2011 Undergraduate Handbook

Contents Welcome

3

Enrolment information Important dates

5

Admission and enrolment procedures

5

Undergraduate enrolment - where to from here 7 Preparing for degree level study

Assignments: late policy

35

Missed examinations

35

Scholarships and prizes

35

Academic honesty, cheating and plagiarism 36

Advice and support for students Improve your English language skills

38

Tertiary Foundation Certificate Biology

8

DELNA

38

Tuäkana Programme

8

ELSAC

38

Planning a degree programme

WAVE student support service

39

BSc (Biological Sciences)

9

SBS Staff/Student Liaison Committee

40

BSc(Hons)

9

Harassment

40

BTech in Biotechnology

9

Information Commons

41 41

BSc & BSc(Hons) Biomedical Science

10

Student Learning Centre

BSc & BSc(Hons) Bioinformatics

10

University Library

42

BSc Ecology

11

Careers

43

Research Section

44

Academic programme structure

12

Transition points structure

12

General Education

12

Postgraduate programmes

13

Academic information Academic year

14

Field Trip dates

15

Staff and facilities Staff directory

51

Buildings and facilities

56

Research and teaching facilities

58

Student support services

59

Campus maps

60

Course descriptions Stage I courses

16

Stage II courses

19

Stage III courses

23

Further information Teaching and attendance

32 33

Awards of marks and grades Requirements for Honours

34

Applications for aegrotat and compassionate consideration 34 SBS examination grades 2

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Disclaimer Although every reasonable effort is made to ensure accuracy, the information in this document is provided as a general guide only for students and is subject to alteration. All students enrolling at The University of Auckland must consult its official document, the Calendar of The University of Auckland, to ensure that they are aware of and comply with all regulations, requirements and policies.

Cover photo: Matthew Coutts & Mazdak Radjainia

Kia Ora Welcome

to the School of

Biological Sciences

As the new millennium unfolds, the impact of biology on our lives continues to broaden. New developments have carried the discipline into applications not even thought possible as little as a decade ago. For the new generation of biologists it is more imperative than ever to keep the subject in perspective, because the future lies in developing skills in both the molecular and whole organism / ecosystem aspects of the discipline. Indeed, one of the advantages of studying biology at The University of Auckland is the wide range of subject areas which are taught and the subsequent possibility of integrating both molecular and whole organism aspects of biology in a single degree. Students who major in Biological Sciences are required to include a broad range of courses at undergraduate level and many continue with a more specialised focus at PGDipSci, BSc(Hons), MSc and PhD level. Courses from the Biological Sciences schedule are an integral part of a variety of other programmes including BSc/ BSc(Hons) Biomedical Science, BSc(Hons) Bioinformatics, BSc (Ecology), BSc/BSc(Hons) Food 2011 School of Biological Sciences Undergraduate Handbook |

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Science, BSc Marine Science, BSc/BSc(Hons) Medicinal Chemistry and BTech Biotechnology. I am confident that the School is offering an exciting and challenging education in the biological sciences and I look forward to working with you over the next few years as you proceed through your degree programme. Details specific to Biological Sciences courses are included within this publication. Further information on the structure of particular programmes or specialisations is available in the Science Faculty Prospectus and in the University Calendar. The staff of our Student Resource Centre are available to provide further guidance and assistance and enquiries are most welcome. Best wishes

Dr Judy O’Brien Deputy Director (Academic) School of Biological Sciences

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Enrolment Information Important Dates Closing dates for applications for admission in 2011 1 December 2010

Deadline for new students to submit Application for Admission if 2011 programme includes Summer School courses. Application for Admission also closes 1 December for all students applying to Optometry and to Sport and Exercise Science.

8 December 2010

Deadline for new students to submit Application for Admission if 2011 programme includes Semester One and Semester Two courses only. If you are a new student, only one Application for Admission is required. Applications received after these dates may be accepted if there are places available.

Admission and enrolment procedures New students For all students not enrolled at The University of Auckland in 2010, apply online at www.auckland. ac.nz/apply_now. If you are unable to access our website, please call 0800 61 62 63 or visit the Student Information Centre at 22 Princes Street, Auckland. This is open Monday to Friday from 8am–6pm and Saturday 9am–12noon during peak times. Student Information Centre Room 112 Level 1 (Ground Floor) The ClockTower Building 22 Princes Street Auckland City Campus Phone: +64 9 923 1969 or 0800 61 62 63 Fax: +64 9 367 7104 Email: [email protected]

The closing date for most undergraduate Science applications is 8 December 2010. If you want to take courses at Summer School, or wish to apply to Sport and Exercise Science or the Bachelor of Optometry, applications close 1 December 2010. Only one application is required.

After submitting your application: Your application will be acknowledged by email. Your application will be assessed and, if successful you will receive an “Offer of a place in a programme” . You may receive a conditional offer, but final approval will be dependent on fulfilment of the conditions of admission to the University and the programme.

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During the application process, you will be given a Net ID and password, which will allow you to access Student Services Online. Here you will be able to monitor the progress of your application and check if further documentation is required. Once you have accepted an offer of place, you will gain access to the Enrolment module on Student Services Online. You can then proceed to enrol in courses online. Postgraduate students may need to contact their department for enrolment to be completed.

time, you may not enrol in new courses for that semester, and if you are unable to continue a course a “withdrawal” appears on your academic record. Withdrawing from courses can be done with consultation of the Associate Dean (Academic Programmes) until the third week before the end of lectures. However, tuition fees are not refundable in these cases. The regulations for changing courses are outlined in the latest version of The University of Auckland Calendar. Enrolment instructions received by students will indicate how to go about adding and deleting courses once semesters have begun.

Returning students If you are currently enrolled at The University of Auckland in 2010 and are applying for a new programme (for example MSc after completion of BSc(Hons)), you should apply using Student Services Online. Visit www.auckland.ac.nz/ apply_now. You will be able to enrol through Student Services Online, but if you would like help, please call 0800 61 62 63 or visit the Student Information Centre or the Faculty of Science Student Centre (Ground Floor, Building 301, 23 Symonds Street). Postgraduate students may need to contact their department for enrolment to be completed. The University of Auckland will be open for enrolment from November 2010 to the end of February 2011. You are welcome to attend at any time during normal office hours to seek academic or enrolment advice or assistance in completing your enrolment. NB: Enrolment for BIOSCI 106 and 107, and all Stage II and III BIOSCI courses will open on 15 December 2010.

Changing courses Choose carefully at the beginning. It is however, possible to add and delete courses within the first two weeks of each semester, without penalty (ie tuition fees are refunded for deletions). After this

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Departmental advice If you have queries about particular courses, or require academic advice, information about prerequisites or relevant background to a course of study, the following SBS staff are available to assist:-

For Stage I: Director Stage I Teaching Ms Mandy Harper Director, Stage I Teaching Biology Building Room 101, Phone: + 64 9 373 7599 Ext 87794 [email protected]

For Stage II & III Stage II & III Course Coordinator Mrs Libby Hitchings Advanced Courses Coordinator Biology Building Room 104 Phone: +64 9 373 7599 Ext 88703 [email protected]

Undergraduate enrolment - where to from here? Enquire Visit www.auckland.ac.nz or contact our student advisers for any information you need. Phone: 0800 61 62 63 | Email: [email protected] Student Information Centre: Room 112, ClockTower, 22 Princes St, Auckland

Apply for a place in a programme(s) Do you have internet access, or can you come on to campus to our help labs?

Yes

No

• Log on to www.auckland.ac.nz

Phone: 0800 61 62 63 (or +64 9 923 1969 if overseas)

• Click on Apply Now. • Complete the online Application for a place in your programme(s) of choice. • You will receive an acknowledgement email asking you to provide specific certified documents (and in some cases to complete other requirements*) before your application can be assessed. The letter or email will also tell you how to complete the next steps.

Email: [email protected] The ClockTower Call Centre will forward required information to you.

Offer Your application will be assessed and, if successful, you will receive an “Offer of a place in a programme”. This normally happens from mid January.** You may receive a conditional offer but final approval will be dependent on fulfilment of the conditions of admission to the University and the programme.

Accept Accept or decline your offer of a place in a programme online. Remember – you still need to enrol in your courses!

Enrol in your choice of courses Enrol in courses via Student Services Online using your login and password. This system can be accessed from www.auckland.ac.nz For help with choosing courses you can: • talk to staff for advice and listen to talks on various programmes at Course Advice Day in late January/February 2011 • refer to www.science.auckland.ac.nz or to publications relating to your programme, or to The University of Auckland Calendar. For programme publications call 0800 61 62 63. The Calendar is for sale in bookshops or can be accessed from www.auckland.ac.nz Click on “Current Students” then “University Calendar” in the Quick Links box • go online to check the timetable for your chosen courses • for more information visit the Faculty of Science Student Centre, Ground Floor, Building 301, 23 Symonds Street • or call 0800 61 62 63.

Pay your tuition fees.

*For some programmes, you may be required to submit supplementary information (eg, a portfolio of work, referee reports, an online form) or to attend an interview/audition. If you have not already done this, any outstanding requirements will be explained in the acknowledgement letter – ensure that you follow them up as quickly as possible. **You can also check the status of your application online using your login and password (if you don’t know these, check the instructions on your acknowledgement letter). If you are not offered a place in the programme(s) of your choice, you will receive a letter outlining alternative options. Please follow the advice on the letter or get in touch with the ClockTower Call Centre. Your final offer of a place is dependent both on you gaining admission to the University (which for school leavers may be dependent on your final school results) and assessment by the faculty offering the programme.

You are now a University of Auckland student. Congratulations!

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Preparing for degree level study The University of Auckland Tertiary Foundation Certificate Biology BIOSCI 91F, 92F The Foundation Programme comprises English and Maths plus two other subjects, from a choice of courses, including two offered in Biology (one per semester). The courses are full time and are designed as preliminary courses to Stage one for students with inadequate educational backgrounds. The CUAP approved Tertiary Foundation Certificate is recognised by institutions throughout New Zealand. The Semester One Biology course BIOSCI 91F provides an introduction to unity in biological sciences. The structures and processes common to all living things at the cellular and molecular levels are introduced in the first half of the course. Genetic principles and processes and an overview of evolutionary concepts are explored in the second half. Laboratory classes complement and reinforce lecture material and several are computer-based utilising multi-media learning tools. In Semester Two concepts introduced in BIOSCI 91F are further developed with an emphasis on the diversity of living things (including bacteria, plants, fungi and animals). Fundamentals of classification and ecology are introduced and the study of a current topic in biology is used to develop research and critical thinking skills. Practical classes are both laboratory and fieldbased. Assessment includes in-course assignments, tests and practical evaluations, together with one final two hour examination per course. Students gaining high grades are well prepared to

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continue in any of the Stage I Biology courses, especially BIOSCI 101. Successful students are also qualified for entry to polytechnics, for courses such as nursing, food technology or laboratory technician training or for entry into teacher training. For further information on the Tertiary Foundation Certificate please contact Gill Stringer (Secretary) Room 403, Level 4, Arts 1 Building 18 Symonds Street Phone: +64 9 373 7599 ext 84145 Fax: +64 9 373 7429 [email protected]

Tuäkana Programme The Tuäkana Programme provides peer tutorial assistance for Mäori and Pacific Island students taking first year Biology courses. The programme is supported by the School of Biological Sciences and cooperates with similar programmes in Science departments and in the Faculty of Medicine and Health Sciences. Students are contacted early in the academic year to arrange meeting times. The Programme is based in Room 111 at the Student Resource Centre. Biology Programme Coordinator: Professor Michael Walker Email: [email protected]

Planning a programme in Biological Sciences The Bachelor of Science (BSc) programme offers the opportunity for many subject majors in scientific areas, including Biological Sciences. The BSc programme can be completed in a minimum of 6 semesters. All Stage I courses and almost all other courses for BSc have a value of 15 points. A BSc degree requires 360 points of which: • at least 180 points are above Stage 1. • at least 75 points at Stage III including 60 points in a first major or 45 points in a second major, • 30 points of General Education. Not more than 30 points from outside the Science schedule.

A typical workload will involve 4 courses per semester, an average of 8 courses (120 points) per year.

BSc(Hons) This programme requires students to have completed the requirements for the Degree of BSc including at least a B average in 90 points at Stage III, with at least 60 points in Biological Sciences. With the permission of the Director 15 points at Stage III in related courses may be substituted. To complete BSc(Hons) students must pass courses with a total value of 120 points including a 45 point dissertation.

BSc (Biological Sciences) To major in Biological Sciences, students will require: • BIOSCI 101 • at least 45 points from BIOSCI 100, 102, 103, 104, 106, and 107 • a minimum of 15 points in at least 2 of the following groups:BIOSCI 201-203 BIOSCI 204, 205, 208 BIOSCI 206, 207, 210 • at least 60 points from BIOSCI 320 - BIOSCI 396 if a first major or 45 points if a second major. See individual course descriptions (listed pages 20 to 32) for details about each course including point value, semester taught, campus, prerequisites, exam/course weightings, and the names of course co-ordinators.

Bachelor of Technology (BTech Biotechnology) A programme of study leading to the degree of Bachelor of Technology in Biotechnology is offered jointly between the School of Biological Sciences and the Department of Chemical and Materials Engineering in the School of Engineering. This programme may be awarded with Honours and requires four years of study in which a defined set of topics within the Faculties of Science and Engineering are covered in the first three years. In the final year students study a set of specialist courses specific to this programme and undertake a project in Biotechnology. Entry to this programme is competitive.

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Selection Criteria for the BTech BioTechnology First year students must meet the required rank score for entry to BTech (Biotechnology). See Faculty of Science prospectus. Students who achieve a GPA of 5(B Average) in their first year will be eligible to be considered for selection into Part II at the end of their first year. Further information relating to this programmme can be obtained from Coordinator: Dr Kerry Loomes, School of Biological Sciences Phone: +64 9 373 7599 Ext 88372 Email: [email protected]

BSc and BSc(Hons) Biomedical Sciences

therapeutics, cellular and molecular biomedicine, microbiology and immunology, cardiovascular biology, genetics and development, neurobiology, nutrition, and reproduction, growth and metabolism, all areas which reflect Auckland’s research strengths in Biomedical Science. Bachelor of Science (Honours) students will complete a fourth research year focused on the field with exposure to a range of advanced methods. Third year students not going on to Honours can complete a PGDipSci followed by MSc. Further information relating to this programme can be obtained from Coordinator: Margaret Goldstone, Associate Dean (Academic Programmes) Faculty of Science, Phone: +64 9 373 7599 Ext 88622, Email: [email protected]

The BSc and BSc(Hons) in Biomedical Science are three and one year degree programmes respectively, for selected very able students.

