels and humans cloned and sequenced. The phylogenetic analysis performed. A molecular appraisal of host-range K1L gene of zoonotic buffalopox virus: Genetic analysis of host-range (K1L) gene of buffalopox virus isolated from buffaloes and humans from an outbreak. The sequence analysis revealed the ORFs of 855 bp. Phylogenetic analysis revealed clustering of BPXV isolates with VACV. Sequence and phylogenetic analysis of ankyrin gene of Camelpox virus: Sequence and phylogenetic analysis of ankyrin gene of camelpox viruses isolated from outbreaks (2009-10) in Delhi, and Jaisalmer and Barmer district of Rajasthan. Isolation and characterization of zoonotic buffalopox virus (BPXV) from outbreaks in Maharashtra; & Meerut, U.P.
Area of specialization of the centre The location of The BIF has been identified in newly developed VTCC facility at NRCE, Hisar. The National Research Centre is a specialized Animal Sciences Research Institution of Indian Council of Agricultural Research performing research and developmental work on various aspects of equine health and prodiction Veterinary Type Culture Collection Centre (VTCC) at NRCE, Hisar as a National Repository of Microorganisms of Animal origin including Recombinant cultures and Plasmids. Presently the Centre is maintaining a microbial Repository with more than 500 accessioned bacteria, 25 virus and hundreds of viral and bacterial clones. Bacterial isolation and biochemical and molecular identification by cloning and sequencing of 16S rRNA and important housekeeping genes is done. This data is used to infer phylogenomics and identification work. Whole Genome Sequencing of Pasteurella multocida and genome analysis work.
Future activities Procurement/installation of the suggested/sanctioned hardwares/softwares. Centre plans to hold and organize short term sensitization and orientation programmes on Application of Bioinformatics tools for the students at the institute. Contact details : Coordinators: 1. Dr. R K Vaid, Senior Scientist, VTCC, NRCE, Sirsa Road, Hisar E-mail:
[email protected] 2. Dr. Sanjay Kumar, Senior Scientist, NRCE, Sirsa Road, Hisar E-mail:
[email protected] Ph. - +91-1662-275787, 276748, 276151, 275114Fax - +91-1662-276217 Website: www.nrce.gov.in
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National Research Centre on Mithun (ICAR), Dimapur, Nagaland Coordinator: Dr. Kishore Kumar Baruah Summary of the progress made by the centre from its inception: The Centre has been sanctioned on 31st March 2012. 1.
His Excellency, Government of Nagaland, Sri Nikhil Kumar inaugurated the Bioinformatics centre of NRC on Mithun (ICAR), Jharnapani, and Nagaland on 30th May, 2012. Dr. Madhan Mohan, Adviser, Department of Biotechnology, Govt. of India, New Delhi also graced the occasion as Guest of Honour.
2.
Organized a three day training for Undergraduate and post graduate students of College of Biotechnology, Nagaland University on Bioinformatics and its application in Molecular Biology
3.
Procurement of Software and Hardware are already been made.
Major research activities in biotechnology and its related fields : (i)
Conservation and propagation of quality Mithun germplasm in Nagaland.
(ii)
Application of endocrine biotechniques for induction of mother-neonate bonding in Mithun (Bos frontalis).
(iii) Elucidating the physiological and genomic regulation of ovarian follicular development for reproduction augmentation in Mithun (Bos frontalis). (iv) Veterinary type culture: Rumen microbes (Network Project). (v)
Isolation and characterization of fibre degrading microbes and manipulation of rumen ecosystem in Mithun (Bos frontalis) for improving fibre degradation.
(vi) Genetic studies on Mithun (Bos frontalis). (vii) Genetic study of leptin gene and its association with growth and nutritional performance of Mithun (Bos frontalis). (viii) Standardization of superovulation and embryo transfer protocols in Mithun. (ix)
Isolation and characterization of botanicals from NEH region for their antibacterial or antimethanogenic activities.
Area of Specialization: Reproductive physiology and endocrinology.
Major achievements made during 2012-13: i.
First mithun calf (Mohan) born through embryo transfer technology (ETT) from cryopreserved embryo at the National Research Centre on Mithun on 12th May, 2012.
ii.
World’s first ever mithun calf (Bharat) through embryo transfer technology born at the National Research Centre on Mithun on 27th March, 2012.
Infrastructure facilities in the Bioinformatics Centre: a.
Hardware: Server (High end), Server (Medium), 10 no. of Computer set with printers
320
b.
Software:
1.
Windows 2008 Server with License and Red Hat Linux Enterprise Edition 4
2.
Microsoft ISA Server 2005 for Proxy server(optimum configuration)
3.
Microsoft Visual Studio, NET, MS SQL Server, MS Office 2010(Standard) and Anti Virus Package (multi user up to ten)
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Details about Staff members working in the centre: Nil Educational activities: Imparting training to scientists, students etc. Papers/published or presented in the conferences: 6 Initiation of R&D activities in Bioinformatics: Yes Details of Training/ Workshop organized and total no of user trained: Organized a three day training for Undergraduate and post graduate students of College of Biotechnology, Nagaland University on Bioinformatics and its application in Molecular Biology Impact shown by the Centre: Students and scientists have been attracted in the field of Bioinformatics.
Proposed activities for 2013-14: i.
Interlinking of the Institutes in the region SASARD, Nagaland University, College of Biotechnology and Patkai College
ii.
Organization of training/workshop for the scientists, teachers and students of Biotechnology, Bioinformatics and other related disciplines on Bioinformatics and its application in molecular biology research
Contact details:
Name of the coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
Dr. K. K. Baruah Jharnapani, Medziphema, Dimapur, Nagaland-797106 03862-247327 (O) 03862-247341
[email protected] www.nrcmithun.res.in Dr. K. K. Baruah, Principal Scientist
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North East Institute of Science and Technology (NEIST), Jorhat Coordintor: Dr. Rajib Lochan Bezbaruah Progress made by the centre since its inception : The Bioinformatics Infrastructure Facility (BIF) at Biotechnology Division, CSIR-NEIST, Jorhat was established on 2nd February, 2008 under the Biotechnology Information System Network (BTISnet) scheme of the Department of Biotechnology, Govt. of India to promote innovation in biology teaching through Bioinformatics. With the goal to facilitate and expose students and researchers from different academic institution of North-East India this centre has successfully serving a vital role in the field of Bioinformatics teaching. The centre is profoundly devoted in R&D work with a great intensity to medicinal chemistry, Computer Aided Drug Design and microbial genomics data analysis.
Objectives
To serve bioinformatics and computational facility to researcher in relation to wet laboratory experiment.
To conduct training and workshop for promoting bioinformatics application in biological research and development.
To provide basic and core Bioinformatics knowledge for PG and UG students coming from different academic Institutions in India and aboard (ARDA, Thailand and LAUTECH, Nigeria).
To strengthen the Human Resource Development in the field of Bioinformatics.
Important Activities During 2012-2013(January) Human Resource Development The Centre has so far trained more than 120 Research Scholars, PG/UG Students, and Teachers in Genomics, Computer aided drug design and other applied areas of Bioinformatics.
The workshop-cum-hands on training on molecular biology and diversity mapping, 15th to 24th November, 2011 The workshop-cum-hands on training on molecular biology and diversity mapping of organisms was held during 15th to 24th November, 2011 under the banner of Biotechnology Division, Biotech Hub and Bioinformatics Infrastructure Facility of NEIST, Jorhat. The program was sponsored by Department of Biotechnology, Govt of India. The training covers both hand on and theory sessions of distinguished field of Molecular Biology and Bioinformatics. Some of the topic highlighted in the training session was Next Generation Sequencing , iOmics: All bioinformatics pipelines biologist need in the internet using cloud computing, Statistical bioinformatics- discovering the biological information, Metagenomics data analysis, Polyphasic microbial taxonomy etc . Dr. GNS Reddy, Scientist from CSIR-CCMB, Hyderabad and Dr. A Talukdar, Chief Scientific Officer from Geschickten Bioscience, Bangalore was invited as resource person of the training program. Short Term Training Course on Bioinformatics Tools for Genomics Research
March 19-21, 2012 The Short Term Training Course on Bioinformatics Tools for Genomics Research was organized in Bioinformatics Centre, Biotechnology Division, during March 19-21, 2012 as mandate program of the Centre. Total 13 students from different Institutes of India were participated in the Training program.
Upcoming Bioinformatics Training Training Code NEIST-02
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Title Chemo Informatics and its role in Computer aided drug dersign.
Date
Duration
March 26th-28st , 2013
3 days
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Monthly Bioinformatics Bulletin The centre is publishing its monthly News letter “Bioinformatics up to date” from June 2008 to January 2013 continuously in NEIST official website (Error! Hyperlink reference not valid./biotechnology.html). We are continuously getting good feedback from different R&D organizations with their motivational view. The new edition of news letter is under construction. Licensed Computational Resource facilities of the Centre 1. Molegro Virtual Docker 4.3.0 ( Date of Expiration of license 16/6/2013) 2. ChemBio Office Ultra 12.0 3. SigmaPlot 11.0
Other Open source Resources The Centre is working on both Windows and Linux Platform. Till date, more than 300 open source software/servers were installed and used by Trainee and student in the field of Phylogenetics, CADD, MD simulation, Docking etc.
Training Programme The six Students from Dibrugarh University successfully completed their M.Sc dissertation work during 1st March to 15th June, 2012. The seven students from Integrated M.Sc. in Bioscience and Bioinformatics, of Tezpur University successfully completed their Summer Training program during 2nd June to 30th June, 2012
Other R and D Supporting Facilities of the Centre 1.
Dedicated 24 hour high speed internet facility.
2.
E-Journal facility (DeLCON).
Research Papers Published 1.
Singh S, Gogoi BK, Bezbaruah RL. Racemic resolution of some DL-amino acids using Aspergillus fumigatus Lamino acid oxidase; Curr Microbiol. ; 2011 Jul; 63(1):94-99.
2.
Salam Pradeep Singh, T. C. Bora and R. L. Bezbaruah. Molecular Interaction of Novel Compound 2-Methylheptyl Isonicotinate Produced by Streptomyces sp. 201 with Dihydrodipicolinate Synthase (DHDPS) Enzyme of Mycobacterium tuberculosis for its Antibacterial Activity ; Indian Journal of Microbiology ; 2012, DOI: 10.1007/ s12088-012-0252-4
3.
Salam Pradeep Singh, Sarangthem Vivek, Rajib Lochan Bezbaruah, and Madhumita Barooah. Prediction of the three-dimensional structure of serine/threonine protein kinase pto of Solanum lycopersicum by homology modelling; Bioinformation. 2012; 8(5): 212–215. Published online 2012 March 17. doi: 10.6026/97320630008212
4.
TC Bora, HP Dekaboruah, N Saikia, R Saikia, A Yadav, P Bordoloi; Bioprosepcting microbial diversity from NorthEast Gene pool; Science and culture, Nov-Dec( 2011), 446-450.
5.
Dhrubajyoti Gogoi, RL Bezbaruah, M Bordoloi, R Sarmah, TC Bora . Insights from the docking analysis of biologically active compounds from plant Litsea genus as potential COX-2 inhibitors; Bioinformation; 2012; 8(16). doi: 10.6026/97320630008212.
6.
Salam Pradeep, Rajib Lochan Bezbaruah and Tarun Chandra Bora. Insilico studies of 2-methylheptyl isonicotinate produced by Streptomyces sps. 201 againstdihydrodipicolinate synthase enzyme of Mycobacterium tuberculosis. Journal of Biophysical Chemistry, Vol 3, No.3, 2012 .
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Contact Details
Coordintor : Dr. Rajib Lochan Bezbaruah Co-corrdinator : Dr. Ratul Saikia Bioinformatics Centre, Biotechnology Division, CSIR- North East Institute of Science and Technology Jorhat-785006, Assam Email:
[email protected]/
[email protected] Web site: www.rrljorhat.res.in Contact: 0376-2372951/2370086(O)
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North Eastern Hill University, Nehu Campus, Shillong Coordinator: Prof. Pramod Tandon Summary of the progress made by the centre from its inception: The Bioinformatics Centre (BIC) at North-Eastern Hill University (NEHU), setup and funded by DBT, GOI under the BTISnet program started functioning from November 1999 with a view to catering to the needs of the scientific community in the farflung northeastern region of the country and to augmenting their research activities through information inputs.
BIC, NEHU:
Information node of BTISnet: part of the National Bioinformation Network and functions as an information base in various areas of Biosciences and Biodiversity for the entire north-east ever since its inception.
Identified as one of the seven Bio-Resource Information Centre (BRICs) and portal development under the first phase of Indian Biodiversity Information Network (IBIN), DBT.
Nodal centre of North East Bioinformatics Network (NEBInet) comprising of 28 BIFs in NER.
Nodal centre for operating DBT-sponsored Online Access Facility of Library Resources (OAFLR): covering 36 Secondary and Senior Secondary Schools in NER through 8 BIF-BTBI Coordinators in te states of Arunachal Pradesh (6), Assam (24), Meghalaya (6) and Mizoram (6).
Identified as one of the 18 nodal Centres in NER to operate and monitor DBT e-Library Consortium (DeLCON) facility (that comprises more than 900 selective Journals).
DBT-sponsored Bioinformatics National Certification Examination Centre (BINC): one of the nine Examination Centres, commenced and operational w.e.f. 2008 onwards.
Major research activities in biotechnology and its related fields : NEPIAC Characterization of parasite biodiversity in mammalian livestock (cattle, sheep, goat, pig etc.) and other food animals in NER of India by integration of comparative genomics and molecular systematics of helminth parasites with defined geographic distribution, genetic variability among the different geographical isolates was carried out. Collation of data with regard to zoonotic parasites with emphasis on helminth parasites and suebsequently an Integrated web-based database system was designed. The first release (1.0) of the proposed database, trial hosting in intranet and open source accessible system, testing and users feedback were made available on September 24, 2012.
IBIN Dr. Ganeshaiah had a visit to the BIC, NEHU and overviewed the inhouse databases suggesting to take up 2 databases primarily the Helminth Parasite Spectrum in North-East India (Database developed using MS-Access and VB6.0). The mosquito database of North East India (web enabled) with front-end: MS-Visual Studio 2005/2008 and Back-End: MS-SQL was to be also incorporated in the IBIN portal. The BIC technical team visited UAS, GKVK for furthering and fine tuning the database with Dr. Ganeshaiah’s team and enhanced the searchability of the database by including Search by scientific name, Search By host and Search by Locality. Currently, we are working on the ‘Helminth parasite database’, of which 121 species have been formatted and entered into the system.
NER Twinning In the first phase of the NER Twinning project, we have identified three food-borne trematodes (two gastrointestinal and one lung fluke) of zoonotic importance namely Fasciolopsis buski, Artefechinostomum surfratyfex and Paragonimus westermani for the next generation sequencing using Illumina platform. De novo whole genome sequencing and assembly and sequence informatics for all the three parasites and transcriptome sequencing for Fasciolposis buski only were carried out owing to budgetary constraints. Scholars from NEHU had frequent visits to Prof. A. Bhattacharya’s (PI from JNU) lab for getting the requisite training on DNA and RNA Poly A+ preparation and total isolation. JNU scholars also made a visit to
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Prof. V. Tandon’s (PI from BIC, NEHU) lab and imparted hands on training to NEHU scholars. There were several in silico meetings arranged at JNU for design of the Bioinformatics pipeline initially for nematodes as the data was available. Two meetings of PIs in the twinning programme were held at JNU, in which the research group from ICAR, PUSA, NewDelhi participated and shared their experiences and expertise on plant nematode projects. After adequate processing of the parasite samples they were sent to M/s. Genotypic Technologies for NGS sequencing and analysis. The short and long library constructs for all the three samples were subjected to bioanalyzer profiling for whole genome sequencing and is under progress. The Bioanalyzer profle for transcriptome sequencing for Fasciolopsis buski was perfect and is completed.
Area of specialization: Biodiversity Informatics Major achievements made during 2012-13:
Organized DIT-sponsored workshop on “Recent Trends in Genome Analysis” and launched the NEPIAC database developed in-house on the public domain during September 24-27, 2012.
Participation and Launch of the IBIN database in the eleventh meeting of the Conference of the Parties (COP 11) held in Hyderabad, India, from 8 to 19 October 2012.
The Deputy Coordinator participated and gave an oral presentation at INCOB 2012, Bangkok, Thailand
The Information Officer participated and gave an oral presentation at INCOB 2012, Bangkok, Thailand
The Deputy Coordinator presented a keynote speech on “Human trematodiases in India: present situation” in the XI EUROPEAN MULTICOLLOQUIUM OF PARASITOLOGY organized by the European Federation of Parasitologists and and was the only scientist to be invited from India as a keynote speaker in University of Agricultural Sciences and Veterinary medicine, Calea Manastur 3-5, Cluj-Napoca, Romania: 25-29 July 2012.
Infrastructure facilities in the Bioinformatics Centre: A.
Computer & Communication facility Leased Line Internet Connectivity, Implementation of LAN on a Structured CAT 5 UTP Cabling Network using Switches and Hubs, Servers (3 nos.), PCs (20 nos.), & Workstations (2 nos.), Printers (3 nos.), Scanner (1 no.), UPS (3 nos.), Projector (1 no.), etc.
B.
Scientific Software packages Accelrys Gene 2.5 (Sequence Analysis Work Bench), Matlab 7.0, Winspirs ver 4.1 for Biotechnological Abstracts, Reference Manager.
C.
Databases & other information resources Derwent Biotechnological Abstracts (July 1987 - March 2006), Reference Update Delux Edition (July 2002 - June 2004), Parasitology Database obtained through MOE&F. and other application Softwares from Microsoft, RHEL, SQL, Adobe and Apple etc.
D.
Facility procured through DIT sanctioned NEPIAC project: Apple Work Group Cluster (HPCC), Apple Desktops, UPS, SPSS, iWork, iNquiry
E.
DeLCON facility through DBT, GOI
Details about Staff members working in the centre: S. N. 1. 2. 3. 4. 5. 6. 7. 8.
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Name of the staff Mr. Devendra Kumar Biswal Mr. Manish Debnath Mr. Welfrank Thongnibah Mr. Graciously Kharumniud Mr. Santosh Kumar Vishwakarma Mr. Pradeep Kumar Kar Mr. Gary Victor Mr. Nirmal Das
Designation Information Officer Senior Technical Assistant Computer Operator Technical Assistant Technical Assistant Data Entry Operator Technical Assistant Data Entry Operator
Working since July 2006 November 1999 March 2007 March 2007 March 2007 November 2005 April 2012 April 2012
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Absorption Status permanent - do -
- do Contractual Contractual
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Educational activities i)
Delivered lectures and conducted practical classes on “Bioinformatics and Molecular Taxonomy” for participants of Refresher Courses in Zoology, November, 2012 conducted by the Academic Staff College, NEHU, Shillong.
ii)
Organized DIT-sponsored workshop on “Recent Trends in Genome Analysis” and launched the NEPIAC database developed in-house on the public domain during September 24-27, 2012.
iii)
Delivered lectures and conducted practical classes on “Bioinformatics and Molecular Taxonomy” for participants of Refresher Courses in Botany, April, 2012 conducted by the Academic Staff College, NEHU, Shillong.
iv)
The Information Officer participated in a 10-day training program on Genome Informatics and HPCC at IIT, Delhi during August 16-25, 2012
v)
Mr. Manish Debnath, STA, BIC, NEHU attended the DBT-sponsored two weeks long training program during July 2nd – 13th , 2012 (second batch) at Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC) , Kharghar, Navi Mumbai
vi)
The Information Officer participated in the 18th DeLCON Nodal Officers meeting, organized at ICGEB, New Delhi on 4th July 2012.
vii) The Information Officer participated in the National Symposium on “Bioinformatics: Challenges in the postgenomic area” on February 2nd, 2012 at University of Jammu and DBT BTISnet-Coordinator’s Meeting during February 03-04, 2012, Vaishno Devi University.
Papers/ published or presented in the conferences:
Biswal DK, Debnath M, Kumar S, Ranganathan S, Tandon P.(2012) Phylogenetic reconstruction in the Order Nymphaeales: ITS2 secondary structure analysis and in silico testing of maturase k (matK) as a potential marker for DNA bar coding (BMC Bioinformatics 2012, 13(Suppl 17):S26 doi:10.1186/1471-2105-13-S17-S26)
Biswal DK, Ramachandran S, Chatterjee A, Tandon V (2012). Phylogeography and genetic variation of Paragonimus westermani (Trematoda: Digenea) and its position within the genus Paragonimus: an in silico study using ITS2 sequences. (oral presentation at INCOB 2012, Bangkok, Thailand)
Kumar S, Biswal DK, Tandon V (2012). In-silico analysis of Caspase-3 and -7 proteases from blood-parasitic Schistosoma species (Trematoda) and their human host. (under review in Bioinformation)
Goswami LM, Prasad PK, Biswal DK, Chatterjee A, Tandon V. (2012) Crustacean-borne infections with microphallid metacercariae (Digenea: Microphallidae) from focal areas in Meghalaya, north-east India. Journal of Helminthol. May 22:1-8.
Sharma SK, Dkhar J, Kumaria S, Tandon P, Rao SR. (2012) Assessment of phylogenetic inter-relationships in the genus Cymbidium (Orchidaceae) based on internal transcribed spacer region of rDNA. Gene. Mar 1;495(1):10-5. doi:10.1016/j.gene.2011.12.052.
Sharma SK, Mehra P, Kumari J, Kumar S, Kumaria S, Tandon P, Rao SR. (2012) PhysicalLocalization and probable transcriptional activity of 18S-5.8S-26S rRNA gene loci in some Asiatic Cymbidiums (Orchidaceae) from northeast India. Gene. May 15;499(2):362-6. doi: 10.1016/j.gene.2012.03.007.
Kehie M, Kumaria S, Tandon P. (2012) In vitro plantlet regeneration from nodal segments and shoot tips of Capsicum chinense Jacq. cv. Naga King Chili. 3 Biotech. Mar; 2(1): 31-35.
Initiation of R&D activities in Bioinformatics: Research Projects: Completed
A database on medicinal plants (nearly 400 species) under the “Network project Development of database of the Indian Himalayan region” –S.K. Barik (PI), Umashankar (Co-PI), N. Chrungoo (Co-PI) and Veena Tandon (Co-PI) sanctioned by NMPB, Department of AYUSH, MH & FW, Govt. of India, (2008-10).
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“North-East Parasite Information and Analysis Centre (NEPIAC): an in silico approach” – (Veena Tandon (PI), Devendra Kumar Biswal (Co-PI) and S Ramachandran (Co-PI) with IGIB and TCGA, New Delhi) - sanctioned by DIT, GOI
Ongoing
Collaborative project with JNU, New Delhi on “Next Generation Sequencing and Genome Information of Parasite Biodiversity of medico-veterinary significance in North-East India” to Veena Tandon (PI), Devendra Kumar Biswal(Co-PI) and Alok Bhattacharjee (PI), JNU, New Delhi under DBT NER Twinning Programme (2011-14) vide sanction no. BT/48/NE/TBP/2010 dated March 14, 2011.
Establishment of Portal for Indian Bioresource Information Network (IBIN) - Veena Tandon (PI), Devendra Kumar Biswal (Co-PI) under National Bioresources Development Board (NBDB, DBT) (2011-2014) vide sanction no. BT/PR14571/NDB/52/187/2010 dated March 04, 2011.
Databases/Software packages developed i)
The Helminth Parasite Spectrum in Northeast India (http://www.nehu.ac.in/BIC/HelMinth_Parasite_NE/default.htm)
ii)
Mosquito Fauna of North East India – with Special Reference to the Medically Important Vectors
iii)
Traditional Fermented Foods and Beverages of the Sikkim Himalayas
iv)
Helminth Parasite of Freshwater Fishes in India (under progress)
v)
NEPIAC Web Portal (under progress)- launched on September 24, 2012
vi)
IBIN first phase national portal to be launched in October 2012.
Details of Training/Workshop organized and total no of user trained
Delivered lectures and conducted practical classes on “Bioinformatics and Molecular Taxonomy” for participants of Refresher Courses in Zoology, November, 2012 conducted by the Academic Staff College, NEHU, Shillong.
Organized DIT-sponsored workshop on “Recent Trends in Genome Analysis” and launched the NEPIAC database develpoed inhouse on the public domain during September 24-27, 2012.
Delivered lectures and conducted practical classes on “Bioinformatics and Molecular Taxonomy” for participants of Refresher Courses in Botany, April, 2012 conducted by the Academic Staff College, NEHU, Shillong.
Impact shown by the Centre: Nodal Cntre for North Easter Bioinformatics Network One of the BRIC nodes for IBIN portal BINC exam centre Upgraded to DIC in 2010 till date
Proposed activities for 2013-14 A.
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Research Programmes:
Extensive transcriptome and comparative genomics analysis would be carried on the Next Generation Sequencing (NGS) data that was generated in the first phase of the twinning project.
Knowledge-base generated would contribute to novel genes, pathways that can be utilized to study the genomics, proteomics and interactome of parasites at molecular level for development of potential therapeutic drugs and other products.
NGS on identified Orchids of North East India
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Contact details: Name of the Coordinator
Prof. Pramod Tandon,
Deputy Coordinator Postal Address
Prof. Veena Tandon Bioinformatics Centre North-Eastern Hill University Shillong 793 022 (0364) 255 0150/ 272 2312/272 1241/ 272 1242/272 2214/ 272 2244 (0364) 255 0150/ 255 0300
[email protected],
[email protected];
[email protected],
[email protected] http://www.bicnehu.ac.in Devendra Kumar Biswal, Information Officer
Phone Number Fax No. Email Website Name of Contact Person
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North Eastern Regional Institute of Science & Technology (Deemed University), Nirjuli Coordinator: Dr. S. Sureshkumar Singh Summary of the progress made by the centre from its inception: Bioinformatics Centre (DBT-BIF) in NERIST was establishment in February, 2008 with financial assistance from DBT, Govt. of India for promotion of Biology Teaching though Bioinformatics (BTBI). In this regard, a sum of Rs. 29.04 lakhs (Rupees Twenty Nine Lakhs and Four Thousand) only had been received from DBT by the Institute during 2008-2012 towards the establishment of BIF as well as for recurring grants. The DBT, New Delhi had given approval for extension of financial support to the BIF during the next five years plan (2013-2017).
Major research activities in biotechnology and its related fields;
Isolation, characterization and identification of natural pigments of food and industrial values from filamentous fungi
Exploration of microbial diversity and microbial role in As-contaminated groundwater of North Eastern states (Arunachal Pradesh and Assam)
Development of nuclear and chloroplast genome sequences for development of DNA barcodes in selected Musa species occurring in North Eastern India
Tissue culture of Aquilaria agalocha, a medicinally important tree species and field trial adopting biotechnological approach
Area of specialization:
Natural product biology, mol. phylogeny, drug discovery & biodiversity database
Major achievements made during 2012-13:
Awarded Best Poster Award for the research poster on “Genome characterization and phylogenetic analysis of wild and cultivated bananas (Musa spp.) of Meghalaya, North East India using morphological, molecular and bioinformatics approaches” during National Symposium in Bioinformatics in Bioinformatics held at University of Jammu on 2nd February, 2012
Dr. S. Sureshkumar Singh has been awarded DBT-National Biotechnology Associateship 2012-13 by DBT, Govt. of India, New Delhi
Infrastructure facilities in the Bioinformatics Centre:
High End Server, Med-End, Desktop Computers (10 nos. HCL TBL), Laser Printer (HP 2015N), Officejet (HP 6488);Flatbed Scanner (HP G3010), 2KVA Uniline Online UPS (IGBT), Genious Pro bioinformatics software; Internet & Networking Facility includes 24 MBPS Super Speed Combo Broadband (BSNL) for the BIF Centre and 1 GBPS Leased Line Internet (BSNL) from the Institute LAN through NKN
Details about Staff members working in the centre: Sl
Name
Designation
Specialization
1.
Dr. S.Sureshkumar Singh
Assistant Professor & Coordinator
Natural Product biology, Molecular Phylogeny & Database
2.
Dr. M.L. Khan
Professor & Dy. Coordinator
Biodiversity & Conservation Biology
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Working Since 2006
Status
1992
Regular
Regular
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Educational activities
The centre has provided available infrastructure facility of computation and internet facility to many of the graduate and post-graduate level and research scholars of the institute for project and research works in the centre.
BIF-NERIST being a member of DBT Electronic Journal Consortium (DeLCON) has enabled unlimited access to more than 900 hundred full text online journals in Biotechnology, Bioinformatics, Life Sciences, and allied disciplines through the IP enabled LAN.
Papers/ published or presented in the conferences (bioinformatics only) :
N. Bareh, S. Sureshkumar Singh and Ch. Roshan (2012) Genome characterization and phylogenetic analysis of wild and cultivated bananas (Musa spp.) of Meghalaya, North East India using morphological, molecular and bioinformatics approaches. In: Proc. National Symposium in Bioinformatics in Bioinformatics,University of Jammu on 2nd February, 2012;
Initiation of R&D activities in Bioinformatics:
Development of a digital database on banana (Musa spp.) resources of NE India (In-house research);
Computational and biochemical approaches for in-silico discovery and screening of drug like-leads; Antidiabetic and antihypertensive compounds from Clerodenrum spp. in NE India (ongoing collaborative project under DBT-NER Twinning programme with Centre for Bioinformtics, Pondicherry University)
Details of Training/Workshop organized and total no of user trained
Number of training conducted
:
03
Number of user trained
:
>150
Impact shown by the Centre:
Since its establishment, BIF-NERIST has been an essential component of teaching and research in bilogy, biotechnology and allies subject in the institute as well as for the surrounding institutes.
Proposed activities for 2013-14
Training programme on Bioinformatics Tools and Techniques (22-23, February, 2013)
Training programme on Application of Bioinformatics in Biological and biotechnological Research (30-31st August, 2013)
Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
Dr. S. Sureshkumar Singh Bioinformatics Centre (DBTBIF), Dept. of Forestry, NERIST, Nirjuli-791109, Arunachal Pradesh 0360 2257059 0360 227872; 2258533
[email protected] ;
[email protected] http://www.nerist.ac.in Dr. S. Sureshkumar Singh
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North Orissa University, Baripada Coordinator: Dr. Hemanta Kumar Sahu Summary of the progress made by the centre from its inception: Since its inception, five students were selected based on open interviews for the above programs and they were provided training by the faculty of Bioinformatics department of the University. They successfully completed the training with stipend as per provisions. A National Seminar on Bioinformatics was organised. The BIF centre has conducted National Seminar on Bioinformatics for teachers, research scholars and students. M.Sc. M. Phil and PhD scholars of Botany, Zoology and Biotechnology used the Bioinformatics Infrastructure Facility for their research activities. Students and faculty of Dept. of Bioinformatics have published Bioinformatics related research papers and presented posters and oral presentations in various organizations of repute.
Major research activities in biotechnology and its related fields : Post graduate departments of North Orissa University are actively engaged with research activities in Botany, Zoology, biotechnology and bioinformatics by research scholars and teachers. Area of specializations: Computational Biology, Molecular Phylogeny, Wildlife & Conservation Biology
Major achievements made during 2012-13: Some students have carried out their M.Sc. Bioinformatics dissertation works under the guidance of Dr. Bibhuti Prasad Barik. Infrastructure facilities in the Bioinformatics Centre: Servers and Computers.
Details about Staff members working in the BIF centre and Dept. of Bioinformatics: Sl. No. 1.
Name
Designation
Specialization
Working Since
Dr. Hemanta K. Sahu
Wildlife & Conservation Biology
2012
2.
Dr. Bibhuti P. Barik
Coordinator, Bioinformatics Infrastructure Facility Lecturer in Bioinformatics, P.G. Dept. of Bioinformatics
Computational Biology
2004
Educational activities North Orissa University runs M.Sc. Bioinformatics on self financing mode since 2004.
Research Papers/ published: B.P. Barik and K. Tayung. (2012). Molecular differentiation of Fusarium spp. with varied lifestyles based on TEF1 alpha gene sequence analysis. Interdisciplinary Sciences: Computational Life Sciences, (Springer), 4: 1-8. K. Tayung, B.P. Barik and U.B. Mohapatra. (2012). Advances in Life Sciences. Studium press, USA. (ISBN:1-933699-69-8). B.P. Barik, M.K. Mahato and K. Tayung. (2012) Molecular phylogeny and secondary structure analysis of some salt tolerant proteins. In Advances in Biotechnology (Accepted). Ahmed, Rahim Ali,K.Prusty,J.Jena,C.Dave, S.K.Das, H.K.Sahu and S.D.Rout (2012). Prevailing Human-carnivore conflict in Kahna-Achanakmar corridor, Central India. World journal of Zoology 7(2):158-164. ISSN : 1817-3098. Sahu,H.K., S.K.Das and N.Palei (2012). Some observations on White-bellied Sea eagle (Haliaeetus leucogasteri) in Bhitarkanika National Park, Eastern India. Tigerpaper 39(1): 6-9. D.P.Sahoo, H.K.Sahu, S.K.Dutta and H.S.Upadhyay (2012). Sighting of Red-necked keelback (Rhabdophis subminiatus) in Similipal Tiger Reserve, Orissa, India. Tigerpaper 39(1): 31-32.
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Sahu,H.K., and S.K.Das (2012). Human-Elephant conflicts in Mayurbhanj Elephant Reserve Orissa, India. Gajah 36: 17-20. R.K.Mohanta, B.S.Adhikary, H.K.Sahu and K.K.Swain (2012).The biological values and conservation status of sacred groves in the Balasore WL division, Odisha- A case study. International Journal of Conservation Science 3(3): 207-216. S.K.Das, R.A.Ahmed, S.K.Sajan, N.Dash, P,Sahoo, P.Mohanta, H.K.Sahu, S.D.Rout and S.K.Dutta (2012). Diversity, distribution and species composition of Odonates on buffer areas of Similipal Tiger Reserve, Eastern Ghat, India. Academic Journal of Entomology 5(1): 54-61. S.Das, S.S.Ram, H.K.Sahu,D.S.Rao, A.Chakraborty, M.Sudarshan and H.N.Thatoi (2012) . A study on soil physico- Chemical, microbial and metal content in Sukunda chromite mine of Odisha, India. Environmental Earth Sciences. Palei, N.C., H.S.Palei and H.K.Sahu (2012). Human-elephant conflict in Keonjhar, Odisha: Implications for Conservation. North Orissa University J. of Sci. & Tech.1(1): 51-55. Ecological study on Avifauna of Bhitarkanika (A.K.Nayak, H.K.Sahu & S.K.Dutta) (2012). Himalaya Publishing House Pvt. Ltd. , Mumbai: 182 pp. (ISBN- 978-93-5051-682-9). Swallowtail Butterflies of Manas Biosphere Reserve of North East India : A Pictorial Guide (K.Choudhury, H.Singha, H.K.Sahu) (2012). Aaranyak, Guwahati, Assam. 102 pp. (ISBN- 81-903669-6-3). Vertebrate fauna of Hadagarh Wildlife Sanctuary (H.K.Sahu, B.K.Parida, P.P.Mohapatra, H.S.Palei and S.K.Dutta (2012). Himalaya Publishing House Pvt. Ltd. , Mumbai: 153 pp. (ISBN- 978-93-5051-539-6). Coastal Biodiversity of Undivided Balasore district (U.B.Mohapatra, H.K.Sahu, A.K.Biswal, S.D.Rout (2012). Himalaya Publishing House Pvt. Ltd. , Mumbai: 106 pp. (ISBN: 978-93-5097-126-0). Proceedings/Invited Talks/Training programs participated Dr. Hemanta Kumar Sahu: Indian Science Congress at KIIT, Bhubaneswar from 3.1.2012 to 7.1.2012. Fifth DST-SERB School in Herpetology at North Orissa University from 24.2.12 to 9.3.12. National Conference on Integrated Coastal Zone Management at Marine Science Department of Berhampur University from 24.2.2012 to 25.2.2012. National Seminar on Man and Environment at Zoology Department of Berhampur University from 10.6.2012 to 11.6.2012. National Seminar on Wildlife Research with special reference to Herpetology at North Orissa University, Baripada from 10.3.2012 to 11.3.2012. Summer Research Training Programme on Molecular Techniques at Sengunthar Arts and Science College, Thiruchingode, Tamil Nadu from 23.5.2012 to 01.06.2012. National Seminar on Suastainable management of Environment in mining areas at Barbil College, Barbil, Orissa from 18.8.2012 to 19.8.2012.