BSc & BSc(Hons) Bioinformatics The first two years of the BSc provide foundation teaching. First year students will take core courses from the Overlapping Year One, in common with students enrolled in health sciences programmes. These include courses in biological sciences, chemistry and physics. Students wishing to apply for entry into Medicine for 2011 need to include Population Health (POPLHLTH 111) as one of their first year courses. Students are strongly encouraged to include biological sciences, chemistry, physics or statistics as electives. In the second year, Biomedical Science students will complete core courses in disciplines fundamental to biomedical science. These include anatomy, biochemistry, cellular and molecular biology, genetics, microbiology, pathology, pharmacology and physiology. In Year 3, students may specialise in a particular area of biomedical science. The inter-disciplinary options available will include cancer biology and 10 | 2011 School of Biological Sciences Undergraduate Handbook

Bioinformatics involves the development and application of computational methods with the aim of extracting information from biomolecular and genetic data to answer questions in biology, biotechnology and medicine. In Year 1, BSc students will take a selection of courses from Mathematics (MATHS 108 or 150), Statistics (STATS 101, 108 or 125), Biology (BIOSCI 101, 106, 107), Computer Science (COMPSCI 101, 105) and Chemistry (CHEM 110). In Year 2 there is a requirement for specified courses in Biology (BIOSCI 201, 202), Computer Science (COMPSCI 220, 230), Mathematics (MATHS 208 or 250) and Statistics (STATS 210). However, students can now begin to specialise in areas of their choosing by selecting elective courses from Biology, Mathematics, Statistics and Computer Science. In Year 3, all students must take BIOSCI 359 (Bioinformatics) and COMPSCI

369 (Computational Biology). Other courses can be drawn from a list that will allow further specialisation. BSc(Hons) students complete 75 points from BIOSCI 743, 744, 789 and a further 45 points from a list of BIOSCI, COMPSCI, MATHS and STATS courses.

What if I want to continue study? Students who complete this BSc specialisation could go on to study for PGDIpSci and MSc in a range of subject areas, including Biological Sciences, Biosecurity, Geography, Environmental Sciences and Statistics.

For further information please contact: Dr Howard Ross Phone: +64 9 373 7599 Ext 86160 Email: [email protected]

The BSc (ecology) programme includes:

BSc Ecology This programme deals with the scientific study of the interactions between animals, plants and microbes and their environment. There are four strands: Conservation Ecology and Biosecurity; Ecology, Evolution and Behaviour; Marine and Coastal Ecology; Quantitative Ecology and Modelling. These allow students to follow their particular interests while they develop a core understanding of Ecology and the necessary skills for its application.

Core Courses 105 points: BIOSCI 101, 104, 206, 209, ENVSCI 101, 201, STATS 101 OR 108 15 points: BIOSCI 102, 103 15 points: GEOG 101, 102 45 points: BIOSCI 202, 203, 204, 205, 207, 208, 210, GEOG 201, 205, 210, GEOLOGY 202, 205, MARINE 202, STATS 210, 220 and include one of the following options: Conservation Ecology and Biosecurity 45 points: BIOSCI 394, 396, ENVSCI 311 At least 30 points: BIOSCI 320, 321, 330, 333, 395, ENVSCI 301, GEOG 320, 330, STATS 302, 341, 351

Who should take the degree? Potential careers include: - Conservation careers (eg. with Department of Conservation, Regional Councils. - Biosecurity and pest management (eg. with MAF Biosecurity NZ, Councils) - Careers in ecological restoration (in terrestrial and aquatic environments) - Environmental policy and science advisory roles (eg. Ministry for the Environment, NGOs) - Teaching careers in ecology - Environmental education and community liaison (eg. DOC, Councils) - Ecological and environmental research (eg. with research agencies, consultancies)

Ecology, Evolution and Behaviour 45 points: BIOSCI 322, 337, 396 At least 30 points: ANTHRO 349, BIOSCI 320, 330, 335, 347, 394, 395, ENVSCI 301, GEOG 334, GEOLOGY 303, STATS 302, 330, 341, 351 Marine and Coastal Ecology 45 points: BIOSCI 329, 330, 333, MARINE 302 At least 30 points: BIOSCI 322, 328, 330, 335, 337, 347, 394, 395, ENVSCI 301, 310, 311, GEOG 331, 351, GEOLOGY 303, MARINE 302, STATS 302

2011 School of Biological Sciences Undergraduate Handbook | 11

Quantitative Ecology and Modelling 60 points: ENVSCI 310, STATS 302, 330, 341 At least 15 points: GEOG 317, 319, STATS 351, 380

Further information is available from the Science Student Centre. The Student Centre is open Monday to Friday 8.30am-5pm. Faculty of Science Student Centre Ground floor, Building 301 23 Symonds Street Phone: +64 9 373 7599 Ext 87020 Fax: +64 9 373 7431 Email: [email protected] Web: www.science.auckland.ac.nz

Academic programme structure Points structure From 2006, all courses were changed to a different points value. Students enrolled in a normal fulltime course of study now complete 120 points per year. The courses in most undergraduate degrees carry a value of 15 points and a normal fulltime enrolment is eight courses per year. A total of 360 points passed is required to complete the BSc degree

Transition points structure Transition regulations apply to all students who have continued enrolment during the transition period having commenced study in their programme at this university prior to the 2006 academic year. They also apply to students who commence study in an undergraduate degree in the 2006 academic year having commenced but not completed study in a different undergraduate programme at this university between 2001 and 2005. 12 | 2011 School of Biological Sciences Undergraduate Handbook

The Transition regulations were written to ensure that students are able to complete their qualification without disadvantage in terms of duration of study or the proportion of their qualification to be completed. Transition regulations are available in the Transition Regulations Handbook. This handbook is available from the Science Faculty Student Centre, the Short Loans Library and online at www.science.auckland.ac.nz/transitionregulations.

General Education Courses in General Education are a distinctive feature of University of Auckland bachelors degrees. General Education is aimed at producing graduates with flexibility, critical thinking skills, and an appreciation and understanding of fields outside of their usual area of study. The General Education programme consists of high quality, intellectually challenging

courses taught by some of the University’s best teachers and researchers. Students must take two General Education courses (30 points) in their degree. These can be taken at any time during the degree. Students will choose General Education courses from schedules which list courses available to their particular degree. The schedules have been developed so that students will take General Education courses that allow them to explore areas of interest outside of their degree subjects. The General Education schedules are: A) Music, Art and Contemporary Issues B) Humanities and Social Sciences

The requirement for General Education applies to students who enrol at The University of Auckland from 2006 to begin their first undergraduate degree. Students enrolled prior to 2006 are not required to include General Education as part of their degree. Special arrangements will apply to students transferring from another tertiary institution with credit. Students are encouraged to seek advice on General Education in their degree from the Science Student Centre.

Postgraduate programmes From 2006, most Masters programmes became one year degrees preceded by either a one year Bachelors Honours degree or a Postgraduate Diploma.

C) Business and Society D) Life Sciences E) Physical Sciences F) Mathematical and Information Sciences G) Communication H) Languages

Doctoral students Doctoral degrees remain essentially the same in structure and duration. The structure of the PhD is now recorded on the academic transcript in new points in accordance with the 120 points system. For named doctorates which include courses with points, the courses have been re-weighted as part of the 120 point structure.

The courses available to students will depend on the subjects in which they are enrolled. For example, students enrolled in a Biological Sciences course will not be able to take General Education courses from Schedule D Life Sciences. In some cases, courses are available both as part of the General Education programme and as part of the portfolio of regular degree courses. If students are taking a dual purpose course as part of the General Education programme, they will enrol in the G version of the course (e.g. HISTORY 103G). The classes and programme of study will be the same for all students. For available courses and the information required for course selection, see www.auckland. ac.nz/generaleducation. 2011 School of Biological Sciences Undergraduate Handbook | 13

Academic information Academic year 2011 Summer School – 2011 Lectures begin

Thursday 6 January

Deadline to withdraw from summer school courses

1 week before the end of lectures

Lectures end

Friday 11 February

Study break/exams*

Monday 14 February - Wednesday 16 February

Summer School ends

Wednesday 16 February

Semester One – 2011 Semester One begins

Monday 28 February

Mid-semester break/Easter

Friday 11 April - Tuesday 26 April

Graduation

Thursday 28 April - Friday 6 May

Deadline to withdraw from first semester courses

3 weeks before the end of lectures

Lectures end

Saturday 4 June

Study break/exams*

Saturday 4 June - Monday 27 June

Semester One ends

Monday 27 June

Inter-semester break

Tuesday 28 June - Saturday 16 July

Semester Two – 2011 Semester Two begins

Monday 18 July

Mid-semester break

Monday 29 August - Saturday 10 September

Graduation

Tuesday 20 September - Thursday 22 September

Deadline to withdraw from second semester courses

3 weeks before the end of lectures

Lectures end

Saturday 22 October

Study break/exams*

Saturday 22 October - Monday 14 November

Semester Two ends

Monday 14 November

Semester One – 2012 Semester One begins

Monday 27 February 2012

*Aegrotat and Compassionate Applications must be submitted within 1 week of the date that the examination affected took place. The medical certificate must date to the actual day of the examination. Deadline for withdrawal from double semester courses is three weeks before the end of lectures in the second semester. 14 | 2011 School of Biological Sciences Undergraduate Handbook

Field Trip Dates BIOSCI 104

Two one-day weekend field trips: either 19 or 20 March, North Head, and either 30 April or 1 May, Rangitoto

BIOSCI 206

Compulsory field trip: Saturday 19 March, Wenderholm, 9-5.30pm Residential field trip (either marine, behaviour or terrestrial): 15-19 April, 11-14 April, 17-21 April

BIOSCI 207

8 October, Muriwai

BIOSCI 320

2-night field trip: 5pm Friday 11 March - 5pm Sunday 12 March 23 March 2-5pm

BIOSCI 323

Compulsory field trip: 5-7 September (Mon-Wed) inclusive

BIOSCI 328

Compulsory 2-day residential field course at Leigh Laboratory: Trip 1: 12-13 April (Tues-Wed) inclusive Trip 2: 14-15 April (Thurs-Fri) inclusive

BIOSCI 329

Compulsory 3-day field trip in second half of mid Semester break: Stream 1: 5-7 September (Mon-Wed) inclusive Stream 2: 8-10 September (Thurs-Sat) inclusive

BIOSCI 330

Laboratories: Saturday 2 April and Sunday 3 April

BIOSCI 333

Residential field trip 19-20 March

BIOSCI 337

Compulsory field trip in mid semester break: Chronobiology 26 August (leave 4pm) - 28 August inclusive or Behavioural Ecology 29-31 August inclusive or Bird Behaviour 8-11 September inclusive

BIOSCI 394

Field Trips/Lab Wednesdays all day 16 March, 4 May, 25 May

BIOSCI 396

Field trip 1: 4 March (leave 4 pm) - 6 March inclusive Field trip 2: 13 May (leave 4pm) - 15 May inclusive Laboratory 1: Wednesday, 9 March 9.30-12.30 Laboratory 2: Wednesday, 25 May evening

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Course descriptions Stage I courses (1st Year) Seven 15 point courses offered at Stage I provide an introduction to the biological sciences. Students intending to major in Biological Sciences are required to have taken 4 Stage I Biology courses (including BIOSCI 101) in order to have an appropriate foundation in molecular biology, plant and animal biology and ecology. The courses BIOSCI 101/102/103/104 provide the most suitable combination for students interested in whole organism biology, while courses BIOSCI 101, 102 or 103, 106 and 107 offer the best choice for students who prefer the more molecular/genetic aspects of biology. More than four biological courses may be selected thus allowing students to keep the full range of biology open to them. Students wishing to enter into the Biomedical Science programme should take BIOSCI 101, 106, 107 and either BIOSCI 102 or BIOSCI 103 as their elective, plus CHEM 110, PHYSICS 160 and MEDSCI 142. This combination of courses will allow students who do not get selected into the Honours programme to continue with a BSc in Biological Sciences. To be considered for entry into Medicine, students must take POPLHLTH 111 as their elective. It is important to gain further information from sources listed below when planning your degree programme, as entry to second and third year courses is based both on academic merit and successful completion of specified 1st year courses. Check the schedule for prerequisites in the Calendar. All Biological Sciences students are strongly advised to take at least one Stage I Chemistry course. Preferably, students should have taken Biology at least to NCEA Level 2 and have a background in other science subjects. Students enrolling in limited entry courses will be 16 | 2011 School of Biological Sciences Undergraduate Handbook

considered in rank order according to their best 80 credits at NCEA Level 3 or higher (or equivalent) over a maximum of five approved subjects, weighted by the level of achievement attained in each set of credits.

Photo: Libby Hitchings

BIOSCI 100 BIOSCI 100G Antarctica: The Frozen Continent (15 Points) (on-line delivery) Second Semester A general introduction to Antarctica and its environs including the Southern Ocean and the sub-Antarctic islands. Emphasis will be placed on the evolution of Antarctica and how resident plants, animals and microorganisms are adapted to cope with the extreme environment. Specific topics to be addressed include the history of Antarctic exploration and its impact on the development of Antarctic science, Antarctic ecosystems, Antarctica as a wilderness region, and the impact of humans including the exploitation of resources and the effects of pollution. This course is suitable for students with both science and non-science backgrounds. Weekly tutorials will be held Monday and Wednesday 2-3 pm Coordinator: Dr Rochelle Constantine Assessment: Incourse 60% (Test 20%, 2 Essays 25%, On-line Quiz 10%, Literary Research Assignment 5%) Examination 40%

Recommended textbook: D. McGonigal. Antarctica: Secrets of the Southern Continent. Simon & Schuster See also http://www.antarctica.org.nz

processes will be highlighted. Coordinator: Mr David Seldon Assessment: Incourse 60%, (Theory 40%, Practical 20%) Examination 40% Recommended textbook: Campbell Biology, Reece et al. (2011) 9th Edn., (Pearson Benjamin Cummings).

BIOSCI 101 Essential Biology: From Genomes to Organisms (15 Points) (City) First Semester An introduction to the structures and processes which are common to micro-organisms, animals and plants at the cellular, molecular and biochemical levels. Genetic principles and processes and an overview of evolution and evolutionary concepts are included. This course includes guest lectures given by graduate students in research fields relevant to course content. This course assumes a knowledge of NCEA Level 3 Biology and at least NCEA Level 2 Chemistry. BIOSCI 103 Comparative Animal Biology Coordinator: Ms Amanda Harper Assessment: Incourse 60%, (Theory 40%, Practical 20%) Examination 40% Prescribed textbook: Campbell Biology, Reece et al. (2011) 9th Edn., (Pearson Benjamin Cummings).