Dr. Bibhuti Prasad Barik: ITS2 RNA secondary structure revealed close affinity between endophytes and pathogens: A case study in endophytic Fusarium and Curvularia species. International conference on microbial world: recent innovations and future trends and 53rd Annual conference of association of microbiologists of India (AMI)-2012; KIIT University, Bhubaneswar, Odisha. Page Ethnobotanical knowledge and drug discovery: past, present and future. In: Annual conference of Odisha Bigyan Congress 2012, Dept. of Geology, Utkal University, Bhubaneswar, Odisha, Page 90. Mathematical perspectives of computational life sciences. National conference on soft computing and data mining, 2012, Dept. of Mathematics and Computer Science, U.N. College, Nalagaja, Mayurbhanj, Odisha, Page 82-85. Molecular differentiation of Fusarium spp. With varied life styles based on TEF1 alpha gene sequence analysis. Proceedings of the DBT Sponsored National Symposium on Bioinformatics: Challenges in the post-genomic era. 2012, Bioinformatics Centre, School of Biotechnology, University of Jammu, Jammu. Page 70.
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UGC sponsored National Seminar on Biodiversity: Status, Loss and Conservation. 2012, Udala College, Udala, Mayurbhanj, Odisha., Page 88-91. Biodiversity Informatics, UGC sponsored Seminar on the need of ethnobotanical studies of Similipal in the district of Mayurbhanj, 2012, Odisha. B.B. College, Baiganbadia, Odisha. UGC-SAP (DRS) sponsored National Seminar on Current Trend of Wildlife Research in India with special reference to Herpetology, P.G. Dept. of Zoology, North Orissa University, Baripada, Odisha, 10-11 March, 2012. Scientific Paper Writing organized by the National Academy of Sciences, India, Lucknow, 06-08. January 2012. Initiation of R&D activities in Bioinformatics: We are trying to put our effort for R&D activities in Bioinformatics in our University.
Details of Training/Workshop organized A National Seminar on Bioinformatics was organized. The BIF centre has conducted National Seminar on Bioinformatics for teachers, research scholars and students.
Impact shown by the Centre: Students and faculty of Dept. of Bioinformatics have published Bioinformatics related research papers in National and International journals and presented posters and oral presentations in various organizations of repute.
Proposed activities for 2013-14 National seminars and training programs will be organized to develop manpower and awareness in the field. The BIF will provide research exposure to college teachers and students of other Universities and institutes.
Extension of Studentships/Traineeships. Research collaboration with other BIF/Bioinf. Centres: Research collaborations will be made with experts of phylogenetics, microbiologists and wild life biologists working in reputed organizations. To carry out new research initiative for data mining applications in Bioinformatics. Publication of Annual e-news letters in Bioinformatics and development of a Bioinformatics portal. Initiative to validate the outcome of Bioinformatics resources: The academic institutions will utilize the bioinformatics services. The research findings will be published in peer reviewed national and international journals.
Contact details: Name of the Coordinator Postal Address
Phone Number Fax No. Email
Name of Contact Person
334
Dr. Hemanta Kumar Sahu Coordinator, Bioinformatics Infrastructure Facility Reader and Head, P.G. Dept. of Zoology NORTH ORISSA UNIVERSITY, Sriram Chandra Vihar, Takatpur,Baripada, Odisha. 757003. 09437177845 06792-255127 hks_nou@ yahoo.com; hks_nou01@ rediffmail.com
[email protected] Dr. Hemanta Kumar Sahu
Bio Informatics Infrastructure Facility (BIFs)
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Orissa University of Agriculture & Technology, Bhubaneswar Coordinator: Mr. S.K Pradhan Summary of the progress made by the centre from its inception: Bioinformatics Infrastructure Facility Centre at Orissa University of Agriculture & Technology, Bhubaneswar is involved in the research activities in the area of Structural bioinformatics, Sequence analysis, Genomics, Computational Phylogenetics & Database development. The infrastructure facilities of the centre has utilized by students, research scholar, scientist and faculties of the universities and other research & educational institutes near by the centre. The numbers of databases designed to keep records of pest, diseases, cultural practices in agriculture & allied sciences. The centre has also trained more than four hundred personnel by organizing workshop and providing dissertation facilities to the under graduate & Post-graduate students.
Major research activities in Biotechnology and its related fields :
The centre provides computer facilities and Bioinformatics support to the neighbouring departments like Department of Microbiology of College of Basic Science & Humanities, Department of Animal Breeding & Genetics of College of Veterinary Science and Animal Husbandry and Department of Biotechnology, Plant Pathology, Horticulture, Soil Science and Biochemistry, Plant Breeding and Genetics, Agricultural Meterology under College of Agriculture, Bhubaneswar and also other Colleges like BJB College & Department of Biotechnology, College of Engineering & Technology.
The Centre allows Ph.D. and M.Sc. students from different institutions for doing their dissertation works in the field of Bioinformatics.
Besides, the centre is actively involved in various research activities related to agriculture & its allied subjects with good publication records.
Area of specialization: Structural bioinformatics, Sequence analysis, Genomics, Computational Phylogenetics & Database development
Major achievements made during 2012-13: During the year 2012-13, the most notable achievements by the researcher working at the are Risk factors of breast cancer in Indian context; a systematic review, In Silico Design of Primer for In Vitro Cloning of DREB1A: A Regulatory Gene Associated with Abiotic Stress, Homology Modeling and Docking Studies of FabH (â-Ketoacyl-ACP Synthase III) Enzyme Involved in Type II Fatty Acid Biosynthesis of Chlorella Variabilis: A Potential Algal Feedstock for Biofuel Production and Identification and Characterization of Differentially Expressed Transcripts in the Gills of Freshwater Prawn (Macrobrachium Rosenbergii) under Salt Stress.
Infrastructure facilities in the Bioinformatics Centre: The project, “Creation of Bioinformatics Infrastructure Facility (BIF) for the promotion of Biology Teaching through Bioinformatics (BTBI) scheme of BTIS-net” was approved on 3rd November, 2006 with 100% support from the Department of Biotechnology, Government of India. The BIF Centre is sustained by a well furnished computer laboratory, fast internet connectivity with two high end servers, one medium end server, ten numbers of desktop computers, operating systems like Windows XP, Windows 2003 server enterprise edition, Redhat Linux enterprise edition, software like Accelry’s Discovery Studio 3.5, Microsoft Visual Studio 2005, Microsoft Office 2007, Microsoft SQL server 2005. In addition, one scanner, one HP Laser Jet 3055 printer, one HP DeskJet D2360 printer, one photo copier and also many open source software belong to the field of Data mining, Protein modelling, Evolutionary analysis etc are available to assist in various research as well as official activities.
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Details about Staff members working in the centre: Sl. No. Name 1. Mr. Sukanta Kumar Pradhan 2.
Mr. Surya Narayan Rath
3.
Mr. Mahesh Chandra Patra
Designation Specialization Asst. Professor, HOD & Bioinformatics & Coordinator Computational Biology Asst. Professor & CO-PI Bioinformatics & Computational Biology Research Associate Computational (April 2011 to till date) structural Biology
Working Since 6th Jan 2010
Status Engaged in the Department
6th Jan 2010
Engaged in the Department
April-2011
Purely Temporary
Educational activities The Department of Bioinformatics, Orissa University of Agriculture and Technology is offering regular two years M.Sc. degree in Bioinformatics with an intake capacity of 32 students per year. Since its inception in 2002, the department has successfully completed 11 years of education and research with 9 batches of students already passed out with good placement records. The department is equipped with well furnished class rooms, one experiment laboratory, two computer laboratories with 32 desktop computers to fulfill the practical needs of the students and a library having the facility of latest books and journals. The BIF Centre provides the infrastructure facility to the PG students of the department and also students of other colleges for carrying out their project work and also helping them to learn advance bioinformatics software application in research.
The list of Dissertation works carried out by students in the BIF Centre YEAR
NO. OF STUDENTS 6 1
2012-13 2012-13 2012-13
2
2012-13
2
INSTITUTION/UNIVERSITY Department of Bioinformatics, OUAT BJB (A) College, Bhubaneswar Dept. of Agriculture Biotechnology, College of Agriculture, Bhubaneswar Dept. of Zoology, College of Basic Science & Humanities
DURATION (IN MONTHS) 4 2 4 4
Papers/ published or presented in the conferences: Research Papers
336
1.
Sahu B, Mohanty DS, Pradhan SK, Rath SN, Joshi A, Risk factors of breast cancer in Indian context; a systematic review. Int J Comput Models Algorithms Med (Accepted 2012).
2.
Gangasagar PS, Rath SN, Mohanty IC, In Silico Design of Primer for In Vitro Cloning of DREB1A: A Regulatory Gene Associated with Abiotic Stress. Biotechnology, Bioinformatics and Bioengineering (Accepted: 2012).
3.
Misra N, Patra MC, Panda PK, Sukla LB, Mishra BK, Homology Modeling and Docking Studies of FabH (âKetoacyl-ACP Synthase III) Enzyme Involved in Type II Fatty Acid Biosynthesis of Chlorella Variabilis: A Potential Algal Feedstock for Biofuel Production. J Biomol Struct Dyn: iFirst, 2012, 1–17.
4.
Barman HK, Patra SK, Das V, Mohapatra SD, Jayasankar P, Mohapatra C, Mohanta R, Panda RP, Rath SN, Identification and Characterization of Differentially Expressed Transcripts in the Gills of Freshwater Prawn (Macrobrachium Rosenbergii) under Salt Stress. The Scientific World Journal 2012: Article ID 149361, doi:10.1100/ 2012/ 149361.
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Book Chapters 1.
Analysis of chromate reductase producing bacteria: a bioinformatics approach by S. K. Pradhan, H.N. Thatoi , S. N. Rath , S. K. Das and M. C. Patra, Advances in Biotechnology edited by H.N. Thatoi & B.B Mishra, Studium Press, LLC, USA (In Press-2012).
2.
IT in BT –Data Mining to Knowledge Discovery by Snehasish Mishra, Sukanta ku. Pradhan and Rajanikant Mohapatra, Encyclopedia of Information Science and Technology, Third Edition (Accepted-2012).
Sequence submission in EMBL-ENA 1.
Accession#:
HF545883
Description:
Ganoderma sp. M1 partial 28S rRNA gene, strain M1
Authors:
Thatoi H.N., Singdevsachan S.K., Rath S.N., Mishra P.B.K., Patra
J.K., Pradhan S.K. 2.
Accession#: HF545884 Status:
Confidential until 30-OCT-2012
Description:
Ganoderma sp. M3 partial 28S rRNA gene, strain M3
Authors:
Thatoi H.N., Singdevsachan S.K., Rath S.N., Mishra P.B.K., Patra
J.K., Pradhan S.K. 3.
Accession#:
HF549034
Description:
Eleusine coracana partial DREB1A gene for dehydration responsive element binding factor1A, culti var Dibyasinha
Authors:
Mohanty I.C., Gangasagar P., Rath S.N.;
Sequence submission in NCBI-Genbank 1.
Accession#:
JX122856
Description:
Escherichia coli strain o9 16S ribosomal RNA gene, partial sequence
Authors:
Pradhan, S.K., Priyadarshini, S., Sardar, K.K., Sahoo, L., Das, S.K.,
Mohanty, M., Rath, S.N. and Patra, M.C.
Delivered Talks in Conferences 1.
“Cloning and molecular characterization of DREB1 a transcription factor from Ragi (Eleusine coracana L.)”, Gangasagar P*, Mohanty LC, Rath SN. International Conference on Biotechnology Advances: Omics Approaches and Way Forward, December 20-22, 2012 organized by Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar, Odisha, India.
2.
“Computational insight into interactions of respirasomes in the electron transfer pathway of Acidothiobacillus ferroxidans”, Patra MC*, Panda PK, Parida BK, Rath SN, Pradhan SK. International Conference on Biotechnology Advances: Omics Approaches and Way Forward, December 20-22, 2012 organized by Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar, Odisha, India.
3.
“Analysis of chromate Reductase Producing Bacteria: A Bioinformatics Approach”, Pradhan SK*, Thatoi HN, Rath SN, Das SK, Patra MC. National conference on Science for Shaping the Future of India, October 18-19, 2012, organized by Indian Science Congress Association Bhubaneswar Chapter, Odisha, India.
4.
“Homology modeling and molecular dynamics simulation of human serum paraoxonase 1 (PON1) in a HDL environment”, Patra MC*, Rath SN, Pradhan SK, Maharana J, National conference on Science for Shaping the Future of India, October 18-19, 2012, organized by Indian Science Congress Association Bhubaneswar Chapter, Odisha, India.
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Initiation of R&D activities in Bioinformatics: The Centre has procured the Accelry’s Discovery Studio 3.5 and started working in the field of structural bioinformatics and started working in new research topics like structural & functional analysis of laccase and chromate reductases.
Details of Training/Workshop organized and total no of user trained This year the centre is going to organize the workshop in March 2013
Impact shown by the Centre: No. of M.Sc(Bioinformatics) students trained
32
No. of M.Sc(Agril. Biotechnology) students Trained 08 Provided the bioinformatics know how & skills to the research scholar, Scientist & faculties of sister departments of the university. No. of Paper Published: 04 No. of Book Chapter :02 No. of Sequence submitted: 04
Proposed activities for 2013-14 The centre is involved in various research activities in the field of Agriculture, Animal Husbandry, Fishery Science, Medicine and database development programmes utilizing the financial aids from DBT, Government of India, New Delhi. The centre has some prospective research plans related to the following subject areas:
Sequence and phylogeny study of a newly isolated E. coli strain o9 using the 16s-rDNA sequence deposited in Genbank (Acc. No: JX122856).
Structure prediction and active site identification of Paraoxonase family of proteins
Structural & functional annotation of fungal Laccase using computational techniques.
Studying the structural features of chromium reductases of bacteria
Sequence and structure analysis of Cytochrome p450 across different species.
Study on bioremediation of chromate (Cr6+) using chromium reducing bacteria.
Two days Seminar-cum-Workshop is going to be organized in March 2013.
Migration plan of Accelry’s Discovery Studio 3.5 will be procured which includes the bundles with modules such as: DS Base – 1 Licenses - consisting of DS Standalone, DS MMFF, DS Biopolymer, DS Protein Refine, DS DMOL3 Molecular, DS CHARMm, DS Catalyst Score, DS Catalyst Conformation, DS Analysis, DS QUANTUMm, DS Protein Refine to strengthen the research activities of the centre.
Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
338
Mr. S.K Pradhan Bioinformatics Infrastructure Facility Centre, Department of Bioinformatics, Orissa University of Agriculture & Technology, Bhubaneswar, Odisha +91-06742565761 +91-06742565760
[email protected] www.ouat.ac.in Mr. S.N. Rath, Co-PI & Asst. Professor
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Presidency University, Kolkata Coordinator: Dr. Abhijit Datta Summary of the progress made at DBT-CENTRE FOR BIOINFORMATICS (BIF-BTBI) at Presidency University (Formerly Presidency College), Kolkata (NAAC A+ Accredited) : The Centre has started working under the guidance of Dr. T. Madhan Mohan, Advisor, DBT, during the last quarter of 2006. Following points are to be mentioned: 1.
Relocation of the facility has been done to the new site (to accom-modate 40 terminals, Server, Workstations) in the Derozio Building, Presidency University, Kolkata.
2.
The EC meetings have been convened as per DBT guidelines;
3.
LAN, 24x7 - 2 Mbps Internet connectivity and graphics facility of the Bioinformatics Laboratory are working full time.
4.
Procurement of the new hardware and software has been completed as per recommendations by the expert members.
5.
List of Experts in the field of Bioinformatics is being updated regularly, required for the Workshop / Training Program conducted by DBT Centre for Bioinformatics, Presidency University, Kolkata from time to time;
6.
Probable schedule of the Workshops / Training Program to be taken up during the next financial year is under execution;
7.
Dynamic updation and modifications of the website bioinfo-presiuniv.edu.in is continuing;
Major research activities in bioinformatics and its related fields at Presidency University, Kolkata: Bioinformatics work groups from different constituent Departments of the University are growing and making inroads in respective disciplines/fields of Life Sciences. Area of Specialization: RNA Biology; Virtual Screening of Natural Compounds.
Major activities of the centre during the year 2012-13: Formally celebrated the Inaugural Day on Founder’s Day, National Workshop conducted on Structural Bioinformatics, Genomics & Proteomics in the Bankim Sabhagriha which was inaugurated by Dr. T. Madhan Mohan and two National Workshops on QSAR & QSTR and another on Bioinformatics in general were completed successfully. One International Seminar on Computational Chemistry, Drug Discovery and Design was also completed last year.
Infrastructure facilities in the bioinformatics centre: A.
Computer & Communication facility: One IBM Server 226 has been installed as per DBT specifications; Forty Desk tops are installed as terminals as per DBT specifications; One HP Workstation is being installed for modeling works; Software to run these systems and Sony LCD Projector purchased; One independent Broadband (2 Mbps) connection with unlimited download facility is running for the users / students; One Fortigate Firewall has been installed for net security of the Centre.
B.
Scientific Software packages: Flex X, E, Pharm;
C.
Databases & other information resources: Antagomir, Lantibiotics, Serpin, TARMI Tool (Developed indigenously).
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Details about staff members working in the centre: Research Assistant: Sayak Ganguly, M.Sc.; Diploma in Bioinformatics. 2.
Educational Activities & Types of services to provide: Downloaded and purchased packages are being made available to the Under Graduate and Post Graduate students of different Life Departments as well as to the Research Scholars of the University and other Institutes of the locality. In future all types of facilities will be offered depending on the availability of the suitable Software. Initiative to validate the outcome of bioinformatics resources: A high profile Advisory Committee has been constituted to formulate the future course of action at this Centre. With the help of suggestions of the honourable members the facilities are being designed to cater not only the students of Presidency University, Kolkata, but also the students of the nearby Universities, Government Colleges, other affiliated Colleges and share with other National Institutions. The excerpts of the suggestions were proposed along with the EFC inputs.
Papers published / presented in the Conference: Tanusri Nandi, Sohini Gupta, Sayak Ganguli and Abhijit Datta. 2012. Structural analyses of argonaute and its homologues in oryza sativa and hordeum vulgare. International Journal of Biology, Pharmacy and Allied Sciences 2012, 1(9). Sayak Ganguli, Manoj Kumar Gupta, Sasti Gopal Das and Abhijit Datta. 2012. Feature extraction from gene expression data files. International Journal of Engineering Inventions, 1 (2): 15-16 Sayak Ganguli, Sasti Gopal Das and Abhijit Datta. 2012. Using SVM for identifying epigenetic patterns in microsatellites in human sex determining genes and its homologues. Journal of Pharmaceutical Sciences and Research, 4: 1692–1696
Book Chapters:
Whispering Death – Bioinformatics of RNA Induced Silencing (Chapter 1); Sayak Ganguli and Abhijit Datta
Bioinformatics – Sequence, Function and Therapies (Chapter 18) Abhijit Datta and Sayak Ganguli -In “Advances in Life Sciences: Principles and Applications” (STUDIUM PRESS, USA)
Conference Attended: Sayak Ganguli – Invited speaker and Panelist – Next Generation Sequencing Congress, Asia Singapore; Oct 1 – 2, 2012 Talk Show on Career Guidance and Bioinformatics Awareness: Sayak Ganguli – Invited Guest on ‘Tara Guide’ – to speak on Bioinformatics as a Career prospect, September 11, 2012, TaraTV. Initiation of R & D activities in Bioinformatics: R & D programmes on RNA secondary structures, Dof Domain and other interesting storage proteins are being initiated. Twenty four communications have been published in peer reviewed International journals. Proposals from Research work groups have been invited from different Bio-Science Departments of the University, to be carried out utilizing the Bioinformatics Infrastructure Facility at Presidency University, Kolkata. Details of Training/Workshop organized and total no. of user trained: One National workshop was conducted on Structural Bioinformatics, Genomics & Proteomics in the Bankim Sabhagriha, Presidency University, Kolkata with 48 participants. Two National Workshops on QSAR & QSTR were held in collaboration with APT Software with 40+40 participants. So far ~640 users have been trained at this Centre.
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Impact shown by the Centre: Research Projects initiated under Dr. Abhijit Datta (as PI) during 2012: Identification of Conserved Regulatory RNA Structural Elements in HIV-1 Genome and Designing Inhibitory Aptamers Funding Agency - DBT, Govt. of India Duration – 3 Years (2012-2015), No. of Personnel – 3 Total Cost – 30,97,332 Development of RNAi Information Database (RNAiIDB) Funding Agency - DBT, Govt. of India Duration – 3 Years (2012-2015), No. of Personnel – 5 Total Cost – 24,68,200 Future activities of this Centre will include: As proposed in EFC inputs Summer School / Winter School on Bioinformatics for Research Scholars and Students, Training Programmes for Post graduate, Under Graduate students and Teachers from the Undergraduate Colleges, Post Graduate Departments of different Colleges and Universities. National level Seminars, Workshops on emerging fields of Bioinformatics. Offer Post M.Sc. Traineeship/Studentship to the students coming from different Bioscience disciplines. To conduct research in the areas viz. Dedicated and derived Genomic/Clinical/ Biotechnology Database Development, Analyses using Bioinformatics tools, In silico Modelling and Development of study modules for different levels of teaching. To introduce (Memorial) Lecture Series in Bioinformatics. To observe and celebrate BIOINFODAY each year, as annual meet, to attract students in this field. This Centre aspires to become full-fledged Bioinformatics Centre in near future.
Contact details :
Name of the Coordinator:
Dr. Abhijit Datta
Postal Address:
Presidency University 86/1, College Street Kolkata 700073
Phone Number:
+919830116667
email:
[email protected];
[email protected]
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Queen Mary’s College, Chennai Coordinator : Dr. K.S. Meena Progress made by the centre since its inception : The Bioinformatics Infrastructure Facility Centre (BIFC) was established in 2010 sponsored by the Department of Biotechnology Government of India for the promotion of Biology teaching through Bioinformatics. The centre supports free access to internet facility services to students as well as staff members right from its inception. So far four National level workshops have been conducted in addition to periodic discussions on Nanotechnology and Biotechnology. A two days conference on “Cheminformatics and Computational Drug Design” was held on 20th and 21st March 2012.Fifteen post graduate students, seven M.Phil scholars and 4 Ph.D scholars utilized this facility centre for their research work. Special classes on Bioinformatics for P.G students have been taken using this facility centre. Database on “Photo sensitizers” is at the verge of completion. Area of specialization: Cheminformatics and drug development.
Future Activities: The BIFC is planning to conduct a refresher course for college teachers in Bioinformatics in collaboration with the UGC and the Academic Staff College, University of Madras. The centre has a draft plan to start a P.G Diploma course in Bioinformatics for the purpose of employment creation and development in research. The BIFC centre is planning to arrange guest lectures in Bioinformatics for P.G and research scholars. The centre has plans to collaborate with the Cancer Institute Adyar and Sankara Nethralaya Chennai.
Contact details :
Name of the Coordinator : Dr. K. S. Meena Postal Address: Coordinator, BIFC of DBT, Queen Mary’s College (Autonomous),Chennai- 4. Email :
[email protected], Tel : (044) 28446692
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Rajiv Gandhi University, Itanagar Coordinator: Prof. R. K. Singh Summary of the Progress made by the centre from its inception: The bioinformatics centre established in 2007 provides basic infrastructural support to the researchers and post-graduate students of the University and nearby institutions. In last 5 years, the centre offered seven traineeship & studentships for research work and training. The centre also guided both internal and external students to complete their dissertation works. Besides imparting bioinformatics related training to the students, the centre has been involved in creating some databases based on the information generated by faculty of the university and other institutions. The databases being developed are: (1) Orchid database of Arunachal Pradesh; (2) A herbarium database on the plant of Pakhui wild life sanctuary and (3) A Data base on Anti-malarial plants of Arunachal Pradesh (in collaboration with Regional Research Institute of Ayurveda, Itanagar).
Major research activities in biotechnology and its related fields : The faculty members of the institution carry out research in the fields of microbial enzymes, biofertilizers and Phytomedicine.
Area of specialization: Biodiversity research, Ethnobotany, microbial enzymes and biofertilizers
Major achievements made during 2012-13: Compilation of information and creation of database on anti-malarial plants of Arunachal Pradesh
Infrastructure facilities in the Bioinformatics Centre: The hardware and software facilities available in the centre are as follows: Hardware: Server (HP ML 350G5 & 370 G5), Desktop (13), Printer (2), Scanner (2), Digital still and movie camera (2). Software: Geneious Pro V 5.4, Visual audio, Red Hat Linux, Swiss-PdbViewer, Rasmol, MolMol, Clustal W, Phylodraw, CN3D, ArgusLab, Mega2
Details about Staff members working in the centre: Sl.No. Name
Designation
Specialization
Working Since
Status
1. 2.
Coordinator RA
Microbiology Bioinformatics
July 2009 2008-2012
Regular Temporary
Prof. R. K. Singh Mr. R. D Kangabam
Educational activities The centre conducts regular classes for the students on Computer application and Bioinformatics. It also provides basic knowledge about bioinformatics tool to M. Sc students to complete their project work on bioinformatics related topics. The core staff of the centre guided two external summer trainees on projects entitled (1) Screening of Natural Molecules against Avain influenga through Molecular Docking and (2) Molecular Modelling of PINK1 protein and its interaction with other associated proteins. Three M.Sc. students of the University also completed their project work with support and guidance from the centre.
Papers/ published or presented in the conferences : (i)
Identification of 6-gingerol target proteins: A structural physiochemical properties based approach. InCoBASCB Asia Joint Conference, Kuala Lumpur, Malaysia 30 Nov.-2 Dec. 2011.
(ii)
Effect of missense mutation on PINL1 protein structure: A molecular modeling approach. InCoB-ASCB Asia Joint Conference, Kuala Lumpur, Malaysia 30 Nov.-2Dec. 2011.
(iii) Gogoi D, Verma AK, Joseph MS, Singh RK and Singh SP (2011). Ligand based Virtual Screening on some of the anti cancer phytochemicals to develop a novel inhibitor of â-catenin against Cancer. Patkai Journal of Multidisciplinary Research 1: 1-15.
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Initiation of R&D activities in Bioinformatics: The centre on its own has not taken any major research programmes. A few small project works on “in silico drug designing” have been successfully completed up by the trainees and students.
Details of Training/Workshop organized and total no of user trained The centre organized two workshops in which 14 faculty members and 32 research scholars were imparted training on basics of bioinformatics. The centre also organized several training programmes for M.Sc. students of the University in which approx. 130 students participated.
Impact shown by the Centre: Creation of biodiversity related databases.
Proposed activities for 2013-14 (i)
Workshop for postgraduate students on “Creation of biodiversity databases” from 11-16 March 2013.
(ii)
Workshop for graduate and postgraduate students on “Bioinformatics tools and techniques” from 04-08 March 2013.
Contact details: Name of the Coordinator Postal Address
Phone Number Fax No. Email Website Name of Contact Person
344
Prof. R. K. Singh Centre of Bioinformatics facility Faculty of Life Sciences Rajiv Gandhi University, Itanagar 791 112 Arunachal Pradesh 0360-2278511 0360-2277317, 2277889
[email protected] www.rgu.ac.in Prof. R. K. Singh
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S. Kula Women’s College, Nambol Coordinator: Mr. W. Robindro Singh Summary of the progress made by the centre from its inception: The Bioinformatics Infrastructure Facility (BIF), funded by the Department of Biotechnology, Govt. of India is well equipped with advanced technology and well maintained by the Department of Biotechnology, S. Kula Women’s College, Nambol, Manipur. The Centre is mainly focused on the Biodiversity of the endangered species of Manipur and Phylogeny analysis of Banana of Manipur. The Centre has appointed Two Research Assistants, One Traineeship, One Studentship and One Technical Assistant, One Post of Information Officer is needed for the Centre in the near future. The BIF Centre of S. Kula Women’s College, Nambol, Manipur has been organized one National Seminar on “Application of Bioinformatics in Biodiversity” on 25th and 26th October, 2009 under the sponsorship of UGC. The Centre has been organized six (6) training Programme and Five (5) Outreach Lecture Programme at the nearby Institutions on the Applications of Biotechnology and Bioinformatics.
Major research activities in biotechnology and its related fields : Some of the major research activities undertaken by the Centre and Biotechnology Department of the S. Kula Women’s College are given below:
Micropropagation of Medicinal Pants of Manipur.
Undergoing database development on Biodiversity of Endangered Species of Manipur.
Undergoing database development on “Indigenous medicinal plants of Manipur.
Phylogenetic tree construction and analysis of Banana of Manipur.
Phytochemical analysis of medicinal plants of Manipur.
Area of specialization: Plant molecular biology & Molecular design of nucleic acid structures.
Major achievements made during 2012-13:
A 2-day Training Program on “Metabolic pathway related to bioinformatics” was organized by the Centre during 30th -31st, March, 2012.
One Day Outreach/extension Lecture program on “Application of Bioinformatics & Smart Board Teaching” was organized by the Centre at the Nambol L. Sanoi College, on 13th December, 2012.
Four bananas Cultivar of Manipur have been sequenced.
Presented Two Papers on a National Seminar.
20 banana samples were collected from different district of Manipur.
Regular classes on Bioinformatics and its application for undergraduate students.
One Day Outreach/extension Lecture program on “Application of Bioinformatics in Biosciences” was organized by the Centre at the Kamakhya Pemton College, Hiyangthang on 02nd January, 2013.
Infrastructure facilities in the Bioinformatics Centre: Sl. No. 1. 2. 3. 4.
Particulars of Item
Quantity
IBM System X 3400 Server High end with 17” IBM TFT IBM System X 3200 Server with 17” IBM TFT IBM Think Centre 6072, 2GB Memory with 17” TFT Display Laser Jet Printer P3005DN
1 No. 1 No. 10 Nos. 1 No.
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Laser Jet Printer 3390MFP UPS 5.0KVA online, Digital Model, Numeric with SMF Batteries Software: Radha Enterprise Linux ES 4.0, Windows Svr. Std. 2003 R2 Win32, ISA Server Std. Edn. 2006, Visual Studio Pro 2008 Win32 (5 User License), SQL Svr. Std. Edn. 2005, Office Pro 2007 Win32 (10 User License), Symantec Antivirus 10.0 Business Pack (15 User), Lenovo Think Centre MS 57E Intel Core-2-Duo Processor E7300 with 17” TFT Display Dell 1525 Intel Core-2-Duo Laptop Computer with Windows Vista Dell 1525 Intel Core-2-Duo Laptop Computer without Windows Software: Geniuos Pro, Dreamweaver and Cold Fusion (CS4), PAUP, NTSYS
8. 9. 10. 11.
1 No. 1 Set 1 Set Each
10 Nos. 1 No. 1 No. 1 Set Each
Details about Staff members working in the centre: Sl. No. Name 1. Mr. W. Robindro Singh
Designation Head/Coordinator
2. 3. 4. 5. 6. 7.
Co-coordinator Research Assistant Research Assistant Traineeship Studentship Tech. Assistant
Mr. N. Surchandra Meitei Mrs. S. Meenakshi Devi Mrs. M. Kheroda Devi Miss N. Sonia Devi Mrs. Ch. Bijaya Devi Mr. L. Shyam Singh
Specialization Working Since Plant molecular biology 2004 & Bioinformatics Fishery 1997 Bioinformatics 2010 Biotechnology 2011 Biotechnology 2012 Microbiology 2012 2009
Status Regular Regular Contract Contract Contract Contract Regular
Educational activities:
Introduced an advanced Diploma Course (COC) on Bioinformatics in Biodiversity under the financial support of UGC since 2010.
Papers/ published or presented in the conferences:
Presented two papers in a National Seminar sponsored by UGC on 27th – 28th September, 2013:
1.
Micropropagation and Conservation of Alpinia galangal
2.
Genome characterisation of wild banana (Musa laterita) of Manipur.
Initiation of R&D activities in Bioinformatics:
Introduced an advanced Diploma Course (COC) on Bioinformatics in Biodiversity under the financial support of UGC.
Regular classes on Bioinformatics and its application for undergraduate students and College Teachers.
Regular extension Programme on Bioinformatics and its application.
Details of Training/Workshop organized and total no of user trained The BIF Centre of S. Kula Women’s College, Manipur has been organized Six (6) Training/Workshop Programme on different topics related to Bioinformatics and its related topics and also organized five (5) outreach programme at the nearby Institutions. The Capacity of the Centre is 25 number and about 150 participants has been trained by the Centre.
Impact shown by the Centre:
To give the awareness and importance of Biotechnology and Bioinformatics.
Proposed activities for 2013-14
346
To organize a training Programme on Application of Bioinformatics in Environment & Biodiversity from 17 to 20 January, 2013.
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To organize a training Programme on Computational Techniques for Biology from 28 to 31 March, 2013.
Organization of regular outreach programme on Biotechnology and Bioinformatics at the Hilly District.
Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
Mr. W. Robindro Singh S. Kula Women’s College, Nambol, Manipur 0385-2453192/09402728115
[email protected] Mrs. S. Meenakshi Devi
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XXIVnd All India BTISnet Coordinators’ Meeting
February 03-04, 2013
Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow Coordinator: Dr. Suraksha Agrawal Summary of the progress made by the centre from its inception. The project entitled “Establishment of Bioinformatics Infrastructure Facility (BIF) for the promotion of Biology Teaching through Bioinformatics” was started under the BTISnet program w.e.f. 22nd September 2006. During the current year, the center (a) provided bioinformatics support facilities to the entire institute and to neighboring institutions, (b) organized three training courses on bioinformatics, and (d) providing six-month training to M.Sc. & M.Tech. Students as part of the curriculum.
Major research activities in biotechnology and its related fields : SGPGI is a premier medical teaching and research institution. Several departments, including Immunology, Genetics, Neurology, Pathology, Microbiology, Gastroenterology and Urology have active research programs.
Area of Specialization of the centre Research and educational activities in of Biomedical information sciences.
Major activities of the centre during the year: i.
Three days training-cum-workshop on “Bioinformatics: Principles, Techniques and Applications” during July 29-31, 2011. The main objective of the course was to impart introductory knowledge about principles underlying bioinformatics and practical application of bioinformatics tools and techniques for gene and protein analysis to students and researchers.
ii.
Three days training-cum-workshop on “Workshop on Scientific Paper Writing” during December 08-11, 2011.
iii.
Two days training-cum-workshop on “Bioinformatics: Principles, Techniques and Applications” during January 20-21, 2012.
iv.
Six days training-cum-workshop on “01-Course in Bioinformatics” during October 01 – 06, 2012.
Infrastructure facilities in the Bioinformatics Centre Computer & Communication facilities Sl. No 1 2 3 4 5 6 7 8 9 10 11 12
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Equipments CISCO 1700 Series Router CISCO 2950 Series Switch XEON 3.2 GHz Processor dual processor with 2GB RAM, 72X5 GB HDD 2Mbps Internet connectivity through VSNL Lease Line Fourteen PCs: Intel Pentium IV with 1GB RAM, 80GB HDD Hp LaserJet P3500dn Printer HP Color LaserJet 3800 Printer HP Scanjet 8290 digital flatbed scanner Xerox Copier WC 420 CP Sharp Digital DLP Multimedia Projector 6 HP Laptops D-Link Wireless Router
Bio Informatics Infrastructure Facility (BIFs)
February 03-04, 2011
XXIVnd All India BTISnet Coordinators’ Meeting
Scientific Software packages v.
Licensed Software OS and Packages
Sl No. 1 2 3 4 5 6 7 8 9 10 11 12
vi.
Name Redhat Linux Enterprise Edition 4 Microsoft Visual Studio Professional Edition Microsoft ISA Server MS Window 2003 Server Edition MS SQL Server 2005 Standard Edition MS Office 2007 Professional Plus Semantic Antivirus Corporate Edition Discovery Studio 2 GCG Package Prism Graph Pad version 5.0 SPSS version 16.0 MATLAB 2008
Free Bioinformatics Software
Downloaded software from World Wide Web ftp sites under General Public License: BioEdit, spdbv, rasmol, Cn3D, Jemboss, Emboss, NCBI BLAST, Treeview, Phylip, MEGA, DAMBE, ClustalW, Chimera, BioPerl.
Details about staff members working in the centre Name Aditya N. Sarangi Shambhavi Srivastava Manmohan Pandey
Designation Senior Research Officer
Specialization Bioinformatics
Period of work June 2007-continuing
Absorption status Temporary
Research Officer Research Assistance
Bioinformatics Bioinformatics
October 2006 -continuing March 2010-continuing
Temporary Temporary
The institute’s faculty at the centre Name Dr.Suraksha Agrawal Dr. Rakesh Aggarwal
Designation Professor, Department of Medical Genetics (Coordinator, DBT Project, Biomedical Informatics Centre) Professor, Department of Gastroenterology
Types of services provided The centre provides computational facilities, bibliographic searches, bioinformatics related services like primer design, analysis of DNA and protein sequences and database development to researchers and medical professionals. More than 50 users from various department of SGPGIMS and near by universities in Lucknow has been using this facility. Centre is also organizing short term training program in bioinformatics for students, researchers and medicos.
Educational activities. The Institute considers requests from universities and colleges for project work towards partial fulfillment of postgraduate degrees.
Papers/ published or presented in the conferences : i.
Sarangi AN, Lohani M, Aggarwal R, Prediction of essential proteins in prokaryotes by incorporating various physico-chemical features into general forms of Chou’s pseudo aminoacid composition. Accepted for publication by Protein and Peptide Letter.
ii.
Trivedi N, Sarangi AN, Naik S, Aggarwal R., Identification of potential drug targets in M1 strain of Streptococcus pyogenes by differential genomics, Online J Bioinformatics, 12(1):149-169, 2011
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XXIVnd All India BTISnet Coordinators’ Meeting iii.
Sarangi AN, Srivastava S., Phylogenetic analysis of swine & human hepatitis E virus, Indian J Med Res 133, 2011, pp 548-549
Initiation of R&D activities in Bioinformatics: Current work is going on in silico studies of hepatitis E virus using bioinformatics tools and techniques. The centre is also developing its local WWWBLAST Server.
Details of Training/ Workshop organized and total no. of user trained Sl. No 1.
Tra Training / Workshop name Bioinformatics: Principles, Techniques & Applications
Duration July 29-31, 2011
No. of trainees 22
2. 3.
Workshop on Scientific Paper Writing Bioinformatics: Principles, Techniques and Applications
December 08-11, 2011 January 20-21, 2012
25 16
4
01-Course in Bioinformatics
October 01 – 06, 2012
21
Impact shown by your centre on the growth of biotechnology and allied areas. The Centre has designed in house database for highlighting the research achievements of SGPGI and organized workshopcum-training programs in which students, researchers and medicos are trained.
Proposed activities for 2013-14 i)
Centre is planning to start diploma and certificate course in the field of Biomedical Informatics from the coming academic year. The centre is planning to organize regular training program and workshop for students, researchers and academicians. Centre will find linkages with different research organizations, universities to promote bioinformatics education and research. Centre will develop various software tools and databases related to medical sciences.
ii)
Development of clinical database.
Contact details: Name of the Coordinator Postal Address Phone Number Email Website Name of Contact Person
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Prof. Suraksha Agrawal Department of Medical Genetics, SGPGIMS, Raebareli Road, Lucknow (UP) 226014 India 091-522 -668700-800 Ext 4338, 4346, 4347
[email protected],
[email protected] http://biomedinfo.sgpgi.ac.in/ Prof. Suraksha Agrawal
Bio Informatics Infrastructure Facility (BIFs)
February 03-04, 2011
XXIVnd All India BTISnet Coordinators’ Meeting
Sant Gadge Baba Amravati University, Amravati Coordinator: Dr. Prasad A. Wadegaonkar Summary of the progress made by the centre from its inception: Bioinformatics Infrastructure Facility has been established at Sant Gadge Baba Amravati University. This facility is housed in Post Graduate Department of Biotechnology. This facility was inaugurated on 28th December 2007 by Hon’ble Vice Chancellor Dr.(Ms) Kamal Singh, in the presence of Dr. Gulshan Wadhwa, Principle Scientific Officer and Information Officer, Apex Centre, DBT, New Delhi. Various training programs have been organized and facility is being used regularly by students, researchers and faculty for open access, books, video lectures and journal on various subjects.
Major research activities in biotechnology and its related fields : Department of Biotechnology, SGB Amravati University is actively engaged in research mainly in the area of Plant, Nonobiotechnology and Bioprocess Technology. Research has been supported by various funding bodies such as UGC, DST, DRDO, etc. DST has sanctioned funds under DST-FIST scheme while UGC has supported department under SAP program.
Area of specialization: Biotechnology Major achievements made during 2012-13:
Provided dedicated computer facility to students and researchers with LAN based portal with collection of books in PDF format and other learning resources.
BIF has also extended the network facility to classroom, laboratories of faculties and DST FIST computer laboratory.
One server is also providing support to UGC scheme for coaching of SC, ST and Minority Community students for NET and SET for lecturership.
i-Bioseminar Series : Weekly one our lecture series has been started for students and research scholars of Biotechnology, Botany, Zoology and Microbiology Departments.
Infrastructure facilities in the Bioinformatics Centre: Servers – 02, Desktops – 20, Network Printer – 01, DeskJet- 01, Scanner – 01, Photocopier -01, Router – 01, Internet through NME-ICT project – 1.0 Gbps, Software – Geneious, Discovery studio, FlexX, Sigma ScanPro, Prism GraphPad, Visual Studio, Academic Licences for ACD/Chemsketch, Chemaxon, Marvin Sketch, VMD, Ligplot
Details about Staff members working in the centre: Sl. No. Name 1. Dr. Prasad A. Wadegaonkar 2. Mr. S.D. Kove
Designation Coordinator
Specialization Biotechnology
Co-Coordinator
Biotechnology
Working Since Status 2007 Associate ProfessorBiotechnology Department 2010 Assistant ProfessorBiotechnology
Educational activities
E-portal (Open access lectures) has been developed which provides links to more than 300 hours video based lectures on Bioinformatics, Biochemistry, Molecular Biology Immunology etc.
E-portal for Teaching elective paper on Drug Discovery http://wprasad.webs.com/drugdiscoveryelective.htm
E-portal for resources generated during last workshop http://wprasad.webs.com/
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Papers/ published or presented in the conferences : 1.
Wadegaonkar V.P. and Wadegaonkar P.A. (2012). Withaferin A targets apoptosis inhibitor cIAP1: A potential anticancer candidate. Journal of Applied Pharmaceutical Science 2(3), 154-157. DOI 10.7324/JAPS.2012.2527
2.
Jaiswal J.V. & Wadegaonkar P.A. & Hajare S.W. (2012). The Bioflavonoid Galangin Suppresses the Growth of Ehrlich Ascites Carcinoma in Swiss Albino Mice: A Molecular Insight. Appl Biochem Biotechnol. DOI 10.1007/ s12010-012-9646-3
3.
Hade S.N. (2012). Exploration of new therapeutic potentials of phytoconstituents in anti-inflammatory plants by PASS. Journal of Chemical and Pharmaceutical Research 4 (4), 1925-1937.
4.
Wadegaonkar P.A. and Wadegaonkar V.P. (2012). Withanone as an inhibitor of survivin: A potential drug candidate for cancer therapy. International Biotechnology Symposium and Exhibition, Deagu, South Korea (Sept. 16-21, 2012).
5.
Pilley H.H. (2011). In-silico prediction of structural and functional aspects of a hypothetical protein of Capnocytophaga canimorsus CC5. Journal of Advanced Bioinformatics Applications and Research. 2(3), 206210
Initiation of R&D activities in Bioinformatics: Validation of Complementary and Alternative Medicine using Bioinformatics approach.
Details of Training/Workshop organized and total no of user trained National Workshop cum Training Program on “Computational Approaches to Phylogenetic Analysis” (26 – 28, March 2012). Twenty participants, thirty participants of refresher course (Life Sciences) and forty students were benefited by training course.
Proposed activities for 2013-14
Extend on going activities of the centre
Integrate available in-silico facility with wet lab facility available in Biotechnology Department for Research
Developing tutorials and lectures for teaching Bioinformatics.
Organizing workshop and training program for research scholars and faculties teaching Bioinformatics in colleges.
Organizing Webinars and Interactive Lecture series with collaboration with IISER and other institutes.
Training to students through studentship and traineeship.
Contact details: Name of the Coordinator Name of the Co-coordinator Postal Address
Phone Number Fax No. Email Website Name of Contact Person
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Dr. Prasad A. Wadegaonkar Mr. S.D. Kove Bioinformatics Centre of BTISNet, Department of Biotechnology, Sant Gadge Baba Amravati University, Amravati 444602 (Maharashtra) +919422157263, 0721-2662207/08 ext 267 0721-266
[email protected],
[email protected],
[email protected] https://sites.google.com/a/sgbau.ac.in/bioinformatics-centre-of-btisnet/ , www.sgbau.ac.in Dr. Prasad A. Wadegaonkar
Bio Informatics Infrastructure Facility (BIFs)
February 03-04, 2011
XXIVnd All India BTISnet Coordinators’ Meeting
Sardar Vallabhbhai Patel University of Agriculture & Technology, Meerut Coordinator: Dr. Jitender Singh Summary of the progress made by the center from its inception: The Bioinformatics Center (BIC) at Sardar Vallabhbhai Patel University of Agriculture & Technology has been setup in September. 2006 with the support of Department of Biotechnology (DBT), Ministry of Science & Technology under the Biotechnology information System Network (BTIS) program. The center is specialized in the field of Biotechnology and has been catering the need of teaching, training and research using bioinformatics tools related to different departments of college of Biotechnology of the University & other nearby organizations.
Major activities of the center during the year 2012-13
Organized summer trainings for undergraduate and post-graduate students.
Developed Website of Center and databases.
Teaching of UG and post-graduate courses of bioinformatics and biotechnology.
Traineeship and Studentship is awarded for strengthening the research and training activities in the area of bioinformatics biotechnology.
Project works of M.Sc, B.Tech, M.Tech, M.Phil students carried out and guided Ph. D scholars.
Molecular characterization of a new phytoplasma based on 16Sr DNA region infecting Tomato (Solanum lycopersicum) and Brinjal (Solanum melongena) in India was done.
Molecular detection, cloning and in-sillico analysis of genomic components of tomato leaf curl virus associated with leaf curl disease in Chilli(Capsicum annum L.) was carried out successfully.
Molecular detection and cloning of cry 1 and cry 2 genes of Bacillus thurigiensis isolates from Meerut zone.
21 days “Hand on Training on Molecular Biotechnology Tools and their Application in Agriculture” conducted from December 19, 2012 to January 08, 2013 with collaboration with Bioinformatics facility, DBT sponsored and Centre of Excellence in Agriculture Biotechnology.
Infrastructure facilities in the Bioinformatics Center: Computer & communication facility
Desktops Intel Pentium Dual Core 2.8 GHz
Server (Medium end)
Desk-jet Printer HP 1020
Laser printer (Network) HP 3600N
Notebook Hp
Toshiba photocopier Machine
Server (High end)
LCD Projector
Internet facility
Video conferencing facility
Scientific Software packages Lasergene 7.2 DNA sequence analysis software,Mega 5.0 and Adobe Pro C56, BioEdit, Geneious Pro, Treecon and Modeler
Types of services provided:
Teaching of graduate and postgraduate course in Bioinformatics.
Scientific literature search and retrieval.
Biological database development.
Students project training in bioinformatics.
Students research work in bioinformatics.
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Educational activities with details of placement:
Students of B.Tech (Biotech) are being periodically trained through offering six month bioinformatics course.
M.Tech in Biotechnology has been started.
The project training is given to students.
Initiation of R&D activities in Bioinformatics: The following research proposals are being developed for post graduate students.
“Cloning and molecular characterization of lectin gene from garlic (Allium sativum).
In sillico-identification and comparative analysis of candidate gene encoding proline in Lens cullineris. Jitender Singh, Juhi Bhardwaj, Pankaj Kumar, Priya Tomar, Anchal Rani, Rosy Rani Amit Kumar Singh and Anil Sirohi submitted Journal of Legume Research - An International Journal.
Identification and Molecular Characterization of a new phytoplasma infecting peach (Prunus persica) in India submitted to Australisian disease Notes.
Singh J, Rani A, Kumar P, Baranwal VK, Saroj PL, Sirohi A, 2012. First report of a 16SrII-D phytoplasma ‘Candidatus Phytoplasma australasia’ associated with a tomato disease in India. New Disease Reports 26, 14. [http://dx.doi.org/ 10.5197/j.2044-0588.2012.026.014].
Future activities: 2012-13
To develop advanced for central bioinformatics training.
Database generation on adopted agricultural crops (cereals, pulses, vegetables, horticulture, forestry and oil seeds etc) by the farmers as well as on potential agricultural crops scientifically recommended for their adoption in their respective zones.
To organize 21 days summer trainings for the undergraduate and postgraduate students and faculty training course on Bioinformatics.
To support and promote different ongoing teaching programmes in relation to Bioinformatics of the university and Collaborative institutions and organizations
Advance Diploma and post graduate degree course will be started in Bioinformatics if approved.
To develop Bioinformatics training manuals.
Modernization of the present infrastructure facility.
To support and promote different ongoing teaching programme of the university in the subjects of information technology, bioinformatics and biotechnology.
Contact details: Name of the Coordinator
Dr. Jitender Singh
Postal Address
Bioinformatics Center, College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture Technology, Meerut. 0121-2888534, Mobile: 09410455334 0121-2888534
[email protected]; jeets_80@rediffmailcom
Phone Number Fax No. Email Website Name of Contact Person
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Dr. Jitender Singh
Bio Informatics Infrastructure Facility (BIFs)
February 03-04, 2011
XXIVnd All India BTISnet Coordinators’ Meeting
Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar Coordinator:Prof. Nazir A Ganai Summary of progress made by the centre since its inception : The Bioinformatics Centre in SKUAST Kashmir was established in January 2007 as Bioinformatics Infrastructural facility under BTISNet program of DBT. The Bioinformatics lab developed under the program is well equipped and made fully functional for the use of the students, research scholars and the faculty. The centre has made available a variety of bioinformatics tools for the use of the researchers. The Bioinformatics lab supports broad band internet connectivity to 14 departments in the College, and also the classrooms for web-based learning. The centre has developed the e-learning portal in veterinary sciences under domain name www.starelearning.org. Bioinformatics has been incorporated as a 2 credit course each at graduate level, Masters level and at Doctorate level. The Centre has developed three MIS tools (Management information systems) for management and analysis of the livestock research data viz. FARMMAN 1.0 , MateSoft1.0. Sheep Manager 1.0.
Major Research activities:
Transcriptome profiling of the double humped camel: The sequence data on ~ 21000 cDNA of the double humped camel generated through NGS.
Development of Camel Genome information Resource
Microarray analysis for differential expression of the genes under cold stress: 5 tissues of pashmina goat involved in thermo-regulation in mammals have been been collected for microarray analysis through cross genome hybridization of the cattle genome on Agilent platform. The data is now being analysed for fold change and cluster analysis.
qPCR for validation of the microarray data
Genetic diversity of the 12 silkworm races using microsatellite marker analysis
Areas of Specialization The main area of specialization is the functional genomics, where in the data on differential expression is being generated through microarray analysis and its validation through qPCR. The bioinformatics forms the backbone for the analysis of such data.
Infrastructure Facility at Bioinformatics Centre Equipment
: Computers -15 Nos, Servers -2 Nos, LCDs – 4 Nos, 10KVA UPS, 20 KV stabilizer, Printer 2 Nos., Net-working of the 14 departrments
Communication facility
: Broad band internet connectivity from the BSNL
Software Tools
: Genious pro, PHYLIP, Mutation Surveyor, Primer 3, Moodle, AS-Reml, Exom-Ed, SYSTAT
Staff Members: Name Dr Nazir A Ganai Dr Firdos A Malik
Desig Professor, and Coordinator BIF, SKUASTK RA
Specialization Genomics Bioinformatics
Status Permanent temporary
Educational activities:
Development of the e-learning portal www.starelearning.org for supporting biology teaching at UG level.
Teaching of 2 hour credit course on Bioinformatics at Masters and PhD level.
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Development of tutorials on the various aspects of bioinformatics tools –
Bioinformatics for Beginners
–
BLAST Tutorial
–
Primer Design Tutorial
–
Tutorial on Phylogenetic Analysis
–
Tutorials on GENE BANK, SWISS Plot, EMBL
–
Genious Pro Tutorial
Training-cum-Workshop Name of Training-cum-Workshop 1. Bioinformatics Tools & Bio-techniques in Crop & Animal improvement 2728 Feb 2007. E-learning tools and practices. 25-26 March 2008
2.
No of Trainees 15
20
3. Brainstorming on “e-learning as a cutting edge teaching and learning methodology on 25 March 2008
35
4.
Advanced Techniques in Animal Disease Diagnosis
15
5.
Essential Molecular Techniques Feb 2010
20
6.
Development and management of e-modules for e-learning March 25-28, 2010
18
7.
Application of Bioinformatics in Genomics 6-8 Feb 2012
25
Services Provided The centre supports teaching of the Bioinformatics course at UG, and PG level. It also offers training to the faculty and research scholars on fundamental aspects of Bioinformatics. It supports high speed internet connectivity to the Post graduate students for literature search, sharing of resources, support to R & D activities of other departments. It also supports the e-learning portal for web-based teaching and learning in the class-rooms.
Future Activities:
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Building e-resources: o
Strengthening and updating of the e-learning portal www.starelearning.org developed by the centre.
o
Provide open access to the e-resource www.starelearning.org in veterinary sciences in the country.
o
To design and develop interactive tutorials in bioinformatics
Research in Bioinformatics: o
Develop database on the transcriptome of the pashmina goat and double humped camel.
o
Design and develop sheep & goat genome resource database with gene annotations.
o
Build and maintain online web application for sheep & goat research management across 7 different research stations in the state of J & K
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XXIVnd All India BTISnet Coordinators’ Meeting
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Collaboration: o
Collaborate for research in bioinformatics with other institutes viz. NBAGR, NDRI, IIIM
o
Extend support of bioinformatics facilities to other sister institutes in the region.
Trainings: Advanced trainings in areas of : o
Functional genomics for absolute and relative gene expression using Real Time PCR
o
Analysis of the microarray data for gene annotations and gene network analysis
o
Whole genome scanning for QTL mapping
Contact details :
Name of Coordinator:
Dr Nazir A Ganai
Postal Address
Division of Biotechnology Faculty of Veterinary Sciences and Animal Husbandry Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shuhama 190006 Srinag
Phone No
0194-2262642, 2262612, 9419018745
Email:
[email protected],
[email protected]
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Shri Mata Vaishno Devi University, Katra Coordinator: Prof. V.Verma Summary of the progress made by the centre from its inception: The Bioinformatics Infrastructure Facility (BIF) Centre in the School of Biotechnology, Shri Mata Vaishno Devi University, has been established with the kind help and support of the Department of Biotechnology, Govt. of India in 2007. The facility is headed by Prof. V. Verma, Dean College of Engg. as the Co-ordinator of the BIF centre. The BIF centre at SMVDU, setup and funded by DBT under the BTISnet program started functioning from October 2008 and is currently catering to the needs of more than 100 students and several research scholars of the School of Biotechnology.
Major research activities in Biotechnology and its related fields : School of Biotechnology is working in the areas of applied microbiology, fermentation, plant biotechnology and bioinformatics. Extramural funding from DST, DBT and UGC for carrying out projects in the respective areas is available with faculty members.
Area of specialization: Microbial and Plant Biotechnology
Major achievements made during 2012-13: ?The XXIII Annual Bioinformatics Coordinator’s Meeting was held at Matrika Auditorium of Shri Mata Vaishno Devi University, Katra on Feb 3rd – 4th, 2012. The Meeting was inaugurated on 3rd February 2012 by Padma Shri Prof. R.N.K Bamezai, Vice- Chancellor, SMVDU and presided over by Prof. M. Vijayan, Chairman, Computational Biology and Systems Biology Task Force, DBT; Dr. T. Madhan Mohan, Adviser DBT and Prof. A. S. Kolaskar, Vice-Chancellor, KIIT University, Bhubaneswar. In addition, papers were presented at International and national conferences.
Infrastructure facilities in the Bioinformatics Centre: The following equipments were procured and installed for proper functioning of the centre.
Computer Hardware: High-end Server Sunfire x400 M2, Entry –level Server Sunfire x2200 M2, Workstations Sun Ultra20 M2 (4 nos), Desktop computers (Dell make, 10 nos), Video Conferencing System (Sony make), Scanner (HP make), HP laserjet Printer (HP make), Photocopier (Canon make), Online UPS 5KVA (APC make).
Computer Software: DNASTAR Lasergene, Tripos SXBYL-X and other licensed System Softwares like Window XP 2, Red hat Linux Enterprise Edition 4, MS Office 2007 etc.
Communication Facility: Internet, working telephone and fax connectivity.
Details about Staff members working in the centre: Sl.No. Name 1.
Designation
Specialization
Working Since
Status
Under appointment
Educational activities The centre was used for teaching and carrying out lab exercises in bioinformatics for students of M.Sc. Biotechnology and B.Tech. Industrial Biotechnology. The BIF facility was used by research scholars and Faculty for research purpose and for literature surveys.
Papers/ published or presented in the conferences:
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Slathia PS and Sharma P. Predicting conserved epitopes in the variants of amastin protein of Leishmania major and designig an epitope based immunogenic DNA vaccine. 2012. International Journal of Infectious Diseases Vol. 16Supplement 1, Page e314.
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Sharma S, Slathia PS and Verma V. Jatropha curcas as a source for biodiesel: its limitations and need for new resources. Journal of biofuels. 2012. 2 (2), 98-106.
Slathia PS and Sharma P. In Silico Prediction of Conserved Epitopes in Pneumococcal Surface Protein A (PspA) of Streptococcus pneumoniae for Designing DNA Vaccine. ICIB 2012, Patiala. Nov. 2012
Slathia PS, Gupta G and Sharma P. Use of bioinformatics tools for designing a DNA vaccine based on conserved epitopes located in the variants of structural polyprotein of chikungunya virus with IL-15 as adjuvant. 2nd Antivirals Congress. Nov. 2012, Boston, USA.
Initiation of R&D activities in Bioinformatics: R&D activities have been started for molecular modeling and drug design as well as for immunoinformatics. The above presentations in conferences clearly show this. Mr. Parvez Singh Slathia, Lecturer who is working in the bioinformatics center from inception has been granted a UGC funded Minor project in molecular modeling and drug docking.
Details of Training/Workshop organized and total no of user trained The XXIII Annual Bioinformatics Coordinator’s Meeting was held at Matrika Auditorium of Shri Mata Vaishno Devi University, Katra on Feb 3rd – 4th, 2012.
Impact shown by the Centre: The centre is catering to the need of students, scholars and faculty in School of Biotechnology. Workshops have been organized in past years for training in house research scholars and other universities. The facility has also been used to impart training to college faculty from different colleges in Jammu region.
Proposed activities for 2013-14
Developemnt of database on endophytes from important medicinal plants of J&K Himalayas.
Infrastructure and expertise development in Genome analysis and System biology for drug target identification in infectious microbes with particular emphasis on selected bacterial and protozoan parasites
Metabolic pathway analysis for enhancement of bioactive molecule production.
Comparative genome analysis of selected medicinal plants for novel Gene identification and interaction network studies.
In silico prophylactic vaccine candidate prediction for major infectious diseases.
Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website
Prof. V.Verma Fast track postal address: Office of VC SMVDU, c/o PRO Office of SMVDU,15-C (2nd Ext.) Gandhi Nagar, Opp. Bahu Plaza, Jammu 180003 Tel. (Direct) 01991 285692 (PABX) 01991 285524,285535, 285699 ext.2386, 2384, 2300 FAX 01991 285506
[email protected] /
[email protected] www.smvdu.ac.in
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Sri Padmavati Mahila Visva Vidyalayam (Women’s University), Tirupati Coordinator: Dr. Palempalli Uma Maheswari Devi Summary of the Progress made by the centre from its inception: The Bioinformatics Facility Centre is established with the procurement of sanctioned hardware, software and other infrastructure. From the day of inception, the BIF Centre is concentrating on providing Lab facility and professional assistance for Bioinformatics projects and practicals for students including Research Scholars belonging to various branches of life sciences, Pharmaceutical Sciences and Engineering courses in the University. The proposed areas of specialization of the centre are viz. Protein Modeling & Computer Aided Drug Designing followed by Pharmacophore Analysis. Computational Genome and Proteome Analysis, System Approaches to Biology: Molecular Simulation, Interaction & Networking, Genetic Diversity and Molecular Phylogenetic Analysis. The centre was further strengthened with latest soft wares like GCG Wisconsin Package, MATLAB, DISCOVERY STUDIO (DS). The centre developed data bases on Aggressive Weed Parthenium and one endangered species endemic to Tirumala Hills cycas-beddomei.
Major research activities in Biotechnology and its related fields at your institution: Production of Keratinases and Strain improvement. Aluminium induced stress in neurological development Ergothioneine in neuro protection DNA bar coding Role of GA in induced DSS Colitis.
Area of specialization: Microbial Technology, Plant Biotechnology, Animal Biotechnology, Neuro toxicology, Seri biotechnology, Bioremediation, Neutraceuticals and Chemo prevention.
Major achievements made during 2012-13: Insilco analysis of anti-inflammatory potential of Xanthones Comparative docking on flavanoids as COX-2 inhibitors
Infrastructure facilities in the Bioinformatics Centre: A.
Computer: Computer Hardware: High End Server - 1 No. Medium Server - 1 No. HP DX2280 Computers with LCD Monitors - 18 Nos. HP Laptop 6710B - 1 No. HP Laserjet Printer 300 SDN - 1 No. HP Office Jet K7108 - 1 No. HP Scanjet G2410 - 1 No. Canon IR2016J Copier - 1 No. LCD Projecstor - 1 No. 5.0 KVA online UPS system with 26 AH/12V/20 Nos. – 1 No.
B.
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Scientific Software Packages:GCG Wisconsin Package, MATLAB, Discovery Studio (DS)
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Details about Staff members working in the centre: Sl. No. 1. 2. 3. 4. 5. 6.
Name Ms. Subha Laxmi Nayak Srila Mondal K. Krishnaveni Lopamudra Palai S. Sirisha B. Anusha
Designation Specialization Working Since Research Assistant Studentship Gall Bladder Cancer 2008-09 Traineeship Tyrosine Kinase Inhibiotrs 2008-09 Traineeship CETP Inhibiotrs 2008-09 Traineeship Malaria Vaccines 2009-10 Traineeship Diabetes-II 2009-10
Status Completed Completed Completed Completed Completed
Educational activities Under studentship program, one candidate has completed her project on the topic “Identification of Novel Markers for Gall Bladder Cancer Using SAGE” Under Traineeship Program, two candidates have completed their projects on the topics (i) “Molecular Docking Studies on Tyrosine inase Ibhibitors in the Treatment of Chronic Myleiod Leukemia” and (ii) “Molecular Modelling and Docking Studies of Some Novel Inhinitors of CETP against Cardiovascular Disease”.
Papers/ published or presented in the conferences: 1.
Navya A., Nanda Kumar Y. Hari Prasad O. Santhrani T. and Uma Maheswari Devi P. “In vivo and in silico Analysis Divulges the Anti- inflammatory Activity of A-Mangostin”. International Journal of Applied Biotechnology and Biochemistry. 2 (1): 69-80, 2012.
2.
Navya. A, Jayasimha Rayalu. D and Uma Maheswari Devi. P, “Docking Studies On Xanthones of Mangosteen as Cox-2 Inhibitors”. IJABPT, 2(3): 263-268, 2011.
3.
Presented a paper on “Computational Tools to Predict Anti-inflammatory potential of á-Mangostin” in National Conference at Sri Yogi Vemana University, Kadapa, A.P.
4.
Presented a paper on “Comparative docking studies on Mangostins as COX-2 and iNOS inhibitors” in National Conference at Sri Venkateswari Institute of Medical Sciences, Tirupati, A.P.
5.
Presented a paper on “Computational Tools to Predict the Drug-likeness of á-Mangostin” in international Conference at Sri Padmavati Mahila Visva Vidyalayam (Women’s University), Tirupati, A.P.
Initiation of R&D activities in Bioinformatics: 1.
Docking studies on Xanthones of Mangosteen as Cox-2 Inhibitors.
2.
Computational Tools to Predict Anti-inflammatory Potential of Xanthones and Flavanoids.
Details of Training/Workshop organized and total no of user trained One batch with one studentship and two traineeships and second batch with two traineeships completed “Six Month Training Programme”.
Impact shown by the Centre: 1.
Due to Impact of BIF Centre, this University has introduced a Post Graduate Course in Bioinformatics.
2.
Further one paper on Bioinformatics with 4+2 credits introduced in the curriculum of all life sciences and B. Tech Industrial Biotechnology.
Proposed activities for 2013-14 1.
Insilco Analysis for analyzing the role of Ergothioneine on B-amyloid peptide induced in Alzehmeirs.
2.
Homology modeling of laccases in the degradation of textile dyes.
3.
Structure Prediction of Novel Drug Molecules in Diabetes-II.
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Additional details: Name of the Coordinator Postal Address
Phone Number Fax No. Email Website Name of Contact Person
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Dr. P. Uma Maheswari Devi Head, Dept. of Applied Microbiology, Sri Padmavati Mahila Visva Vidyalayam, Tirupati, 517502, Andhra Pradesh. 09848894900
[email protected] Spmvv.ac.in Dr. P. Uma Maheswari Devi, cell: 09848894900
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Sri Krishnadevaraya University, Anantapur Coordinator: Prof. Chitta Suresh Kumar Summary of the progress made by the centre from its inception The Center main aim is to encourage and build the knowledge of Bioinformatics in all fields of biology. The BIF organizes the course of Bioinformatics and Computational Biology to PG students of Biochemistry, Biotechnology, Microbiology, Zoology etc., of host as well as nearby institutes. The facility also provides support for retrieval of material for seminar presentations, online literature survey and data analysis, bioinformatics analysis and use of specialized molecular modeling and drug design software. In addition the DBT-BIF is also offering PG Diploma in Bioinformatics and Drug Design. The BIF is helping M.Sc. and Ph.D. students of Bioinformatics in teaching, research projects and finalizing their dissertations/thesis. If it is continued after the period of 5 years it would be great helfull for all the students and teachers to develop more skills of advance computational biology.
Major research activities in biotechnology and its related fields at your institution
Identification of New potent Drugs against the Cancer Apoptosis Proteins
Identification of New insilico theories against Cancer related disorders
Genomic analysis of Mycobacterium tuberculosis for Protein targeted In Silico Drug Design
Plasmodium falciparum genome analysis for development of anti-malarial drugs and vaccine development using in silico techniques
Protein Networking
Sequence analysis of genes involved in salt stress in ground nut and fox-tail millet
Proteomic approach and studies on salt stress protein expression
Area of Specialization of the centre: Molecular Modeling, Dynamics, Docking and Drug Design.
Major activities of the bioinformatics facility (BIF) during the year 2012-2013 The BIF organizes the course of Bioinformatics and Computational Biology to PG students of Biochemistry, Biotechnology, Microbiology, Zoology etc., of host as well as nearby institutes. The facility also provides support for retrieval of material for seminar presentations, online literature survey and data analysis, bioinformatics analysis and use of specialized molecular modeling and drug design software. In addition the DBT-BIF is also offering PG Diploma in Bioinformatics and Drug Design. The BIF is helping M.Sc. and Ph.D. students of Bioinformatics in teaching, research projects and finalizing their dissertations/thesis.
Quantifiable major achievements
122 new Drug Targets identified for S. Pneumonia (Paper is under Communicated in JMM)
New Resveratrol analogs are prepared based on Computational Screening which are proving very good target to accelerate apoptosis in cancer cells
Screening of best Drugs against cancer related disorders
Infrastructure facilities at BIF Computer & Communication facility : Server (High end) for Database/Application Server- 3 No., Server (Medium) for Porxy & File Server-1No, desk tops (including internet clients) -20, HP-printers -4Nos, Scaner -2, copier -1, LAN with dedicated BSNL – broad band & Reliance net. Scientific Software packages: Public domain software, MODELER, Open Eye, R package, HYPERCHEM, VectorNT, Autodock, PyrXv11, AutoDock Vina, Visualization Softwares. Bioinformatics programs. Databases & other information resources: Public domain databases.
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Details about staff members working in BIF (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status): Prof. Chitta Suresh Kumar, Professor of Biochemistry, since from August, 2008.
Educational Activities
The Centre is helping M.Sc. and Ph.D. students of Bioinformatics in teaching, research projects and finalizing their dissertations/thesis of host and nearby institutions
Offering PG Diploma course in Bioinformatics and Drug Design to PG students.
Supporting to R&D activities in the field of Bioinformatics of the host and nearby Institutes.
Additionally the BIF is used by students who come for short term projects at S.K. University College of Engineering and College of Pharmacy, from other colleges and universities
All the post graduate and diploma students were easily absorbed by the Pharmaceutical and Biotech Industries as they have excellent hands on training in using Bioinformatics tools.
Papers published or presented in the conferences with reference to BIF (2011-12) Name of the Seminar/Conference/Symposia etc International Symposium on Chemistry and Chemical Biology of Natural Products at IICT during 2-4th August, 2012 National symposium on immunological methods at Dept. of Microbiology, S.K. University during 21st – 23rd of March, 2012
Presentations Oral Poster 0 4 3
4
1.
Catalysis by molecular iodine: a rapid synthesis of 1,8-dioxo-octahydroxanthenes and their evaluation as potential anticancer agents. Bioorg Med Chem Lett. 2012 Mar 15;22(6):2186-91. PMID: 22365759.
2.
Molecular docking and dynamics simulations of A.niger RNase from Aspergillus niger ATCC26550: for potential prevention of human cancer. J Mol Model. 2012 Sep 16. [Epub ahead of print] PubMed PMID: 22983653.
3.
Nutrigenetic screening strains of the mulberry silkworm, Bombyx mori, for nutritional efficiency. J Insect Sci. 2012;12:15. doi: 10.1673/031.012.1501. PubMed PMID: 22934597; PubMed Central PMCID: PMC3467092.
4.
Molecular characterization of Mtb-OMP decarboxylase by modeling, docking and dynamic studies. Interdiscip Sci. 2012 Jun;4(2):142-52. Epub 2012 Jul 29. PubMed PMID: 22843237.
5.
InCl3-catalysed synthesis of 2-aryl quinazolin-4(3H)-ones and 5-aryl pyrazolo[4,3-d]pyrimidin-7(6H)-ones and their evaluation as potential anticancer agents. Bioorg Med Chem Lett. 2012 Aug 1;22(15):5063-6. Epub 2012 Jun 13. PubMed PMID: 22749421.
6.
Ultrasound mediated catalyst free synthesis of 6H-1-benzopyrano[4,3-b]quinolin-6-ones leading to novel quinoline derivatives: their evaluation as potential anti-cancer agents. Bioorg Med Chem. 2012 Jan 15;20(2):759-68. Epub 2011 Dec 8. PubMed PMID: 22202437.
7.
Comprehensive structural and functional characterization of Mycobacterium tuberculosis UDP-NAG enolpyruvyl transferase (Mtb-MurA) and prediction of its accurate binding affinities with inhibitors. Interdiscip Sci. 2011 Sep;3(3):20416. Epub 2011 Sep 29. PubMed PMID: 21956743.
8.