BIOSCI 102 Plants, Microbes & Society (15 Points) (City) Second Semester A multi-disciplinary approach is taken to studying the relationships between plants, microbes, and humans. The course begins with an introduction to the key characteristics of plants and microbes, and demonstrates how they are used for food and pharmaceuticals. The impact of plants and microbes on human health, as well as their role in a variety of industrial and biotechnological

(15 Points) (City) Second Semester A comparative approach to the study of animals focusing on the processes which underlie and unite all animal life. Emphasis will be placed on evolutionary relationships and history, and on the relationship between form and function and the predictability of animal design. Reference will be made to the New Zealand fauna and to other animals of economic or evolutionary importance where appropriate. The practical component of this course involves animal dissection. This is an essential part of the course. No exemptions are possible. Coordinator: Dr Brendon Dunphy Assessment: Incourse 60% (Theory 40%, Practical 20%), Examination 40% Prescribed textbook: Campbell Biology, Reece et al. (2011) 9th Edn., (Pearson Benjamin Cummings). 2011 School of Biological Sciences Undergraduate Handbook | 17

)BIOSCI 104 BIOSCI 104G New Zealand Ecology and Conservation

entry course. Students are strongly advised to complete BIOSCI 101 and CHEM 110 before enrolling in BIOSCI 106.

(15 Points) (City) First Semester Coordinator: Mrs Libby Hitchings An introduction to the diversity of animals and plants in New Zealand including endemic, native and introduced species; biogeographical and evolutionary relationships; community structure and inter-relationships; behaviour and ecology; Maori perspectives in biology; and current conservation, environmental, social, animal welfare, and economic issues relevant to New Zealand biology.

Assessment: Incourse 60%, (Theory 40%, Practical 20%) Examination 40%

Coordinator: Dr Rochelle Constantine

BIOSCI 107 Biology for Biomedical Science: Cellular Processes & Development

Assessment: Incourse 60% (Theory 40%, Practical 20%), Examination 40% Prescribed textbook: Parsons et al. 2006 Biology Aotearoa, Pearson Education, NZ. Recommended textbook: Campbell Biology, Reece et al. (2011) 9th Edn., (Pearson Benjamin Cummings). Field trip:

Two compulsory Saturday or Sunday field trips. Either 19 or 20 March (North Head) and either 30 April or 1 May (Rangitoto)

BIOSCI 106 Foundations of Biochemistry

(15 Points) (City) Second Semester This course will consider biochemical reactions as essential elements of life processes with reference to the genes that control them. Material covered includes: the molecular structure and action of proteins, the synthesis and metabolism of carbohydrates and fats in the fed and starved states, and elements of enzymology, energetics, metabolism, nutrition and hormonal control in health, physical performance and disease. Reference will be made to specific biomedical examples where appropriate. This is a limited 18 | 2011 School of Biological Sciences Undergraduate Handbook

Recommended textbook: Campbell, M.K., Farrel, S.O. Biochemistry. 6th Edn. Thomson.

(15 Points) (City) First Semester The cellular and tissue level basis of mammalian form and function. Special emphasis on cellular structure and processes including membrane transport, muscle types and function, blood and the immune response, and basic neurobiology. Selected topics in human and experimental embryology will also be covered. Practical component includes labs on cell histology, human embryology and muscle physiology. This is a limited-entry course that assumes knowledge of NCEA Level 3 Biology and at least NCEA Level 2 Chemistry. Coordinator: Dr Mel Collings Assessment: Incourse 60% (Theory 40% Practical 20%) Examination: 40% Prescribed textbook: Tortora, G. and B. Derrickson. Principles of Anatomy and Physiology. 12th Edn. Wiley Recommended textbook: Campbell Biology, Reece et al. (2011) 9th Edn., (Pearson Benjamin Cummings).

Stage II courses (2nd Year) The Stage II offering consists of a selection from ten courses. It is designed to provide a balanced and integrated approach to genetics, ecology, evolution, biochemistry, microbiology, plant and animal studies. Stage II courses provide a basis for further specialised study and are prerequisites for certain Stage III courses. For example, students advancing in either biochemistry or cellular & molecular biology should take both BIOSCI 201 and BIOSCI 203 at Stage II. To advance to Stage III courses, most students will require at least 3 courses from the Stage II selection. Most have limited entry based on the grade point average (GPA) calculated from results attained in previous semesters.

A minimum of one course (15 points) must be taken from at least 2 of the following groups: Group 1: BIOSCI 201 Sem I (City) Cellular & Molecular Biology BIOSCI 202 Sem 2 (City) Genetics BIOSCI 203 Sem 2 (City) Biochemistry Group 2: BIOSCI 206 Sem 1 (City) Principles of Ecology BIOSCI 207 Sem 2 (City) Adaptive Design BIOSCI 210 Sem 2 (City) Evolution and the Origins of Life Group 3: BIOSCI 204 Sem 1 (City) Principles of Microbiology BIOSCI 205 Sem 2 (City) Plant, Cell and Environment BIOSCI 208 Sem 1 (City) Invertebrate Diversity

Biometry (Biological Statistics). All students in Biological Sciences are strongly advised to include BIOSCI 209 BIOMETRY in their undergraduate programme.

BIOSCI 200 Current Topics on the Biology of Humans (15 points)

This is not available in 2011

BIOSCI 201 Cellular and Molecular Biology (15 points) (City) First Semester The basic structures of biomolecules, the structure of cells and their organisation into tissues and organs, and viruses, are examined first. This is followed by a study of the nucleus, DNA, RNA and protein synthesis and the regulation of gene expression. Further sections deal with recombinant DNA technology, cellular development, cancer, and the basis of immunity. Prerequisites: BIOSCI 101, 30 points from (BIOSCI 102-107, MEDSCI 142) and 15 points from CHEM 110, 120, 150 Coordinator: Dr Ken Scott Assessment: Incourse 40% (Theory 25%, Practical 15%), Examination 60% Textbook:

Lodish et al. (2004) Molecular Cell Biology. 6th Edn, Freeman.

Students intending to advance to the postgraduate level in Biological Sciences should note the importance of a sound basis in 2011 School of Biological Sciences Undergraduate Handbook | 19

Practical 25%) Examination 50%

BIOSCI 202 Genetics (15 points) (City) Second Semester

Recommended textbooks: Berg et al., (2002) Biochemistry. 6th Edn. W.H. Freeman

The basic principles of mutation, recombination and genetic mapping are established in this course. These principles are then developed in a variety of prokaryotic and eukaryotic organisms. Laboratory work uses molecular, microbial and eukaryotic material to explore the key features of heredity.

Lodish et al. (2004) Molecular Cell Biology, 6th Edn, Freeman

BIOSCI 204 Principles of Microbiology Prerequisites: 30 points from Stage I Biological Sciences including BIOSCI 101

(15 points) (City) First Semester

Coordinator: Assoc. Prof. Brian Murray Assessment: Incourse 62.5% (Theory 37.5%, Practical 25%), Examination 37.5% Recommended textbooks: Griffiths, Miller, Suzuki et. al. An Introduction to Genetic Analysis. 8th or 9th Edn. WH Freeman Pierce B.A., Genetics: a conceptual approach. 3rd Edn, W.H. Freeman.

This course provides an introduction to the diversity, physiology and functions of microorganisms (prokaryotes, eukaryotes, viruses) as individuals and as communities. The fundamental roles of microorganisms in ecosystems, health and disease are considered alongside methods for their isolation and study. Microbial applications in biotechnology, food production, agriculture and industry are also discussed. Prerequisites: BIOSCI 101 and at least 15 points from BIOSCI 102, 106, 107

BIOSCI 203 Biochemistry

Coordinator: Dr Susan Turner

(15 points) (City) Second Semester

Assessment:

Incourse 50% (Theory 30%, Practical 20%), Examination 50%

Textbook:

Prescott, Harvey & Klein Microbiology, 6th or 7th Edn. (2005) McGraw-Hill.

This course presents core areas of modern biochemistry. Emphasis is on macromolecular structure and function. Areas covered include protein structure, oxygen and carbon dioxide transport in humans and other species, metabolism in mammals, proteases and human disease, cholesterol metabolism and transport and signal transduction.

BIOSCI 205 Plant, Cell and Environment Prerequisites: BIOSCI 101, 106 and 15 points from either CHEM 110 or 120 Coordinator: Assoc. Prof. Tom Brittain Assessment: Incourse 50% {Test 25% 20 | 2011 School of Biological Sciences Undergraduate Handbook

(15 points) (City) Second Semester Unlike animals, plants cannot move to respond to changes in their environment. Plants have evolved

diverse signaling systems and the ability to grow towards their essential resources. This course explores the intricate ways plants function: how they are able to respond to developmental and environmental signals at the whole plant and cellular level.

trip to Wenderholm) Residential field trips (Either Marine 15-19 April, Behaviour 11-14 April or Terrestrial 17-21 April)

Prerequisites: BIOSCI 101 and 15 points from BIOSCI 102, 104, 106, 107

BIOSCI 207 Adaptive Design

Coordinator:

Dr Karine David

(15 points) (City) Second Semester

Assessment:

Incourse 50% (Theory 25%, Practical 25%), Examination 50%

Prescribed Textbook: Taiz, L., and Zeiger, E. Plant Physiology. 4th Edn. Sinauer.

BIOSCI 206 Principles of Ecology (15 points) (City) First Semester Ecology is the study of living organisms (plants, animals and microbes), their relationships with one another and with their environment. This course examines ecosystem processes, factors that affect distribution and interactions of organisms, population ecology, and applications of ecology such as restoration and conservation. The key principles of ecology are taught in a New Zealand context emphasising an experimental approach.

Organisms are found in almost all habitats on earth, from the abyssal depths of the oceans to the tops of mountains. The course covers the principles of evolutionary adaptation to different habitats and their application to behaviour, morphology,physiology and life histories. Comparative examples are drawn from diverse life forms and contexts, including the biology of dinosaurs, how animals navigate, the evolution of ageing, foraging, parental care and communication, costs and benefits of sex and an evolutionary account of human nutritional biology. Prerequisites: BIOSCI 101 and 15 points from BIOSCI 102-104, 106, 107 Course Co-ordinator: Dr Stuart Parsons Assessment: Incourse 60% (Practical 20%, Test 40%) Examination 40% Field Trip:

8 October Muriwai

Prerequisites: BIOSCI 101, 104 and 15 points in either STATS 101 or 108

BIOSCI 208 Invertebrate Diversity

Coordinator: Dr James Russell

(15 points) (City) First Semester

Assessment: Incourse 70% (Practical Assignments 40%, Test 30%), Examination 30% Prescribed textbook: Molles, Ecology 4th Edn. McGraw-Hill Field trips:

19 March (one day compulsory

Invertebrates make up over 95% of animal species. This course explores the biology of invertebrates with an emphasis on structure, function, life histories, behaviour and ecology. Invertebrate diversity is examined in a variety of 2011 School of Biological Sciences Undergraduate Handbook | 21

environments, using New Zealand examples where possible, and provides the basis for advanced courses in conservation and marine ecology.

Biometry: The Principles and Practice of Statistics in Biological Research, 3rd Edition. W.H. Freeman & Co., New York.

Prerequisites: BIOSCI 101 and 103 Coordinator: Dr Mary Sewell Assessment: Incourse 60% (Theory 20%, Practical 40%) Examination 40%

BIOSCI 210 Evolution and the Origins of Life

Recommended text: Anderson, D.T. (2001). Invertebrate Zoology. Oxford University Press.

Part 1 covers basic concepts in evolutionary biology including Darwin and the theory of evolution by natural selection, phylogenetics, population genetics, molecular evolution, speciation and extinction. Part 2 explores the extent to which Darwin’s theory of evolution by natural selection can explain the origins of biological complexity i.e. the evolutionary history and origins of life and topics ranging from life in the primordial soup, through to the history and origins of cells, sex, societies and language.

BIOSCI 209 Biometry (15 points) (City) First Semester Biological patterns and processes are inherently variable. Quantitative description and analysis of biological variability is essential for making progress in all areas of biological research and statistics is central to this endeavour. This course provides an introduction to statistics for biologists. Topics include the description of data, probability distributions, experimental design, model building, regression (including multiple and logistic regression), one and two-way analysis of variance, nested ANOVA, chi-squared goodnessof-fit tests, and multivariate plots. It is strongly recommended that students have taken mathematics to Year 13 level. Prerequisites: 15 points in either STATS 101 or 108 and 30 points from Biological Sciences, Environmental Sciences or Geography. Coordinator: Dr Wayne Stewart (Statistics) Assessment: In course test 15%, Assignments 20% (5% each), Quizzes 5% and Examination 60% Textbook: Sokal, R.R. & Rohlf, F.J. 1995. 22 | 2011 School of Biological Sciences Undergraduate Handbook

(15 points) (City) Second Semester

Prerequisites: BIOSCI 101 and 15 points from BIOSCI 102-104, 106, 107 Coordinator: Dr Mat Goddard Assessment: Incourse 45% (1 Essay @ 15%, 2 Lab reports @ 15% each)) Examination 55% Prescribed textbook: Stearns, S. and Hoekstra, R., Evolution: An Introduction, 2nd edition 2005, Oxford University Press Recommended textbook: Origin and Early Evolution of Life, 2002, T. Fenchel, Oxford Uni Press

Stage III courses (3rd Year) A wide range of specialist courses is offered at Stage III. Most have limited entry based on the grade point average (GPA) calculated from results attained in previous semesters. At least 4 Stage III courses are required to major in Biological Sciences.

BIOSCI 320 Pure and Applied Entomology

BIOSCI 321 Plant Pathology

(15 points) Tämaki (Labs in City) First Semester

(15 points) (City) First Semester

An introduction to the systematics and evolution of insects describing the major lineages and discussing the role insects play in different ecological systems and their behaviour. This course also examines the role of insects as pests (including as vectors of disease) and describes various control measures and how these methods are integrated. Practicals include a 2-night field trip, and insect collection.

Microorganisms are of major importance to horticulture and agriculture. This course examines the biology of plant pathogens, plantmicrobial interactions at the cellular and molecular level, and the epidemiology and control of plant diseases. Practicals will focus on techniques for isolation, culture, identification and study of plant pathogens.

Prerequisites: BIOSCI 103 and 15 points from Stage II Biological Science courses Coordinator: Dr Greg Holwell Assessment: Incourse 70% (Test 30%, Assignments 20%, Insect Collection 20%). Examination 30%. Field trip: Compulsory 2-night field trip 11-12 March. 23 March 2-5pm Recommended textbooks: Gullan, P.J. & Cranston, P.S. The Insects: An Outline of Entomology. 3rd Ed. Chapman and Hall.

Prerequisites: BIOSCI 204 or 205 Coordinator: Assoc. Prof. Mike Pearson Assessment: Incourse 60% (Theory 30%, Practical 30%), Examination: 40% Textbook: Agrios, G.N. Plant Pathology. 5th Edn. AP. If you are interested in crop protection we suggest you take BIOSCI 320 and 321 together.