Protein-protein docking on molecular models of Aspergillus niger RNase and human actin: novel target for anticancer therapeutics. J Mol Model. 2012 Feb;18(2):653-62. Epub 2011 May 12. PubMed PMID: 21562828.
9.
Azadirachtin interacts with retinoic acid receptors and Inhibits retinoic acid-mediated biological responses (2011) , J. Biol. Chem; http://www.jbc.org/cgi/doi/10.1074/jbc.M110.169334
Initiation of R&D activities at Bioinformatics Facility : Research activities carried out by the centre are as follows: 1). UGC, New Delhi sanctioned Major Research Project on Homology modeling of Mtb proteins and the program is actively going on.
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2). B.Tech Project work on Homology modeling and Docking Studies on S. Pneumonia DNA Gyrase by Sai Ramya Sree, Navya Keerthi, Satyabhama University, Chennai. Details of Training/ Workshop organized and total no. of user trained: 2 workshops organized. 1). National Workshops Protein Modeling of Drug Targeted Proteins in Bioinformatics Era during 26-28th December, 2008 and 50 participants trained. 2). “Bioinformatics Workshop for Pharmacy Students” during 3-5th Jan. 2009. Thirty six students of M. Pharmacy students were trained in basic tools of Bioinformatics in sequence analysis.
Impact shown by your BIF on the growth of biotechnology and allied areas. Primary impact of this centre is the manpower training in Biotechnology at levels that includes undergraduates, postgraduates and research scholars numbering about 350, of Biochemistry, Biotechnology, Microbiology, Botany, Zoology and Sericulture, Chemistry, Physics disciplines of Host University and nearby Institutes.
Proposed Future Activities for 2013-14 :
To offer M.Sc./Ph.D. in Bioinformatics programs from next academic year if financial support for staff is provided by DBT, New Delhi.
To develop computational models/Multimedia interactive educational aids for easy understanding of the biotechnology and related topics
To organize training programs on various advanced topics of Bioinformatics to update the skills and knowledge of Scientists and Researchers.
Implementing R&D in Bioinformatics Training programs in Drug Discovery, Systems Biology.
Hands-on Bioinformatics training for the students and staff of rural schools. Intensive efforts will be made once the center is fully established with faculty sanctioned and supported by DBT, New Delhi.
Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of the contact person
Prof. Chitta Suresh Kumar DBT-BIF, Dept. of Biochemistry, Sri Krishnadevaraya University, Anantapur-515001, A.P. India +91-8554-255466 (M) +91-9849669899
[email protected] www.bic-sku.org Prof. Chitta Suresh Kumar
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Sikkim State Council of Science and Technology, Gangtok Coordinator: Dr. B. C. Basistha Summary of the progress made by the centre from its inception: Sub-DISC centre, Sikkim was established in the year 2001 in Sikkim State Council of Science and Technology with the support from Department of Biotechnology, Government of India. The centre has made remarkable progress since its inception. It has become a scientific information retrieval centre for the researcher of the state. The centre caters not only the scientific information need of the state but also of the national and international researcher working in the flora and fauana of the Himalayan region. Database: The Bioinformatics SubDISC has prepared a database of various important flora and fauna species of Sikkim. This includes Orchids, Rhododendrons, Medicinal Plants, Birds, Butterflies, Crop Diseases, rare, endangered and threatened plant species of Sikkim Himalaya and Scientific personals of Sikkim.
Meeting/Training:
The Bioinformatics SubDISC, Sikkim State Council of Science & Technology has successfully conducted XVIIIth All India BTISnet Coordinators’ Meeting in the year 2007.
Conducted Ist NEBInet Coordinators’ Meeting in Gangtok in the year 2008.
Every year the Centre is conducting two major training program on Bioinformatics based on Annual BTISnet Training Calendar, among the Scientists, Research Scholars, Research Assistants and Assistant Professors.
News Letter: The centre is publishing its quarterly News Letter “BIOGYAN”. The online version is uploaded in the centre’s website wwww.bioinformaticssikkim.gov.in E-library: The centre is providing free access of online e-journals to the Scientists, Researchers, SRFs, JRFs, Research Assistants and Students of the state, with the support of DeLCON Consortium, Department of Biotechnology, Government of India. Library: The centre has well maintained library. The library consists of good quantity of books from fields of Bioinformatics, Biotechnology, Environment and Biodiversity, Molecular Biology and Information Technology.
Book:
The centre has compiled all the published research papers on biodiversity of Sikkim Himalaya in three volumes, I,II,III. The book has become useful for the researcher working on biodiversity of Sikkim. The research topic of the all the research paper is being uploaded in the website. Full text is given on request.
Research Publication: The centre has published research papers on various national and international journals. Some of the recent publications are as under:
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Sushen Pradhan, B. C. Basistha, Radha Basnett, Asok Banerjee. (2012). Chromatographic Techniques are used for identification of basic bioactive compounds of Hippophae salicifolia of Sikkim Himalaya. Glimpse of Biodiversity. 32-39.
Sushen Pradhan, B.C. Basiatha, K.B. Subba. (2012). Aerial nodulation in Hippophae salicifolia from secret forest of Sikkim Himalaya. Australian journal of Botany. Communicated.
Bharat C Basistha and Arneb Sen .(2011) Sea buckthorn and its microsymbiont- a review. NBU Journal of Plant Sciences. 5 67-84.
Arvind K. Goyal, Bharat C. Basistha, Arneb Sen and Sushil K. Middha. (2011). Antioxidant profiling of Hippophae salicifolia growing in scared forest of Sikkim, India .Functional Plant Biology, 38, 697-701.
B.C. Basistha & A. Sen (2012). Genetic diversity of Frankia associated with root nodules of Hippophae salicifolia growing in the sacred forests of Lachen, North Sikkim (Communicated Biologica).
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Research articles in Book:
Laydong Lepcha,B.C.Basistha & M.L.Arrawatia (2012). Landslides: A threat to Bio-resource of Sikkim Himalaya. Sikkim Biodiversity Significance and Sustainability, pp.80-91.
S.Pradhan, B.C Basistha,R.Basnett &A.Banerjee (2012). Chromatographic Techniques used for Investigation of Basic Bio-active Constituents of Highly Potent Species –Hippophae salicifolia from Hidden Forest of Sikkim. Sikkim Biodiversity Significance and Sustainability, pp. 80-91.
Sushen Pradhan, Manjila Sharma, K.B.Subba, Dhanraj Chhetri & B.C.Basistha (2012). Effect of growth regulators on in-vitro multiplication of Citrus jambhiri Lush. Sikkim Biodiversity Significance and Sustainability, pp.128-133.
Rajdeep Gurung, S.R. Lepcha & B.C. Basistha (2012). Intellectual Property Rights (IPR) in Sikkim Himalayas : A future Perspective. Sikkim Biodiversity Significance and Sustainability, pp. 193-198.
Biological animation package:
The centre has prepared Biological database on HIV AIDS and Mitosis & Meiosis. The prepared animations package were distributed to the schools and Colleges. The animation helps the students to understand Biology and bring interest to uptake career in Biological Sciences.
Recently the centre is preparing animation on Plant Physiology. The animation will be distributed to the schools and colleges.
Major research activities in Biotechnology and its related fields at your institution:
Research on plant species of Sikkim Himalaya
Preparation of Database on floral species of Sikkim Himalaya
Area of specialization: Biodiversity, Biotechnology and Bioinformatics Major achievements made during 2012-13:
On 9th August, 2012, the Centre conducted training on DELCON Science Direct Journals, which was attended by Scientists, Research Scholars, Research Assistants working in Sikkim State Council of Science & Technology.
On 07th December, 2012, the Centre conducted training on Documentation of Ethno-traditional knowledge by using Bioinformatics Tools. The Resource Persons of the training were Dr. Bharat Kumar Pradhan, Survey Expert, Sikkim Biodiversity Conservation and Forest Management Project, JICA Institute, Shri. L.K. Rai, Scientist, GBPANT Institute, Government of India and Mr. Laydong Lepcha, Information Officer, Bioinformatics Centre, Sikkim State Council of Science & Technology. The training was attended by Scientists, Junior Research Fellows, Research Assistants from JICA and Sikkim State Council of Science & Technology.
The centre has prepared an important first list database of rare, endangered and threatened plant species from Sikkim Himalaya. The same is uploaded in centre’s website www.bioinformaticssikkim.gov.in.
Fifth Volume of the news letter “BIOGYAN” has been published and is been made online at our website: http// www.bioinformaticssikkim.gov.in.
The centre has prepared animation software of Plant Physiology and Life Science quiz, which will be distributed to the colleges and schools. The software will be very useful for the students to understand Biology.
Infrastructure facilities in the Bioinformatics Centre: Hard wares:-The Centre is equipped with a dual processor server, 17 P-4 PCs, 2 Laptops, 1 Scanners, 2 DeskJet laser printers, 1 Nikon Coolpix S6000 digital camera. Software: Geneious Pro Bioinformatics Software, Quick Heal Internet Security. Internet facility: The centre has 100 Mbps 24 hours internet connectivity provided by the State National Informatics Centre through RF Antenna. The previous one from BSNL was non functional as there was not enough service and internet was too slow and disruptive. Bio Informatics Infrastructure Facility (BIFs)
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Details about Staff members working in the centre: Sl.No. Name 1. Dr. B. C. Basistha 2.
K.B. Subba
3.
Laydong Lepcha
4.
Karun Chettri
Designation Specialization Additional Director and Cyto-genetics Coordinator Co-Coordinator and Sustainable development Assistant Scientific Officer Information Officer Env. & Biodiversity, Bioinformatics and Disaster Mitigation Data Entry Operator BTech
Working Since 2001
Status Permanent
2012
Permanent
2004
Temporary
2011
Temporary
One vacant post each of Technical Assistant and Data entry operator is going to be filled up shortly via interview.
Educational activities
The centre has been providing scholarship for the students undergoing Biological studies.
The centre has prepared and distributed Biological animation packages on HIV AIDS and Biological Life Processes (Mitosis &Meiosis) to the schools and Colleges of Sikkim. The animation helps the students to understand Biology and bring interest to uptake career in Biological Sciences.
Papers/published or presented in the conferences:
Dr. B.C. Basistha (2009). Presented a paper on Understanding agro- techniques of Sea buckthorn in Sikkim Himalayas at International Sea buckthorn Association Conference (ISA) 2009 at Belukuriha , Russia held from 1st-6th September 2009.
Sharma,M.,Pradhan,S.Subba,K.B.Basistha,B.C. Effect of growth regulators on the in-vitro multiplication of Nucellar Seedlings of Citrus reticulaata Blanco. Journal of Hill Research.Vol.22.No.2.2009.pp.110-113.
Pradhan,S.,Sharma,M. Subba,K.B. & Basistha,B.C. Effects of various cultural conditions on in-vitro germination of immature seeds of Citrus reticulata Blanco. Journal of Hill Research.22(1):39-42,2009.
Basistha,B.C.,Sharma,N.P.Lepcha,L.Arrawatia,M.L. & Sen.A. A Ecology of Hippophae salcifolia D.Don of Temperate and Sub Alpine Forests of North Sikkim Himalayas – A case study- Paper accepted for Journal of Symbiosis,USA Inc.
Basistha,B.C. Understanding agro-technique of Sea buckthorn in Sikkim Himalayas. Proceedings of International Seabuckthorn Association
Initiation of R&D activities in Bioinformatics: Details of Training/Workshop organized and total no of user trained Impact shown by the Centre: The centre has shown excellent impact in case of Biological research in the state.
Proposed activities for 2013-14
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a.
Conducting trainings/seminars/workshops and sensitization programs on Bioinformatics and Biotechnology.
b.
Conduct training on application of GIS in Biodiversity database and Management.
c.
Conduct training on application of PERL Bioinformatics for retrieving and analyzing Biological Database.
d.
Database on local banana species of Sikkim
e.
Database on Bamboos of Sikkim Himalayas.
f.
Publish a compiled book of research articles on Ethno-traditional knowledge of Sikkim and other places, from various published journals to support academic research. The book shall be allocated in the library of Bioinformatics Centre only.
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g.
Publication of a Bioinformatics newsletter “Biogyan” current bioinformatics advancements, biodiversity informatics and research activities.
c.
Encouragement to young researchers to take up research in the field of Bioinformatics and Biotechnology through studentship and traineeships.
d.
Collaboration with others research institutes of the state as well as other national institutes to take research work in the field of Bioinformatics and Biotechnology.
e.
Publication of Bioinformatics research papers on National/International Journals.
Contact details: Name of the Coordinator Postal Address
Dr. B.C. Basistha
Sikkim State Council of Science & Technology, Dept. of Science & Technology and Climate Change, Development Area, Gangtok- 737101, East Sikkim Phone Number 03592-208370 Fax No. 03592-208764 Email
[email protected],
[email protected],
[email protected] Website www.bioinformaticssikkim.gov.in Name of Contact Dr. B.C. Basistha, Person Additional Director, Sikkim State Council of Science & Technology
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Sri Venkateswara College, New Delhi Coordinator: Dr. N. Latha Progress made by the centre from its inception The Bioinformatics Infrastructure Facility (BIF) at Sri Venkateswara College, University of Delhi commissioned in July 2007 has been promoting teaching of biology through Bioinformatics at various levels. The centre has organized training programs/workshops for research scholars, post graduate, undergraduate students, college faculty and school teachers in areas of bioinformatics,computational biology,drug discovery and development. The centre also offers a course in Bioinformatics to post graduate Botany students at University of Delhi. The center is involved in a 3 month certificate programme in bioinformatics to undergraduate students. The centre is facilitating students to train in the area of Bioinformatics who are actively involved in the project under DBT-Star College Scheme Student Innovation Projects and Delhi University funded Student Innovative Projects. Besides these training activities, the centre is also actively involved in research in protein modeling, lead molecule design, immunoinformatics and systems biology.
Areas of specialization Major research areas of the centre include Protein modeling and simulations, lead molecule design, immunoinformatics and interaction network analyses.
Infrastructure facilities in the bioinformatics centre A.
Computer & Communication facility: The existing infrastructure includes unlimited internet connectivity (TATA WiMax), Sun Workstations M2 (18), 2 Servers (1-High End Compute & 1- Web Server), One 64 Processor-8-node Cluster, 2 Gigabit Switch for LAN, 2 Laser Network Printers, HP dc7900 Desktops (5), 1 HP Touchsmart IQ500 PC, HP Pavillion dc6767tx Laptop and one Inspire mini Dell Laptop, 24 Port D-link Gigabit Rack Switch (3), external hard drives (4), 1 Sharp Notevision DLP Projector, 2 Uniline UPS (5 & 10 KVA) and one wireless router.
B.
Scientific Software packages: Schrodinger package for Protein modeling, molecular docking, pharmacophore modeling and QSAR analysis, Muse from Tripos, Gromacs 4.5.5, Autodock 4, Phylip, Modeller 9.10, SPDBV, ArgusLab, ACD Cherm sketch, MedChem Designer, Cytoscape, Navigator, Pymol, CYGWIN, MEGA 4, etc.
C.
Databases & other information resources: Library of bioinformatics Books – 113
Major activities of the centre during the year Teaching & Training Activities
Add on Course in Bioinformatics : 3 months Short Term Course for graduates 26 final year students pursuing degree programs in Biochemistry, Botany, Zoology, Physics and Life Sciences at Sri Venkateswara College are selected for this course. This 3 month course covers lectures by experts working in the area of Computer Fundamentals, Genomics, Proteomics and In silico drug design. In addition, hands-on session exposes the students to various Bioinformatics tools & softwares available in the public domain. Evaluation at the end of the course & certificate
Short Term Training Programme in Bioinformatics: 6 months duration for post-graduates( M.Sc/ M.Tech)Around 12 postgraduate students from various institutes across the the country have been trained.
Continous Training Program in Bioinformatics : Around 5 undergraduate students have been trained for 13 months short term training program in bioinformatics at any given time.
Workshops Organized:
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Basics in Bioinformatics for Undergraduate Students- Jan 10-12, 2013
Workshop in Computational Approaches for Lead Optimization – Dec 22-23, 2011
Workshop on Bioinformatics for Life Sciences Faculty – July 27-30, 2011
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Workshop in Recent Advances in Computer Aided Drug Design – Dec 3-4, 2010
Refresher Course in Biotechnology & Its applications (Interdisciplinary), July 30- August 4, 2009
National Conference on Drug Discovery & Development , Jan 21-23, 2009
Instructional Workshop in Bioinformatics for School teachers, April 24-25, 2008
Bioinformatics Workshop for School Teachers – Jan 3-4, 2008
The Second ASEAN India Bioinformatics Workshop- Dec 14-16, 2006
Papers published or presented Recent Publications: 1.
Nidhi Jatana, Sarvesh Jangid, Garima Khare, Anil K. Tyagi & N. Latha “Molecular modeling studies of Fatty acylCoA synthetase (FadD13) from Mycobacterium tuberculosis: a potential target for the development of antitubercular drugs” (2011) Journal of Molecular Modeling, Volume 17, Number 2, 301-313. (DOI: 10.1007/s00894010-0727-3).
2.
Nidhi Jatana, Aditya Sharma & N. Latha “Pharmacophore modeling and virtual screening studies to design potential COMT inhibitors as new leads” (2012) Journal of Molecular Graphics and Modelling (DOI: 10.1016/ j.jmgm.2012.10.010)
Poster Presentations: International Conferences
Poster presentation at Albany 2011: Nidhi Jatana, Aditya Sharma and N. Latha entitled “Integrating CADD methodologies for the design of novel COMT inhibitors” at Albany 2011: 17th conversation from June 14-18, 2011 at State University of New York, Albany, NY, USA.
Poster presentation at INCOB 2011: Sonika Malik, Suchi Sharma, Brijesh Rathi, B. K. Singh and N. Latha entitled “Structure prediction and peptidomimetics based inhibitor design for CARD15/NOD2 using computational approaches: Implications in Crohn’s disease ” in InCoB-ISCB Asia Joint Conference 2011 held from 30th Nov 2011-2nd Dec 2011 in Kuala Lampur, Malaysia.
National Conferences
Workshop on “Molecular Modelling and Drug Design” Centre for Modelling Simulation and Design, University of Hyderabad ( 2010)
International Conference on “Open Source for Computer Aided Drug Discovery” Institute of Microbial Technology, Chandigarh ( 2009)
National Conference on Drug Discovery and Development ,Sri Venkateswara College, New Delhi ( 2009)
International Symposium on “Emerging Trends in Tuberculosis Research: Biomarkers, Drugs and Vaccines” , ICGEB, New Delhi ( 2008)
Staff Members: Name Nidhi Jatana
Designation SRF
Specialization Molecular modeling & lead molecule design
Period of Working December 2007- till date
Avijit Podder Neelu Singh
SRF SRF
Genomics and Systems biology De-novo Inhibitor Design
June 2012- till date August 2012- till date
Suchi Sharma
JRF
Molecular modeling & network analyses
December 2010- till date
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Contract details:
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Name of the Coordinator
:
Dr. N. Latha
Postal Address
:
Associate Professor, Department of Biochemistry & Coordinator, Bioinformatics Infrastructure Facility, Sri Venkateswara College, University of Delhi, Dhaula Kuan , New Delhi 110021
Phone Number
:
011-24111742
Fax No
:
011-24118535
Email:
:
[email protected]
Website:
:
www.bic-svc.ac.in
Name of contact person
:
Dr. N. Latha
Email
:
[email protected]
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Sri Venkateswara Institute of Medical Sciences University, Tirupati Coordinator: Dr. A. Umamaheswari Summary of the progress made by the centre from its inception: Sri Venkateswara Institute of Medical Sciences (SVIMS) was established by Tirumala Tirupati Devasthanams, Tirupati, in the year 1993 to provide the most advanced medical care to the poor and the needy at an affordable cost and became University by State Act in the year 1995. The Department of Bioinformatics was established in the year, 2003 and the university is first of its kind to start post graduate course in Bioinformatics in the state of Andhra Pradesh. SVIMS University is the only medical science institute to have a DBT sponsored BIF in South India. Since its inception on 10th March, 2007, the centre became a focal point for providing training, communication and computational facilities to the teachers, researchers and students of various medical specialties of the university and neighboring institutions. The centre was further extended to develop a molecular modeling laboratory with HPZ800 workstation, Sun Microsystems workstation, Schrodinger software 2011, Discovery Studio 2.0. Being a medical science institution, constant efforts have been made by the centre to implement Bioinformatics techniques in healthcare through collaborative works with medical specialties of our institute as well as pharmacy departments of neighboring institutes. Two BIF executive committee meetings were conducted by the centre, the second BIF executive committee meeting was chaired by Padma Bhushan Dr. Mrs. Manju Sharma. She appreciated the progress made by the centre.
Major research activities in biotechnology and its related fields : I.
Stem cell Isolation, evaluation and characterization.
II.
Molecular characterization of drug targets from Staphylococcus aureus ATCC 12600.
III.
Prevalence of factors influencing endothelial function in paediatric obesity.
Area of specialization: Molecular Modeling and Drug Design, Reverse Vaccinology, Bioinformatics e-learning modules and Biological database development, Medical informatics.
Major achievements made during 2012-13: I.
Paper entitled “Discovery of potent MurC inhibitor of Leptospira interrogans through structure based drug designing”, by Pradhan D, Priyadarshini V, Munikumar M, Sandeep S, Pradeep N, Hema K and Umamaheswari A, won Association of Biotechnology & Pharmacy junior scientist award 2012 (1st Prize) in “International Conference on Environment impact on human health and therapeutic challenges” organized by Dept. of virology, SV University, AP, India from 20-22nd Dec 2012.
II.
Paper entitled “Genome-based approaches to develop epitope-driven subunit vaccines against infective endocarditis” by Priyadarshini V, Pradhan D, Munikumar M, Sandeep S and Umamaheswari A, won best paper presentation award in National seminar on “Emerging Trends in Biotechnology: Challenges and Opportunities” organized by Dravidian University, Kuppam, from 13th -15th Mar 2012.
III.
Paper entitled “Homology modeling, docking and molecular dynamics simulations reveal potential inhibitors of Legionella pneumophila MurB reductase” by Priyadarshini V, Pradhan D, Munikumar M, Sandeep S and Umamaheswari A, won best poster award in 3rd National seminar on computer aided drug design organized by Dept. of Bioinformatics, SVIMS University, Tirupati from 29th -30th Dec. 2011.
IV.
Three M.Sc. Bioinformatics students were selected as for BCIL Bioinformatics industrial training programme (BIITP) 2012-13.
Infrastructure facilities in the Bioinformatics Centre: Details about Staff members working in the centre: Sl. No.
Name
1.
Mr. Dibyabhaba Pradhan
Designation
Specialization
Working Since
Status
Project Assistant
Bioinformatics
17/3/2008
Not absorbed
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Educational activities The Department of Bioinformatics offers M.Sc. Bioinformatics (15 seats) and Ph.D. (6 seats).
Papers/ published or presented in the conferences: Papers published - 09 I.
Pradhan D.,Priyadarshini V., Munikumar M., Swargam S., Umamaheswari A and Aparna B (2012) Para-(benzoyl)phenylalanine as a potential inhibitor against LpxC of Leptospira spp.: Homology modeling, docking and molecular dynamics study. Journal of Biomolecular Structure & Dynamics. http://dx.doi.org/10.1080/07391102 .2012.758056 (In Press)
II.
Munikumar M., Priyadarshini V.,Pradhan D., Umamaheswari A. and Vengamma B (2012) Computational approaches to identify common subunit vaccine candidates against bacterial meningitis. Interdisciplinary Sciences: Computational Life Sciences (In Press).
III.
Anjum M., Pradhan D., Priyadarshini V., Munikumar M., Sandeep S., and Umamaheswari A. (2012) Identification of potent antagonists against BACE-1 through structure based virtual screening approach. Journal of Clinical and Scientific Research (In Press).
IV.
Priyadarshini V., Pradhan D., Munikumar M., Sandeep S., Umamaheswari A. and Rajasekhar D (2012) Molecular modeling, docking and dynamics studies of Biotin carboxyl carrier protein of acetyl-CoA carboxylase to discover potential inhibitors. Journal of Clinical and Scientific Research (In Press).
V.
Munikumar M., Priyadarshini V., Pradhan D., Swargam S., Umamaheswari A and Vengamma B (2012) In Silico Identification of common putative drug targets among the pathogens of bacterial meningitis. Biochemistry and Analytical Bioichemistry 1:8.doi:10.4172/2161-1009.1000123 (OMICS Publishing Group)
VI.
Navya P., Hema K., Munikumar M., Swargam S and Umamaheswari A. (2012) Molecular docking of a beta-2microglobulin drug target. Online Journal of Bioinformatics 13(1):93-201.
VII. Hemanthkumar M. and Umamaheswari A. (2012) Homology model of sugarcane soluble acid invertase. Online Journal of Bioinformatics 13(1):93-201. VIII. Sandeep S., Priyadarshini V., Pradhan D., Munikumar M. and Umamaheswari A. (2012) Docking and molecular dynamics simulations studies of human protein kinase catalytic subunit alpha with antagonist. Journal of Clinical and Scientific Research 1(1):15-23. IX.
Umamaheswari A., Pradhan D. and Hemanthkumar M. (2012) Computer aided subunit vaccine design against pathogenic Leptospira serovars. Interdisciplinary Sciences: Computational Life Sciences .4(1):38-45.
Papers presented-20
374
I.
Munikumar M, Priyadarshini I.V., Pradhan D, Sandeep S, Pradeep N, Hema K and Umamaheswari A. In silico identification of common putative drug targets among the pathogens of bacterial meningitis was presented and published in “International Conference on Environment impact on human health and therapeutic challenges” organized by Dept. of virology, SV University, AP, India from 20-22nd Dec 2012.
II.
Priyadarshini I.V., Pradhan D, Munikumar M, Sandeep S, Pradeep N, Hema K and Umamaheswari A. In silico identification of potential inhibitors against acetyl-coA carboxylase, biotin carboxyl carrier protein associated with infective endocarditis was presented and published in “International Conference on Environment impact on human health and therapeutic challenges” organized by Dept. of virology, SV University, AP, India from 2022nd Dec 2012.
III.
Pradhan D, Priyadarshini V, Munikumar M, Sandeep S, Pradeep N, Hema K and Umamaheswari A Discovery of potent MurC inhibitor of Leptospira interrogans through structure based drug designing was presented and published in “International Conference on Environment impact on human health and therapeutic challenges” organized by Dept. of virology, SV University, AP, India from 20-22nd Dec 2012.
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IV.
Priyadarshini I.V., Pradhan D, Munikumar M, Sandeep S, Pradeep N, Hema K and Umamaheswari A. In silico identification of potential inhibitors against acetyl-coA carboxylase, biotin carboxyl carrier protein associated with infective endocarditis was presented and published in National conference on pharmaceutical industry and academic partnership-for professional excellence organized by Sri Padmavathi Mahila Visvavidyalayam (Women’s University) Tirupati Tirupati, From 5 and 6 October 2012.
V.
Lakshmi Narayana Rao C., Ramesh G., Pradhan D and Umamaheswari A Structure based virtual screening to discover potent antagonists for human PPIF: a drug targer of cardiovascular disease was presented and published in National conference on pharmaceutical industry and academic partnership-for professional excellence organized by Sri Padmavathi Mahila Visvavidyalayam (Women’s University) Tirupati Tirupati, From 5 and 6 October 2012.
VI.
Geetha Y., munikumar M and Umamaheswari A Identification of novel human growth factor receptor bound protein2 activators through docking studies was presented and published in National conference on pharmaceutical industry and academic partnership-for professional excellence organized by Sri Padmavathi Mahila Visvavidyalayam (Women’s University) Tirupati Tirupati, From 5 and 6 October 2012.
VII. Reshma, Hema K and Umamaheswari A Structure based virtual screening to design novel potent inhibitors for human alpha-1-acid glycoprotein (ORM1) involved in cardiovascular diseases was presented and published in National conference on pharmaceutical industry and academic partnership-for professional excellence organized by Sri Padmavathi Mahila Visvavidyalayam (Women’s University) Tirupati Tirupati, From 5 and 6 October 2012. VIII. Althaf Basha B., Pradeep N and Umamaheswari A Virtual screening design drug molecules for human Cathepsin D was presented and published in National conference on pharmaceutical industry and academic partnershipfor professional excellence organized by Sri Padmavathi Mahila Visvavidyalayam (Women’s University) Tirupati Tirupati, From 5 and 6 October 2012. IX.
Sandhya A., Sandeep S and Umamaheswari A Identification of novel agonist for human apolipoprotein A-1 using structure based virtual screeining was presented and published in National conference on pharmaceutical industry and academic partnership-for professional excellence organized by Sri Padmavathi Mahila Visvavidyalayam (Women’s University) Tirupati Tirupati, From 5 and 6 October 2012.
X.
Deepthi Reddy D., Navya P and Umamaheswari A. Discovery of novel inhibitors for human macrophage colony stimulating factor1 receptor (CSF1R) through molecular docking studies was presented and published in Advanced Biopharmaceutical Strategies-A Regulatory Perspective (ABS 2012)organized by Sree Vidyanikethan College of Pharmacy, Tirupati, Ranganpet , From 13 and 14 July 2012.
XI.
Prasad D.,Pradhan D and Umamaheswari A. Docking studies to discover novel therapeutic antagonists for human sulfhydryl oxidase1. was presented and published in Advanced Biopharmaceutical Strategies-A Regulatory Perspective (ABS 2012)organized by Sree Vidyanikethan College of Pharmacy, Tirupati, Ranganpet , From 13 and 14 July 2012.
XII. Tejaswi G.,Sandeep S and Umamaheswari A. Structure based virtual screening to design novel activators for human HCFII involved in cardiovascular diseases was presented and published in Advanced Biopharmaceutical Strategies-A Regulatory Perspective (ABS 2012)organized by Sree Vidyanikethan College of Pharmacy, Tirupati, Ranganpet , From 13 and 14 July 2012. XIII. Anila N.,Hema T and Umamaheswari A. In silico analysis to explore novel antagonists for human insulin like growth factor binding protein-1 (IGFBP-1) involved in cardiovascular diseases was presented and published in Advanced Biopharmaceutical Strategies-A Regulatory Perspective (ABS 2012)organized by Sree Vidyanikethan College of Pharmacy, Tirupati, Ranganpet , From 13 and 14 July 2012. XIV. Aswini SR.,Priyadarshini I.V.and Umamaheswari A. 10. strategic molecular docking to explore novel inhibitors against human complement component c8 alpha chain was presented and published in Advanced Biopharmaceutical Strategies-A Regulatory Perspective (ABS 2012)organized by Sree Vidyanikethan College of Pharmacy, Tirupati, Ranganpet , From 13 and 14 July 2012.
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XV. Keerthi kumari.,Munikumar M and Umamaheswari A. Discovery of novel human ficolin-3 activators based on molecular docking studies was presented and published in Advanced Biopharmaceutical Strategies-A Regulatory Perspective (ABS 2012)organized by Sree Vidyanikethan College of Pharmacy, Tirupati, Ranganpet , From 13 and 14 July 2012. XVI. Priyadarshini I.V.,Pradhan D.,MuniKumar M.,Sandeep s and Umamaheswari A. Genome-based approaches to develop epitope-driven subunit vaccines against infective endocarditis was presented and published in National Seminar on Emerging Trends in Biotechnology: Challenges and Opportunities organized by Dravidian University, Kuppam , From 13 and 15 March 2012. XVII. Navya P K.,Divya M., Hema K and Umamaheswari A. In silico design of potent agonists for human PPAR gamma, was presented and published in National Conference on Modern Innovations and Approaches in Biotechnology (NCMIAB-2012),organized by Sri Padmavathi Mahila Visvavidyalayam (Women’s University) Tirupati, From 29 February to 1st March 2012. XVIII. Priyadarshini I.V., Pradhan D., MuniKumar M and Umamaheswari A. Structure based virtual screening towards identification of potential thioredoxin reductase inhibitors for infective endocarditis therapy, was presented and published in National conference on Biotech and Biotech Molecules - their Health effects and Therapeutic applications (BAMHT-2012), organized by S.V University, Tirupati, From 24 and 25 February 2012. XIX. Hema K., Harika M,. Navya P and Umamaheswari A. In silico identification of potential antagonists for human Casein kinase II subunit alpha, was presented and published in National Seminar on Advances in Microbial Technology organized by Sri Padmavathi Mahila Visvavidyalayam (Women’s University) Tirupati, From 13 and 14 February 2012. XX. Pradhan D., Priyadarshini I.V., MuniKumar M., Sandeep s and Umamaheswari A. Homology modeling, docking and molecular dynamics simulations for designing potential inhibitors against KDO-8-phosphate synthase of Leptospira interrogans , was presented and published in National Symposium on Bioinformatics: Bioinformatics: Challenges in the post-genomic era organized by University of Jammu, Jammu, on 2nd February 2012.
Initiation of R&D activities in Bioinformatics: I.
Identified potential drug targets and inhibitors against diseases like leptospirosis, infective endocarditis, bacterial meningitis and cancer.
II.
Organizing National level workshops, Continuing medical education (CME) programs, and Guest lecturers for promotion of biology teaching through bioinformatics.
III.
Providing long term training (4-6 month) for M.Sc. Bioinformatics students and short term training (One month) for B. Tech Bioinformatics/ Biotechnology students for partial fulfilment of their degrees.
IV.
Impart training to M.Sc. Bioinformatics students through studentship and traineeship program.
Details of Training/Workshop organized and total no of user trained I.
CME on Antiviral agents was organized by Dept. of Bioinformatics, Biotechnology and Bioinformatics on 1st December 2012.
II.
Dr. M. Rami Reddy, presented a guest lecture on Use of computer aided drug design methods & structural biology in the discovery of new classes of clinical candidates on Diabetes & AIDS on 4th Dec. 2012.
III.
One day training program by Dr. Rathore on Schrodinger software suite was organized by Dept. of Bioinformatics on 5th Dec. 2012.
IV.
Dissertations completed: Fifteen M.Sc. dissertations were completed utilizing Bioinformatics Infrastructure Facility in the academic year 2012-13.
Impact shown by the Centre: The main objective of the Bioinformatics centre is Bioinformatics teaching and Research. The Bioinformatics centre is actively involved in teaching Bioinformatics subjects to M.Sc. Bioinformatics and M.Sc. Biotechnology students of SVIMS
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University. The centre regularly conducts National workshops/seminars and CME programs to promote Bioinformatics knowledge among life science researchers, M.Sc. students and UG students. The centre promotes research activities in Bioinformatics through Ph.D. Bioinformatics program. It also offers research training to M.Sc. Bioinformatics students of SVIMS University, Neighboring University (SV University & SPMVV University, Tirupati) to complete their dissertation works for partial fulfillment of their M.Sc. Degree. The studentships, Traineeships were utilizing BIF for their research training program. So far 95 dissertations (93 M.Sc. & 2 B.Tech) in the field of Bioinformatics were completed through training programs of Bioinformatics centre. The students of M.Sc. and Ph.D courses of SVIMS University and neighboring institutes are utilizing state of art facilities at SVIMS Bioinformatics centre for partial fulfillment of their degrees and for conducting advanced research. The research activities carried out by the centre in collaboration with medical specialties of the institute have identified drug targets and potential inhibitors against diseases like leptospirosis, bacterial meningitis, infective endocarditis and cancer causing cell signalling proteins. The infrastructure facility is being utilized by the students, faculty and researchers of departments of Bioinformatics, Biotechnology, Anatomy, Physiology, Physiotherapy, Microbiology, Biochemistry and Nursing.
Proposed activities for 2013-14 I.
Developing user friendly online databases on drug targets and potential inhibitors of leptospirosis, infective endocarditis, bacterial meningitis and cell signaling proteins involved in cancer for usage of these data to scientists worldwide.
II.
Collaboration with IIT, Madras and Dept. of pharmacy for synthesis and in vitro analysis of proposed lead molecules. Probing, Industrial collaboration for developing drug molecules.
III.
Exploring collaboration with Bioinformatics centre, University of Pune for developing clinical databases.
IV.