If you are interested in crop protection we suggest you take BIOSCI 320 and 321 together.

2011 School of Biological Sciences Undergraduate Handbook | 23

BIOSCI 322 Evolution of Genes, Populations and Species (15 points) (City) Second Semester A thorough understanding of evolutionary principles and applications is critical for study in a wide variety of fields, including ecology, physiology, microbiology, development, molecular biology, biomedicine and bioinformatics. This course progresses from the basic Stage II material to explore the most recent theoretical advances in evolutionary thought, and how they can be applied at the DNA, population and species levels. SBS staff present their current research in fields including: •

conservation genetics and biogeography

•

phylogenetics and speciation

•

experimental molecular evolution and the mechanisms of selection

•

sexual selection

•

genome evolution

Practical work includes phylogenetic analyses, computer simulations, and hands-on lab research into the conservation genetics of endangered species using PCR techniques.

plants with a comprehensive survey of the characteristics and distributions of the major plant groups. Coverage will also include classical and phylogenetic approaches to plant identification, and applications of systematics. Practical work will focus on tools for identifying plants, introduction to plant diversity in the lab and field, and development of a herbarium collection. Prerequisite: BIOSCI 102 or 104 and 30 points at Stage II in Biological Sciences, Environmental Science or Geography. Coordinator: Dr Bruce Burns Assessment: Incourse 60% (Incourse Test 20%, Plant ID and test 5%, 2 assignments 15%, 20%) Examination: 40% Prescribed textbook: To Be Advised Field trip:

A compulsory residential field course will be held during the Semester Two mid-Semester break 5-7 September inclusive. Other optional day trips will be announced in class.

Prerequisite: BIOSCI 202 and 210 Coordinator: Dr Shane Lavery Assessment: Incourse 50% (Terms Test 20%, Practical 30%) Examination: 50% Prescribed textbook: D.J. Futuyma, Evolutionary Biology, 3rd Edition or D.J. Futuyma, Evolution (2009) 2nd Edition (Sinauer).

BIOSCI 323 Plant Diversity (15 points) (City) Second Semester An introduction to plant systematics, plant reproductive strategies, and the evolution of 24 | 2011 School of Biological Sciences Undergraduate Handbook

BIOSCI 328 Fisheries and Aquaculture (15 points) (City) First Semester Harvest and capture of aquatic organisms and inter-relationships with aquaculture. Fisheries and aquaculture are treated not as distinct disciplines but in the context of integrating exploitation and sustainable environmental integrity. Case studies include deepsea and coastal fisheries, and shellfish culture. Prerequisites: BIOSCI 207 or 208 Coordinator: Dr Neill Herbert (Leigh Marine Laboratory)

Assessment:

Incourse 50% (Field Course Assignment 30%, Test 20%) Examination 50%

Recommended textbook: Jennings, S, Kaiser MJ, Reynolds JD. Marine Fisheries Ecology Blackwell Science, Carlton, Victoria, Aus. Field trip:

A residential field course at the Leigh Marine Laboratory during the Semester 1 mid Semester break is compulsory and fulfils the practical requirements of the course. The dates are 12-13 April 2011 or 14-15 April inclusive.

BIOSCI 330 Freshwater and Estuarine Ecology (15 points) (City) First Semester The structure, biodiversity and ecology of lakes, streams, wetlands and estuaries and linkages with near-shore marine habitats. Emphasis is placed on the role of science in monitoring and managing these ecosystems. Case studies include impacts of Auckland’s urban sprawl on stream, estuarine and near-shore marine habitats, and local estuaries as nurseries for fish. Prerequisites: BIOSCI 206, or BIOSCI 104 and 15 points from BIOSCI 205, 207, 208 and STATS 101 or 108 Coordinator: Dr Richard Taylor (Leigh Marine Laboratory)

BIOSCI 329 Biology of Fish (15 points) (City) Second Semester A comprehensive coverage of the biology of fishes including their evolution, diversity and organismal biology. Coverage includes habitats of particular interest to New Zealand such as Antarctica, the deep sea, coral and temperate reefs, and New Zealand’s lakes and rivers.

Assessment: Incourse 50% (Field Report 20%, Essay 20%, Lab Report 10%) Examination 50% Field trip/laboratory: 2 and 3 April

BIOSCI 333 Marine Ecology (15 points) (City) First Semester

Prerequisites: BIOSCI 207 or 208 Coordinator: Assoc. Prof. Kendall Clements Assessment: Incourse 50% (Essay 10%, Practical 40%), Examination 50% Field trip:

A compulsory 3 day field trip will be held in the second half of mid-Semester break, either 5-7 or 8-10 September.

Recommended textbook: Helfman, Colette, Facey, Bowen. The Diversity of Fishes. 2nd Edn. Wiley-Blackwell (2009)

Marine ecology includes patterns and processes in the ecology of benthic and pelagic plants and animals, including how environmental factors and physiology influence species distribution and abundance. Lectures cover: measuring biodiversity at population (including molecular), species and ecosystem levels; ecology of phytoplankton and seaweeds including factors that influence their growth and productivity; plant-herbivore interactions and chemical ecology; and interesting case studies related to research at the university. Practical work includes collecting and analysing ecological data with regard to landscape (habitat and community) biodiversity, and a laboratory study of nutrient uptake in seaweeds.

2011 School of Biological Sciences Undergraduate Handbook | 25

Prerequisite:

Coordinator: Associate Professor Mark Costello (Leigh Marine Laboratory) Assessment:

Assessment: In course 45% (15% examination, 30% practical), Examination 55%

Field trip:

Residential at Leigh Marine Laboratory. 19-20 March

Recommended textbook: Kaiser M., et al. (2005) Marine Ecology: Processes, Systems and Impacts. Oxford University Press, Oxford.

BIOSCI 335 Ecological Physiology 15 points) (City) Second Semester This course focuses on the strategies used by animals to cope with physical and biological challenges in the environment. Accordingly, we work at the level of the individual and the interface between physiological, biochemical or molecular approaches on the one hand, and ecology on the other. The adaptive strategies employed by a range of species, with an emphasis on aquatic organisms, in response to physical factors such as temperature, oxygen and food availability are considered. Energetics and nutrition are emphasised. The course aims to meet the needs of students with ecological interests wishing to recognise the experimental approach to solving problems in environmental biology. The practical work is project oriented with some laboratory work. Prerequisites: BIOSCI 207 or 208 Coordinator: Dr Tony Hickey Assessment:

Theory Test 10%) Examination 50%

BIOSCI 206, or 104 and 15 points from BIOSCI 205, or 207 or 208 and STATS 101 or STATS 108

Incourse 50% (Practical 40%,

26 | 2011 School of Biological Sciences Undergraduate Handbook

BIOSCI 337 Animal Behaviour (15 points) (City) Second Semester This course will provide you with an introduction to all major facets of the study of animal behavior with special attention to its evolution and ecological significance. In addition to identifying major patterns and processes of animal behavior, we will discuss observational and experimental techniques used to study behavior and explore major theoretical models directing past and current research in this field. Topics include methods for the observation and quantification of behaviour, natural selection and evolution of behaviour, orientation, circadian rhythms, neural and physiological mechanisms of behavior, communication, aggression, sexual reproduction, parental investment, mating systems, and social behaviour. Knowledge of BIOSCI 206 is recommended. Prerequisites: BIOSCI 207 and (STATS 101 or 108 or BIOSCI 209) Coordinator: Prof. Mike Walker Assessment:

Incourse 65% ( Practical 30%, Theory Test 35%), Examination 35%

Field trip:

One compulsory field trip will be held in mid semester break. 4pm Friday 26 August Wednesday 31 August

Recommended textbook: Krebs, J., Davies, N. (1993). An Introduction to Behavioural Ecology. Third Edition. Blackwell.

MOLMED 201, MEDSCI 202

BIOSCI 340 Plant Cell Biology and Biotechnology

Restriction:

(15 points) (City) Second Semester

Coordinator: Dr Mike Taylor

This course focuses on selected topics in Plant Biotechnology and Plant Molecular Science. The lectures are presented by staff who are actively researching these areas from the University and from the nearby Crown Research Institute - Plant and Food Research. The information presented comes from application of a range of approaches - plant molecular biology, genetics, genomics, phylogenetics, cell biology, chemistry, biochemistry, and physiology. Topics include plant hormones and signalling, structure and biosynthesis of plant cell walls, regulation of flowering time, control of fruit ripening and post harvest quality and engineering of plant colour, health components and resistance to stress. Prerequisites: BIOSCI 201, 202 or 205 Coordinator: Assoc. Prof. Andy Allan Assessment: Incourse 55% (2 Tests 15% each, Practical 25%), Examination 45% Recommended textbook: Taiz, L. and Zeiger, E. Plant Physiology. 4th Edn. Sinauer.

BIOSCI 347 Environmental Microbiology and Biotechnology (15 points) (City) Second Semester The ecology and physiology of microorganisms in natural and engineered environments. Key themes include marine microbiology, the importance of microbial symbioses to life on Earth, and contemporary research methods in microbiology. Processes such as wastewater treatment and the production of bioactives are used to emphasise exploitation of microbial metabolism for environmental biotechnology purposes.

Assessment:

BIOSCI 352 Incourse 50% (Essay 10%, Practicals 25%, Terms Test 15%), Examination 50%

Recommended textbook: Prescott, L.M., Harley, J.P., and Klein, D.A. (2005) Microbiology, 6th Edition. McGraw Hill International edition.

BIOSCI 348 Food and Beverage Microbiology (15 points) (City) Second Semester The use and scientific fundamentals of microorganisms in the production of foods and food additives, nutriceuticals and probiotics. Fermentation-derived food additives and their industrial processes including principles of metabolic engineering. Molecular and applied aspects of the fermentation processes for production of beer and wine including aroma generation and analysis. Microbial food spoilage, pathogens involved, food safety and quality control. Prerequisites: 15 points from BIOSCI 204, MOLMED 201, MEDSCI 202 Restriction:

BIOSCI 352

Coordinator:

Dr Silas Villas-Boas

Assessment:

Incourse 50% (Essay10%, Practicals 25%, Terms Test 15%), Examination 50%

Laboratory:

Two days lab in the first week of mid-semester break.

Prescribed reading: Bibek Ray & Arun Bhunia Fundamental Food Microbiology, 4th Edn, CRC Press (McMillan)

Prerequisites: 15 points from BIOSCI 204, 2011 School of Biological Sciences Undergraduate Handbook | 27

BIOSCI 349 Biomedical Microbiology

Prerequisites: BIOSCI 201 and 203

(15 points) (City) First Semester

Coordinator: Dr Chris Squire.

The major biochemical, physiological and genetic systems involved in the biology of microorganisms affecting human health. Properties of micro-organisms important in pathogenesis and virulence, and examples of infectious diseases. The molecular response of the host cells during infection. The molecular basis for antimicrobial therapy, acquisition of resistance, and vaccination. Use of micro-organisms in medical biotechnology. Prerequisites: BIOSCI 201 and either 204 or MEDSCI 202

Assessment: Incourse 50% (Practical 20% from laboratory reports and Theory, 30% from two tests). Examination 50% Recommended textbooks: 1. C. Branden & J. Tooze. Introduction to Protein Structure. 2nd Edn. Garland. 2. Berg, J.M., Tymoczko, J.L., and Stryer, L., (2007) Biochemistry. 6th Edn. 3. Lehninger, Principles of Biochemistry, 2nd Edn Worth. no that OR Matthews, Van Holde, Ahern, Biochemistry, 3rd Edn.

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Coordinator: Dr John Taylor Assessment: Incourse 50% (Theory 30%, Practical 20%) Examination 50% Reference material will be recommended.

BIOSCI 351 Molecular Genetics (15 points) (City) First Semester

BIOSCI 350 Protein Structure and Function (15 points) (City) First Semester The relationship of molecular structure to protein function will be emphasised. Techniques for the purification, characterisation and production of native and recombinant proteins and threedimensional structure determination will be combined with a description of protein structure. Specific groups of proteins will be selected to illustrate structure/function relationships and protein evolution. This course provides an excellent background for students who wish to take BIOSCI 353, “Cellular Regulation, Hormones and Growth” in Semester 2. For reasons of health and safety, students must enrol in this course in time for the first lab in Week 1 of the semester.

28 | 2011 School of Biological Sciences Undergraduate Handbook

The analysis of genetic material in prokaryotes, viruses and eukaryotes is addressed in this course. The means by which genetic information is transferred and the mechanisms underlying genome diversity will be examined, together with the study of eukaryote genomes at the level of chromosome structure and organization. The molecular mechanisms underpinning mutation and sequence diversity in the human genome will be discussed, with a focus on heritable human disorders and disease modelling. Prerequisites: BIOSCI 201 and 202 Coordinator: Assoc. Prof. Brian Murray Assessment: Incourse 50% (Theory 30% [2 tests @ 15% each], Practical 20%), Examination 50% Recommended textbooks: Introduction to Genetic Analysis. Griffiths AR et al. Freeman & Co. (8th or 9th Edn)

The Evolution of the Genome, Gregory TR (ed.)

BIOSCI 354 Gene Expression and Gene Transfer

Human Molecular Genetics, Strachan T. & Reid, A.P. (2nd or 3rd Edn)

(15 points) (City) Second Semester

Recombinant DNA, Watson J et al. (2nd Edn) at no

e th e not Pleas ok extbo overs the t e n o c t. uately q onten e d a rse c e cou entir

BIOSCI 353 Molecular and Cellular Regulation (15 points) (City) Second Semester The molecular mechanisms which mediate intracellular sorting, targeting and posttranslational modification of biologically active molecules and the networks of intracellular and extracellular signals which regulate cell function form the focus of this course. The roles of growth factors, oncogenes, plasma membrane receptors, nuclear receptors, ion channels and membrane transporters are emphasised. For reasons of health and safety, students enrolling in this course must enrol in time to attend the first lab in Week 1 of Semester. Students who plan to take this course should consider enrolling in BIOSCI 350 (“Protein Structure and Function”) which provides an excellent background. Prerequisites: BIOSCI 201 and 203

This course focuses on the molecular biology of plant and animal cells. It stresses genomes and genomics, gene expression and genetic engineering. Topics include: regulation of eukaryotic gene expression and eukaryotic diversity and complexity (including the transcriptome, enhancers, transcription factors and RNAi silencing); whole genome sequencing and microarray analysis of expression of the genes in a genome; methods of gene transfer in plants, insects and animals with genetic engineering for crop improvement and viral vectors for gene therapy in humans. Prerequisites: BIOSCI 202 and either 201, 203 or 205 Coordinator: Professor Richard Gardner Assessment: Incourse 55% (Theory 30%, Practical 25%) Examination 45% Recommended Textbooks:: Watson et al. Molecular Biology of the Gene. 6th Edn. (Pearson, Benjamin Cummings). Lodish et al., Molecular Cell Biology. 6th Edn. (2004)

BIOSCI 356 Developmental Biology and Cancer (15 points) (City) First Semester

Coordinator: Assoc. Prof. Nigel Birch Assessment: Incourse 50% (Practical 20%, 2 Tests 10% x 2, Essay 10%), Examination 50% Recommended textbook: Lodish et al, Molecular Cell Biology. 6th Edn. (2004)

Molecular, cellular and genetic aspects of normal and perturbed development focusing on a variety of model systems including Caenorhabditis elegans, Drosophila, the zebrafish and the mouse. Molecular events underlying the development of body form, the contribution of stem cells to the different tissues of the body, and abnormalities of development that contribute to cancer.