Developing e-learning modules on Bioinformatics, Organizing National level workshops, Continuing medical education (CME) program and Guest lectures on Molecular modeling and drug designing; Providing short term and long term training programs for M.Sc. and B.Tech students for partial fulfillment of their degree along with regular M.Sc. and Ph.D. Bioinformatics courses offered by the Department.
Contact details: Name of the Coordinator Postal Address Phone Number Email Website Name of Contact Person
Dr. A. Umamaheswari SVIMS Bioinformatics Centre, Sri Venkateswara Institute of Medical Sciences University, Alipiri Road, Tirupati – 517 507 0877-2287727
[email protected] http://svimsbic.org Dr. Amineni Umamaheswari, Associate Professor & Head, Department of Bioinformatics
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Sir Venkateswara University, Tirupati Coordinator: Prof. K. Yellamma Summary of the progress made by the centre from its inception: The Bioinformatics Infrastructure Facility (BIF) was established in the Department of Zoology, Sri Venkateswara University, with the financial assistance from the Department of Biotechnology (DBT), Ministry of Science and Technology, Government of India, New Delhi. The BIF was inaugurated by our honorable Vice Chancellor, Prof. N. Prabhakar Rao on 25th June 2010, with the initial grant of Rs. 20 lakhs. The center has acquired two servers, 10 desktops systems with latest configuration, Printer, Scanner, Photocopier, KVA UPS Backup power supply and 4Mb BSNL Broadband Wi-Fi internet connectivity. Subsequently, the DBT has released Rs.6.88 lakhs as second installment for the year 2011-2012 to strengthen the facility further and with the recruitment of supporting personnel Viz. Research Associate, Traineeship and Studentship and Contingency. All these facilities existing are being extended to the Faculty, Research Scholars and Students of all disciplines of Life Sciences in this University to carry out their Research work and Project works in the field of Bioinformatics and Computational Biology.
Major research activities in biotechnology and its related fields:
Development of Database for anti-ulcer compounds from herbal sources.
Molecular dynamics and docking studies of human potassium channel.
Protein-Protein docking studies on scorpion toxins with GABA-gated chloride channel
Development of new inhibitors against breast cancer.
Identification and molecular modeling of proteins involved in Alzheimer’s Disease and subsequent designing of novel inhibitors for these selected proteins.
Area of specialization:
Genomics & Proteomics.
Database Development.
Molecular modeling and Drug design.
Ethno-pharmacology.
Neuroinformatics on Alzheimers Disease.
Molecular Biology.
Major achievements made during 2012-13:
Executio of Academic projects for M. Sc Bioinformatics students
Development of Database for anti-ulcer compounds from herbal sources
Molecular dynamics and docking studies of human potassium channel
Protein-Protein docking studies of scorpion toxins with GABA gated chloride channel
Development of new inhibitors against breast cancer
Infrastructure facilities in the bioinformatics centre:
378
Desktop Systems
:
10
Printer
:
01
Scanner
:
01
Photocopier
:
01
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KVA UPS Backup power supply
:
01
4Mb BSNL broadband with Wi-Fi internet connectivity.
Details about Staff members working in the centre: (2012-13) Educational activities Sl. No. 1. 2. 3.
Name K. Praveen P. Usnan Taj V. Kalpana
Designation Traineeship Studentship Studentship
Specialization Bioinformatics M.Sc -Bioinformatics Student M.Sc - Bioinformatics Student
Working Since 29-12-2012 29-12-2012 29-12-2012
Status Temporary Temporary Temporary
To Execute project works by M.Sc. Bioinformatics, M.Sc. Animal Biotechnology and M.Sc. Zoology students as a part of their M.Sc curriculum
Organization of Hands on Training Programmes for the Lectures, Ph.D., M.Phil Scholars, PG students and students of Non-Bioinformatics Programmes.
Development of Database for anti-Ulcer, anti–Cancer and anti- Alzheimer’s compounds from herbal sources and from Seri-byproducts.
Development of Database for different vertebrate animal models representing the phyla and to sequence the functionally similar genes.
Paper published and Research papers presented at the conferences: 2012 -13
Research Paper Publications
:
27
Research Papers presented at the conferences
:
65
Initiation of R&D activities in Bioinformatics:
Development of Database for anti-Ulcer, anti–Cancer and anti- Alzheimer’s compounds form Herbal sources.
Insilco Molecular interactions studies on the Neurotransmitters with Seri-products.
Molecular dynamics and docking studies of human potassium channel.
Protein-Protein docking studies of scorpion toxin with GABA-gated chloride channel.
Development of new inhibitors against breast cancer
Analysis and elucidation of the therapeutic efficiency of Antimalarial drugs.
Identification of therapeutic targets against Chlamydophila pneumoniae AR39.
Identification and molecular modeling of proteins involved in Alzheimers Disease and subsequent designing of novel inhibitors for these selected proteins.
To Submit a Research Proposal to the DBT- BIF on preparation of the Database for different vertebrate animal models representing the phyla and to sequence the functionally similar genes.
Details of Training/Workshops organized and total number of users trained: a)
Training/Workshops organized
b)
Total number of users trained:
c)
:
one
i.
M.Sc. Zoology
:
41
ii.
M.Sc. Bioinformatics
:
25
iii.
M.Sc. Animal Biotechnology
:
28
:
More than 50
Research Scholars of other departments in the campus
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M.Sc. Projects by Bioinformatics and
:
54 students
M.Sc. Animal Biotechnology e)
Training for the Faculty, Research scholars and Students of Zoology, Animal Biotechnology, Biotechnology, Virology, Aquaculture Departments in the area of Bioinformatics tools and techniques : 50
f)
The number of M.Sc. Bioinformatics and M.Sc. Animal Biotechnology students currently doing their M.Sc Projects (2013-2014) : 45
Impact shown by the Centre:
12 students, registered for the Ph.D. Programme in Bioinformatics area in the Department are working utilizing the Bioinformatics Infrastructure facilities.
Proposed activities for 2013-14 To further strengthen the Bioinformatics Infrastructure Facility by I.
Organizing Hands on training Workshops for Lecturers of Degree Colleges, Faculty Research Scholars and PG students of our University and other Universities.
II.
To organize International and National Conferences and Awareness Programmes on selected themes of Bioinformatics.
III.
To arrange Guest Lectures on Latest Trends in Bioinformatics field by eminent scientists from reputed Research Institutions.
IV.
To establish collaborative Research Programmes between our University and other Universities, Reputed Parma companies and Research Institutes.
V.
Purchase of Bioinformatics Commercial Software’s required for execution of R&D activities.
VI.
Expansion of the existing Infrastructure Facilities in this Centre to cater to the needs of all Life Science departments on the Campus by acquiring 10 more computers.
VII. Creation of a separate Website for this Centre.
Contact details: Name of the Co-ordinator Prof. Kuna Yellamma Postal Address Department of Zoology, S. V. University, Tirupati – 517 502 Andhra Pradesh, India Phone Number : Office 0877 2289304 Ext:102 ; Mobile 09885248629, Email
[email protected] [email protected] [email protected]
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St. Aloysius College, Mangalore Coordinator: Fr. Denzil Lobo SJ Workshops Conducted : I.
Workshop on Biological Databases and Sequence Analysis Tools 8th Feb 2012
A one day workshop on ‘Biological Databases and Sequence Analysis Tools’ was conducted on 8th February 2012 by St Aloysius Institute of Management and Information Technology (AIMIT), St. Aloysius College, Centre for Bioinformatics, supported by the Department of Biotechnology, Ministry of Science and Technology, Government of India. The aim of the workshop was acquainting students with the available Biological resources on the World Wide Web and demonstrating the practical applications of Bioinformatics by providing hands on training on the same. 50 students from 3rd year B.Sc Biotechnology and 1 faculty member from St. Aloysius College, Mangalore attended the workshop. Students were introduced to various Biological databases by Prof Deborah Vijay, Department of Bioinformatics, AIMIT, AND then acquainted with the Structural databases and Molecular visualization tools by Ms. Shreya John DCruz, student of 4 th Semeter Msc Bioinformatics. This was followed by a lecture on Alignment and Analysis of Biological sequences by Mr. Lanwin Lobo, Lecturer, Department of Bioinformatics, AIMIT. During these sessions various concepts such as biological databases, visualization tools and sequence alignment algorithms were discussed. The morning session concluded at 1:00 PM with an interactive Question and Answer session where the resource persons clarified the doubts and queries of the participants. During the afternoon session participants were given demonstrations and hands on session on various databases, visualization tools and sequence alignment and analysis tools. This was followed by a talk on “Higher Education, Research and Career prospects in Bioinformatics”, delivered by Prof. Santosh Rebello. II.
Workshop on Bioinformatics Tools and Techniques 22nd Feruary 2012
A one day workshop on ‘Bioinformatics Tools and Techniques’ was conducted on 22nd February 2012 by St. Aloysius College, Centre for Bioinformatics. The aim of the workshop was acquainting students with the available Biological resources on the internet and demonstrating the practical applications of Bioinformatics and Computational tools. 30 students from 3rd year B.Sc Microbiology from St. Aloysius College Mangalore attended the workshop. Students were introduced to the field and various applications of Bioinformatics by Mr. Lijo John, student of 2nd Semeter M.Sc Bioinformatics. Biological databases which included sequence and structural databases by Prof Deborah Vijay, Lecture on Alignment and Analysis of Biological sequences by Mr. Lanwin Lobo, Lecturer, Department of Bioinformatics, AIMIT. During these sessions various concepts such as areas of interest in Bioinformatics and its applications, biological databases, visualization tools and sequence analysis algorithms. The participants were given demonstrations and hands on session on various databases, visualization tools and sequence alignment and analysis tools. This was followed by a talk on “Opportunities for Research in Bioinformatics and Computational Biology in India”, delivered by Prof. Santosh Rebello. III.
Workshop on Computational Biology 23nd Feruary 2012
A one day workshop on ‘Computational Biology’ was conducted on 23rd February 2012 by St Centre for Bioinformatics. The aim of the workshop was to introduce the Computational Biology tools. 21 students from 2nd year M.Sc Biotechnology from St. Aloysius College, Mangalore participated in the workshop. Students were introduced to various Advanced Biological databases - sequence and structural databases by Prof Deborah Vijay. This was followed by a talk on ‘Pharmacology for Ashtama Drugs and Scope of Computational Biology’, delivered by Dr Sharat J Vayttaden from the Graduate School of Biological Medicines, University of Texas Health Science Center, Houston, Texas, USA. Dr Sharat J Vayttaden who is an Alumni of St Aloysius College in his talk spoke about the significance and applications of Computational Biology for Pharmacology in finding new medicines to cure Ashtma. He also guided the students on research and future career path. Lanwin Lobo, then discussed Sequence analysis tools and their applications. Students were introduced to various computational tools available such as Expasy tools for proteomics and Genomics, Restriction Mapping, Global and local Alignment, database searching for similar sequences, ORF finders and other nucleotide and protein analysis tools. IV.
Workshop on Genomics and Proteomics 10th March 2012
A one day workshop on ‘Applications of Bioinformatics in Genomics and Proteomics’ was conducted on 10th March 2012 by Centre for Bioinformatics. The aim of the workshop was to introduce students to the analysis and applications of
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microarray data in genomics and proteomics. 27 students from final year B.Sc Microbiology and B.Sc Biotechnology and 1 faculty from St. Agnes College, Mangalore participated in the workshop. Students were introduced to the principle and working of Microarrays, DNA and Protein Chips by Prof Deborah Vijay. A session on ‘Applications of Bioinformatics in Genomics and Proteomics’ by Mr Lanwin Lobo, who spoke about the significance of biological data and applications of microarray data in analyzing the genome and the proteome. During the afternoon session, participants were given demonstrations and hands on session on various databases, visualization tools and sequence alignment and analysis tools. Participants were also introduced to various data analysis tools available such as Expasy tools for proteomics and Genomics. Workshop on Computational and Structural Biology 26th & 27th March 2012
V.
A two day National Work shop on ‘Computational and Structural Biology’ was conducted on 26th and 27th March 2012 at AIMIT. 50 enthusiastic participants attended the workshop comprising of faculty, research scholars and final year Engineering (B E Biotechnology) and M.Sc Students. The workshop commenced with the inaugural. Prof. Mrs. Deborah Vijay formally welcomed the gathering. Dr. Mrs. Manjula Shantaram highlighted on the advantages of using bioinformatics in various scientific disciplines. The first session, “Introduction to Bioinformatics and Structural Databases’ was taken up by Prof. Deborah Vijay, in which she spoke about the types and importance of various structural databases. Thereafter, the session was taken up by Dr. Balaji S on ‘Structural Analysis and Visualization’. He spoke about various visualization tools and provided a visual demonstration using Rasmol. He also gave us an insight into the art of science and protein structure. Hands on practical session which was led by Ms. Melissa and Ms. Chriselle on various sequence and structural databases. They were also made familiar with molecular visualization tools. The second day of the workshop commenced with the session given by Dr Rio D’souza on Computational algorithms in Bioinformatics. Mr Lanwin Lobo talking on sequence analysis. He spoke about the wealth of information hidden in the genome and how to extract it. In the afternoon session with the hands on session led by Ms Poojitha and Mr Lijo. Proposed New Post Graduate Diploma in Computational Biology from 2013
Post Graduate Diploma in Computational Biology (PGDCB) - I Year
1 2 3 4 5 6 7
Post Graduate Diploma in Computational Biology (PGDCB) - I Year I SEMESTER II SEMESTER Bioinformatics and Biological Databases Genomics and Proteomics Computational Biology Systems Biology Structural Biology Computing and Programming for Biologists Bioinformatics and Biological Databases Lab Perl Programming Lab
Computer Aided Drug Design Python Programming Genomics and Drug Design Lab Python Programming Lab Project / Disseration
Books Published by the Faculty: 1.
Santhosh R., Uma M: “Fundamental Simulation Methodologies Dwelling in Neural Networks-Algorithms, Mat lab Source Code”, LAP LAMBERT Academic Publishing, Germany ISBN 13 : 978-3-8443-2579-9 ISBN 10: 3844325794
2.
Santhosh R., Uma M: “Soft Computing Methodologies for Cluster Analysis & Gene Prediction”, LAP LAMBERT Academic Publishing, Germany ISBN : 978-3-8443-1761-9
Contact details : Bioinformatics Center, Aloysius Institute of Management and Information Technology St. Aloysius College (Autonomous), Beeri, Mangalore – 575 022, Karnataka, India Phone : 0824-2286890, 6490299 e-mail :
[email protected] website : www.staloysius.ac.in
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St. Edmund’s College, Shillong Coordinator: Dr. Samrat Adhikari Objective of the facility The objective of the Centre is to provide analysis of biological data, bibliographic references to published literature in science & technology for the faculty members of the colleges in Shillong.
Area of specialization of the Centre: The main area of specialization is Environmental Biotechnology, Bioinformatics and plant Biotechnology.
Research Projects:
Bioremediation of thallium polluted areas using cyanobacteria (UGC – MRP)
Cloning and expression of acpD gene of cyanobacteria and its protein expression study
Extraction and purification of bioactive compounds from cyanobacteria.
Dyes detoxification study using cyanobacteria.
Databases and other information resources Indian Journal of Biotechnology
BCIL Industrial Directory
Indian journal of Experimental Biology
Journal of Scientific and Industrial research
Indian journal of Plant Physiology and Biochemistry
International journal of Bioinformatics
International journal of Biotechnology
International journal of Biotechnology and Biochemistry
Indian Journal of Biochemistry and Biophysics
Softwaresavailable: MS OFFICE (licensed), Systat 12 (licensed), Genious Pro (Licensed), MySQL, freewares like Rasmol, Phymol, Hex6, Auto Dock, Autodock Vienna, GROMACS (parallel server), AMBER etc.
Details about staff members working in the centre: Sl. No Name DrSamratAdhikari 1.
Designation Head & coordinator
Specialization Absorption status Permanent Protein engineering, environmental Biotechnology & bioinformatics
2 3
MsPhilemPriyadarshini Ms Dolly Sewa
Research Associate TraineeShip
Protein bioinformatics Evolutionary genomics
Temporary Temporary
4 5
Mr P. Sawian MrBikashThakuria
Studentship Traineeship
Microbiology Bioinformatics
Temporary Temporary
6
MrJahnuSaikia
Studentship
Environmental Biotechnology
Temporary
Resources Developed: The Centre has prepared a Virtual Laboratory in Electrophoresis of DNA for under graduate students. 1.
Important activities
Human Resource development:
Two students from Garden City College, Bangalore have undergone a 3 months project in BIF centre.
3 undergraduate students of biotechnology honours were trained for using various software’s in bioinformatics as a part of their project work.
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A workshop was organized in the Biotech Hub where two day sessions were devoted to the bioinformatics.
Development of Laboratory manuals:
The BIF has successfully prepared the SOP (Standard operating procedures) for the undergraduate students.
Types of services provided
Literature search by means of CD ROM, internet databases and freewares available.
Email and internet services to all teachers of all departments and to bioscience students.
Online interactive classes/animations for bioscience students to modernize & update biology teaching for the honors students of the college and also for other colleges of Shillong.
Network connectivity:
The BIF has been recently equipped with dedicated optical fibre broadband connection.
An interactive board has been provided from the college management to facilitate the interactive learning.
Posters presented in National Seminars:
Harold B Pyngrope, PhilemPriyadarshini andSamratAdhikari (2012); A docking interaction and analysis of small peptides of Factor VIIa with Factor IX for prediction of potent drug against hemophilia B using in silico approach: Poster Presented at the Proceedings of National symposium on Bioinformatics: challenges in the post genomic era, 2nd February, 2012, organized by the School of Biotechnology, Jammu University, Jammu, India.
Samudra Prasad Suthradhar, Philem PriyaDarshini and SamratAdhikari (2012); Anin silico based docking and analysis of catalytic site prediction of azoreductase in E. coli with a wide range of industrially important azodyes. Poster Presented at the Proceedings of National symposium on Bioinformatics: challenges in the post genomic era, 2nd February, 2012, organized by the School of Biotechnology, Jammu University, Jammu, India.
Papers Published International Priyadarshini Devi Philem&SamratAdhikari (2012); Homology modeling, docking studies and functional analysis of various azoreductase accessory interacting proteins of Nostoc sp.PCC7120; Bioinformation; Vol 8(7): 296-300. PhilemPriyadarshini Devi and SamratAdhikari (2012): Homology modeling and functional sites prediction of azoreductase enzyme from the cyanobacterium Nostoc sp. PCC7120.Interdisciplinary Sciences computational biology 4:310–318.
International (Under Review) H. B. Pyngrope, PhilemPriyadarshini Devi and SamratAdhikari“Prediction of novel small peptides of Factor VII-a which activates Factor IX responsible for extrinsic pathway of blood coagulation” Interdisciplinary Sciences computational biology (Springer) SamratAdhikari, Samudra and PhilemPriyadarshini Devi “In silico docking analysis of E.coli azoreductase with different industrial dyes” Journal of Molecular Modeling.
Impact shown by the Centre on the growth of biotechnology/bioinformatics and allied areas:
The usage of biology literature by the students have increased notably and the facilities of the Centre are widely being made use of for research, paper presentations and other research activities of the college as well as for interpretation of molecular and sequence related work. All together the centre is planning to submit 6 cyanobacterial sequences of the acpD gene to the Gene bank. Besides these the Centre is planning to crystallize the azoreductase protein.
Future activities:
384
To train faculty, students & research workers to make use of bioinformatics techniques in scientific research from base level to advanced level.
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Purchase software’s like schoringder to strengthen R&D activities in bioinformatics.
To developed an interactive practical databases in biotechnology for students.
To start an e-newsletter facility which would act as a repository for research articles by integrating data generated from Biotechnology division and other affiliated research stations
To have access to all the important paid journals required for a thorough literature survey
To keep up with all the new advances in computer and software for a better research
To have access to some of the important software tools for training the students and teachers
To set up a wet lab for basic practical to go hand in hand research with dry lab work
Contact details: Name of the Coordinator: Dr. Samrat Adhikari Postal Address: Bioinformatics Infrastructure Facility (BIF), St Edmund’s college, Shillong - 793003 Phone: 0364-2220808, Mobile: 9862041757 Email:
[email protected];
[email protected] Website: www.sec.edu.in
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Tezpur University, Tezpur Coordinator: Dr. S. K. Ray Summary of the progress made by the centre from its inception: The DBT funded Bioinfomatics Infrastructure Facility (BIF) is in the 5th year of its activity, housed at the Department of Molecular Biology and Biotechnology, Tezpur University. The Centre has been a support in computational biology to the students of MSc in Biotechnology (2 year programme) as well as Integrated MSc in Biosciences and Bioinformatics (5 year programme) students. In addition the facility has been a support to research scholars as well as faculty members of this Department. Our Centre remains open from 9:00am to 9:00 pm on all working days and on holidays from 10:00am to 6:00pm. We have organized two workshops in the last one year as per the mandate. One is on “protein three-dimensional structure modeling” and the other one is on “Chemo-informatics”. The Centre participated in the all India Coordinators’ meeting held at Jammu in February 2012. From the Centre both the Coordinator as well as the Co-coordinator participated in the DBT funded training at ACTREC, Navi-Mumbai in June and July, 2012. The Centre was involved in coordinating between the North-East participants and Dr. A. K. Varma, the host at ACTREC. Faculty members of Tezpur University that are actively involved in computational biology research and associated with the Centre are as follows: (i) Dr. S. K. Ray (ii) Dr. A. N. Jha (iii). Prof. A. K. Buragohain, and (iv) Dr. M. Mandal from the Department of Molecular Biology and Biotechnology; (i) Prof. R. C. Deka, from the Dept. of Chemical Sciences; and (i) Mr. S. S. Satapathy, from the Dept. of Computer Sciences and Engineering. Regarding the temporary position in the BIF, the Research Associate position was occupied till March 2012 and the vacancy will be filled soon. One studentship has been given to a MSc project students doing work in computational biology. Candidates those joined the traineeship left as soon as they got better opportunity. So it is becoming difficult to get candidates for traineeship. Regarding the infrastructure: this year we will be getting new computers and statistical and bioinformatics software.
Major research activities in biotechnology and its related fields : Facultie members of Tezpur University are working in the following biotechnology and allied fields: Plant biotechnology, Petroleum biotechnology, Microbial biotechnology, Biochemistry, nanobiotechnology, Redox biochemistry, Enzymology, Virulence functions in bacteria. Molecular immunology and Immunogenetics, Radiation and cancer biology, Molecular Toxinology, Human Molecular Genetics, Molecular evolution, in-silico Drug designing, Evolutionary genomics Computational Biophysics, Cardiovascular Biology, Regulation of inflammatory gene expression, Protein ‘arginylation’ and its role in cellular function, Host Pathogen Interaction, Molecular biology of rotavirus, Traditional Medicinal plants
Following research were carried out in the center in the year 2012 (i)
Understanding the evolution of codon usage bias in bacteria
In the genetic code the 61 codons encodes the 20 amino acids which results more than one codon for most of the amino acids, known as synonymous codons. The abundance of these synonymous codons in genomes is not random suggesting the role of evolutionary forces causing this bias in genomes. Interestingly, the extent of codon usage bias is different among different species and different within a genome. Therefore to understand the evolutionary mechanism of this wide spread phenomenon is of significant interest to evolutionary scientists. We are addressing the problem by doing compositional anaylsis of nucleotides at the 4-fold degenerate sites across eight family boxes. Our observation is in the support that selection is important to cause codon usage bias in genomes.
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A docking study with Mycobacterial catalase-peroxidase enzyme and the prodrug Isoniazid
Isoniazid is a first line tuberculosis drug used to treat tuberculosis. This prodrug is activated by Mycobacterial catalaseperoxidase and Ser315Thr mutation is found to affect the activation process. Docking studies were performed in order to find the effect of mutation on isoniazid binding to the active site. It is found that Ser315Thr mutation significantly affects the isoniazid binding to the active site. The change in isoniazid binding pattern is mainly responsible for the isoniazid resistance Mycobacterium tuberculosis. In order to find alternative to isoniazid certain imidazole derivatives are chosen for docking analysis and among them 4-nitro-1H-imidazole-5-carbohydrazide shows very good result. (iii) Amino Acid Preferences in Intrinsically Disordered Proteins It has been established that the intrinsically disordered proteins (IDPs) are functionally as important as the other proteins without having a completely folded conformation under the native, physiological conditions. These unstructured / disordered regions provide advantages in several protein functions. The IDPs of class four with known crystallographic structure have been selected for analysis. The PI values of these proteins are very selective and in the range of 3.5-4.0, which is different from the globular proteins. The amino acid composition of the disordered region sequences has been calculated to find the specificity of these segments and their functional importance. The percentage composition of amino acids of the disordered regions of IDPs has been compared with the percentage occurrence of amino acids in the completely folded (globular) proteins and the results show a qualitative difference from the available data in literature. The investigation done in this project gives a strong indication that the intrinsically disordered proteins are divergent and a comprehensive research is very much needed to understand the specificity of these proteins and also to explore the mechanism of the functions done by IDPs.
Area of specialization: Molecular evolution, in-silico Drug designing and Computational Biophysics
Major achievements made during 2012-13: A.
39 number of participants from various parts of India received training in the workshops conducted by the centre.
B.
Students (32 numbers) of integrated M.Sc. in ‘Bioscience and Bioinformatics’ programme run by the Tezpur University have got extensive training from the centre.
C.
Several (8) papers in the field of bioinformatics have been published in the international reputed journals during the year 2012.
Infrastructure facilities in the Bioinformatics Centre: SN 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
Items Desktop Computers Desktop HP Make High end server - HP ML350 Medium end server - HP ML110 Pinter - HP DeskJet Printer - HP Photo copier Scanner UPS 5.0 KV LCD Projector Godrej Almirah Godrej Book shelf White Board Godrej locker Godrej computer table Godrej revolving chair DNA Star Lasergene 8.1 Bio Informatics Infrastructure Facility (BIFs)
Quantity 15 5 1 1 2 1 1 2 3 1 2 1 1 1 15 15
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Details about Staff members working in the centre: Sl.No. Name 1. Dr. S. K. Ray
Designation Associate Professor
Specialization Molecular Evolution
Working Since 2007
Status Coordinator
2. 3.
Dr. M. Mandal Dr, A. Jha
Associate Professor Assistant Professor
Microbiology Computational Biophysics
2007 2011
Co-coordinator Co-coordinator
4. 5.
Mr. V. J. Baruah Ms. U. Borah
Research Associate Project Trainee
Molecular evolution Bioinformatics
November 2012 November 2012
Educational activities The centre is actively involved in teaching and research activities in the field of bioinformatics and other related areas like chemo informatics. The Bioinformatics Centre is organizing regular training for students, research scholars and scientist from North East and other parts of India. This centre is playing very important role in teaching and hands on training for students of five years integrated M.Sc. programme on ‘Bioscience and Bioinformatics’ conducted by Tezpur University
Papers/ published or presented in the conferences (2012): 1.
Nilakshi Barua, Pubalee Sarmah, Iftikar Hussain, Ramesh C Deka and Alak Kumar Buragohain.()DFT-based QSAR models to predict the antimycobacterial activity of chalcones. Journal of Chemical Biology & Drug Design 2012; April, 79(4),553–559,
2.
Satapathy SS, Dutta M, Buragohain AK, Ray SK. Transfer RNA gene numbers may not be completely responsible for the codon usage bias in asparagine, isoleucine, phenylalanine, and tyrosine in the high expression genes in bacteria. J Mol Evol. 2012 Aug; 75(1-2):34-42.
3.
SP Singh, S Vivek, RL Bezbaruah, M Barooah. Prediction of the three-dimensional structure of serine/threonine protein kinase pto of Solanum lycopersicum by homology modelling. Bioinformation 2012; 8 (5), 212
4.
SP Singh, BK Konwar. Molecular docking studies of quercetin and its analogues against human inducible nitric oxide synthase. Springer Plus 2012; 1 (69)
5.
SP Singh, RL Bezbaruah, TC Bora. Insilico studies of 2-methylheptyl isonicotinate produced by Streptomyces sps. 201 against dihydrodipicolinate synthase enzyme of Mycobacterium tuberculosis. Journal of Biophysical Chemistry 2012; 3 (3), 233-237
6.
SP Singh, R Konwarh, BK Konwar, N Karak. Molecular docking studies on analogues of quercetin with dalanine:d-alanine ligase of Helicobacter pylori. Medicinal Chemistry Research 2012
7.
SP Singh, BK Konwar. In silico structure assessment analysis of core domain of six protein data bank entries of HIV-1 Integrase. Journal of Computational Biology and Bioinformatics Research 2012; 4 (1), 1–7
8.
SP Singh, TC Bora, RL Bezbaruah. Molecular Interaction of Novel Compound 2-Methylheptyl Isonicotinate Produced by Streptomyces sp. 201 with Dihydrodipicolinate Synthase (DHDPS) Enzyme of Mycobacterium tuberculosis for its Antibacterial Activity. Indian Journal of Microbiology, 2012; 1-6
Initiation of R&D activities in Bioinformatics: The Centre is actively involved in research activities in different aspects of Bioinformatics such as (i)
Genome compositional analysis
(ii)
Amino acid composition in unfolded protein sequences
(iii) Protein and drug interactions. The Centre is planning to start genome sequence database.
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Details of Training/Workshop organized and total no of user trained Sl No 1 2
Name of the programme National Workshop on Chemical Informatics Workshop on tools of proteomics
Date
Duration
21– 24 March, 2012 21-22 June 2012
4 2
Users Trained 16 23
Impact shown by the Centre: a.
The centre is giving hands on training to the faculty members and research scholars of the north east India.
b.
The University is running a five years integrated M. Sc. course on ‘Bioscience and Bioinformatics’ and this centre is providing the human resource and infrastructural facilities for smooth running of the programme.
c.
M.Sc. and Ph.D. students of this university are regularly availing the facilities of the centre for their research work.
d.
Several international publications in reputed journals came out from this centre
e.
Many faculty members and students of the University have initiated quite a few research works related bioinformatics in recent past.
Proposed activities for 2013-14 1)
Organization of a series of trainings on bioinformatics and computational biology to teachers, Ph.D scholars and M.Sc students.
2)
The Centre is looking forward to merge bioinformatics and experimental research in the direction of sequencing genomes of interesting as well as novel prokaryotes.
3)
The University in the 12th plan had proposed creating a microbial genomic data base to which the Centre is looking forward very much. Our objective to make the Centre an active Centre of genomic research.
4)
Collaborative research with other Universities and Institutes of India.
5)
Regular updating of the dedicated website.
6)
Studentship and Traineeship for various bioinformatics works as per DBT’s provision.
Contact details: Name of the Coordinator Postal Address
Phone Number Fax No. Email Website Name of Contact Person
Dr. Suvendra Kumar Ray Coordinator, Bioinformatics Centre Tezpur University Napaam, Tezpur, Dist: Sonitpur Assam- 784 028 Mob: 09954472151; 03712-275406 (Off) +91-3712-267005/6
[email protected],
[email protected] http://www.tezu.ernet.in/bif/ Dr. Suvendra Kumar Ray
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Tripura University, Suryamani Nagar Coordinator: Professor S Banik Summary of the progress made by the centre from its inception: Bioinformatics Centre was established during 2008 in the academic grounds of Tripura University in order to facilitate the Bioinformatics Infrastructure Facility (BIF) in Tripura University, Suryamaninagar 799022, and Tripura with the direct financial support of Department of Biotechnology, Ministry of Science & Technology, and Government of India. The centre is situated at the second floor of Academic Building II with two well equipped laboratories- Laboratory-I as well as LaboratoryII. The Laboratory-I is equipped with instruments. The laboratory-II is for functioning the workshop, training facilities, short course programme, seminar, lecture etc related to bioinformatics. The BIF at Bioinformatics Centre facilitating the activities on teaching biology through different bioinformatics tools all through the year. The centre working on some innovative works such as (i) Development of Fish database of Tripura in particular and North-East India in general and (ii) studies on some information search for "Genetic characterization and Conservation Biology of economically important Siluroid fish Ompok pabda of Tripura". Also, the BIF at Bioinformatics Centre extending the facilitating on bioinformatics training program, workshop, seminar etc.
Major research activities in biotechnology and its related fields: Research studies are going on in Collaboration with National Bureau of Fish Genetic Resources, Lucknow under DBTTwinning project entitled "Genetic Characterization and Conservation Biology of an Siluroid Fish species Ompok pabda of Tripura", funded by DBT, Government of India (on-going). Biology, Population Genetics and captive breeding of Ompok bimaculatus from Tripura: a State Fish for Conservation. in Collaboration with National Bureau of Fish Genetic Resources, Lucknow (completed) Some aspects of Biotechnology and Reproductive Physiology related to Ompok bimaculatus with the financial support of DST, Government of India (on-going).
Area of specialization: Fish Biology and Biotechnology
Major achievements made during 2012-13: The bioinformatics centre of Tripura University achieved its goal in different aspects such asi)
Scientists and Students availed facilities of training on Bioinformatics.
ii)
The Bioinformatics Centre receiving a lot of responses from both M.Sc. students, RET qualified PhD Course work students, Pre-doc research scholars and also from the faculties of different disciplines from different corners of NorthEast India in general and Tripura in particular.
iii)
Research publications done with the help of Bioinformatics Centre-
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a)
Book Edited- S. Banik. 2012. Climate change: effects on freshwater biodiversity-Freshwater Environment : Fauna of India. Lap-Lambert Academic publishing, Germany, ISBN 978-3-8473-3635-8.
b)
S Banik, P Goswami, T Acharjee and S Malla. 2012. Ompok pabda (Hamilton-Buchanan, 1822): An Endangered Catfish of Tripura, India: Reproductive Physiology Related to Freshwater Lotic Environment. J. Environment, U.K 1:45-55.
c)
S Banik and P. Bhattacharya. 2012. Ompok pabo (Hamilton, 1822) of Tripura, India: an endangered fish species in relation to some biological parameters. J. Biol. Sci., U.K. 3:91-97.
d)
S Banik, and S. Saha. 2012. Puntius ticto (Hamilton, 1822) of Tripura, India: Reproductive Physiology and Biology. J. Environment,U.K, 1: 136-141.
e)
S Banik, P Goswami, T Acharjee and S Malla. 2012. Larval rearing technology of Ompok pabda (HamiltonBuchanan, 1822)………Proc. Zool. Soc. Springer (In press).
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v)
PARTICIPATION on behalf of the centre: a)
Interactive program on Fish Bioinformatics held at Central Institute of Brackish water Aquaculture during May 21-23, 2012.
b)
Interactive program on Fish Biotechnology held at BHU during 2012
c)
Interactive programme on preparation of database of fish species of Climbing perch of Tripura at University of Kalyani during 6-10 October 2012.
Research works going on with the aids of Bioinformatics Centrei)
Fish biotechnology
ii)
Fish database
Infrastructure facilities in the Bioinformatics Centre: i)
Equipment for practical studies of bioinformatics,
ii)
Information retrieval facility,
iii)
Research Laboratories-two,
iv)
Class room study facility,
v)
Workshop lab facility,
vi)
Seminar lab facility
vii) BIF Library with standard collections of recent books of modern Biology.
Details about Staff members working in the centre: Sl. No. Name of the staff Designation 1. Dr. S Banik Professor in Zoology Coordinator BIC, TU
2.
Dr. Abir Shib
Research Associate
3.
Tanmoy Acharjee
Traineeship
4.
Papiya Das
Studentship
Specialization 1.Ph.D in Zoology (Conservation of Rare and Aquaculture Fish species) 2. Genetic Characterizations of Ompok pabda. 3. Formation of Fish Data Base of Tripura. Ph.D in Life Science Working on Fish Data Base of Tripura M.Sc. in Zoology: Specialization in Fisheries MSc- 4th Semister in Zoology Working on Fish Data Base of Tripura
Working Since 1990 in Department of Zoology
Status Permanent
2001 in Department of Zoology 2011 in Department of Zoology 2012 in Department of Zoology
Temporary
Temporary
Temporary
Educational activities : i) Class room teaching with the Use of equipment for studies on Informatics. ii) Class room teaching on Bioinformatics. iii) Information search facility for the students of different disciplines of Life Sciences. iv) Research facility for the faculties of different disciplines of Biological Sciences. v) Research facilities for the students/scholars of Biological Sciences. vi) Post Graduate course-project preparation. vii) PhD Course work study-project development.