2011 School of Biological Sciences Undergraduate Handbook | 29

Prerequisites: BIOSCI 201 and 202 Coordinator: Associate Professor Clive Evans Assessment:

Incourse 40% (2 Lab Reports 10%, General Performance 5%, 1 test 25%) Examination 60%

Recommended textbooks: S.F. Gilbert. Developmental Biology. 9th Edn. Sinauer.

Recommended textbooks: E.E. Zieglier & L.J. Filer (eds) Present Knowledge in Nutrition, 7th Edn, ILSI Press Washington DC Further information on journal articles of relevance will be provided during the course.

G. Davis and C. Tickle. Principles of Development. 4th Edn. OUP I.F. Tannock and R.P. Hill. The Basic Science of Oncology. 4th Edn. MacGraw-Hill. R.A. Weinberg. The Biology of Cancer. 1st Edn. Garland t no e tha e not Pleas k o o extb s the one t cover nt. te uately adeq e con s r u o ec entir

BIOSCI 358 Nutritional Science (15 points) (City) Second Semester The scientific basis of nutrition focusing on its biochemistry and physiology linking diet to health and disease. Nutritional aspects of carbohydrates, fats, proteins, vitamins and trace nutrients are covered in an integrated manner as are the clinical aspects of nutritionally related diseases such as obesity, cardiovascular disease, Type II diabetes mellitus and cancer. Reference will be made to a broad range of examples, and a number of specific nutritional topics of current interest will also be included.

BIOSCI 359 Bioinformatics (15 points) (City) Second Semester The methods and especially the applications of informatic and computational approaches to biological problems with specific reference to: internet accessible data base technology, database mining, applications for gene and protein sequence analysis, phylogenetic analyses, three-dimensional protein prediction and structural bioinformatics. Prerequisites: 15 points from Stage II Biological Sciences, and 15 points from Computer Science, and 15 points from Mathematics or Statistics Coordinator: Dr Shaun Lott. Assessment: Incourse 75% (Theory Test 25%, Practical 50%) Examination 25% Recommended textbooks: Mount, David (2004) Bioinformatics. 2nd Edn. Cold Spring Harbour Laboratory. Orengo, C.A., Thornton, J.M., Jones, D.T. (eds) Bioinformatics, Bio Scientific Publishers Ltd (2002)

Prerequisites: BIOSCI 203 Coordinator: Assoc. Prof. Sally Poppitt (Human Nutrition Unit) Assessment: Incourse 50% (Lab Test 10%, Theory Test 20%, Lab Reports 10%, Research Essay 10%) Examination 50%

30 | 2011 School of Biological Sciences Undergraduate Handbook

BIOSCI 394 Conservation Ecology (15 points) (Tämaki) First Semester Conservation of species and ecosystems.

Population ecology, population growth, harvesting, and control, conservation practice, species and ecosystem management. Impacts and control of invasive species. Case studies in the conservation of threatened species. Population viability analysis, international conservation. This course assumes competence in statistics - students are strongly advised to enrol concurrently in BIOSCI 209 if they have not previously passed a first or second year statistics course. BIOSCI 104 is an ideal precursor to this course and ecological knowledge equivalent to its content is assumed. Prerequisite: BIOSCI 104 and 30 points at Stage II in either Biological Sciences or Geography Coordinator: Dr Jacqueline Beggs Assessment: Incourse 60% (Terms test 25%, 3 field trip Assignments=2 @ 15% + 1 @ 20 % = 50%) Examination 25%. Field trips/labs: 16 March, 4 May, 25 May

Recommended textbook: Keast, A. & Miller, S.E. (eds) The Origin and Evolution of Pacific Island Biotas. S.E. Academic Publishing

BIOSCI 396 Terrestrial Ecology (15 points) (Tämaki) First Semester This course surveys the front lines of experimental population and community ecology, focusing on biotic and abiotic factors controlling the distribution and abundance of terrestrial populations of plants and animals. The fundamental ecological processes explored in this course underpin the conservation and management of species and ecosystems. Content: Population dynamics, community composition, exploitation (predation, herbivory, parasitism), competition and facilitation, mutualisms, food web dynamics and contentious issues, such as biological invasions and ecosystem functioning.

BIOSCI 395 Pacific Biogeography & Biodiversity

Prerequisite: BIOSCI 206, or 104 and 15 points from BIOSCI 205, 207 or 208 and STATS 101 or 108

(15 points) (City) Second Semester

Coordinator: Dr Bruce Burns (Tämaki)

The Pacific Ocean with its many remote archipelagoes, represents the grand stage for the study of island biogeography and insular biodiversity. This course will examine those processes across the Pacific. A multi-disciplinary approach involving the study of both plant and animal systematics and biogeography will be a feature of the course. Prerequisite: 30 points at Stage II in either Biological Sciences or Geography Coordinator: Dr Shane Wright Assessment: Incourse 65% (1 Practical Assignment 30%, Theory Test 35%) Examination 35%

Assessment: Incourse 75% (Test 25%, Research Proposal 10%, Research Project 20%, Group exercise 10%) Examination 40% Field trips:

Residential Fieldtrip 1: 4-6th March (Motutapu Island) (Friday evening to Sunday evening) Residential Fieldtrip 2: 13-15th May (Motutapu Island) (Friday evening to Sunday evening)

Laboratories Lab 1: 9:30am-12:30pm, Wed 9th March, Tämaki campus (room to be advised) Lab 2: evening Wed 25th May, Tämaki campus (room to be advised) 2011 School of Biological Sciences Undergraduate Handbook | 31

Recommended textbook: C.R. Townsend, M. Begon & J.L. Harper (2008). Essentials of Ecology. 3rd Edn. Blackwell Publishers.

Further Information Entry to some first year and all advanced undergraduate courses is restricted. Enrolment for BIOSCI 106 and 107 and Stage II and III BIOSCI courses will be on-line using Student Services Online at any time from mid December 2010 to the end of February 2011. Consult the University Calendar or Faculty of Science Student Centre.

For School of Biological Sciences undergraduate information, contact: Student Resource Centre, Level 1, Biology Building, 5 Symonds Street. Phone:

+64 9 373 7599 Ext 87297

Facsimile: +64 9 373 87417 E.mail:

[email protected]

The Student Resource Centre (City Campus) will also provide the names and telephone extension numbers of course co-ordinators who can provide information on specific courses.

Ms Amanda Harper, Director Stage I Teaching Phone: +64 9 373 7599 Ext 87794, Room 101, Biology Building will provide further advice on Stage I courses.

Mrs Libby Hitchings, Senior Tutor, Coordinator Stage II+III Courses Phone: +64 9 373 7599 Ext 88703, Room 104, Biology Building will provide further advice on Stage II and III courses.

32 | 2011 School of Biological Sciences Undergraduate Handbook

Teaching and attendance BIOSCI courses require full attendance at lectures and laboratory classes from day one, week one, to ensure adequate time for preparation and completion of assessments which contribute to final grades. Students who absent themselves (e.g. weeks one and two) from these activities are at risk of failing the course.

Streaming:

Resources in Cecil:

Field trips:

Most Biological Sciences courses now use Cecil as an on-line system to provide supplementary learning resources. The type of material posted on Cecil will vary depending on the course structure and level, as well as individual teaching styles. For example, where a Powerpoint file is used in the lecture, it may be made available afterwards at the lecturer’s discretion, for the purpose of reviewing the material covered. For copyright reasons some material presented in lectures may not be made available digitally.

These range from day trips in some Stage I courses to one week residential trips in advanced courses. See p. 15 for details.

Streaming information for laboratories is posted on course noticeboards in the corridor, Resource Centre, Level 1 Biology Building, prior to the beginning of each semester. You may also find your timetable and your room allocations on Student Services Online “My timetable, grades & course history”.

Residential field trips: For these trips the department has, in the past, arranged food and/or catering on behalf of enrolled students as this option has proved to be the most practical and economical. Where this option is selected, the student will be required to reimburse the department for the costs incurred, likely to be approximately $20 per day.

Laboratories: Performance in laboratory work contributes to the final grade for the relevant course.

Payment is requested two weeks prior to the field trip; cash, cheque and credit card payments are all accepted.

Safety:

Students are welcome to make their own catering arrangements if such an option is practical. If you would prefer to arrange your own food please discuss your plans with the Course Coordinator.

• Students should wear covered footwear during practical classes, and if required, laboratory coats. • No food or drink is allowed in laboratories.

If there are any concerns or queries, please contact the Head of Department.

Tutorials: Tutorials targeting the needs of Maori and Pacific Island students are offered once a week for Stage I students enrolled in BIOSCI 101 - BIOSCI 107. Other tutorials for first and second year courses may be offered during the year.

2011 School of Biological Sciences Undergraduate Handbook | 33

Awards of marks and grades Requirements for Honours

or injury or exceptional circumstances beyond their control. This also applies to tests, but not assignments.

SBS assessment grades 2011

Application forms are available online, or from the relevant campus Student Health and Counselling Services and Examinations Office.

LETTER GRADE

%

The application form must be submitted to the University Health and Counselling Service within one week of the date that the examination affected took place, or if more than one examination has been affected, then within one week of the last of those examinations.

GPA

A+ A A-

90-100 85-89 80-84

9 8 7

B+ B B-

75-79 70-74 65-69

6 5 4

C+ C C-

60-64 55-59 50-54

3 2 1

D+ D D-

45-49 40-44 0-39

Honours GPA: First Class: Second Class (1st Div): Second Class (2nd Div):

Following the decision of Senate on an application for aegrotat or compassionate consideration, a student may apply for reconsideration of that decision no later than four weeks after the student is notified of Senate’s decision. Please refer to The University of Auckland Calendar for the official regulations.

Grade Point Average GPA 7.0-9.0 GPA 5.5-6.9 GPA 4.0-5.4

SBS examination grades This is based on the examination and, in most courses, internal theory tests. All undergraduate courses have a final exam. Practical (lab and/or field):

Applications for aegrotat and compassionate consideration An application may be made for aegrotat or compassionate consideration, by candidates who may have been prevented from being present at an examination, or who consider that their preparation for or performance in an examination has been seriously impaired by temporary illness 34 | 2011 School of Biological Sciences Undergraduate Handbook

This is completely based on exercises, assignments and internally assessed practical examinations, or a combination of these. The weighting of theory to practical marks is given for each course in the course description section of this booklet. NB: To obtain a pass mark in a course it is necessary to pass both practical and theory components.

Assignments: late policy SBS policy is that assignments submitted up to 24 hours after the 4pm deadline on the due date receive an automatic penalty of 20% deduction of marks. After 24 hours, late assignments will NOT be accepted except with a medical or compassionate certificate.

Missed examinations Students who discover that they have missed an examination through their own mistake cannot sit the examination at another time unless it is for a Masters or Bachelors Honours degree. The student must contact the Examinations Office immediately and complete an application for Special Pass Consideration. Please refer to the Examination Regulations in the Calendar.

Scholarships & prizes SBS prizes

Top student in each course

4 Annual prizes

Stage I and Stage II

Frances Briggs Bursary Senior

Stage III Plant Sciences

Frances Briggs Bursary Junior

Stage II Plant Sciences

R. Morrison Cassie Prize

for Biometry

R.E.F. Matthews Prize

for the best student paper on Cellular & Molecular Biology published in the previous year

T.L. Lancaster Memorial Prize

for the best report on indigenous flora and vegetation

Janet Bain McKay Memorial Scholarship

for the outstanding Plant Sciences student intending to advance to MSc

Frances Barkley Scholarship

Stage 1 Mäori & Pacific Island Scholarship

2011 School of Biological Sciences Undergraduate Handbook | 35

Academic honesty, cheating and plagiarism Cheating is viewed as a serious academic offence by The University of Auckland. The University will not tolerate cheating, or assisting others to cheat. Penalties are set by the Discipline Committee of the Senate and may include suspension or expulsion from the University.

What is cheating? Cheating, in the context of University coursework and examinations, is the act of attempting to gain an unfair advantage by violating the principle that lies behind all University work – that of intellectual and scholarly integrity. Work students submit for grading – in coursework and examinations – must ultimately be their own work, reflecting each student’s learning and performance. To cheat is to be intellectually dishonest by passing off as your own, work that has been done by someone else. It is also unjust in that it devalues the grades and qualifications gained legitimately by other students. All staff and students have a responsibility to prevent, discourage and report cheating. Examples of forms of cheating • Copying from another student during a test or examination, whether or not there is collusion between the students involved; • Using the work of other scholars or students when preparing coursework and pretending it is your own by not acknowledging where it came from. This is called plagiarism. Course coordinators, lecturers or tutors are the appropriate people with whom you should discuss how to use and acknowledge the work of others appropriately; • Making up or fabricating data in research assignments, or the writing up of laboratory reports; 36 | 2011 School of Biological Sciences Undergraduate Handbook

• Impersonating someone else in a test or examination, or arranging such impersonation; • Submitting the same, or a substantially similar, assignment that you have done, for assessment in more than one course; • Misrepresenting disability, temporary illness/ injury or exceptional circumstances beyond one’s control, then claiming special conditions; • Using Material obtained from commercial essay or assignment services, including web-based sources.

Group work On the whole, the University requires assessment of the work of individual students. On those rare occasions where the work of a group of students is assessed, group members need to make sure that the workload is shared equally. Course coordinators will determine their own procedures for dealing with cases where the final piece of work reflects unequal participation and effort.

Student support Typically students cheat because they are having difficulty managing workloads, feel that the course content is too difficult or experience difficulties with the language of the course. None of these reasons are justification for cheating. There are many people and services at the University to assist students. Options of people to approach include:

• the course convenor/coordinator, lecturer, tutorial head, lab demonstrator • Head of Department • faculty-level official • Student Learning Centre or Library staff • AUSA or other students’ association representatives • health and counselling services staff. Students should also consult the University’s major academic referencing resource: www.cite.auckland.ac.nz The following website provides further information about the key principles and practices underlying academic honesty, and related resources: www.auckland.ac.nz/honesty

2011 School of Biological Sciences Undergraduate Handbook | 37

Advice and support for students Improve your English language skills All first-year students are required to undertake an assessment that enables us to identify your level of academic English. This free assessment is available via DELNA.