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Papers published or presented in the conferences: i)
S Banik, P Goswami, T Acharjee and S Malla. 2012. Ompok pabda (Hamilton-Buchanan, 1822): New Reports from Freshwater Environment of Tripura, India………J. Environment,UK 1:40-44.
ii)
Ompok bimaculatus: Captive breeding, genetic characterization and conservation. Paper presented in Tripura Science Congress 2011.
iii)
Fish diversity of Tripura : Effects of environment. Paper presented in Tripura Science Congress 2011.
Initiation of R&D activities in Bioinformatics: i)
A collaborative research programme with National Bureau of Fish Genetic Resources, Lucknow is under going entitled "Genetic Characterization and Conservation Biology of an Siluroid Fish species Ompok pabda of Tripura" under the financial support of DBT, Government of India is going on.
ii)
Fish data base construction related to freshwater resources of North-East India.
Details of Training/Workshop organized and total no of user trained: 1.
Lecture program on " Fundamentals of Bioinformatics" :
April 02, 2012
2.
Seminar on " Biology and Bioinformatics" :
July 25, 2012
3.
Hands on Trainings "Tools of Bioinformatics"
August 02-03-, 2012
4.
Hands on Trainings "Computational tools in Biology"
August 29, 2012
5.
Training programme on "Biological data base in Bioinformatics"
January 01-03, 2013
Total no of user: 147 during 2012-2013
Impact shown by the Centre: i)
Use of facilities for training, workshop and seminar etc.
ii)
Awareness development program in the field of BIOINFORMATICS for the students of TRIPURA.
iii)
Use of facilities by faculties of different disciplines.
iv)
Class room teaching for M.Sc students.
v)
Class room teaching for PhD COURSE WORK participants.
vi)
Visit of Scientists related to Subject-Bioinformatics.
Proposed activities for 2013-14 i)
Workshop on 3-days programme on Fish data base and Bioinformatics.
ii)
10-days Course program on DNA Bar coding of Fish and Bioinformatics.
iii)
One week workshop program on Biology and Bioinformatics.
Contact details: Name of the Coordinator Postal Address Phone Number Mobile number Fax No. Email Website Name of Contact Person
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Professor S Banik, Tripura University Bioinformatics Centre, Tripura University (a Central University) Suryamaninagar 799 022, Tripura (West) 0381 237 3787 +919774061712 0381 237 4804
[email protected] http://www.tripurauniv.co.in Professor S Banik, Tripura University
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University of Allahabad Coordinator: Prof. Dwijendra Gupta Progress made by the centre from its inception M.Sc. Program in Bioinformatics started here with our own resources in 2002 is presently running in its 11th Batch. Besides, Bioinformatics is being taught in B.Sc.(Applied Science).Four laboratories have since been added. One Molecular biology Lab and 3 Advanced level Bioinformatics Laboratories for Research, M.Sc.(Bioinformatics) and B.Sc. Applied Science students. Besides, for experimental laboratories in Biochemistry, Molecular Biology and Biotechnology, the existing facilities in the Molecular Biology and Nanobiotechnology Laboratories established by DST-Nanomission grants are being used. Yet another Computer Lab for M.Sc. Bioinformatics students has 30 advanced desktop computers and with internet service. The Bioinformatics Infrastructure Facility was inaugurated on 6th January 2009 by Hon’ble Justice Arun Tandon of Allahabad High Court and Prof. R.G.Harshe, Vice-Chancellor of Allahabad University and has become operational and is open to use by faculty, students and research scholars. Our earlier procured softwares Genocluster, FlexX need fresh licenses. We are shortly purchasing Discovery Studio. Our wet lab is equipped for Proteomics, Protein Biochemistry, Immunology and Nanobiotechnology. The Center organised a 3-Day International Symposium cum Training Workshop on “Recent Trends in Bioinformatics, Systems Biology and Biomolecular Interactions” during January 8-10,2012. with celebrated speakers from Italy, France, Tokyo, Ireland, Australia and Czech Republic with over 80 young participants including B.Sc. Applied Science students.
Major Research activities in biotechnology and its related fields at University of Allahabad Fields of Research in Biotechnology: There are four independent research groups working in Biotechnology and related areas, i.e. Nanobiotechnology, Nanophosphors, GPI anchors etc These projects have become operational as regards the procurement of the equipment is concerned.
Area of Specialization of the Center Fields of Research in Bioinformatics & Computational Biology: Molecular Modeling, Structural Bioinformatics, Metabolic Network Reconstruction, Molecular Docking, Molecular Biology of Cyanobacteria. Major activities of the Center during 2011-12: An International Collaboration is already in force (5th Year) between University of Allahabad (Prof. D.K. Gupta ) and University of Cagliari( Prof. Paul la Colla.
Infrastructure facilities in the Bioinformatics Center: A.
Computer and Communication facility a very high-end work stations (one with two octacore processors, 16 GB of RAM & 3TB HDD, and another is a TESLA workstation) for bio-molecular dynamics, genomics and computeraided structure prediction and computer-aided drug design.
B.
Proteomics and Molecular Biology Laboratory equipped with 2-D Gel Electrophoresis system, PCR and Ultracentrifuge etc.
C.
Scientific and Software packages We are shortly purchasing the Discovery Studio. The earlier procured GenoCluster and FlexX need renewal of licenses.
D.
Databases and other information resources: We are developing our database of activities of the Center of Bioinformatics that includes the projects carried out by the students as part of requirement of curriculum, research papers published by the Biotechnology and Bioinformatics Centers.
Details about staff members working in the Center Presently, we have only one person temporarily employed as Office Assistant on fixed emoluments( Rs 12500 per mensem). UGC has given under its Non-Plan 8 faculty positions (Professor 1, Readers 2, and Lecturers 5) against which recruitment process has been started and these posts are likely to be filled soon. Presently, the core teaching faculty comprises of faculty drawn from different departments vide infra as well as guest faculty:
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Core Teaching Faculty of Bioinformatics 1.
2. 4. 5. 6.
Professor Dwijendra K.Gupta, ( Recombinant DNA, Membrane Molecular Biology, Cell Biology, Immunology, Biochemistry and Genomic DNA and cDNA cloning techniques. Besides, hands-on experience in the area of Genomics and Proteomics and Nano-biotechnology). Professor P.N.Pandey ( Differential Geometry, Biomathematical Modeling. 3. Professor Anoop Chaturvedi (Econometrics, Time series, Life Testing and Reliability, and Liner Models). Dr. Shanthy Sundaram, (Immunobiology, protein structure-function and Genomics and Proteomics Dr.K.N.Uttam (specialty is Diatomic Molecular Spectroscopy). Dr Atul Singh (specialty: Biostatistics)
Types of Service provided: Use of Bioinformatics Infrastructure Facility is open to all.
Educational activities The International Collaboration between University of Allahabad (Prof. D.K. Gupta) and University of Cagliari ( Prof. Paul la Colla) is running in the fifth year. Besides, international collaborations with Italian universities at Turino, Bologna, Parma, Milano and Roma are in force. A number of passed out students are working towards their doctoral degrees on prestigious Italian Govt fellowships in Universities of Bologna,Cagliari, Rome, Parma, Naples, Turino ( all Italy),in Brno (Czech Republic) and University of South Bohemia (Czech Republic)and Göttingen University (Germany), Japan and Netherlands. Collaborative works/ initiatives: Collaborative work in the field of Nanophosphors is going on with a number of laboratories in India.
Initiation of R&D activities: 1.
Nanophosphor-Nanoconjugates based Proteomics and Nanobiosensors Project of DST has been completed..
2.
A project of UGC titled “Molecular dynamics simulations and Docking Studies of acelylcholinesterase for Alzheimer’s Disease” has been started.
Training/ Workshop organized in 2012 3-Day International Conference on International Symposium cum Training Workshop on ““Recent Trends in Bioinformatics, Systems Biology and Biomolecular Interactions” with celebrated speakers from Italy, France, Tokyo, Ireland, Australia and Czech Republic with over 80 young participants including B.Sc. Applied Science students. There were 47 Master’s level student- participants in the Workshop who were given with tutorials and hands-on experience with the problems in Steered Molecular Dynamics, Protein Engineering with Triton and Biomolecular Interactions.
Publications:
394
1.
Ashutosh Mani, P. K.Yadava and Dwijendra K. Gupta (2012) Cold Shock Domain protein from Philosamia ricini prefers single-stranded nucleic acids binding. J. Biomol. Str. Dynamics . 30(5): 532-541.
2.
M. Dwivedi, D. Kumar , V. Tripathi, S.P. Singh and Dwijendra Gupta (2012) Combustion Synthesis and Characterization of Eu-doped Y2O3 Nanoparticles . Adv.Science Letters.4:1-4.
3.
Hina Kalra ..... Dwijendra Gupta ... et al (2012) Vesiclepedia: A Compendium for Extracellular Vesicles with Continuous Community Annotation. PLOS Biology,10(12):1-5.
4.
Pooja Mishra and Paras N. Pandey, (2012) Elman RNN based classification of proteins sequences on account of their mutual information Journal of Theoretical Biology . 311: 40–45.
5.
Ashutosh Mani, Swati Singh, Manish Dwivedi, Vijay Tripathi & D.K.Gupta (2011) An Evolutionary Account of GPI Anchored Proteins. European Journal of Experimental Biology. 1(1)......
6.
Pooja Mishra and Paras N. Pandey, Recursive neural networks for predicting protein folds from their pseudo amino acid composition. Proceedings of 13th International Conference of the International Academy of Physical Sciences (CONIAPS XIII), June 14-16, 2011 at UPES, Dehradun (India)
7.
Pooja Mishra and P. N. Pandey, (2011) (In Press)SVM-based protein fold classification using pseudo amino acid composition and amino acid residue pairs of protein sequences. Adv. Sci. Lett. (2011) (Accepted)
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8.
Pooja Mishra and Paras N. Pandey(2011) A Graph-based Clustering method applied to Protein sequences. Bioinformation 6(10): 372-374.
9.
Manish Dwivedi and D.K. Gupta (2011)A Comparative Genomics based evaluation on Evolutionary aspect of Cystinosin: the Protein defective in Cystinosis, , Journal of Computing, 3( 6) ISSN 2151-9617, 130-134.
10.
S Roy, R Chauhan , N.Maheshwari, S. Gupta , D. K Gupta and Ashok Sharma(2011): In-silico approaches in comparative genomics, structure prediction and functional characterization of secondary metabolite proteins of Mentha sp. Plant Omic Journal. 4(7):354-363.
11.
D.Gupta, D. Kumar, M. Dwivedi, V. Tripathi and S. P. Singh(2012) “Nanophosphors-Nanogold immunoconjugates in Isolation of Biomembranes and in Drug Delivery” In “Nanomedicine for Drug Delivery and Therapeutics” Edited by Dr A. K.Mishra- Australia, Wiley-Scrivener Publishing.
12. M. Dwivedi, D. Kumar , V. Tripathi, S.P. Singh, Marco Brucale and Dwijendra Gupta (2013) A Simple and Facile Method for Preparation and Characterization of CdS Nanoparticles by SEM,TEM and AFM (in preparation).
Presentations/Participations: 1.
Ashutosh Mani & Dwijendra K. Gupta (2011) Identification of novel cold shock response related proteins from Philosamia ricini by 2-D gel electrophoresis. Conference of International Academy of Physical Sciences. June 14-16. University of Petroleum and Energy Studies, Dehradun.
2.
Manish Dwivedi, Vijay Tripathi, and Dwijendra Gupta, A Bioinformatics based Proteomic Approach on Cystinosin Protein Family: Lysosomal Membrane Cystine Transporters, Oral presentation at CONIAPS XII, 22-24 Dec,2010.
3.
Manish Dwivedi, Vijay Tripathi, Shanthy Sundaram and Dwijendra Gupta, Lysosomal Storage Diseases: Application of Nanophosphor-Nanogold-coated Immunoconjugates in Affinity Purification of Lysosomal Membrane Transporter Vesicles.
4.
Manish Dwivedi, Vijay Tripathi, and Dwijendra Gupta, Nanophosphor-Tagged Nanogold Immunoglobulin Conjugates in Molecular Characterisation of Lysosomal transport vesicles- A Proteomics based Study: Preparation and Characterisation of ZnO Nanophosphors.
5.
Manish Dwivedi and Dwijendra K. Gupta, A Comparative Genomics based evaluation on Evolutionary aspect of Cystinosin: the Protein defective in Cystinosis, 1st IFIP International Conference on Bioinformatics ,2010, at SVNIT, Surat.
6.
Manish Dwivedi, Vijay Tripathi, and Dwijendra Gupta, Biogenesis of Lysosome: An Evolutionary Analysis of Lysosomal Associated Membrane Protein -1 (LAMP-1)
7.
Manish Dwivedi, Vijay Tripathi and Dwijendra K. Gupta: Preparation and characterization of ZnO nanophosphors, Poster presented, DST- Nanomission Meeting 2009, Kolkata, INDIA.
8.
Vijay Tripathi, Manish Dwivedi and Dwijendra Gupta, Nanophosphor-Tagged Nanogold Immunoglobulin Conjugates in Molecular Characterisation of Lysosomal transport vesicles- A Proteomics based Study: Preparation and Characterization of Nanophosphors: Mn+2: ZnS, Eu+2:Y2O3.
9.
Vijay Tripathi, Prerna Arora, Nandini Singh, Manish Dwivedi, Shanthy Sundaram and Professor Dwijendra Gupta, Phylogenetic Analysis of the Entire Genome of Influenza A (H5N1) Viruses from China.
10. Ashutosh Mani, Manish Dwivedi, Vijay Tripathi and D.K. Gupta, Phylogenetic based study of GPI Anchored Proteins. Oral presentation at National Conference on Nation for Computing, IndiaCom 2009) 11.
Vijay Tripathi, Ashutosh Mani, Manish Dwivedi and D.K. Gupta, Bioinformatics Based Study on Zbtb7 (Zinc finger and BTB domain containing7A) Proteins. . Oral presentation at National Conference on Nation for Computing, IndiaCom 2009.
12. Participated in “Joint Indo-Canadian Meeting on Development of Low-Cost Lab-on-a-chip Medical Devices for Health Monitoring”, Jan 9-11, 2011 at IIT Bombay.
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Participated in International “Winter School on Nano-Scale Materials and Devices”, Dec. 13-17, 2010 at IIT Bombay.
Lectures Delivered: International/National Conferences and Workshops at : CARI Port Blair
(March2011)
Bologna, Italy
(June 2011)
Namur, Belgium
(September 2011)
Orlando, Florida
(October 2011)
Wilberforce, Ohio
(October 2011)
APS University Reva
(January 2012)
Sobhit University Meerut
(February 2012)
Integral Universiy
( April 2012)
Poltusk Poland
(April 2012)
Case Western Reserve University, Cleveland Ohio
(May 2012)
Wilberforce University Ohio
(May 2012)
Kansas State University, Kansas
(June 2012)
SBC Kolkatta
(November 2012)
CONIAPS Bangkok
(December 2012)
Impact shown. M.Sc. Students from different Universities outside Uttar Pradesh (Shobhit University, Amity University, NOIDA, Banasthali Vidyapeeth-Jaipur, MANIT-Bhopal, Devi Ahilya Vishwavidyalaya-INDORE) are being trained in this Department for their Major projects. Biotechnology based projects are being pursued with the help of the BIF offered by our Center. Future activities We are seeking interaction with Bioinformatics institutions abroad for collaborative research proposals. This includes summer training of our students and researchers in these overseas laboratories in different areas of Genomics and Proteomics,,Transcriptomics and metabolomics. A collaborative project with University of Bologna(Italy) is being submitted. Also, an ESF proposal with Prof. Bruno Samori-Chair and Prof Dwijendra Gupta as Co-Chair has been submitted. Proposed Activities:1. Organise 2 Training workshops in Bioinformatics and Exosome Proteomics 2. Electronic classroom by participating institutions in India including MANIT Bhopal We require funds fro DBT under its BTIS-Net scheme to the tune of Rs 1 crore atleast to upgrade our facilities. The hardwares purchased in previous grant period are out of date and need funds to upgrade and service them. Additional details: M.Sc. Bioinformatics program has a novel feature amongst all the teaching programs run at this University, i.e. it is credit-based. The courses are divided into level 0, level 1, level 2, and level courses. Each course has an appropriate minimum requirement. There is a minimum number of credits (12) that each student has to complete in each semester The Courses have been revised again recently.. Contact details : Name of Coordinator: Professor Dwijendra Gupta Postal Address: Prof. Dwijendra Gupta, Coordinator-Chair, Center of Bioinformatics, Institute of Interdisciplinary Studies, Nehru Science Center & Ex-Head, Department of Biochemistry, Faculty of Science, University of Allahabad, Allahabad 211002 (U.P.) Phone Number: 0532-2461861(o), 09335150718 Cell), and 0532-2541764 (home) Fax # 0532-2461157 Email:
[email protected] [email protected] Website: www.allduniv.ac.in
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University of Hyderabad, Hyderabad Coordinator: Prof. Anand K. Kondapi Summary of the progress made by the centre from its inception: The Bioinformatics Infrastructure facility supported the teaching and research in drug discovery and systems biology of students and faculty members. Research carryout at the facility yielded ten publications in impact peer reviewed Journals. Various Biological resources available at BIF include biological databases as well as web tools to carry out user defined analysis. These resources are freely available at http://bif.uohyd.ac.in. These resources, at BIF website, includes computationally identified mycobacterial regulatory regions, medicinal plants data from North-east region of India, in silico predictions for cynobacterial proteins, integrated knowledge base for HIV, Online tool to identify orthologs etc. We have conducted a 3-day workshop on “Programming in R and applications in Computational Biology”, form Jan 11 to 13, with participants of 60. Facility helped in training more than 100 students from integrated M.Sc. Systems Biology, M.Tech Bioinformatics and Ph.D. students. Software training given to students in the lab includes: Sybel Tripos 8.0, Gold, Silver, Goldmine, CSD System Software 2011 (ConQuest, IsoStar, Mercury, Mogul, Prequest, and Vista) Mat Lab and several open License Softwares. The Bioinformatics Infrastructure facility at University is being used by five students who had come from all over India of different institutes for doing their project work. The facility is made available from morning 9.30 AM to evening 5.30 PM.
Major research activities in biotechnology and its related fields :
Development of molecular therapeutics and diagnostics against infectious (viral, bacteria, parasitic) diseases, cancer, neurological disorders and inflammation.
Development of Bio-intensive-integrated insect pest management.
Transgenic plants
Identification and characterization of bioactive molecules from medicinal plants
Genomic analysis and building gene regulatory networks and systems biology
Metabolomics and metabolic engineering
Nanobiotechnology and biofuels
Area of specialization: Systems Biology and Drug Discovery
Major achievements made during 2012-13:
Published databases: CyanoPhyChe, Mycorrdb, NeMedPlant, CPC
Developed software tools: Orfin
Published 10 papers in peer reviewed journals
Trained 46 master students in drug discovery and systems biology
Offered projects to five students from other universities in the region.
A workshop being held on R package and applications in computational biology
Infrastructure facilities in the bioinformatics centre: Severs:
Servers (One Domain Controller, One File server and One Program Server)
20 systems.
DST PURSE grant and DBT-CREBB supported 8-node Linux cluster
There are 10 web tools/resources presently being hosted. All the resources are freely available at http:// bif.uohyd.ac.in.
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User systems: Databases / Servers developed by students by using BIF facility in 2012 CyanoPhyChe
:
( http://bif.uohyd.ac.in/cpc/)
Mycorrdb
:
(http://bif.uohyd.ac.in/mycorrdb)
NeMedPlant
:
(http://bif.uohyd.ac.in/medplant)
CPC
:
(http://bif.uohyd.ac.in/cpc)
Orfin
:
(http://bifl.uohyd.ac.in/orfin) (Web Server)
Databases developed by students by using BIF facility (under construction) Cyanocis
:
(http://bif.uohyd.ac.in/cyanocis)
Aging
:
(http://bif.uohyd.ernet.in/aging)
Hire
:
(http://bif.uohyd.ac.in/hire)
Conflore
:
(http://bif.uohyd.ac.in/conflore )
Tarc
:
((http://bif.uohyd.ac.in/Tarc)
Details about Staff members working in the centre: Educational activities
Facility support practical and project work of M.Tech Bioinformatics and IMSc Systems Biology program
Facility also provide support of PhD students and post-doctoral fellows in Bioinformatics and Systems Biology
Papers/ published or presented in the conferences : Research Publications from the work carried out at BIF:
398
1.
Arun PV, Bakku RK, Subhashini M, Singh P, Prabhu NP, Suzuki I, Prakash JS. CyanoPhyChe: A Database for Physico-Chemical Properties, Structure and Biochemical Pathway Information of Cyanobacterial Proteins. PLoS One. 2012;7(11):e49425. doi: 10.1371/journal.pone.0049425. Epub 2012 Nov 21.
2.
Rathore RS, Reddy NR, Kondapi AK, Reddanna P, Rami Reddy M, Use of quantum mechanics/molecular mechanics-based FEP method for calculating relative binding affinities of FBPase inhibitors for type-2 diabetes, Theor Chem Acc 131:1096 (2012).
3.
Midha M, Prasad NK, Vindal V (2012) MycoRRdb: A Database of Computationally Identified Regulatory Regions within Intergenic Sequences in Mycobacterial Genomes. PLoS ONE 7(4): e36094. doi:10.1371/ journal.pone.0036094
4.
Meetei, Singh P, Potshan P, Nongdam A, Prabhu NP, Rathore RS, Vindal V, NeMedPlant: a database of therapeutic applications and chemical constituents of medicinal plants from north-east region of India (Database), Bioinformation 8(4): 209-211 (2012).
5.
Midha M., Polavarapu R., Meetei PA, Krishnan H., Mohareer K., Vindal V, OrFin: A web tool for detection of putative Orthologs(Server), Bioinformation 8(15): 738-739 (2012).
6.
Arun PVPS, Bakku RK, Subhashini M, Singh P, Prabhu NP, et al. (2012) CyanoPhyChe: A Database for PhysicoChemical Properties, Structure and Biochemical Pathway Information of Cyanobacterial Proteins. PLoS ONE 7(11): e49425. doi:10.1371/journal.pone.0049425
7.
Golzarroshan B., Siddegowda MS, Li H, Yathirajan HS, Narayana B, Rathore RS, Imatinib (Gleevec@) conformations observed in single crystals, protein–Imatinib co-crystals and molecular dynamics: Implications for drug selectivity, Journal of Molecular Structure 1018 (2012) 107–112.
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8.
Karthikeyan NS, Gunasekar R, Sathiyanarayanan KI, & Rathore RS (2012): Synthesis and Molecular Structure of New Macro Acyclic Mannich Derivatives: Symmetrical and Unsymmetrical 2-[(E)-(Benzylideneamino) (aryl)methyl]cyclododecanone, Synthetic Communications: An International Journal for Rapid Communication of Synthetic Organic Chemistry, 42:23, 3429-3440 (2012).
9.
Kannapiran P, Prabhakar M, Rathore RS, Bommakanti A, Kondapi AK. HIV-1 Associated Topoisomerase IIâ Kinase: A Potential Pharmacological Target for Viral Replication. Curr Pharm Des. 2012 Dec 18. [Epub ahead of print]
10.
Brahma SS, Srinidhi M, Shivashankar SA, Narasimhamurthy T, Rathore RS, New metal-organic precursors for MOCVD applications: Synthesis, characterization, crystal structure and thermal properties of mixed-ligand Mg(II) complexes, Journal of Molecular Structure 1035, 416–420 (2013)
Initiation of R&D activities in Bioinformatics:
Initiated molecular therapeutic development through an integrated modeling of the molecular structures and simulation of interaction of bioactive molecules in developing novel therapeutics.
An integrated plant form of genomic and proteomics being developed for modeling biological interaction through systems approach being developed at the centre by faculty members.
Details of Training/Workshop organized and total no of user trained Work shop on R package and applications in computational biology, participants registered are sixty, work shop to be held from 11 to 13 Jan, 2013.
Impact shown by the Centre: Infrastructure at the centre has been strengthened the research in drug discovery and systems biology and allied areas of faculty members, and research students, Several databases are developed by faculty members and were hosted at centre. As a result the quality of publications significantly enhanced.
Proposed activities for 2013-14 Work shop on R package and applications in systems biology, July 1 to 3, 2013
Contact details: Name of the Coordinator Postal Address
Phone Number Fax No. Email Website Name of Contact Person
Prof. Anand K. Kondapi Bioinformatics Infrastructure Facility School of Life Sciences University of Hyderabad Gachibowli 500046 India 040-23134570 040-23010145
[email protected],
[email protected] http://bif.uohyd.ac.in Mr, J, Rajesh
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University of Jammu, Jammu Coordinator: Prof. M. K. Dhar Summary of the progress made by the centre from its inception: The Bioinformatics Centre at University of Jammu, was established during January 2007 as the Bioinformatics Infrastructure Facility (Training Code: JUBIF-01) under the Biotechnology Information System Network (BTISnet) programme of the Department of Biotechnology, Government of India. During the first six months, the process for procurement of the hardware was completed. In the next phase several softwares were purchased and installed. The Bioinformatics lab was made functional for the use of students, research scholars, faculty and research scientists. During the last one year, the Coordinator delivered lectures as a resource person, during various Refresher courses and training programs, organized by various departments of the University and also the affiliated colleges. The Centre organized demonstrations, hands on training sessions and awareness programmes on applications of Bioinformatics in solving the biological problems. Bioinformatics has been incorporated as a 4-credit course in the course curriculum of M.Sc Biotechnology, Microbiology, and Biochemistry. The Centre is organizing the teaching work and is also conducting practical classes. The Bioinformatics Centre offers dedicated internet facility and training to M. Sc., M. Phil., and Ph. D. students for using the online and offline softwares to assist in their research programmes.
Major research activities in biotechnology and its related fields: The centre is focusing mainly on in-silico analysis using Bioinformatics softwares. The centre promotes Bioinformatics awareness. Research projects and interdisciplinary research in collaboration with wet lab Biotechnology research programmes are being carried out.
Areas of specialization of the centre: The main areas of specialization are Genomics, Proteomics and Metabolomics.
Major activities of the centre during the year 2012-13: a)
National Symposium on “Bioinformatics: Challenges in the post-genomic era” (February 2nd 2012)
A one day National Symposium on Bioinformatics: “Challenges in the post-genomic era” sponsored by Department of Biotechnology, Govt. of India was organized by the Bioinformatics Centre, University of Jammu. The symposium was inaugurated by Jenab Aga Syed Mehdi Ruhullah, Hon’ble Minister of Science & Technology, J&K State in presence of Prof. R. N. K. Bamezai, Vice-Chancellor, SMVDU, and Dr. Madhan Mohan, Adviser DBT. Eminent scientists, academicians, and scientific dignitaries across the globe were present in the symposium. The symposium was attended by Scientists, Teachers and Research Scholars from various Universities, Colleges and research institutions of India. National symposium had four sessions, namely (i) Plenary session (ii) Technical session-I (iii) Technical session-II (iii) Technical session-III. In the plenary session was plenary lecture was delivered by Prof. Bikram Singh Gill, Kansas State University, USA on the theme of symposium “Bioinformatics-Challenges in the post-genomic era”. Other prominent speakers were Dr. T. Mohapatra, Director, Central Rice Research Institute, Cuttack, Dr. Saurabh Raghuvanshi, Delhi University South campus, Prof. Manoj K. Dhar, Coordinator Bioinformatics Centre, University of Jammu, Prof. N.K. Chrungoo, NEHU, Shillong, Prof. S. Krishnaswamy, Madurai Kamraj University, Madurai, Dr. Debasisa Mohanty, NII, New Delhi, Prof. Deepti Deobagkar, Pune University, Dr. D. Sundar, IIIT, New Delhi, Dr. N. Manoj, IIT, Madras, Prof. Indira Ghosh, JNU, New Delhi. b)
Awareness in Bioinformatics
In order to create awareness about Bioinformatics, the coordinator delivered popular lectures in the Departments Computer Sciences and Information Technology and Environmental Sciences of the University of Jammu and also in the affiliated colleges. The Centre organized short training sessions and awareness programmes on applications of Bioinformatics in solving the biological problems.
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Item Computers Servers Printers Scanners Communication facility Scientific software packages
Quantity Thirty (30) Two (High-End and Medium) Two (hp1020n, hp2600n) Two Telephone connection Geneious PRO (Bioware, New Zealand), Discovery Studio(Accelerys, U.S.A), NTSys, PHYLIP, TREE VIEW, RAPDPLOT
7. 8.
Databases and other information resources Database acquired Journal
Science (AAAS)
Details about staff members working in the centre: Name Prof. M. K. Dhar
Mohit Kumar Sharma
Designation Director School of Biotechnology& Coordinator Bioinformatics Centre R. A
Specialization Genomics and Proteomics
Period of working
Absorption status Permanent Faculty
Bioinformatics/Data Analyst
17- 09- 2007 till date
Temporary
Types of services provided: The Centre offers training on fundamental topics in Bioinformatics for technical staff and students of Jammu University. Literature search, sharing of resources, support to R&D activities in Life Sciences for PG student projects, imparting teaching in Bioinformatics for PG students. The centre is involved in creating awareness among undergraduate and postgraduate students and faculty regarding the basics of Bioinformatics and its applications.
Educational activities with details of placement: As a part of the M Sc program, the centre conducts Bioinformatics courses for M.Sc Biotechnology, Biochemistry and Microbiology students of the University of Jammu.
Initiative to validate the outcome of bioinformatics resources: The large number of users at the Centre and the research activities validate the outcome of bioinformatics resources.
Collaborative works/Initiatives: Databases/Software packages developed: Apple Database (Under process) Papers published or presented in the conference/ Thesis submitted: The following papers have been communicated to the press. i)
Mohit Kumar Sharma, Manoj K. Dhar, Sanjana Koul 2012. Bioinformatics: An introduction and Overview. International Journal of Engineering and Research e-ISSN: 2278-067X, p-ISSN: 2278-800X, www.ijerd.com Volume 3, Issue 8 (September 2012), PP. 88-99
ii)
Mohit Kumar Sharma, Manoj K Dhar, Vladimir B Bajic 2008. Using Bioinformatics Tools to create a database for transcription Factors. Abstract Book of 3rd J&K State Science Congress 26-28 February, 2008.
iii)
Khalid Zaffar Masoodi and Manoj K. Dhar (2012) Cloning and functional analysis of carotenoid biosynthesis genes from carrot (Under review).
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iii)
Yash Paul Khajuria (2010) Organization of disease resistance genes in apple and molecular characterization of Venturia inaequalis (Cooke) Winter. Ph. D. Thesis, University of Jammu, Jammu.
iv)
Khalid Zaffar Masoodi (2010) Studies on cloning and functional analysis of some carotenoid biosynthesis genes. Ph. D. Thesis, University of Jammu, Jammu.
v)
Gurmeet Kour (2010) Studies on cloning, mapping and expression of amplified DNA sequences in Plantago lagopus L. Ph. D. Thesis, University of Jammu, Jammu.
vi)
Balbir Kour (2010) Biotechnological approaches towards development of disease resistant beans. Ph. D. Thesis, University of Jammu, Jammu.
Initiation of R&D activities in Bioinformatics: The centre has initiated some in house research projects in the area of cancer biology especially esophageal cancer. We are performing expression analysis of several genes and annotating some of the putative genes. We have also initiated a mega project on Apple genomics and the centre is providing full assistance in building the database.
Details of Training/ Workshops organized and total no. of users trained: The Centre conducted various lectures and is involved in teaching full fledged course on Bioinformatics in M.Sc. Biotechnology, M.Sc. Biochemistry and M.Sc Microbiology programmes of the University.
Impact shown by the centre on the growth of biotechnology and allied areas: The Centre has initiated several programmes for introducing Bioinformatics to the students as well as faculty of the University. The usage of e-mail and Internet has increased notably and the facilities of the Centre are widely made use of for presentations and other research activities.
Future activities: The focus will be on research activities in Bioinformatics and the centre plans to start the P. G. Diploma course on Bioinformatics. The Centre proposes to hold a National Level Symposium and training programme for University and college teachers during the month of February, 2013. The other routine services of the Centre would be continued efficiently.
Contact details: Name of the Coordinator: Postal address:
Phone Number: Fax: E-mail:
402
Prof. M. K. Dhar School of Biotechnolgy University of Jammu, Dr. B.R.Ambedkar Road Jammu -180006 91-191- 2433655, 91-191-2456534 0191-2456534
[email protected],
[email protected]
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University of Kalyani, Kalyani Coordinator: Dr. Alpana Seal Summary of the progress made by the centre from its inception : DBT funded BIF centre at University of Kalyani is in function for last six years as a commendable platform to serve all the Life Science Departments of this University, as well as, the neighboring institutes. The centre is now being used by the faculty members, researchers, M.Sc. students and project workers from home University and other Universities/Institutions. Scientific Software packages like GCG, DS Suite, Geneious Pro, Matlab, AMBER, GOLD, CSD and other scientific program packages free for academicians are available to the users. The database CSD and in house database DB Dehydrogenase (http://www.bifku.in/DBD/) has been rationalized. Training programs in bioinformatics and computational biology are going on in a regular basis for M.Sc. students, researchers and others. Since its inception, nine national workshops have been arranged on various fields of bioinformatics and last one was on “Protein Folding” and “Molecular Modeling, Dynamics & Simulation” organised in November, 2012. More than 200 pupil have been trained in the workshops, 12 students completed their dissertation, among them 5 enjoyed DBT funded studentship and 4 traineeship. Total 8 research papers have been published in various international journals. Frontier research of this centre is on protein-ligand and protein-protein interactions, modeling studies of membrane system, cluster and self assembly study.
Major research activities in Biotechnology and its related fields : A.
Department of Biochemistry and Biophysics: I) Molecular modeling of sulfur compounds metabolizing proteins (in collaboration with Bose Institute, Kolkata) & modeling of protease inhibitor interaction and membrane system. II) Molecular Mechanism of Artificial Transformation of E. coli with Plasmid DNA. III) Structural Elucidation of the Molecular Mechanism of Biological Sulfur Oxidation
B.
Department of Molecular Biology and Biotechnology: I) Molecular Phylogeny of Indian Shad Tenualosha ilisha inferred using mitochondrial DNA partial gene sequences. II) Molecular Breeding of Rice with Special Reference to Marker Assisted Gene Pyramiding for Biotic Stress Resistant III) An Investigation on Somaclonal Variance of certain Aromatic Plants using Biochemical and Molecular Approaches. IV) An Investigation on in vitro selection of Aluminium Stress Resistance of a leguminous crop and its rhizobial counterpart for their potential exploration in acid soil tract. v) An exploration of in vitro somatic embryogenesis of two important medicinal plants and their biomodulatory mechanism vi) Identification of DNA markers associated with disease and pest resistance in Mulberry. vii) A study on induction of somatic embryos and over-expression of SAM Decarboxylase in Limonium sinensis through transgenesis.
Area of Specialization of the centre: a) Molecular Modeling & Dynamics b) Computational Biology
Major activities of the centre during the year 2012-13:
National workshop on “Protein Folding” and “Molecular Modeling, Dynamics & Simulation” was arranged during 26th - 30th November, ‘12.
Four research papers have been published.
A new research laboratory has been established.
Our in-house database on dehydrogenase was updated on web (http://www.bifku.in/DBD/) and published.
Databases & other information resources:
DB Dehydrogenase was updated(In house)
Cambridge structural database
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Details about staff members working in the centre
Shri Rajabrata Bhuyan, Research Assistant
Paper published from this center in 2012-13
Suman K. Nandy, Rajabrata Bhuyan, Alpana Seal. Modeling Family 2 Cystatins and their interaction with Papain. Journal of Biomolecular Structure and Dynamics, 2012, (in Press). DOI:10.1080/07391102.2012.706403.
Suman K. Nandy, Rajabrata Bhuyan, Alpana Seal. DB Dehydrogenase: an online integrated structural database on enzyme dehydrogenase. Bioinformation, Volume 8(20): Bioinformation 8(20): 1000-1002 (2012).
Bagchi A., Structural insight into the mode of interactions of SoxL from Allochromatium vinosum in the global sulfur oxidation cycle. Mol Biol Rep. 2012 Dec; 39(12):10243-8. doi: 10.1007/s11033-012-1900-9.
Sourav Singha Roy, Monobesh Patra, Rakhi Dasgupta & Angshuman Bagchi. A structural insight into the prokaryotic heat shock transcription regulatory protein s32: an implication of s32-DnaK interaction. Bioinformation 8(21): 1026-1029 (2012).
Future activities: For supra molecular simulation, we need powerful workstation like IBM blue gene or very high end workstations and SGI machines to enhance our research on :a) Modeling studies of membrane system, b) Structural Bio-informatics to develop novel drug molecules, c) Cluster and self assembly study, d) Interaction studies on protein-protein and protein-ligand complexes. We also want to develop more databases & bioinformatics tools. A new practical classroom for M.Sc. students should be established. We will continue to provide a bioinformatics hand for research and development in this locality in future also.
Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
404
Dr. Alpana Seal Department of Biochemistry and Biophysics, University of Kalyani, Kalyani - 741235, West Bengal. 033 2582 3405(O), 033 2321 2106(R), 9830795655(M)
[email protected],
[email protected] http://www.bifku.in/ Dr. Alpana Seal
Bio Informatics Infrastructure Facility (BIFs)
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University of Kerala, Thiruvananthapuram Coordinator: Dr. Achuthsankar S. Nair Summary of the progress made by the centre from its inception: The DBT-BIF centre at university of Kerala works as a part of Centre for Bioinformatics established in 2005 and upgraded as the Dept. of Computational Biology and Bioinformatics in 2011. The Department was established as an interdisciplinary Department for teaching, research and extension in Bioinformatics and Computational Biology and has completed its 7th year of operation in 2012. In 2010, Centre for Systems and Synthetic Biology and in 2012, a Centre for Venom Informatics have been established as a part of this Department. The department maintains a rich and well updated and professionally designed web site of international standards at dcb.keralauniversity.ac.in. Research publications continue to be modest, but growing. One high impact paper by a Research Scholar in the reputed BMC Bioinformatics Journal has now been labeled “Highly Accessed”. Best citation achieved so far is 40. Good impact factor publications are close to 10 so far (Impact factor form 1 to 4). A number of training programmes and wokshops were conducted under the auspices of DBT-BIF and the major one was Bioinformatica Indica 2012. A national symposium on Soft Computing & Computational Synthetic Biologyhas held on 7th and 8th december2012.
Major research activities in biotechnology and its related fields : Bio-Sequence (DNA, miRNA, AA) Studies using Digital Signal Processing, Protein-Protein Interaction Networks, Protein Sub-cellular Localization Prediction,Protein Structure Analysis, Immunoinformatics of Cancer, Programming Languages for Synthetic Biology,Small Gene Identification, Insilico Study of Extremophiles, Molecular evolution of RNA Viruses, Computer Aided Drug Design based on Natural Products, Investigations into non-coding DNA,Snake Venomics,Transcriptomics & Genomics.
Area of specialization: Computational Biology/ Rational Drug Discovery, Venom Informatics, System and Synthetic Biology.
Major achievements made during 2012-13: (1) Award of 3 Ph.D degrees and submission of 6 Ph.Ds from this department. (2) 25% Campus placement for students of third batch of M.Sc Computational Biology students (3) Conduct of Bioinformatics National Certification Examination at our Department (4) Establishing four on-line Bioinformatics tools in the web (6) Establishment of Centre for Venom Informatics (7) A book titled “BIOINFORMATICS”(Malayalam version) published by DC books.(8) Provided training for 37 project students from within and outside Kerala.
Infrastructure facilities in the bioinformatics centre: The centre has a full-fledged Informatics Lab. To complement the insilico biology work going on at the Department, a well equipped microbiology and bioelectronics lab has been set up recently. This provides complete research facility for microbiology, molecular biology, phytochemistry, bioelectronics and clinical studies.. With the establishment of the wet lab, a long felt balance of bio and informatics has been achieved. The project on Snake Venom detection Biosensor (SVDB) provides a system and method for detecting quantitative extent of envenomation and to monitor the venom clearance from the body using species specific diagnostic biosensor.
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Details about Staff members working in the centre: Sl.No. Name Designation 1. Dr. Achuth sankar S Nair Head
Specialization Computational Biology
2.
Dr. Oommen V. Oommen
Emeritus Professor Zoology
3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14.
Dr. P.R sudhakaran Dr. M. Vijayakumar Dr. Yusuf Akkara Vipin Thomas Umesh P. Aswathy B.L Rani J.R. Sherin K. Renga Nayaki G. Sunitha P. Jayamol Saleena Y.
Senior Scientists Professor Asst. Professor Lecturer Lecturer Lecturer Lecture Lecturer Lecturer Lecturer Technical Assistant Research Associate
Working Since Status 2005 Associate Professor & Head 2005 Retired Professor
Biochemistry Computer science Botany Bioinformatics Bioinformatics Bioinformatics Bioinformatics Bioinformatics Bioinformatics Bioinformatics BS.c, PGDCA Computational Biology
2012 2011 2011 2011 2011 2011 2011 2012 2010 2011 2011 2011
Retired Professor Adjunct Professor Adjunct Professor Contract Contract Contract Contract Contract Contract Contract Contract Contract
Educational activities Ph D in Computational Biology and Bioinformatics, M Phil (Bioinformatics) 10 seats (7th batch in 2011), M Phil (Computer Aided Drug Designing) 10 seats (1th batch in 2013), M Sc (Computational Biology) 10 seats (5thbatch in 2012)
Papers/ published or presented in the conferences :
406
1.
Amjesh R, Achuthsankar S. Nair and Suganan V.S, “Diversity of Hepatitis C Virus in southern India based on 5’UTR sequence” Indian Journal of Virology,http://dx.doi.org/1007/s13337-012-0103-2012.
2.
Amjesh R, Achuthsankar S. Nair and Suganan V.S, “Structure based virtual screening for Allosteric site binding inhibitors of Hepatitis C Virus RNA dependent RNA Polymerase”,Journal of Bioinformation, 8(15):716-719, 2012.
3.
Aswathi B.L., BaharakGoli, Achuthsankar S. Nair , A Novel Algorithm for Prediction of Hub Proteins from Amino acid sequences in Eukaryotic proteome using global Amino acid features, , Advances in computing and information technology– Springer, Vol. 198 , pp.204-211, 2012.
4.
Aswathi B.L., BaharakGoli, RenganayakiGovindarajan, and Achuthsankar S. Nair, “A Novel Algorithm for Prediction of Hub Proteins from primary structure in Eukaryotic proteome using Di-peptide compositional skew information and Amino acid sequence likeness”, Prospects in Bioscience: Addressing the issues – Springer , pp. 31-33, 2012.
5.
Aswathi B.L, BaharakGoli, RenganayakiGovindarajan and Achuthsankar S. Nair, “A Novel algorithm for Hub protein identification in Prokaryotic proteome using Di-peptide composition and Hydrophobicity ratio”, Ecofriendly Computing and Communication Systems Communications in Computer and Information Science – Springer, Volume 305, pp. 204-211, 2012.
6.
BaharakGoli, Aswathi B.L., Achuthsankar S. Nair , “A Novel Algorithm for Prediction of Protein Coding DNA from Non-coding DNA in Microbial Genomes Using Genomic Composition and Dinucleotide Compositional Skew”,Advances in computing and information technology– Springer, Vol. 198 , pp. 535-542, 2012.
7.
BaharakGoli, Aswathi B.L., Achuthsankar S. Nair, “Naïve Bayes Based Classification for Short Microbial Genes Using Chaos Game Representation”, Prospects in Bioscience: Addressing the issues – Springer, pp. 33-36, 2012.
8.
BaharakGoli, Aswathi B.L., Achuthsankar S. Nair, “New Feature Vector for Recognition of Short Microbial Genes”, Eco-friendly Computing and Communication Systems Communications, Computer and Information Science – Springer, Vol. 305, pp. 222-229 , 2012.
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BaharakGoli, Aswathi B.L, Chinu Joy, Achuthsankar S. Nair, “New feature Vector for Recognition of Short Microbial Genes”, Proceedings of the Eco-friendly Computing and Communication Systems Communications, Computer and Information Science, Vol 305, 2012, pp. 222-229.
10.
Anaswara Krishnan S., Dileepkumar R. & Oommen V. Oommen “Aristolochia Indica, Plant anti-dote to replace serum therapy for snake bite treatment” Proc 24th Kerala Science Congress, Kottayam., 29-31 January 2012, page no 569.
11.
Anaswara Krishnan S., Dileepkumar R., Vipin Thomas and Oommen V.Oommen. “Interaction of bioactive compounds against snake venom phospholipase A2s- A molecular docking approach” International Conference on Advances in Structural Biology, Kannur., 15-17th march 2012, page no. 36-37.
12.
Biji C.L, Achuthsankar S Nair, Sudhakaran P.R., “The Use of S Transform in Bio-Sequence Analysis” Proceedings of the National Conference on Applied Linear Algebra & Transform Techniques, Thiruvananthapuram, pp.91-98, 10-11th July 2012.
13.
SarithaNamboodiri, Alessandro Giuliani, Achuthsankar S Nair, Pawan K Dhar, “Looking for a sequence based allostery definition: A statistical journey at different resolution scales”, Journal of Theoretical Biology, Vol 304, pp.211-8, July 2012.
14.
Anju C.P, Anusooya N.J, Deepasree M, Deepak O.M, Krishnan Namboothiri P.K, “De Novo designing of HDAC inhibitors in cancer therapy”, International Journal of Pharmaceutical Sciences and Health Care,Vol 4, pp. 59-66,, Aug 2012.
15.
Radhika A, Sudhakaran PR, “Upregulation of macrophage-specific functions by oxidized LDL: lysosomal degradation-dependent and -independent pathways”, Mol Cell Biochem,doi: 10.1007/s11010-012-1459-8. 372(1-2):18190. Epub 2012 Sep 30.
16.
Binu S, Soumya SJ, Sudhakaran PR, “Metabolite control of angiogenesis: angiogenic effect of citrate”, J PhysiolBiochem, Nov 20 2012[Epub ahead of print].
17.
Soman S, Raju R, Sandhya VK, Advani J, Khan AA, Harsha HC, Prasad TS, Sudhakaran PR, Pandey A, Adishesha PK, “A multicellular signal transduction network of AGE/RAGE signaling”, J Cell Commun Signal. Nov 19 2012. [Epub ahead of print].
18.
Abdul Rahiman Anusha, Vinod Chandra S S, “Prediction of Antisense Oligonucleotides using Structural and Thermodynamic Motifs”, Bioinformation, Vol. 8(23), pp. 1162-1166, November 2012.
19.
SilpaBhaskaran, Achuthsankar S Nair, Umesh P,“Cell phenomena are reminiscent of electric circuits”, IEEE Potentials (To appear in 2013).
Initiation of R&D activities in Bioinformatics: Four software developed by the centre are now available on-line: (i)
CGRex: A Software for generating CGR Signatures of bio-sequences Developed with DIT, Govt of India support
(ii)
HumLocoProt is on-line software predicting sub-cellular localization of human proteins, available at www.locoprot.in
(iii) Cgress (DNA compression algorithm) available at www.cgress.in (iv)
Repam (Calculating scoring matrices, which is a correct version of parm). Available at www. repam.in
Details of Training/Workshop organized and total no of user trained. The Department organized a series of training programmes / Workshops in the field of Bioinformatics. 1.
Bioinformatica Indica international symposium during 12-14th January 2012 (81 delegates)..
2.
One day seminar on “Biological Data Curation” was organized by DBT- BIF center jointly with SciGenom Labs Pvt. Ltd., on July 7th 2012 (50 participants).
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A workshop on “Spoken Tutorial for Python” jointly with IIT Bombay during 1-14th November 2012.
4.
Two-day National Symposium on “Soft Computing & Computational Synthetic Biology”, organized by DBT-BIF on December 7th – 8th 2012(40 delegates).
Impact shown by the Centre: Please refer to sections 4, 7, 8, 9, 10.
Proposed activities for 2013-14 1.
Workshop on python and Scilab in collaboration with IITB.
The above two workshops aims at spreading the use of FOSS (Free & Open Source Software, for example Linux & LaTeX) in India, through audio-visual self-learning tools, known as ‘Spoken Tutorials’. 2.
National seminar on NGS (Next Generation Sequencing)
The workshop will cover NGS technologies, bioinformatic tools and also on the impact of NGS platform on modern medicine. 3.
Bioinformatica Indica 2013 Dec/2014 January.
4.
Bioinformatics Video YouTube channel.
The video ‘A Flavor of Bioinformatics’ is now available in TubeDCB for public viewing. The link is: https://www.youtube.com/ watch?v=aldo_Pp2l6Q.
Short term training program and /Seminars in: Computer Aided Drug designing, Python for Bioinformatics, Molecular Visualization, Sequence Alignment, Data Compression in Bioinformatics, Soft Computing in Bioinformatics, Research Methodology for Bioinformatics, System Biology.
Contact details: Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
408
Dr.Achuthsankar S. Nair Department of Computational Biology and Bioinformatics, University of Kerala, Karyavattom Campus, Thiruvananthapuram 695581, Kerala. +914712308759 +914712308759
[email protected] www.dcb.res.in Dr.Achuthsankar S. Nair
Bio Informatics Infrastructure Facility (BIFs)
XXIVnd All India BTISnet Coordinators’ Meeting
February 03-04, 2011
University of Madras, Chennai Coordinator: D.Velmurugan Summary of the progress made by the centre from its inception: Major research activities of the centre is computer aided drug discovery using commercial softwares; Molecular Modeling and Docking studies using GLIDE Schrödinger Suite USA, Homology Modeling using MODELLER and various online servers, Molecular Dynamics using GROMACS, AMBER; Screening of large databases to find the lead compound and designing the ligands using their pharmacophore properties and subjecting them for the docking studies to find the binding affinity of the receptor and lead compound.
Major research activities in biotechnology and its related fields:
INDO-JAPAN Project: Identification of Efflux Pump Inhibitors to Gram Negative organism using Bioinformatics tools and Invitro Analysis and Crystallographic studies of Target membrane Protein Inhibitor Complexes.
Virtual Screening of TCM natural compound database against NorM MATE transporter Channel.
Virtual Screening of Asinex and Toslab compound database screening against nsP3 macrodomain in Chikungunya virus.
Molecular Docking and Simulation studies of Natural compounds against AcrB efflux pump.
Area of specialization: Docking and Molecular Dynamics.
Major achievements made during 2012-13:
Poster presented during 2nd National conference on Toxinology (2012), hosted by Department of Biochemistry, University of Mysore “A Pharmacophore Modeling And Molecular Dynamics Simulation Based Approach To Find Novel Inhibitors Of Daboia Russellii Phospholipase A2”.
Poster presented during 41st National Conference on Crystallography (2012) hostedby CAS in Crystallography and Biophysics, University of Madras.“Pharmacophore Modeling Based on Crystal Structure and MD Ensembles of MDM2-peptide Complexes”.
Poster presented in NSC2012 seminar “Competitive Inhibition study of nsP3 macro domain in Chikungunya virus using Molecular Dynamics Simulation & Free Energy Calculation”.
Presented a paper on “Insilico docking study towards Anti-inflammatory - Drug Design” in International symposium on recent trends in Macromolecular Structure and Functions organized by CARI, Port Blair on Jan 27th, 2012.
Presented a poster on “Insilico docking study towards Anti-inflammatory Drug Design” in 4th National symposium cum workshop on recent trends in Structural Bioinformatics and Computer Aided Drug Design, organized by Alagappa University, Karaikudi on Feb 22nd, 2012.
Presented a paper on “Potent Aromatase Inhibitors for estrogen dependent Breast Cancer-Structure Based Drug Design” in National conference on High throughput Bioinformatics held during Aug 23rd & 24th, 2012, Karunya University, Coimbatore.
Presented a poster on “Structure based drug design towards potent anti-proliferative agents” in National Seminar on Crystallography organized by University of Madras held during 8th-10th 2012 October 2012.
Presented a poster on “Modelling studies on Ethanomedicinal compounds towards curing inflammation” in Toxinology Society of India organized by University of Mysore during 10th 12 August 2012.
Presented a Poster on Modelling Studies On Phospholipase A2 Using Plant Compounds- in 41st National Seminar on Crystallography (2012) – conducted by CAS in Crystallography and Biophysics, University of Madras – Cash awarded
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Presented a Poster on Docking Analysis Of Gingerol And Its Derivatives Against Obesity - in 41st National Seminar on Crystallography (2012) - conducted by CAS in Crystallography and Biophysics, University of Madras.
Poster presented on Structure Based Drug Design Of Marine Compounds For Curing Breast Cancer - S.Suhitha, R. Selvakumar, S.Karthiga Devi, D.Velmurugan in the Conference ‘Integrated approach to Herbal Technology’ conducted by Asthagiri herbal research foundation and Sri Ramachandra University at CLRI Jan (3-4) 2013.
Poster presented on Structure Based Drug Design of Herbal compounds for curing Dengue and Chikungunya S.Karthiga Devi, S.Suhitha, Kutumbarao and D.Velmurugan in the Conference ‘Integrated approach to Herbal Technology’ conducted by Asthagiri herbal research foundation and Sri Ramachandra University at CLRI Jan ( 3-4) 2013.
Infrastructure facilities in the Bioinformatics Centre: Equipments
Color LaserJet printer 3600 (1Number)
HP Core2 Duo PCs (6 Numbers)
Workstations with Linux Compatibility (4 numbers)
HCL PCs for Windows (10 numbers)
HP Network Printer (2 Numbers)
Linux Compatible Laptop (2 numbers)
Internet (4Mbps)
Softwares Schrodinger Suite 2010 version (including Induced Fit Module), GOLD
Details about Staff members working in the centre: Sl.No. Name 1. A.Mary Thangakani 2. R.Selvakumar
Designation RA RA
Specialization Computer Applications Biophysics
Working Since May 2011 Sept 2012
Status Temporary Temporary
Educational activities Apart from the Trainees and studentship, students and research scholars from various Colleges and Universities use Bioinformatics Infrastructure facilities for their project work and for the research. Currently more than 25 students are using this centre for their academic projects. Research scholars and faculties from universities and colleges use this infrastructure facility for their research work.
Papers/ published or presented in the conferences
410
Distinct position-specific sequence features of hexa-peptides that form amyloid-fibrils: application to discriminate between amyloid fibril and amorphous â- aggregate forming peptide sequences BMC Bioinformatics (in press). A.M. Thangakani, S. Kumar2, D. Velmurugan and M.M. Gromiha (2013)
Design and docking studies of peptide inhibitors as potential antiviral drugs for dengue virus NS2B/NS3 protease D. Velmurugan, U. Mythily and K. Rao. (2013) Protein and Peptide Letters (in press).
How do thermophilic proteins resist aggregation? A.M. Thangakani, S. Kumar, D. Velmurugan and M.M. Gromiha (2012) PROTEINS: Structure, Function and Bioinformatics, 80:1003-15.
Sequence analysis and discrimination of amyloid and non-amyloid peptides M.M. Gromiha, A.M. Thangakani, S. Kumar and D. Velmurugan (2012) Comm. Comp. Inf. Sci. 304, 447-452.
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Structure-Based Discovery of Anti-Viral Compounds for Hepatitis B & C, Human Immunodeficiency, and Dengue Viruses Pp.187-211 D. Velmurugan, U. Selvi, U. Mythily, K. Rao, R. Rajarajeshwari and Sangeetha.(2012) Current Bioinformatics 7, 187-211.
Structure based design of compounds from natural sources for diabetes and inflammation, 8(22): 1125-1131 (2012) Sivasubramanian Suhitha ,Krishnaswamy Gunasekaran & Devadasan Velmurugan
Designing of Protein Kinase C â-II Inhibitors against Diabetic complications: Structure Based Drug Design, Induced Fit docking and analysis of active site conformational changes. Balakrishnan Vijayakumar& Devadasan Velmurugan Bioinformation 8(12): 568-573 (2012)
Molecular docking and ex vivo pharmacological evaluation of constituents of the leaves of Cleistanthus collinus (Roxb.) (Euphorbiaceae) Subramani Parasuraman, Ramasamy Raveendran, Balakrishnan Vijayakumar, Devadasan Velmurugan Subramani BalamuruganIndian Journal of Pharmacology | April 2012 | Vol 44 | Issue 2 203
Selection of an improved HDAC8 inhibitor through structure-based drug design. Balakrishnan Vijayakumar, Appavoo Umamaheswari, Ayarivan Puratchikody, Devadasan Velmurugan Bioinformation7(3):134-141(2011).
Oral Presentations:
Oral presentation in CLRI conducted by Asthagiri herbal research foundation and Sri Ramachandra University (2013), Structure Based Drug Design of Herbal compounds towards curing Inflammation, Cancer, Diabetes and Tuberculosis – Prof.D.Velmurugan.
Oral Presentation at University of Mysore (2012), Structure Based Drug Design towards curing inflammation – Prof. D.Velmurugan.
Oral Presentation at Manipal University, Manipal (2012), Structure Based Drug Design towards curing inflammation – Prof. D.Velmurugan.
Initiation of R&D activities in Bioinformatics
INDO-JAPAN Project: Identification of Efflux Pump Inhibitors to Gram Negative organism using Bioinformatics tools and Invitro Analysis and Crystallographic studies of Target membrane Protein Inhibitor Complexes.
Structure based discovery of anti-virus for treatment of Chikungunya virus infections.
Structure based design of Dengue virus protease inhibitors.
Major computational work using the BIF computing facilities for the three collaborative projects under DBT scheme with North-Eastern Universities (NEHU, Shilong, Tezpur University and Mizoram University) on isolation of active compounds from natural products towards curing snakes bites, along with wetlab work. Bioinformatics tools are used in finding respective macromolecular targets and also in field of the structure based drug design for further studies.
Details of Training/Workshop organized and total no of user trained
Interactive Workshop (Internationsl) on System’s approach to Modern Biomolecular Technology December 1516, 2011. Number of users trained are 30.
1st National conference on Toxinology 2011 and 1st Annual Conference on Toxinological Society of India December 17-18, 2011.
Impact shown by the Centre:
In addition to the research team of the coordinators in using BIF facilities many PIs from University of Madras and neighbouring universities use this facility for their research work.
Many students doing their Masters programme in Bioinformatics are greatly benefited by the BIF.
In Research publications related to work carried out with BIF facility , due acknowledgment is made.
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Proposed activities for 2013-14 National seminar on Structural Bioinformatics and Structure Based Drug Design and Hands on Session on Crystal Structure Determination of Small Molecules – to be held during February 15-17 , 2013.
Contact details: Name of the Coordinator Postal Address Phone Number
Prof. D. Velmurugan, University of Madras, Guindy (Maraimalai) Campus, Chennai-600 025 044-22301929, 09841075847
Fax No. Email Website
044-22300122
[email protected] http://bif.unom.ac.in/
Name of Contact Person
Mrs. A. Mary Thangakani, Research Assistant.
[email protected]
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University of North Bengal, Siliguri Coordinator: Dr Arnab Sen The center has every modern facility of information and communication including necessary hardware and software. There were a number of publications in journals and posters presented in national and international conferences on the relevant areas.
Major research activities in Biotechnology and its related fields: At NBU major research activities are clustered in the arenas of molecular genetics, microbial biotechnology, plant tissue culture, immunology, microbial genomics, transgenics, genomics and proteomics of nitrogen fixing bacteria and food pathogenic bacteria.
Area of specialization of the centre: Microbial genomics, molecular modeling, molecular dynamics, structural bioinformatics & molecular phylogenetics
Major activities of the centre during the year 2011-12: A National Conference on “Biology and Bioinformatics of economically important plants and microbes- BBCon2012” was organized on Feb 17th-19th 2012 at University of North Bengal. Two regional workshops on sequence analysis and bioinformatics were organized in Kalimpong College on 27th September, 2012 and St Xavier’s College, Siliguri, on 1st December, 2012. Two volumes of the official newsletter of the NBU Bioinformatics Facility “BIOINFOLINE” (ISSN No. 0974-9403) have been published. Research work relating to the characterization of bacterial genomes and proteomes on the basis of codon usage, comparative genomics and evolutionary analysis, phylogenetic analysis, proteome analysis, molecular modeling and molecular dynamics has been done.
Infrastructure facilities in the bioinformatics centre: Computer and communication: One DellTM Rack Mount Server, One Apple IMAC machine, One HP laserjet Colour Printer, One HP Scanjet Scanner, 0.22 PCs with OS, Two High end servers and a Medium end server, One Toshiba make Laptop, One Laser printer (network), one DeskJet printer, One Canon make Photocopier, one Sony make LCD Projector, CISCO 1700 Leased line Router. Scientific and Software packages: Two Windows 2003 Server with license, 10 Windows XP Professional with license, 8 Windows VISTA with License, Microsoft ISA Server 2005 for Proxy Server, one Microsoft Visual Studio, .NET, MS SQL Server (Std.), MS Office 2003, Fedora 7 Linux, Ubuntu Linux, Red-Hat Entreprise Linux, 14 Quick Heal AVG Antivirus Package. Acclerys Gene Package, MAUVE, GRIL, GENOME BROWSER, BIOEDIT, CODONS, CODON W, MATLAB 5.0, MODELLER 9v7, Autodock, CLUSTAL W, CLUSTAL X, DNAsp 4.0, MEGA 4.0, TREEVIEW, MR. BAYES, PHYLODRAW, CHIMERA, SPDBV, RASMOL, PHYLIP, PAUP, HYPHY, GLIMMER, HUMMER, AMORPHA, GENETRACE, GROMACS, CHEMDRAW, Cn3D, SPLITSTREE, DAMBE, VMD, Jcat, Argus Lab, C++ and PERL.
Other resources: 10 Mbps Line from Reliance and BSNL.
Details about staff members working in the center: Serial No. 1 2 3
Name of the Staff Ayan Roy Tanmayee Mishra Krishanu Ghosh
Designation Research Associate Studentship Holder Data Entry Operator
Working Since October 2011- till date January 2009-June 2009 and June 2010 till date September 2009
4
Sanghati Bhattacharya
Traineeship Holder
October 2011- April 2012
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Types of service provided: The center provides access to the faculty members, research scholars and students from nearby universities, colleges and research institutions interested in working in the field of bioinformatics.
Educational activities with details of placement: Four PhD students (Subarna Thakur, Ayan Roy, Arnab Kr. Chakraborty & Sanghati Bhattacharya) are currently engaged in their research work utilizing the facility. Mr. Saubashya Sur and Mr. Uttam Kumar Mondal have already been awarded their Ph.D. degree. Besides faculty members, students and research scholars from other departments, institutes and nearby areas utilize this facility.
Collaborative work and initiatives: The Coordinator Dr. Arnab Sen has set up International collaboration with the Department of Microbiology, University of New Hampshire, USA. Dr. Sen also has collaboration with Bioinformatics Centre of Bose Institute, Kolkata and Maharani Lakhsmi Ammanni College for Women, Bangalore.
Databases and software developed: We have developed programs for codon usage analysis and another for phylogenetic analysis. A database named BAMBOOINFOLINE- a database for North Bengal bamboo’s (http://www.bamboodb.ind.in/) has been developed. We are also currently engaged in designing a database on secretome analysis of Mycobacterium “MycoSec”
Initiation of R&D activities in Bioinformatics: The Coordinator’s group is actively engaged in research in the field of genomics and proteomics of nitrogen fixing bacteria and food pathogenic bacteria. Protein structure prediction, biological sequence analysis, phylogenetic study, molecular modeling and molecular docking are the major thrust areas. Two PhD students (S Thakur & Ayan Roy) are actively pursuing their research work.
Details of Training/ Workshop organized and total number of user trained: Three National Level Workshops on Bioinformatics were held. About 50 participants (students, research scholars and faculties) in total from different disciplines of biological sciences were provided training on biodiversity informatics, database, alignment tools, phylogeny software, molecular evolution, homology modeling and molecular docking. One regional workshop on bioinformatics has been organized in Gaur College (Malda) on 22nd March 2011.
Frankia Genome sequencing project collaborating laboratory: The Coordinator of NBU Bioinformatics Facility, Dr. Arnab Sen has a long-term collaboration with Dr. Louis S. Tisa, Department of Microbiology, University of New Hampshire, USA. He along with Dr. Louis S. Tisa has been working towards the complete genome sequencing of five Frankia strains collected from different parts of the world. DNA sequencing for Frankia strains Eul1c has been completed and is available in public domain.
Research publications from the Centre (2012-13):
414
1.
Goyal AK, PK Ghosh, Ak Dubey and A Sen (2012). Inventorying bamboo biodiversity of North Bengal: a case study. Int. J. Fund. Appl. Sci. 1:5-8
2.
Thakur S, AK Bothra, S Sur and A Sen (2012) Molecular dynamics simulation of pr-1 protein from Solanum tuberosum provides an in-depth view of its structural features. In ‘Microbial Resources for Crop Improvement’; BN Chakraborty and U Chakraborty (ed.); Satish Serial Publishing House Pp 173-181.
3.
Saha, S, S Sur, A Bothra and A Sen (2012). A homology model for 16S rRNA tertiary structure of Frankia. NBU J Pl. Sc.6:89-94.
4.
Mondal, U, A Sen and A Bothra (2012). Bioinformatics of pathogenic food bacteria. NBU J Pl. Sc.6:9-17.
5.
Thakur S, A Bothra and A Sen (2012) In silico studies of Nifh protein structure and its post-translational modification in Bradyrhizobium sp. ors278. Int. J Pharm Bio Sc (accepted)
6.
Mishra T, Das AP and Sen A (2012). Phytochemical screening and in vitro antioxidant profiling of solvent fractions of Canna edulis Ker Gawler. Free radicals and Antioxidants. (In press)
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7.
Sen A, S Thakur, A Bothra, S Sur and L Tisa (2012). Identification of TTA codon containing genes in Frankia and exploration of the role of tRNA in regulating these genes. Archives of Microbiology.194: 35-45.
8.
Kundu S, A Bothra, LS Tisa and A Sen (2012). In silico analysis reveals the role of horizontally transferred genes in shaping the pathogenecity of Xanthomonas. Ind J Biotechnol. (In press)
9.
Sur S, AK Bothra and A Sen (2012) Proteome analysis reveals the influence of isoelectric point and amino acid usages on the lifestyle of nitrogen fixing microorganisms. Ind J Biotechnol. (In press)
10.
Kundu S, A Bothra, LS Tisa and A Sen (2011). In silico analysis reveals the role of horizontally transferred genes in shaping the pathogenecity of Xanthomonas. Ind J Biotechnol. (accepted)
11.
Chakraborty D, UK Mondal, A Sen and AK Bothra. IUP J Biotechnol. 5(3) in press.
12.
Sur S, AK Bothra and A Sen (2011) Bioinformatics of Nitrogen fixation – a review, In Recent studies in biodiversity and traditional knowledge in India. C Ghosh & AP Das (eds.) pp35-43.
13.
Mishra T, AK Goyal, SK Middha and A Sen (2011) Antioxidative Properties of Canna edulis Ker Gawler. Ind. J Nat. Pro. Res. 2:315-321.
14.
Sur S, AK Bothra and A Sen (2011) Proteome analysis reveals the influence of isoelectric point and amino acid usages on the lifestyle of nitrogen fixing microorganisms. Ind J Biotechnol. (accepted)
15. Sen A and AK Misra (2011) Frankia and actinorhizal symbiosis. In: Microorganisms in Sustainable Agriculture and Biotechnology (ed. Satyanarayana T. Johri BN and Prakash A). Springer Science+Business Media B.V. DOI 10.1007/978-94-007-2214-9_7 (in press) 16.
Goyal AK, BC Basistha, A Sen and SK Middha (2011). Antioxidant profiling of Hippophae salicifolia D. Don growing in sacred forests of Sikkim, India. Functional Plant Biol. 38(9) 697-701.
17.
Goyal AK, SK Middha and A Sen (2011). In vitro antioxidative profiling of different fractions of Dendrocalamus strictus (Roxb.) Nees Leaf Extract. Free Radicals and Antioxidants. 1:42-48
18.
Mondal UK, A Pal, A Sen and AK Bothra (2011). Bioinformatic study of pathogenicity related genes of three species of Helicobacter. Int. J Appl. Biotech. Biochem. 1(2): 193-200.
19.
Thakur S, Z Patra, M Biswal and A Sen (2011). Exploration of proteis with signal peptides and their respective genes in some actinomycetes: a bioinformatics approach. Int. J. Integrative Biol. 11(2): 97-102.
20.
Basistha BC and A Sen (2011). Sea buckthorn and its microsymbiont-a review. NBU J Pl. Sc.5:67-84.
21.
Mishra T, AK Goyal, P Mondal and A Sen (2011). Free radical scavenging activity of different ornamental and cultivars of Canna available in Eastern India. NBU J Pl. Sc.5:41-45.
22.
Mondal UK, A Sen and AK Bothra (2011). Characterization of pathogenic genes through condensed matrix method, case study through bacterial Zeta toxin. International journal of Genetic Engneering and Biotechnology. 2(1): 109-114.
Future activities:
Development of MycoSec- database on secretome of Mycobacterium
Annotation and analysis of five Frankia genomes whose sequencing has been undertaken.
Bioinformatics analysis of nitrogen fixing and food pathogenic bacterial genomes.
Molecular modeling of some nitrogen fixing proteins and bacterial toxin proteins.
Publication of Newsletter and conducting various training programs/workshops and seminar/ conference in bioinformatics in North Bengal and adjoining areas.
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Contact details: Coordinator: Dr. Arnab Sen NBU Bioinformatics Facility, Department of Botany, University of North Bengal, Siliguri-734013 Phone: +91-353-6528172, Fax: 0353-2699106 E-mail:
[email protected],
[email protected] Deputy Coordinator: Dr. Asim K Bothra Chemiinformatics Bioinformatics Laboratory Department of Chemistry Raiganj (University) College, Raiganj-733134 Phone: 9474441570; E-mail:
[email protected]
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University of Rajasthan, Jaipur Coordinator : Dr. Sumita Kachhawaha Summary of the progress made by the centre from its inspection: The bioinformatics infrastructure facility (BIF) was established on 22nd September, 2006 under BTISNET programme funded by DBT Govt. of India. University has provided independent accommodation for BIF, with 24 hours high speed internet, telephone and electricity supply. BIF centre runs successfully in a well, air conditioned lab, located in CCT building.
Major research activity in biotechnology and its related fields : a.
The university has biotechnology and its related field of study in the department of Botany, Zoology, Biotechnology, Microbiology and Chemistry at the level of UGC, PG and Ph. D.
b.
The board research activity in these departments include transgenesis, plant tissue culture, secondary metabolites, molecular taxonomy, biodiversity, reproductive biology, immunology, biochemistry, neuroscience, bioinformatics, metabolomics, system biology and convergence of technology.
Area of specialization of the centre: a.
Transcriptome data analysis-analysis of gene expression profiling and metabolomics profiling of complex disease particularly the Brest Cancer. b. Plant diversity and evolutionary biology.
b.
Metabolomics profiling of medicinal plants. d. Genetic transformation.
Infrastructure facility of Bioinformatics centre: (i)
12 Desktops
(ii)
2 servers
(iii) Laser jet printers (HP 2430dtn). (iv)Inkjet Printer (HP 1200). (v)
Scan jet Scanner.
Details about the team members working/ associated with the centre: Name Dr. Sumita Kachhawaha Dr. Nupur Mathur
a. b.
Designation Coordinator Dy. Coordinator
Area of specialization Plant biotechnology Animal biotechnology
Types of service provided: a.