Diagnostic English Language Needs Assessment (DELNA) DELNA is only available to students who have accepted a place and enrolled at The University of Auckland. It cannot be used to exclude you from a particular programme and the results do not appear on your academic record. The screening is a 30 minute compulsory assessment that includes a vocabulary task and a text editing task. It enables us to quickly identify whether or not you need assistance with the demands of academic English. If you do require assistance, you will undertake the second part of the assessment. You should book your screening assessment during Orientation Week or the first week of semester by going online to: www.delna.auckland. ac.nz/booking The diagnosis is only necessary if your screening results suggest you need assistance with academic English language skills. This two-hour assessment includes a listening, reading and writing task. It enables us to recommend appropriate English language enrichment options. If you do need to improve your skills, you will be invited to discuss your needs with the DELNA Language Adviser and guided to sources of 38 | 2011 School of Biological Sciences Undergraduate Handbook

effective English language enrichment within the University. For more information visit www.delna.auckland.ac.nz

English Language Self Access Centre (ELSAC) ELSAC is the place where you can: • Get advice about your particular English language needs for university study • Use a huge variety of English language resources • Come any time for as long as you like, Monday to Friday between 9am and 5pm. Visit the ELSAC space, real and virtual, and chat to Siew, Rebecca or Penny — we’re all experienced English language teachers. ELSAC services are free for as long as you are enrolled at The University of Auckland.

ELSAC Level 1, Kate Edger Information Commons Phone: +64 9 373 7599 ext 82134 Email: [email protected] For more information visit www.elsac.auckland.ac.nz

WAVE student support service The W.A.V.E Department exists to provide a support network, a voice and services to improve the quality of student life at The University of Auckland. W.A.V.E is an acronym to describe the four major areas that the department works in: Student Welfare, Student Advocacy, Student Voice and Student Education. If a student is unhappy about something at the University or needs help sorting out a problem, the dedicated W.A.V.E. team is there to help.

Welfare Hardship Grants

Voice

If a student need help with food, accommodation, travel or medical costs they can apply for an AUSA Hardship Financial Assistance Grant. The Welfare Officer also provides emergency food parcels for students in need.

Voice is another term for student representation. Student representation exists at all levels throughout the University and is coordinated through the W.A.V.E department. This ensures that students are represented at every level possible at the University. A class rep is a student who volunteers at the start of each semester to represent the interests of the students in their courses to the lecturers.

Contact: [email protected]

Parents Space There is a dedicated kitchen and study area for students to use, with or without your children, at AUSA House on 4 Alfred Street. The resources that are available include; port-a-cot, high chair, change table, TV/stereo, computer & printer, children’s toys & books, kitchen facilities, study spaces and lounge chairs.

Contact: [email protected]

Education The Education Vice President’s role is to bring your concerns about education matters to the wider community.

Contact: [email protected]

Contact: [email protected]

Advocacy

Other WAVE Services

The Student Advocacy team has the skills and dedication to ensure that students are treated fairly and with respect while you study at The University of Auckland. The Student Advocates offer prompt, confidential and quality support to any student who has an academic grievance or any other concern about the University services. We also provide general legal advice on issues within the wider community, such as tenancy and employment. Contact: [email protected]

Tämaki Student Association The TSA office is based at the Tämaki Campus and is open from Monday – Friday between 10am-2pm. The services offered include a dedicated Parents Space for students, sports equipment, free lockers, lost property, emergency food parcels, AUSA Hardship Grant applications, class party applications, photocopying and free phone for local calls. Contact: [email protected] 2011 School of Biological Sciences Undergraduate Handbook | 39

Epsom Tai Tokerau Student Association The ETTSA office is located at the Epsom Campus to support students studying there. Students can organise the catering for a class party, loan sport equipment, buy a locker to store books, apply for a hardship grants, and be issued with an access card for the fitness centre and pool, and obtain stickers for MAXX bus discounts from the Office Administrator. Contact: [email protected] Location: Auckland University Students’ Association, 2nd floor Kate Edgar Building. Text or phone: 021 272 7026 or +64 9 309 0789 ext 202. www.ausa.org.nz

SBS Staff/Student Liaison Committee An SBS Staff/Student Committee, comprising undergraduate and postgraduate student representatives and academic staff, provides a forum where issues concerning courses and lectures and general academic developments may be discussed. Meetings are held 4 times per year, in advance of Science Faculty meetings. Student representatives from the School Committee attend the Faculty of Science Liaison Committee, and SBS Library Committee meetings. AUSA runs training sessions and workshops for class representatives throughout the year and publishes a monthly newsletter which is sent to representatives.

Harassment Harassment in the form of unwanted, unacceptable or offensive behaviour, or discrimination on any grounds by staff or fellow students can be dealt with by approaching any member of the Contact Network or the Mediator. The Contact Network is a group of staff and student representatives who will ensure that confidentiality is maintained when approached by students, and any action will only be taken with the agreement of the complainant. www.auckland.ac.nz/mediation

40 | 2011 School of Biological Sciences Undergraduate Handbook

Information Commons

Student Learning Centre

Designed as information hubs, the Information Commons give you computer access and learning support, as well as proving group and individual study areas. You’ll find these facilities at our City, Grafton, Tämaki and Epsom campuses.

The Student Learning Centre facilitates the development of effective academic learning and performance skills for all students enrolled at the University. Qualified tutors of the Centre provide learning instruction, advice and support through workshops, individual consultations, and online resources.

Use one of the Information Commons computers or laptops to access your coursework through Cecil (the University’s e-learning system), send email and browse the internet, and to complete coursework using MS Office, Adobe Master Collection and other software. You can retrieve information from the library databases, e-journals, ebooks and electronic course materials - including recommended readings. You also have access to printers, scanners and photocopiers. Wireless networking technology is available. At the Kate Edger Information Commons on the City Campus you will find computer training rooms, the Student Learning Centre, a Disabilities Resource room, the Library’s Short Loan service and the English Language Self-Access Centre (ELSAC). The IC helpdesks provide walk-in, roaming, email and telephone support with all aspects of student computing resources and services. If you want to develop your IT and information literacy you can attend a training course, use electronic resources on the Library and Information Commons web sites or ask a staff member for help. Information Commons Phone: +64 9 373 7599 ext 82333 Email: [email protected] www.information-commons.auckland.ac.nz

Skills areas covered include: • learning skills, eg, reading, note-taking, learning styles • writing skills, eg, question analysis, planning and structuring, summarizing and paraphrasing, referencing, editing. - thinking Skills, eg, critical thinking, constructing arguments - test and exam skills, eg, multi-choice and short answer questions, exam essays, exam sitting strategies • self-management skills, eg, time/workload management, motivation, academic assertiveness • computer skills, eg, MS Word/Excel/PowerPoint; SPSS; EndNote • mathematics and statistics support for specific credit courses • support for students with English as an Additional Language (EAL), eg, sentence structure, paragraph writing, academic style. The Centre caters for the academic needs of Māori students through its Te Puni Wananga programme, and for the needs of Pacific students through the Fale Pasifika programme. In addition, the SLC has specialist tutors who can provide assessment, instruction, and support for students with specific learning disabilities. It is necessary to register with the SLC to utilise its services; this costs $10 for the calendar year. 2011 School of Biological Sciences Undergraduate Handbook | 41

University Library Te Tumu Herenga General Library

Services

Most science serials are now available electronically. The majority of the science book collection is shelved on Level M where you will also find printed serial collections for biology, marine science, chemistry, computer science, food science, geology, physics, mathematics and statistics. Geography, computer science and psychology serials are shelved with the book collection.

Visit the subject librarians in Science Information Services on level M. Consultation sessions are available during visits made by the Subject Librarian to the Departments.

Tāmaki Library has resources in computer science, physics, psychology and sport and exercise science. Leigh Marine Research Laboratory Library has marine science resources.

Other Library services include Ask a Librarian Service, Enquiry Desk, Information Commons Help Desk, Inter-Campus Library Delivery Service, Interlibrary Loan and Document Delivery and the Short Loan Collection.

Subject librarians Visit the subject librarians in Science Information Services on Level M. Consultation sessions are available during visits made by the Subject Librarian to the Departments.

Courses, tours and training

Borrowing and accessing resources

Tours and hands-on courses will give you the confidence to use the University Library, its Information Commons service and all its resources. If you are a new student, the following courses are recommended:

Your student ID card is your Library card. Use it to access the photocopiers, printers and to borrow items. You also have 24-hour access via the Library website.

• Library and Resources Overview: an introduction to the University Library resources and services. • Database Searching: how to choose and use databases. • Uni IT Essentials: covers University IT facilities, Netaccount and NetID, Cecil, Webmail, wireless and other electronic resources. To book a Library course visit www.library.auckland.ac.nz/booking

42 | 2011 School of Biological Sciences Undergraduate Handbook

General Library 5 Alfred Street, City Campus Phone: +64 9 373 7599 ext 88044 www.library.auckland.ac.nz Subject Librarians Visit the subject librarians in Science Information Services on Level M. Consultation sessions are available during visits made by the Subject Librarian to the Departments. Biological Sciences and Marine Science Subject Librarian John Lavas Level M, General Library Phone: +64 9 3737 599 ext 87247 Email: [email protected]

Careers Careers advice A science degree from The University of Auckland will give you a foundation of knowledge and skills that can lead to a wide range of career opportunities. Our graduates begin their careers in research organisations, local government, central government, universities, commerce and industry, international and community organisations. You may begin your career in a science position, or in a position that is not directly science related but where your science knowledge and skills are of benefit. University Careers Services can assist you with your career planning and job search throughout the course of your studies. Their website - www. auckland.ac.nz/careers - contains a wealth of invaluable career resources. University Careers Services provides assistance to science students through careers information and advice, job search and career research workshops in the Careers Service, plus seminars and a drop-in service at a variety of times and locations in the Science faculty. For job vacancies, career events, information on internships and current graduate career opportunities, as well as information about employer presentations on campus, visit www.auckland.ac.nz/careerhub. University Careers Services is located in The ClockTower, 22 Princes Street, and at Tāmaki Campus. For information about opening hours, please see www.auckland.ac.nz/careers.

2011 School of Biological Sciences Undergraduate Handbook | 43

Research Section Biodiversity, Biosecurity & Conservation

Ecology, Evolution and Behaviour

Dr Jacqueline Beggs – invertebrate ecology, conservation biology, invasive species.

Ever since Darwin, the theory of evolution has been the primary unifying concept in biology. Research within the Ecology, Evolution and Behaviour Section focuses on the interactions among organisms and their environment, and the dynamic nature of these interactions across space and time. It also focuses on the changes that occur at the level of populations of organisms as a consequence of evolutionary process. Our research is integrative and multidisciplinary, involves a wide range of organisms (from microorganisms to whales), environments (terrestrial and marine), levels of biological organisation (molecules to ecosystems) and experimental approaches (both laboratory and field). EEB provides exciting opportunities for career-minded students in both fundamental and applied science.

Dr Bruce Burns - plant ecology, forest dynamics, conservation biology, biodiversity management in urban and rural environments. Professor Mick Clout – conservation biology, vertebrate ecology and behaviour, invasive species. Dr Rochelle Constantine - Affiliate – conservation biology of whales and dolphins, behavioural ecology, population recovery, spatial ecology Dr Anne Gaskett - Affiliate - refer to Ecology, Evolution and Behaviour for research interest. Dr Greg Holwell - Affiliate - refer to Ecology, Evolution and Behaviour for research interest Dr Mike Pearson - Affiliate - refer to Microbiology for research interest. Dr James Russell - island conservation, quantitative ecology, community and population biology, animal ethics and environmental values. Dr Margaret Stanley – terrestrial community ecology: emphasis on invasion ecology (all stages of invasion process + impact) and pest management; indirect effects in multi-trophic systems; pollination and seed dispersal in a community context. Dr Shane Wright – rates of evolution and the influence of productivity/available energy, with comparisons being made between tropical and temperate congeners amongst plants, birds and marine fish.

44 | 2011 School of Biological Sciences Undergraduate Handbook

In PBRF rankings Ecology, Evolution and Behaviour at the University of Auckland has consistently received outstanding FTE-weighted quality scores - among the highest given to a Biological Sciences Subject Area across New Zealand. The section is comprised of 15 researchers with the following interests: Prof. C. Scott Baker (80% appointment with Oregon State University) – molecular ecology and evolution of whales, dolphins and porpoises. Associate Professor Kendall Clements - fish biology; evolution and speciation, ecology, herbivory, digestion, and nutrition in fishes. Dr Rochelle Constantine - Affiliate - refer to Biodiversity, Biosecurity & Conservation for research interest. Dr Brendon Dunphy - Affiliate - Molluscan ecophysiology and aquaculture, fish physiology

Dr Todd Dennis - Spatial and movement ecology; Bayesian models of movement behaviour; geographic information science; ecography; animal welfare; satellite telemetry; homing and migration; chronoecology of birds, mammals, fish and other animals. Dr Anne Gaskett - Ecology and evolution of deceptive and mutualistic plant-animal interactions, such as pollination. Study species include native orchids, mosses and insects. Dr Greg Holwell – Evolutionary and behavioural ecology of sexual reproduction: sexual selection, sexual conflict, genital morphology, sperm competition, sexual cannibalism, reproductive anatomy and physiology. Research focuses on terrestrial invertebrates including praying mantises, flies, beetles, moths, spiders and millipedes. Dr Shane Lavery – (Academic Leader) applications of molecular and genetic techniques to questions in marine ecology and evolution, including molecular taxonomy, phylogenetics, speciation, phylogeography, connectivity, paternity and individual identification. Professor John Montgomery – fish biology and sensory neuroscience; hydrodynamic receptors; electroreception; nocturnal predators; reef fish and larval settlement. Associate Professor Brian Murray – molecular cytogenetics, plant population biology and breeding systems. Associate Professor Richard Newcomb (80% appointment with Plant and Food Research) - olfaction in insects and humans, sensory science, evolutionary genetics, speciation Dr Stuart Parsons – (Research Leader) bioacoustics, behaviour ecology and sensory ecology of birds, bats and insects. Dr Howard Ross – the application of phylogenetic analysis to a wide range of

problems: the evolution of bird song, when considered to comprise gene-like memes; the timing and path of human settlement of the Pacific; using genomic sequences to determine the species identity of specimens; and estimation of adaptive evolution in viral genomes Dr Mary Sewell – reproduction and development of marine invertebrates, Antarctic larval biology, lipid metabolism. Professor Michael Walker – animal behaviour in space and time: emphasis on the processes and events occurring in sensory cells that detect magnetic fields and lunar rhythms and control annual migrations of animals.