Education: centre helps in education of biology to the following course: (i)
M.Sc. in Zoology, Botany, Microbiology and Biotechnology.
(ii)
B.Sc. in biotechnology.
(iii) Training to the students of the Life sciences students. b. Research. (iv) Centre provides access to bioinformatics tools to university researchers and faculty members.
Publications: 1.
Barupal DK, Kind T, Haldiya P, Wohlgemuth G, Kothari SL, Pinkerten K and Fiehn O (2012). MetaMapp: Mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity. BMC Bioinformatics 2012, 13:99.
2.
Khurana-Kaul V, Kachhwaha S and Kothari SL (2012). Characterization of genetic diversity in Jatropha curcas L. germplasm using RAPD and ISSR markers. Indian Journal of Biotechnology 11, 54-61.
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Dangi B, Jain R, Kachhwaha S and Kothari SL (2012). Assessment of Diversity in Terminalia bellerica Roxb. Using morphological, Phytochemical and molecular markers. National Academy Science Letters 35, 27-35.
4.
Solanki PS, Krishna Mohan M, Ghosh P and Kothari SL (2012). Analysis of structurally conservedatomic interactions in structural homologs of nicotinamide adenine dinucleotide binding dehydrogenases. Journal of Computational Biology and Bioinformatics Research 4, 28-33
5.
Jain D, Kachhwaha S, Jain R and Kothari SL (2012). Isolation and characterization of cry genes from indigenous strains of Bacillus thuringiensis taken from desert soils of Rajasthan. Indian Journal of Biotechnology 11, 491494
6.
Solanki PS (2011). Studies on structural evolution of proteins adaptations to temperature in extremophiles. (Ph.D. Thesis, Awarded)
Contact details:
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Name of the Coordinator
: Dr. Sumita Kachhwaha
Dy. Coordinator
:
Dr. Nupur Mathur
Postal Address
:
University of Rajasthan, Jaipur, 302 004
Phone No.
:
0141 2703439
Email
:
[email protected]
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Vidyasagar University, Midnapore Coordinator : Prof. Bikas Ranjan Pati Summary of the progress made by the center from its inception This centre, situated in the Department of Microbiology is functional since August 2007.The first aim of establishing this center in a rural university of West Bengal was to disseminate the idea and knowledge about bioinformatics in the remote corners of southern parts of the state. Since the Inception till date, we have organized 15 workshops and one refresher course from which more than 370 participants have benefitted. The target group of those programs also ranged from undergraduate students to senior college and university teachers of the allied subjects accordingly. A direct result of this awareness is evident from the inclusion of Bioinformatics in course curricula of masters and undergraduate levels under the University. This year our centre installed WI-FI facility in the Department for wider use. To disseminate the knowledge among the students in a more efficient manner, we have organized one more workshop-cumtraining titled “Introduction to Bioinformatics” for undergraduate students in this year. Another seminar cum workshop on machine learning exclusively for research scholars and teachers of all science disciplines will be held by March, 2013.
Major research activities in biotechnology and its related fields Our faculties are actively engaged in research in different aspect of biotechnology. Major fields of research are:a.
Structural and functional studies of different industrially important enzymes like amylases, keratinases, tannase, chitinase etc
b.
Structure – function relationship of proteins
c.
Codon usage study of viral genes
d.
Analysis of biological problems with machine learning methods
e.
Surface Response Curve analysis
f.
Microbial enzyme (amylase, tannase, xylanase, chitinase) production and scale up process.
g.
Production of microbial polysaccharides and antibiotics.
h.
Antioxidant and anti-diabetic constitute from medicinal plants.
i.
Development of new fish feed
j.
Study of microorganisms involved and process standardization, enhancement and optimization of ethnic beverages
Area of specialization of the center The application of bioinformatics and biostatistics has been made possible in the above mentioned research works through this facility. Apart from these we are also interested in a.
Conserved region, motif finding and structural analysis of different enzymes of interest
b.
Designing probes for enzymes of interest
c.
Structure prediction, docking , energy minimization and molecular dynamics
d.
Evolutionary studies
e.
Applying machine learning techniques in deciphering properties of different types of genes.
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Infrastructure facilities in the bioinformatics centre Computer & Communication facility Computer Hardware : IBM X3650 server, IBM X3400 server, Lenovo quad core (Intel xeon processor @ 2.33MHz) think centre, Apple iMac PC (one No.),55 inch Lcd Monitor (one No.),public address system, Lenovo desktop PCs (20 nos),HP hiend Desktops (5 Nos.), Laptop (one), Assembled desktop with core2duo processor, 4GB RAM (one),Printers-3 (laser and Desk Jet), Photocopier (one), Scanner (one), External HD (one), external DVD writer (one). Communication facility: Twenty four hours leased line internet facility(upto 1Gbps) and one dedicated telephone (no. 03222 – 274173) are available in this center.
Scientific software packages Gromacs, Haddock, Discovery studio (Visualiser), Modeller, PAML, Autodock, Design Expert, Bio-ID, Genius Pro, MEME Suite, BlockMaker, ActivePerl, Codon W, Clustal, PHYLIP, MEGA 4.0, Linux OS, Sigma plot 11.0 with enzyme kinetics, Rapidminer , Vector NTI (Invitrogen) 11 , R, Tiberius etc.
Details about staff members working in the center There is no permanent staff in our center. Following departmental faculty and staff are actively engaged in this center – Prof. B. R. Pati (Coordinator of BIF center) Dr. K. C. Mondal (Co-coordinator, BIF Center and HOD, Microbiology Department) Dr. P.K. Das Mohapatra (Faculty, Microbiology Department) S.No. 1.
Name Designation Mr. Partha Sarathi Das RA, BIF center
2.
Ms. Shilpee Pal
Studentship, BIF center
Specialization Microbiology, Machine Learning, R, biological networks Docking, Modelling,Codon usage studies
Working Since July 2009
Status On yearly contract
September,2012
Temporary
Mr. J. Chalak (Staff, Microbiology Department)
Educational activities
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A.
Granting access to Internet & e-journal facilities through UGC infonet consortium by the PG students, Ph D scholars and faculties.
B.
Sequence and structural data retrieval and storage for specific purposes in line with the interests of the Department.
C.
Providing library facilities through departmental and central library for references on bioinformatics
D.
Allowing students to have a hands-on practice on different local and online tools of bioinformatics. This also helps them to facilitate their research works under the broad head of microbiology, biotechnology, botany, aquaculture and related disciplines as offered in the institute.
E.
Different students of related disciplines use this facility extensively for their project works in bioinformatics or statistical analysis.
F.
The centre also helps the students of MSc. Microbiology second semester to study the theoretical and practical aspects of bioinformatics portion of their syllabus.
G.
This year the Department of Microbiology has initiated an UGC-Sponsored One-Year PG diploma in Quality control and assurance in Microbial Technology. The course also has modules on bioinformatics and the necessary support for that (theory and practical sessions) is being provided by BIF.
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Papers published or presented in the conferences Banerjee A, Jana A, Pati BR. , Mondal KC. , Das Mohapatra PK. Characterization of Tannase Protein Sequences of Bacteria and Fungi: An In Silico Study. The Protein Journal. 2012. 31(4): 306-327.
Paper Communicated Pal S, Banerjee A, Das Mohapatra PK , Das PS, Pati BR., Mandal KC., Sen A. Evolutionary Study of Dengue Viral Genomes through Bioinformatics. Communicated to Virus Genes. Das PS, Chakraborty S, Ghosh TC,Mondal KC, Pati BR. Neural network based prediction of essential genes of S. cerevisae
Poster Presentation 1.
Das Mohapatra PK, Banerjee A, Sahoo DK, Thatoi HN, Sen Arnab, Pati BR, Mondal KC. In Silico Characterization of Keratinase Protein Sequences of Bacterial Origin. International Conference on Industrial Biotechnology. Organized by BRSI & Punjabi University, Patiala. 21-23 November 2012. Pp 92.
2.
Banerjee A, Jana A, Pati BR, Mondal KC, Das Mohapatra PK. Characterization of Tannase Protein Sequenecs of Bacteria and Fungi – an In Silico Study.International Conference on Frontiers in Biological Researches. Organized by Dept. Of Human Physiology with Community Health, Vidyasagar University. 26-27 February 2012. Pp 91.
Collaborative works/ initiatives in R&D activities
We are working on machine learning methods to apply this system in predicting properties and functions of various genes. Prof. Tapash C Ghosh, Scientist, Bioinformatics Department, Bose Institute, Kolkata is collaborating with us in this study.
We have also been doing research work in collaboration with Dr. Arnab Sen, Coordinator BIF center, University of North Bengal for studies in protein structure prediction, sequence and structure based phylogenetic analysis, hub and non hub protein identification, protein-protein interaction, nucleotide expression and codon usage analysis.
Prof. B. R. Pati, Coordinator, BIF Center and faculties of Department of Microbiology , Dr. K C Mondal and Dr. P K Das Mohapatra is keenly interested in Microbial enzyme (amylase, keratinase, tannase, xylanase, chitinase) production and scale up process; Production of microbial polysaccharides and antibiotics; Biofertilizer production and transfer of technology; Biofuels etc where this BIF Center is helping their group to do various bioinformatics and biostatistics related analyses. The extensive use of software acquired by BIF Center like Sigmaplot and enzyme kinetics, BioID, Design Expert have helped them in pursuit of these research works.
Dr. Indraneel Mukherjee, ISI Kolkata also have been collaborating with us for studies in machine learning and biostatistics (specially solving problems through R) respectively.
Training/Workshop organized and total no of user trained Workshop titled “Introduction to Bioinformatics” for 30 undergraduate students held on and from 12th-13th September, 2012
Impact shown by our center on the growth of biotechnology and allied areas: The centre not only has been successful to create awareness about bioinformatics, it has also attracted the students and teachers of various disciplines. This recent field, at the crossroads of sciences has also helped the scholars of different subject to validate their work and conduct research in their own fields of interest, while using some tools or analytical applications of bioinformatics. Specially the bio-statistical packages have been of great help to them. We wish to continue promoting the high- quality free and open source softwares in coming days too so that financial constraints are reduced for research in bioinformatics.
Future activities:
Amalgamation of in-silico and wet lab facilities through collaboration with the Dept of Microbiology.
Install cluster computing facilities for intensive operations and hosting of web based services.
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Few workshops have been planed and will be organized on Machine Learning, Molecular modeling, Drug designing for teachers, researchers and students.
A proposal for BUILDER program in life science including bioinformatics has been submitted to DBT which is under evaluation now.
Contact details : Name of the Coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
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Prof.(Dr.) Bikas Ranjan Pati (Co-ordinator) Dr. Keshab Chandra Mondal (Co-coordinator) Dept. of Microbiology, Vidyasagar University, Midnapore, WB, Pin 721102 03222-273174 (direct), 03222-276554/555 (Ext. 477), Mobile: 09531506687 03222 – 275329 / 264338
[email protected],
[email protected] www.vidyasagar.ac.in Prof.(Dr.) Bikas Ranjan Pati (Co-ordinator) Dr. Keshab Chandra Mondal (Co-coordinator) Mr. Partha Sarathi Das (RA, BIF Center0
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West Bengal University of Technology, Kolkata Coordinator: Dr. Raja Banerjee Summary of the progress made by the centre from its inception: Department of Bioinformatics, founded in the year 2006 for PG teaching and research and recognized by UGC under its 12B regulation, offers courses in –M. Tech. in Bioinformatics (18 students) and Post B.Sc. Int. Ph.D in Bioinformatics (6 students); for details visit www.wbut.ac.in. The department is recognized as BIF by DBT, New Delhi for “Establishment of Bioinformatics Infrastructure Facility (BIF) for the promotion of Biology Teaching through Bioinformatics (BTBI)”. During last few years at the centre we developed programs for Detailed Hydrogen bond analysis from MD trajectories; analysis of Phi Psi torsion angles and contour plot generation for MD trajectories; Identification and Analysis of functional motifs (NEST) in Proteins. DBT is pleased to continue the programme in the 12th plan period. Besides participation in regular course of teaching and research, the Centre regularly organizes workshops and seminars. Eminent Scientists from different Research Institutes, Universities, R&D organizations from all over the country are invited to deliver seminars on current research topics. The centre also provides training programmes to students and researchers of other institutes and extends laboratory facilities to students of other institutes for pursuing their curricular project work. As an initiative to validate the outcome of bioinformatics resources the center helps in Placement of the students: 95% students are placed either in industry or academics. The Department/centre had also functioned as the DBT nodal centre for Eastern Region for holding the National Eligibility Test for Bioinfo-NET (BINC), jointly organized by DBT and University of Pune / JNU.
Major research activities in biotechnology and its related fields :
Molecular Design and Modeling using short peptide motifs (structure-function relation) applying spectroscopic techniques (especially NMR, CD etc) and computational method (Docking, MD Simulation); an implication towards drug design.
Application of Mass Spectrometry (MSn technique) for de novo sequencing and conformational aspects of proteins and natural peptides
Bioinformatics studies and Spectroscopic studies (FTMS, FTIR, 13C NMR, Powder XRD) for structural behavioural analysis, hetero-polymerization and mass production of a biological pigment
Pharmacophore modeling and database designing for comparative study; Analysis of anion binding motifs in proteins and their functional importance
Developed programs for: a) Detailed Hydrogen bond analysis for MD trajectories b) Phi Psi analysis and contour plot generation for MD trajectories c) Identification and Analysis of functional motifs (nests) in Proteins.
Area of specialization: Identification of functionally active short peptide motifs
Major achievements made during 2012-13: Dr. Banerjee was invited as Visiting Professor to Department of Chemistry, University of Padova, Italy for teaching a course of MSc programme and initiating collaborative research. Workshops Organized: National level Hands-on Workshop on Genomics-Proteomics and Metabolomics held in March 2012. Projects Completed: Design of ‘anion recognition’ short peptide motifs: an approach towards designing ‘model scaffolds’ for binding, approved by DBT, Govt. of India to Dr. Raja Banerjee. Infrastructure facilities in the Bioinformatics Centre: Computer & communication facility Hardware – 2 IBM X226, 2 IBM X206, 1 HP Proliant DL 160 G6, 1 Apple MacPro, 1 Apple 27” LED Display, IBM Intellistation Z Pro, IBM x3650, 1 Apple MacMini,15 TFT Monitors, 2 D-Link v92 modem, 25 Thin clients, 1 Apple MacBookPro, 5 Dell Desktops.
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Scientific software – The laboratory runs primarily on Open Source and free softwares: EMBOSS, EMBASSY, CLUSTALV, ARB, Helix packing, netblast, DSSP, OpenBabel, Genocluster(Jalaja Technologies), GROMACS, YASARA, CHARMM, MOPAC, VMD, RASMOL, SPDBViewer, RASTER3D, Pymol, AUTODOC, MOLWORKS, BkChem, GAMESS; Cerius2 and Discovery Studio2.5 form Accelrys, iNMR, ChemBioOffice Ultra 2010, iGOR, BBEdit, Gaussian 09, GaussView 5, MS Office 2010, Antivirus - 10user Databases and other Information Resources – Our digital library based on KOHA and D- space platforms permits network based access to 13500 e-books and 1800 journals from Springerlink along with CSIR, Academy of science, Science Direct and IOE journals.
Details about Staff members working in the centre: Sl. No. Name 1. Dr. Raja Banerjee, Mr. Subhrangshu 2. Supakar, Ms. Aulie Banerjee, 3.
Designation Associate Professor HOD Bioinformatics Project Officer, Project Officer
Specialization Spectroscopy & Structural Biology Pharm. & Bioinformatics Botany & Bioinformatics
Working Since Status 2005 Regular 2006 2006
Tenure Tenure
Educational activities: Offering courses in –M. Tech. in Bioinformatics (18 students) and Post B.Sc. Int. Ph.D in Bioinformatics (6 students) since 2006. Eminent scientist from premier research institutes are invited to deliver seminars and conducting workshops for the students to enlighten them in the cutting edge research and motivate them in their future academics. Faculty members have research collaboration with premier national and international level institutes like University of Padova, Italy, IISc Bangalore, IIT KGP, Bose Institute, Kolkata etc. MTech students are being trained for master’s project in collaboration with premier institutes
Papers/ published or presented in the conferences :
An Insight into Molecular Structure of Melanin Extracted from Nitrogen fixing Bacterium, Aulie Banerjee, Subhrangshu Supakar & Raja Banerjee* (communicated)
Conformational preferences of ‘C?NN’ short peptide motif towards recognition of anions; Tridip Sheet, Subhrangsh Supakar & Raja Banerjee* (communicated)
Significance of genetic variation in glutathione S-transferase M1 (GSTM1) in the development of breast cancer: a meta-analysis; Pritha Bhattacharjee, Subhadeep Das, Raja Banerjee & A.K. Giri (2011) Perspectives in Cytology and Genetics, 15, 237-254
Banerjee R*, Sudarslal S, Ranganayaki RS, Raghothama S., (2011) Effect of ester chemical structure and peptide bond conformation in fragmentation pathways of differently metal cationized cyclodepsipeptides. Org Biomol Chem. Sep 21;9(18):6234-45.
Initiation of R&D activities in Bioinformatics: Besides Collaboration for research, we have Ekta Incubation Centre, a Technology Business Incubator which proposes to build on competencies of its own resources and those of the networked incubator Entrepreneurship Development Cell (EDC). Details of Training/Workshop organized and total no of user trained National level Hands-on Workshop on GenomicsProteomics and Metabolomics held in March 2012. 30 students, researcher and faculty members were trained Impact shown by the Centre: in teaching and research Proposed activities for 2013-14: Along with the existing programme for promotion of teaching and research in Bioinformatics (thrust area Structural Biology) Setting up of High Performance Computational Platform for working on problems involving parallel codes run on clusters. Molecular dynamic analysis of protein-ligand interactions Fluidity analysis of formulation involving proteins/drug molecules
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Molecular modelling of membrane bound peptide Hybrid QM/MM studies of small molecules Setting up of Structural Biology Laboratory
Contact details: Name of the Coordinator Name of the Co-coordinator Postal Address Phone Number Fax No. Email Website Name of Contact Person
Dr. Raja Banerjee Mr. Subhrangshu Supakar West Bengal University of Technology BF- 142, Sector – 1, Salt Lake, Kolkata – 700 064; W.B 033-23217578, 033-23341031, +91 9433350915 033-23341030
[email protected];
[email protected] Website: www.wbut.ac.in Dr. Raja Banerjee,
[email protected] Mr.S.Supakar,
[email protected]
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Sardar Vallabhbhai National Institute of Technology, SURAT: Coordinator: Dr. Neeru Adlakha Summary of the progress made by the centre from its inception: The Department of Applied Mathematics and Humanities, SVNIT SURAT has conducted a number of activities i n the area of bioinformatics and related areas, since the inception of BIF centre. Four National workshops on Bioinformatics have already been organized in the areas of Bioinformatics and Chemoinformatics.Also the coordinator of the centre is coordinating the activities of Special Interest Group (SIG) on Bioinformatics under Computer Society of India as the Secretary of SIG since April 2010.
Major research activities in Biotechnology and its related fields at your institution: The institute plans to develop a versatile research team in the following areas of computational biology1.
Datamining in Bioinformatics and Computational Biology.
2.
Thermal Modeling of Cancer
3.
Computational Phylogenetics
4.
Neuroinformatics and Computational Neuroscience
5.
Computational cell biology
Area of Specialization of the Centre: Mathematical & Computational Biology Major activities of the centre during the year 2012-2013: An Indo-Austrian project on Thermal Modelling of Cancer is in progress (funded by DST).Also research in above mentioned areas is in progress. A CSIR project entitled Computational Model and Server for Simulation of Ca2+ Dynamics in Myocytes is in progress
Infrastructure facility in the Bioinformatics Centre The procurement of infrastructure is in progress. Details about staff members working in the centre (Name of the staff, Designation, Specialization and period of working. Please indicate their absorption status): There are 10 Research scholars working in the area of Mathematical & Computational Biology. Name of staff Dr. Neeru Adlakha
Designation Associate Professor
Specialization Computational Biology,Datamining
Period of working 12 years
Types of services provided: I)
Training programmes/ workshops in the area of bioinformatics to provide exposure to basic skills of bioinformatics to the students and faculties of biotechnology/ lifesciences, physical sciences and IT, from other institutes of our region and country.
Educational activities with details of placement: 10 candidates are doing PhD in the area of Computational Biology and Bioinformatics.Two Phd Thesis have been submitted.
Initiative to validate the outcome of bioinformatics resources: i)
Feedback of participants in training / workshops.
ii)
Feedback of students and research scholars of educational programme.
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Collaborative works/ Initiatives: We are having collaboration with BTISNET Centre of MANIT, Bhopal. Databases / Softwares packages developed: Nil Papers published or presented in the conferences with reference: Paper published- 05
Presented in conference –05
Initiation of R& D activities in Bioinformatics: We plan to develop computational techniques and softwares on protein-protein interactions and reticulate evolution.
Details of Training / Working organized and total no. Of user trained:Nil Impact shown by your centre on the growth of biotechnology and allied areas. In this you may highlight the details like number of paper published / number of paper published with the help of your centre, how your centre is promoting activities of your organization and neighboring institutions , manpower trained , tool developed , copyrights acquired and other services offered etc The centre has been established last year and four workshops have been organized to train the students, faculties and scholars in the area of Bioinformatics. In all one hundred and thirty two participants from various Institutes of the country have been trained in these workshops. It is proposed to start BTech, MTech and PhD programs in the area of Bioinformatics in the institute in near future. About one hundred and thirty two participants have already been trained by the centre. Two PhD Thesis have been submitted in the field of computational neuroscience
Future activities Proposed National workshop on Statistical modeling for life scientists during October - 2013.
Contact details: Name of the Coordinator: Dr. Neeru Adlakha Postal Address : Associate Professor,Department of Applied Mathematics, SVNIT, SURAT Phone Number: 0261-2201914 , Mobile: + 91 – 9574280428 Email:
[email protected] Website: www.svnit.ac.in Name of contact person (s) : Dr. Neeru Adlakha
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BIF Centre, D. M. College of Science, Imphal Coordinator: Dr. Oinam Shashikumar Singh Summary of the Progress made by the centre from its inception: Since its inception in the latter parts of 2008 under the sponsorship of Department of Biotechnology, Ministry of Science & Technology, Government of India, New Delhi, Bioinformatics Infrastructure Facility Centre, Department of Zoology, D. M. College of Science, Imphal has become an important centre for bioinformatics studies, training, research and popularization.
Major research activities in Biotechnology and its related fields at your institution: (a)
Development of a digital database on Bioresources of North-East India - Through a Network approach among NE states.
(b)
Development of a digital database on microscopic invertebrates of Manipur.
(c)
Development of a digital database on spiders of Manipur.
(d)
Production of monosex populations of fishes through artificial androgenesis and gynogenesis.
(e)
Development of a digital database on the wetland resources of Manipur
Area of specialization: (a)
Ethnobotany and ethnozoology
(b)
Develoment of digital databases on bioresources
(c)
Aquaculture Bioinformatics & Biotechnology
(d)
Conservation Bioinformatics
Major achievements made during 2012-13: (i) Develoment of Database on Bioresources of NE India (Input of secondary data): Bioresources Plant bioresources Medicinal & edible insects Fish
No. of species entered 1200 16 280
No. of families 195 9 12
No. of orders 59 5 33
(ii) Two Ph.D. scholars registered under Assam University, Silchar working on a.
Comparative morphometry of certain fishes......using NTSys software.
b.
Ethnozoology of certain tribes.........& Develoment of a digital database.
Infrastructure facilities in the Bioinformatics Centre: Sl Particular of items 1 Servers/Main/Proxy 2 Computers/Desktops 3 UPS/Inverters with battery 4 Internet connection 5 Video camera # 6 Digital Field camera# 7 Digital SLR Field camera# 8 Interactive Board# 9 Multimedia Projector# 10 Digital stereomicroscope 11 Digital Electronic balance #Procured through Consortium project;
Make IBM Lenovo/Sony/Apple Emerson/6 KVA; Lucas BSNL - 512 kbps Broadband and 2 Mb leased line Sony HDD, 220GB/inbuilt projector Sony Cybershot, 16 mp with GPS, 4 GB Sony GPS 16mp, 10 fps Burst shooting Sharp Sharp Optica Italy Fisher scientific *Being procured for long term training in Bioinformatics.
Quantity 2 nos 12 + 4# +10* 1+1 1 1 1 1 1 1 1
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XXIVnd All India BTISnet Coordinators’ Meeting
Details about Staff members working in the centre: Sl. Name
Designation
Specialization
From
Status
1.
H. Nilima Devi
Research Assistant
M .Sc. Bioinformatics
2009
Continuing
2.
Th. Ajita Devi
Research Assistant
M .Sc. Bioinformatics
2009
Continuing
3.
Bebethoi
Traineeship
M .Sc. Biotechnology
2012
Continuing
4.
Romoni
Studentship
M .Sc. Life Science
2012
Continuing
5.
N. Usharani
Project Fellow
M .Sc. Bioinformatics
2012
Continuing
6.
I. Sarda
Project Fellow
M .Sc. Life Science
2012
Continuing
7.
Th. Anusaya
Project Fellow
M .Sc. Botany
2012
Continuing
8.
N. Bisorjit
Project Fellow
MCA Computer
2012
Continuing
9.
Lucy Pamei
Project Assistant
M. Sc. Life Science
2012
Continuing
Lab Attendant
Matriculate
2012
Continuing
10. Y. Thoibi
Educational activities Till date, the centre has trained about 400 teachers, research scholars and students from universities, colleges and schools by organizing national level training programmes//workshops/national seminars, etc. The Centre also have given short term training guidance to M. Sc. students in Bioinformatics from different universities and institutes in their last semester project work.
Papers/ published or presented in the conferences : 3 papers on ethnobiology being submitted for publication in Indian Journal of Ethnobiology.
Initiation of R&D activities in Bioinformatics: “Analysis of intraspecific variation among fishes using NTSys software” and “Development of Database on Ethnozoology of certain tribes of Manipur” (Research leading to Ph. D. degree from Assam University, Silchar
Details of Training/Workshop organized and total no of user trained Number of training/workshop 7 (seven)
Registered 325
Unregistered 75
Total No. of participants 400
Impact shown by the Centre: The Centre has been playing an active role in bioinformatics studies, training, research and popularization. The Centre has been attracting more teachers and students who want to know more about Bioinformatics and its aplications in modern biologigy.
Proposed activities for 2013-14
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(i)
Long term training on Bioinformatics for graduates in subjects other than Bioinformatics.
(ii)
Opening of Carrier-oriented add-on course in Bioinformatics at undergraduate level.
XXIVnd All India BTISnet Coordinators’ Meeting
February 03-04, 2011
Contact details: Name of the Coordinator Postal Address Phone Number Email Website Name of Contact Person
Dr. Oinam Shashikumar Singh Bioinformatics Centre, D. M. College of Science, Imphal 03852440616 / 9436020795
[email protected];
[email protected] www.dmcollege.ac.in Dr. Oinam Shashikumar Singh
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Bioinformatics Infrastructure facility, University of Hyderabad Coordinator: Prof. Anand K. Kondapi Summary of the Progress made by the centre from its inception: The Bioinformatics Infrastructure facility supported the teaching and research in drug discovery and systems biology of students and faculty members. Research carryout at the facility yielded ten publications in impact peer reviewed Journals. Various Biological resources available at BIF include biological databases as well as web tools to carry out user defined analysis. These resources are freely available at http://bif.uohyd.ac.in. These resources, at BIF website, includes computationally identified mycobacterial regulatory regions, medicinal plants data from North-east region of India, in silico predictions for cynobacterial proteins, integrated knowledge base for HIV, Online tool to identify orthologs etc. We have conducted a 3-day workshop on “Programming in R and applications in Computational Biology”, form Jan 11 to 13, with participants of 60. Facility helped in training more than 100 students from integrated M.Sc. Systems Biology, M.Tech Bioinformatics and Ph.D. students. Software training given to students in the lab includes: Sybel Tripos 8.0, Gold, Silver, Goldmine, CSD System Software 2011 (ConQuest, IsoStar, Mercury, Mogul, Prequest, and Vista) Mat Lab and several open License Softwares. The Bioinformatics Infrastructure facility at University is being used by five students who had come from all over India of different institutes for doing their project work. The facility is made available from morning 9.30 AM to evening 5.30 PM.
Major research activities in Biotechnology and its related fields at your institution:
Development of molecular therapeutics and diagnostics against infectious (viral, bacteria, parasitic) diseases, cancer, neurological disorders and inflammation.
Development of Bio-intensive-integrated insect pest management.
Transgenic plants
Identification and characterization of bioactive molecules from medicinal plants
Genomic analysis and building gene regulatory networks and systems biology
Metabolomics and metabolic engineering
Nanobiotechnology and biofuels
Area of specialization: Systems Biology and Drug Discovery
Major achievements made during 2012-13:
Published databases: CyanoPhyChe, Mycorrdb, NeMedPlant, CPC
Developed software tools: Orfin
Published 10 papers in peer reviewed journals
Trained 46 master students in drug discovery and systems biology
Offered projects to five students from other universities in the region.
A workshop being held on R package and applications in computational biology
Infrastructure facilities in the Bioinformatics Centre: Severs:
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Servers (One Domain Controller, One File server and One Program Server) 20 systems. DST PURSE grant and DBT-CREBB supported 8-node Linux cluster There are 10 web tools/resources presently being hosted. All the resources are freely available at http:// bif.uohyd.ac.in.
February 03-04, 2011
XXIVnd All India BTISnet Coordinators’ Meeting
User systems: Databases / Servers developed by students by using BIF facility in 2012 CyanoPhyChe
:
( http://bif.uohyd.ac.in/cpc/)
Mycorrdb
:
(http://bif.uohyd.ac.in/mycorrdb)
NeMedPlant
:
(http://bif.uohyd.ac.in/medplant)
CPC
:
(http://bif.uohyd.ac.in/cpc)
Orfin
:
(http://bifl.uohyd.ac.in/orfin) (Web Server)
Databases developed by students by using BIF facility (under construction) Cyanocis
:
(http://bif.uohyd.ac.in/cyanocis)
Aging
:
(http://bif.uohyd.ernet.in/aging)
Hire
:
(http://bif.uohyd.ac.in/hire)
Conflore
:
(http://bif.uohyd.ac.in/conflore )
Tarc
:
((http://bif.uohyd.ac.in/Tarc)
Details about Staff members working in the centre: Sl.No. Name Prof. Anand K. 1. Kondapi* 2. Dr.JSS Prakash*
Designation Coordinator, Professor Reader
Specialization Working Since Molecular 1996 Therapeutics Functional Genomics 2010
3
Dr.Vaibhav Vindal
Assistant Professor
Genomics
2008
4
J Rajesh
Sys Adm
Networking and 2008 systems management
Status Permanent (Joint)* Permanent (Joint)* Permanent (Joint)* Temporary
*Faculty at Dept Biotechnology, jointly involved at Centre
Educational activities
Facility support practical and project work of M.Tech Bioinformatics and IMSc Systems Biology program
Facility also provide support of PhD students and post-doctoral fellows in Bioinformatics and Systems Biology
Papers/ published or presented in the conferences : Research Publications from the work carried out at BIF: 1.
Arun PV, Bakku RK, Subhashini M, Singh P, Prabhu NP, Suzuki I, Prakash JS. CyanoPhyChe: A Database for Physico-Chemical Properties, Structure and Biochemical Pathway Information of Cyanobacterial Proteins. PLoS One. 2012;7(11):e49425. doi: 10.1371/journal.pone.0049425. Epub 2012 Nov 21.
2.
Rathore RS, Reddy NR, Kondapi AK, Reddanna P, Rami Reddy M, Use of quantum mechanics/molecular mechanics-based FEP method for calculating relative binding affinities of FBPase inhibitors for type-2 diabetes, Theor Chem Acc 131:1096 (2012).
3.
Midha M, Prasad NK, Vindal V (2012) MycoRRdb: A Database of Computationally Identified Regulatory Regions within Intergenic Sequences in Mycobacterial Genomes. PLoS ONE 7(4): e36094. doi:10.1371/ journal.pone.0036094
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XXIVnd All India BTISnet Coordinators’ Meeting
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4.
Meetei, Singh P, Potshan P, Nongdam A, Prabhu NP, Rathore RS, Vindal V, NeMedPlant: a database of therapeutic applications and chemical constituents of medicinal plants from north-east region of India (Database), Bioinformation 8(4): 209-211 (2012).
5.
Midha M., Polavarapu R., Meetei PA, Krishnan H., Mohareer K., Vindal V, OrFin: A web tool for detection of putative Orthologs(Server), Bioinformation 8(15): 738-739 (2012).
6.
Arun PVPS, Bakku RK, Subhashini M, Singh P, Prabhu NP, et al. (2012) CyanoPhyChe: A Database for PhysicoChemical Properties, Structure and Biochemical Pathway Information of Cyanobacterial Proteins. PLoS ONE 7(11): e49425. doi:10.1371/journal.pone.0049425
7.
Golzarroshan B., Siddegowda MS, Li H, Yathirajan HS, Narayana B, Rathore RS, Imatinib (Gleevec@) conformations observed in single crystals, protein–Imatinib co-crystals and molecular dynamics: Implications for drug selectivity, Journal of Molecular Structure 1018 (2012) 107–112.
8.
Karthikeyan NS, Gunasekar R, Sathiyanarayanan KI, & Rathore RS (2012): Synthesis and Molecular Structure of New Macro Acyclic Mannich Derivatives: Symmetrical and Unsymmetrical 2-[(E)-(Benzylideneamino) (aryl)methyl]cyclododecanone, Synthetic Communications: An International Journal for Rapid Communication of Synthetic Organic Chemistry, 42:23, 3429-3440 (2012).
9.
Kannapiran P, Prabhakar M, Rathore RS, Bommakanti A, Kondapi AK. HIV-1 Associated Topoisomerase IIâ Kinase: A Potential Pharmacological Target for Viral Replication. Curr Pharm Des. 2012 Dec 18. [Epub ahead of print]
10.
Brahma SS, Srinidhi M, Shivashankar SA, Narasimhamurthy T, Rathore RS, New metal-organic precursors for MOCVD applications: Synthesis, characterization, crystal structure and thermal properties of mixed-ligand Mg(II) complexes, Journal of Molecular Structure 1035, 416–420 (2013)
Initiation of R&D activities in Bioinformatics:
Initiated molecular therapeutic development through an integrated modeling of the molecular structures and simulation of interaction of bioactive molecules in developing novel therapeutics.
An integrated plant form of genomic and proteomics being developed for modeling biological interaction through systems approach being developed at the centre by faculty members.
Details of Training/Workshop organized and total no of user trained Work shop on R package and applications in computational biology, participants registered are sixty, work shop to be held from 11 to 13 Jan, 2013.
Impact shown by the Centre: Infrastructure at the centre has been strengthened the research in drug discovery and systems biology and allied areas of faculty members, and research students, Several databases are developed by faculty members and were hosted at centre. As a result the quality of publications significantly enhanced.
Proposed activities for 2013-14 Work shop on R package and applications in systems biology, July 1 to 3, 2013
Contact details: Name of the Coordinator Postal Address
Prof. Anand K. Kondapi Bioinformatics Infrastructure Facility School of Life Sciences, University of Hyderabad Gachibowli 500046 India Phone Number 040-23134570 Fax No. 040-23010145 Email
[email protected],
[email protected] Website http://bif.uohyd.ac.in Name of Contact Person Mr. J. Rajesh
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Cover page design by : Shri P. N. Gautam
Centre of Excellence Distributed Information Centre Distributed Information Sub Centre Bioinformatics Infrastructure Facility (BIF)
Dr. Ashok Sharma
Ph. No. 0522-2718577,
Chief Scientist and Head Biotechnology Division, Coordinator, Bioinformatics Centre CSIR-Central Institute of Medicinal and Aromatic Plants Lucknow-226015
E-mail:
[email protected],
[email protected] army printing press www.armyprintingpress.com Lucknow (0522) 6565333