Microbiology The research interests of this group are wide ranging, and encompass the study of microbial diversity and evolution, industrial, agricultural, environmental, marine, medical and gut microbiology, virus-host interaction, viral characterisation and evolution, and the adaptation of medically-important microbial pathogens to antibiotics and environmental stress through mutation(s). Current research programmes include: • Environmental microbiology research investigates the key factors influencing biofilm development in natural and industrial settings, using traditional methods and molecular techniques of DNA sequencing, microarray, proteome and metabolome analysis. Microbial ecology of stream biofilms provides a research focus with emphasis on rehabilitation of stream ecosystems. Marine systems are also an area of interest, particularly interactions between microbes and host organisms such as sponges

2011 School of Biological Sciences Undergraduate Handbook | 45

• Molecular genetics studies of protozoan parasites involve bioinformatic, genomics, cellular biology, molecular biology and biochemistry to decipher aspects of gene regulation and virulence. Current studies are focused on gene expression of amitochondriate protists such as Trichomonas vaginalis and Giardia lamblia. Coming studies envisage the understanding of virulence and drug resistance in these and related species.

• Evolution and genetics of microorganisms, including evolutionary bioinformatics, yeast ecology and genetics (especially wine yeasts), and evolutionary genetics of viruses.

• Microbial biodiversity in extreme environments, ranging from the desiccated, sub-zero Dry Valleys of Antarctica to geothermal and hydro-thermal vents. Organisms from these studies can be used to design isolation strategies for genes which code for enzymes that have potential uses for industry.

Associate Professor Gillian Lewis environmental microbiology, water quality, microbial ecology, freshwater ecology and restoration.

• Industrial microbiology explores the metabolic abilities of microbial cells to develop new technologies and novel products for industrial applications. Current studies are focused on pigment production via microbial fermentation to be used as natural colorants in the food and pharmaceutical industries. Investigation of microbial processes in wastewater treatment is another key area and is the focus of a microbial genome sequencing and functional genomics programme. • Medical microbiology studies of pathogenic yeasts and bacteria, including the investigation of metabolic attributes that enable different Candida species to survive and grow within the environment of healthy individuals, unraveling the metabolism of pathogenic bacteria in vivo using metabolomics and systems biology. • Plant pathology, including the characterisation of new viruses from horticultural and native plants, development of diagnostic methods for plant pathogens, studies of the molecular interactions between mycoviruses and their fungal hosts. 46 | 2011 School of Biological Sciences Undergraduate Handbook

Dr Augusto Barbosa - medical microbiology, protozoology, molecular genetics and evolution of protists Dr Mat Goddard - evolutionary genetics, population genetics and adaptive evolution of natural and wild yeast populations.

Associate Professor Mike Pearson - (Academic & Research Leader) plant virology, mycoviruses, virus and fungal molecular diagnostics, diseases of temperate and tropical crops. Dr Mike Taylor - marine microbiology, symbiosis, microbial community ecology, marine biotechnology. Dr Susan Turner - environmental and industrial microbiology, wastewater treatment, functional genomics, molecular microbial ecology. Dr Silas Villas-Boas - Microbial metabolism and metabolomics, industrial microbiology, medical microbiology, metabolic engineering, and systems biology.

Molecular, Cellular & Developmental Biology Research progress in modern Biology requires a wide range of experimental approaches. The section Molecular Cellular and Developmental Biology has staff with excellent research skills in biochemistry, molecular biology, genetics, cellular biology and physiology applied to the study of both individual cells and whole organisms. This broad experimental basis provides students with valuable training both through undergraduate

lectures and graduate research supervision. We offer a wide range of interesting and varied research programmes and opportunities for collaborative ventures/research projects.

Dr Judy O’Brien - Deputy Director, Academic – Interest and responsibility for content and delivery of undergraduate and postgraduate teaching programmes in SBS. Research interest in rotavirus structure.

Associate Professor Nigel Birch - The function of serine proteases and their inhibitors (serine protease inhibitors or serpins) in nerve cell growth and connectivity, cognitive function including learning and memory, neurological disorders and stroke, and immune cell function.

Dr Ken Scott (Academic Leader) - Function of DING proteins in mammalian, plant and microbial cells.

Associate Professor Tom Brittain (Research Leader) - Structure and function of metalloproteins, in particular neuroglobin, a protein that protects neurons from cell death. Associate Professor David Christie - Membrane transport proteins. Our two research themes are ‘Membrane transporters required for the uptake of neurotransmitters and nutrients in the brain’ and ‘Ion-channels and receptors involved in the detection of odorant molecules by insects’. Associate Professor Clive Evans - Functional analysis of antifreeze glycoproteins: How do Antarctic fish survive in freezing water? The anhydrobiotic state: How do organisms survive without water? Associate Professor Don Love - Development and analysis of DNA, RNA and chemicalbased insults on gene expression programming using the zebrafish as a model system; modelling multifactorial human disorders using the zebrafish. Developing improved diagnostic techniques for use in clinical genetics. Dr Craig Millar - Estimation of mutation and evolutionary rates, ancient DNA studies of the extinct New Zealand Moa and DNA barcoding the birds of New Zealand and the Antarctic. Understanding the genetic processes that underlie evolutionary change.

Dr John Taylor – Cell biology of virus infection. Interactions between virus and host, protein trafficking in virus infected cells. Rotavirus and the hepatitis B virus. Development of anti-viral vaccines and immunotherapeutic approaches to treat/ prevent virus infections.

Plant Molecular Science Plants are fundamental to functional ecosystems and to successful agriculture, horticulture and forestry industries. Their importance is highlighted in the Plant Molecular Science section by research into plants ranging from native species, key model plants (ie, moss, Arabidopsis, Medicago) through to commercially significant crops. A range of interesting project opportunities awaits graduate students in the Plant Molecular Science Group. Projects can be focused at the level of whole plants and/or on molecular, genetic, cellular and biochemical interactions. They can be based at the School of Biological Sciences or at Crown Research Institutes such as Plant and Food Research, Scion, and AgResearch. Find out more here about Plant Molecular Science research topics and contacts in the School of Biological Sciences and at Plant & Food Research: http://www.molecular-plants.auckland.ac.nz/ The Plant Molecular Science group is made up of the following research groups:

2011 School of Biological Sciences Undergraduate Handbook | 47

Associate Professor Andy Allan - Plant physiology, genetics and genomics of plant pigments and health compounds; anthocyanin, carotenoids, chlorophylls, colourless flavonoids. Biosynthesis, regulation and influence of the environment. Fruit biology (apple, peach, strawberry, kiwifruit, berries). Allelic diversity found in the germplasm and breeding resources, studied at both the genetic and epigenetic level.

Plant Hormone Signalling Dr Karine David We aim at understanding the signalling pathways of the plant hormone auxin, which is involved in virtually every aspect of plant growth and development. The approaches we use are multidisciplinary and combine genetics, molecular biology, biochemistry and proteomic.

Yeast Molecular Genetics Professor Richard Gardner The major interests of the laboratory are to use the tools of molecular gentics to develop improved yeast strains for fermentation, especially of wine.

Plant Cell Walls Professor Philip Harris (Academic and Research Leader) The structure, biosynthesis, degradation and evolution of plant cell walls are studied using advanced chemical and biochemical techniques. Improving wood quality in young trees is another goal.

The Flowering Lab Associate Professor Jo Putterill Utilises the techniques of molecular biology, 48 | 2011 School of Biological Sciences Undergraduate Handbook

genetics, biochemistry with a focus on the model plants Arabidopsis and Medicago. Our projects are directed at understanding how the decision to flower is taken, particularly in response to major seasonal changes.

Proteomics & Biomedicine Members of the Proteomics and Biomedicine Research Section are involved in biomedical research in the areas of metabolic disease mechanisms and malignant melanoma. The group of Professor Garth Cooper and Dr Kerry Loomes utilizes the tools of proteomics, ultrastructural imaging techniques, and cellular and molecular biology to dissect the mechanisms of metabolic diseases. Members of the laboratory are also interested in using proteomic techniques for targeted discovery of novel bioactive peptides to develop new therapies. Current areas of investigation include the regulation of hormone production from pancreatic tissues, the consequences of Diabetes Mellitus on pancreatic function, the biochemical mechanisms underlying insulin resistance, the complications of diabetes including effects on target organs (e.g. the heart), acute pancreatitis and brain proteomics of various neurological disorders. Members of the laboratory are also interested in metabolic syndromes associated with Diabetes Mellitus, atherosclerosis and cancer. Assoc Prof Rod Dunbar’s laboratory focuses on human immunity, especially immune responses to cancer. One project aims to develop new therapeutic vaccines for use in patients with melanoma. These vaccines are designed to stimulate the patients’ own cytotoxic T lymphocytes to kill melanoma cells. The lab is also using the department’s strengths in proteomic technology to study the molecular mechanisms involved in communication between human immune cells. This work aims to develop new methods for modulating immune responses in humans.

Members: Professor Margaret Brimble Professor Garth Cooper Associate Professor Rod Dunbar - Research Leader Dr Debbie Hay Dr Tony Hickey Dr Kerry Loomes Academic Leader Dr Anthony Phillips Associate Professor Sally Poppitt Dr Rob Young

Structural Biology The Structural Biology group consists of some 40 researchers with a common goal of understanding biology at the molecular level, and using that understanding to develop new approaches to disease or new tools for biotechnology. This research is at the forefront of modern biological research, but also draws strongly on the disciplines of chemistry, biophysics and computational analysis. Much of the research in the Structural Biology group focuses on projects of medical importance, investigating the mechanisms of disease, the discovery and structural characterization of new drug targets, structure based drug design and modelling. The group also works actively in areas such as plant growth and insect control. We have strong collaborative programmes with researchers in the Faculty of Medical and Health Sciences in the development of new anti-cancer drugs and the development of molecules that influence the human immune system. We also have strong external linkages, both within NZ (AgResearch, Plant & Food Research) and outside NZ. Prof. Ted Baker, Assoc. Prof. Peter Metcalf, Dr. Shaun Lott, Dr. Richard Kingston and Dr. Chris Squire lead research centred around the use of X-ray crystallography but also involving many

other approaches for discovering protein structure and function: genomics, gene cloning, protein expression, micro-scale crystallization, bioinformatics and modelling, structure-based drug design, protein engineering, NMR and biophysical analysis. Examples of current projects include: 1) investigation of proteins that enable TB to persist, and use of TB protein structures to help design new anti-TB drugs, 2) discovering mechanisms of infectious disease by studying proteins that attach bacteria to human cells, 3) using protein structure to design new anti-cancer drugs, 4) analysing naturally occurring microcrystals that form protective coats around viruses, 5) analysing the mechanisms by which viruses assemble and discovering how they avoid the human immune system. Electron microscopy is central to research in the Mitra lab, where high resolution cryo-electron microscopy techniques are used to elucidate the structure of membrane proteins, virus particles and macromolecular complexes. Assoc. Professor Alok Mitra’s laboratory focuses on understanding structure/ function relationships of biomedically important membrane proteins and molecular machines. These systems, which are usually refractory to structural analysis by most methods, are ideally suited for high resolution investigation using electron cryo-microscopy, for which a state-of-the art facility in SBS has been established. Current research in the lab applies this approach to: 1) structural insights into integral membrane proteins including cation transporters, proteins involved in bacterial drug efflux systems and a protein that imparts antibiotic resistance, 2) understanding the dynamics of membrane channel formation by studying the membrane-inserted state of colicin, a soluble protein toxin that forms ion channels in the 2011 School of Biological Sciences Undergraduate Handbook | 49

lipid bilayer, 3) structural investigations of the anthrax toxin toxic complex, 4) structure and function of large, dynamic macromolecular complexes that include the diabetes and cardiovascular drug target adiponectin, a natural bacterial microinjection protein nano machine, 5) understanding assembly and interaction of viral scaffolding and capsid proteins, and 6) structural elucidation of designed inhibitors of the drug target human aquaporin 1 water channel. Dr Andrew Dingley’s research group applies high-resolution nuclear magnetic resonance (NMR) spectroscopy to study the structure, dynamics and function of proteins. Research interests include structural characterisation of antimicrobial protein-membrane interactions and the dynamics of cytokine mediated intracellular signalling. Projects aim to advance our basic understanding of diseases and underpin the potential development of new therapeutics. Members: Professor Ted Baker - Research Leader Dr Andrew Dingley Dr Richard Kingston Professor Joerg Kistler Dr Shaun Lott Associate Professor Peter Metcalf Associate Professor Alok Mitra - Academic Leader Dr Chris Squire

Teaching & Learning This group consists of senior tutors whose primary roles are in coordinating undergraduate courses. Our focus is on developing teaching practices which are driven and informed by education research. We aim primarily to raise levels of student achievement and encourage life-long learning. The educational environment of 50 | 2011 School of Biological Sciences Undergraduate Handbook

the 21st Century requires consideration of access, multiple learning styles, and other varied demands. We believe the diverse needs of students and other challenges can be met through innovative teaching and learning strategies involving the tools and technologies of the internet age. Our course design strategies aim to reflect consideration of these issues. The group has already been involved in a number of research and development projects. These have predominantly focussed on working with schools in low socioeconomic areas to address issues such as access to recent biological science developments, communication with primary researchers, and increasing the expectations and achievements of their students in tertiary education. The University’s Learning Management System (LMS) Cecil™ has been integral to the successful implementation of visionary developments in course design in the School of Biological Sciences and secondary schools outreach projects. Members: Mandy Harper - Academic Leader Dr Rochelle Constantine Dr Mel Collings Dr Brendon Dunphy Libby Hitchings Selvan Reddy Dave Seldon

Staff and facilities Academic staff in SBS Special Interests

Contact

Cellular and molecular physiology, structural biology

Level 2, Lippincott Cottage, Ext 88250 Email: [email protected]

Molecular virology, cryoelectron microscopy

Ground Floor, Rm 02, Lippincott Cottage, Ext 88764 Email: [email protected]

Yeast genetics, wine science

Level 3, Thomas Bldg, Rm 318E Ext 87234 Email: [email protected]

Health-related microbiol aspects of water quality

Level 3, Thomas Bldg, Rm 348A Ext 87396 Email: [email protected]

Ted Baker

Structural biology, X-ray crystallography

Level 4, Thomas Bldg, Rm 470 Ext 84415 Email: [email protected]

Mick N. Clout

Animal and plant ecology

Tämaki Campus Ext 85281 Email: [email protected]

Garth J.S. Cooper

Cause of diabetes; biology of regulatory peptides

Level 4, Thomas Bldg, Rm 4004 Email: [email protected]

Philip J. Harris

Plant cell walls

Level 3, Thomas Bldg, Rm 315A Ext 88366 Email: [email protected]

John C. Montgomery

Neurobiology

Level 1, Thomas Bldg, Rm 140 Ext 87208 Email: [email protected]

Michael M. Walker

Magnetic sensitivity in animals

Level 1, Thomas Bldg, Rm 1016 Ext 87054 Email: [email protected]

Director: Professor Joerg Kistler

Deputy Director Academic Dr Judith A. O’Brien

Deputy Director Research Professor Richard C. Gardner

Deputy Director Development Associate Professor Gillian Lewis

Professors

2011 School of Biological Sciences Undergraduate Handbook | 51

Associate Professors

Special Interests

Contact

Andy Allan

Plant genetics and physiology

Biohub Room 130 Ext 86631 Email: [email protected]

Nigel P. Birch

Molecular neuroendocrinology

Level 2, Thomas Bldg, Rm 228M Ext 88239 Email: [email protected]

Thomas Brittain

Structure-function studies of haemproteins

Level 4, Thomas Bldg, Rm 402B Ext 88246 Email: [email protected]

David Christie

Creatine transport and brain function, insect odorant receptors

Level 4, Thomas Bldg, Rm 402C Ext 88009 Email: [email protected]

Kendall D. Clements

Marine biology

Level 1, Thomas Bldg, Rm 136 Ext 87223 Email: [email protected]

Rod Dunbar

Molecular immunology development genomic imprinting

Level 4, Thomas Bldg, Rm 452 Ext 85765 Email: [email protected]

Clive W. Evans

Developmental biology, Cancer, Ecotoxicology

Level 1, Thomas Bldg, Rm 144 Ext 87245 Email: [email protected]

Peter Metcalf

Structural biology and Xray crystallography

Level 4, Thomas Bldg, Rm 465 Ext 84810 [email protected]

Alok Mitra

Structural biology/electron Level 4, Thomas Bldg, Rm 420A crystallography Ext 88162 Email: [email protected]

Brian G. Murray

Cytogentics and plant breeding

Level 1, Thomas Bldg, Rm 138 Ext 88334 Email: [email protected]

Michael N. Pearson

Virus diseases of crops

Level 3, Thomas Bldg, Rm 338B Ext 88371 Email: [email protected]

Joanna J. Putterill

Regulation of flowering time

Level 3, Thomas Bldg, Rm 318A Ext 87233 Email: [email protected]

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Senior Lecturers

Special Interests

Contact

Jacqueline Beggs

Invertebrate ecology

Tämaki Campus Ext 86823 Email: [email protected]

Andrew Dingley

Biomolecular NMR spectroscopy and Structural biology

Chemistry, Rm 729A Ext 86801 Email: [email protected]

Mat Goddard

Experimental ecology and evolution

Level 3, Thomas Bldg, Rm 3006 Ext 89537 Email: [email protected]

Richard Kingston

Structural biology of viruses

Level 4, Thomas Bldg, Rm 472A Ext 84414 Email: [email protected]

Shane Lavery

Molecular marine ecology and evolution

Level 1, Thomas Bldg, Rm 126 Ext 83764 Email: [email protected]

Kerry Loomes

Biochemistry, Biotechnology

Level 4, Thomas Bldg, Rm 4020 Ext 88372 Email: [email protected]

Shaun Lott

Structural biology bioinformatics

Level 4, Thomas Bldg, Rm 424A Ext 87074 Email: [email protected]

Stuart Parsons

Behaviour & ecology of bats

Level 1, Thomas Bldg, Rm 1018 Ext 85322 Email: [email protected]

Howard Ross

Evolution of genetic diversity, bioinformatics

Level 2, Thomas Bldg, Rm 284 Ext 86160 Email: [email protected]

G. Kenneth Scott

Growth related proteolysis in human cells

Level 2, Thomas Bldg, Rm 228F Ext 88240 Email: [email protected]

Mary Sewell

Marine biology/ecology

Level 1, Thomas Bldg, Rm 130 Ext 83758 Email: [email protected]

Chris Squire

Structural biology and drug discovery

Level 4, Thomas Bldg, Rm 402A Ext 88806 Email: [email protected]

John Taylor

Cell biology and molecular virology

Level 4, Thomas Bldg, Rm 401A Ext 82854 Email: [email protected]

Susan Turner

Molecular microbial ecology

Level 3, Thomas Bldg, Rm 334D Ext 82573 Email: [email protected] 2011 School of Biological Sciences Undergraduate Handbook | 53

Senior Lecturers cont.

Special Interests

Contact

Silas Villas-Boas

Industrial and medical microbiology

Level 3, Thomas Bldg, Rm 3010 Ext 83762 Email: [email protected]

Shane D.T. Wright

Terrestrial ecology

Tämaki Campus Ext 87715 Email: [email protected]

Augusto Barbosa

Medical microbiology, protozoology

Level 3, Thomas Bldg, Rm 348B Ext 85087 Email: [email protected]

Bruce Burns

Plant ecology and restoration ecology

Tämaki Campus Ext 83135 Email: [email protected]

Karine David

Plant development, hormone signalling

Level 3, Thomas Bldg, Rm 313 Ext 83793 Email: [email protected]

Todd Dennis

Spatial and movement ecology

Level 1, Biohub, Rm 126 Ext 87288 Email: [email protected]

Debbie Hay

Molecular Pharmacology

Level 3, Thomas Bldg, Rm 338B Ext 88229 Email: [email protected]

Anne Gaskett

Behavioural Ecology

Level 1, Thomas Bldg,, Rm 1020 Ext 89509 Email: [email protected]

Greg Holwell

Evolutionary and behavioural ecology of sexual reproduction

Level 1, Thomas Bldg, Rm 139 Ext 83652 Email: [email protected]

James Russell

Island conservation, quantitative ecology

Tämaki Campus Ext 86833 Email: [email protected]

Margaret Stanley

Biosecurity & invasion biology/community ecology

Tämaki Campus Ext 86819 Email: [email protected]

Lecturers

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Special Interest

Contact

Evolutionary biology

Level 1, Biology Bldg, Rm 101 Ext 87794 Email: [email protected]

Mel Collings

Cellular and Molecular Biology

Level 1, Biology Bldg, Rm 111D Ext 89066 Email: [email protected]

Rochelle Constantine

Behavioural ecology

Level 1, Biology Bldg, Rm 103 Ext 85093 Email: r.constantine

Brendon Dunphy

Marine invertebrate biology

Level 1, Biology Bldg, Rm 111C Ext 84929 Email: [email protected]

Elizabeth Hitchings

Biochemistry

Level 1, Biology Bldg, Rm 104 Ext 88703 Email: [email protected]

Dave Seldon

Entomology/Forest Ecology

Level 1, Biology Bldg, Rm 111B Ext 87583 Email: [email protected]

Infectious disease immunology

Level 1, Biology Bldg, Rm 105 Ext 83798 Email: [email protected]

Director Stage I Teaching Amanda A. Harper

Senior Tutors Stage I

Senior Tutor Stage II Mr Selvan Reddy

2011 School of Biological Sciences Undergraduate Handbook | 55

Facilities Buildings and Facilities

SBS Student Resource Centre

City Campus

The SBS Student Resource Centre (SRC) is located on Level 1 of the Biology Building. Opening Hours: 9am-4pm Phone: +64 9 373 7599 ext 87297 Email: [email protected] Website: Student Resource Centre link at www. sbs.auckland.ac.nz.

The School of Biological Sciences is located in three buildings:- the Thomas and Biology Buildings which are joined by a covered walkway over the main drive at Gate 3A Symonds Street, and the Lippincott Cottage housing the School’s administration. Thomas Building, 3 Symonds Street: Research laboratories, Staff offices, Undergraduate teaching laboratory. Biology Building, 5 Symonds Street: Undergraduate teaching laboratories, tutorial rooms, lecture theatres, and computer laboratory. Student Resource Centre.

For further information please contact Tessa Holloway, SRC Manager [email protected] Ext 87297

The SRC provides a wide range of services for all Undergraduate students including:

Lippincott Cottage: Adjacent to the Thomas Building on the main drive at 3 Symonds Street, the administration building houses the offices of the Director and Deputy Director (Academic) as well as the Registrar of the School of Biological Sciences and associated administrative staff. Tämaki Campus The School of Biological Sciences teaches three Stage 3 courses at the Tämaki Campus, located at the corner of Morrin and Merton Roads, Glen Innes. Full teaching facilities including laboratories are available on site. For further information students may contact the SBS Student Resource Centre (City Campus) or staff of the Division of Science and Technology (Tämaki Campus). Bessie D’Sa Ext 86825

Enquiry Desk The SRC staff will be happy to help you with all enquiries, provide general advice and be able to refer you to the relevant course coordinator if you have specific academic questions. A telephone and PC are available at the SRC desk for use by all students – giving access to the internal phone network and all online resources.

Loans, Desk Copy material The SRC carries a wide range of material which can be borrowed for photocopying (1 hour limit) by leaving photo id with the SRC. Materials available include: • Reading material/articles recommended by course coordinators • Past exams/Mid Semester Test papers • Course handouts (often free of charge) • Videos/DVDs • Limited selection of textbooks

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Assignment Hand In Your course manual/coordinator will advise you on the submission deadlines associated with each assignment/lab. If directed to the SRC- please complete and attach an Assignment Sheet (provided) and submit using the Assignment Boxes just to the right of the SRC desk (all boxes will be clearly labelled to avoid confusion!). Boxes are emptied promptly in line with the deadlines specified by your course coordinator. See page 36 for late policy for assignments

Assignment/Lab/Test collection facility Many marked assignments, labs and tests are available for collection from the SRC (on presentation of your Student ID card). Details of assignments/labs available for collection will be shown on the white board near the SRC desk.

SRC Area A number of facilities are available in the SRC area – to support all undergraduates. These include: • a wall mounted electronic noticeboard and class noticeboards displaying class details, lab streams and test results for each course plus general notices detailing BSA plans and Bioscience news/events • intranet access and telephone (university extensions) • a comfortable common area to meet up with friends/discuss courses (with a large group study table) • photocopying and binding facilities • paper & can recycling facilities

Technical Ancillary Services Audio Visual Unit Photographic, graphics and design services, student darkrooms.

Workshop Electrical, precision machine engineering and woodworking.

Field Stations The Leigh Marine Laboratory is located at the Goat Island Marine Reserve, Leigh, on the east coast 95km north of the University. The laboratory offers good diving facilities, access to a 14m research vessel the “Hawere”, on site accommodation, teaching and research laboratories and a library. The Leigh Laboratory is widely used by marine, ecology and biology students and by staff. The School of Biological Sciences also has use of residential facilities on Tiritiri Matangi Island. Some field courses are held there during the year and much postgraduate research in behavioural ecology is carried out on the island.

The McGregor Museum/Seminar Rooms The McGregor Museum, housed in the Biology Building since the 1930s, contains a significant and valuable collection of specimens and skeletons including many rare and extinct species. It is especially notable for its collection of primates, Australian mammals, birds, reptiles and amphibians. Although the emphasis is on vertebrates and their adaptive trends, there are also exhibits of many of the invertebrate groups. The museum collections are displayed in the McGregor Seminar Rooms 1, 2 and 3.

2011 School of Biological Sciences Undergraduate Handbook | 57

Research and teaching facilities Animal sciences: Special facilities include a seawater aquarium; freshwater aquarium; culture and maintenance rooms for mammals, amphibia and insects; environmental chambers with controlled light and temperature; and reversed light cycle rooms for behaviour studies. Research equipment is distributed in physiological laboratories (neurophysiology, ion and water regulatory physiology, cardiac, respiratory and exercise physiology), an insect reference collection room, an electron microscopy laboratory with two microscopes, an evolutionary genetics laboratory, and a histology laboratory. An extensive range of field equipment such as boats, nets, and dredges, vehicles and environmental monitoring instruments is available. Plant sciences: Plant growth facilities include glasshouses, garden space, controlled environment cabinets, and a tissue culture room. The University Herbarium is now sited at the Auckland Museum. Postgraduate students may have access to this collection through Mr Ewen Cameron, Curator of Botany.

Computers: General computer laboratories are available with Macintosh and IBM compatible computers which are linked together on a local area network. More advanced computing including molecular modelling and protein and nucleic and sequence analysis is carried out on a Silicon Graphics system which is available within the School. Computer supported learning: SBS utilises computer supported learning at an undergraduate level. Students are able to use a

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flexible learning environment using Cecil software as the platform. Cecil was designed by the School of Business and Economics and uses latest technologies to enhance teaching programs. Each course has on-line access to resources and self-assessed learning activities with feedback, allowing a student centred approach to pace, place, style and stage of learning. Supplementary lecture material in digital format is provided after the lecture rather than beforehand because educational research indicates that learning outcomes are enhanced when information is integrated from a variety of sources. It is recommended that you read about the topic beforehand (in your course guide and textbook), attend each lecture and then add to your notes using the on-line resources where available. In this way, you will learn much more effectively than you would if you simply printed out a set of prepared notes. Course administration using the same software gives students access to their incourse marks, self-streaming for laboratories, discussion forums and information through a semester calendar. All this is available through the Internet by logging onto the Cecil website either in SBS or at home. SBS has an undergraduate computer laboratory (Basement, Biology Building) which has helpdesk assistance available during semester teaching periods.

Student support services Service

Location

Phone

Accommodation and Conference Services

O’Rorke Hall, 16 Mount Street

Careers Centre

Room 001, The ClockTower

Early Childcare Services Chaplain’s Office

28 Park Avenue, Grafton 18 Princes Street

Disability Services

Room 036, The ClockTower (south wing)

+64 9 373 7599 [email protected] www.auckland.ac.nz/accommodation +64 9 373 7599 ext 88727 [email protected] www.auckland.ac.nz/careers +64 9 373 7599 ext 85894 +64 9 373 7599 ext 87732 [email protected] +64 9 373 7599 ext 82936 [email protected] +64 9 373 7599 ext 88905 [email protected] www.auckland.ac.nz/mediation +64 9 373 7599 ext 84923 www.eo.auckland.ac.nz +64 9 373 7599 ext 84422 +64 9 373 7599 ext 87681

Mediator’s Office

Equity Office

Level 1, The ClockTower (East Wing)

Student Finance Health Services (including counselling) Dental Services International Students’ Information Centre

Room 108, The ClockTower Level 3, Student Commons Level 3, Student Commons Auckland International Old Choral Hall

Recreation Centre

Building 314, 17 Symonds Street

Scholarships Office

Room 012, The ClockTower

Student Advocacy Network

AUSA House 3 Alfred Street

Student Information Centre

Room 112, The ClockTower

Student Learning Centre

Level 3 Information Commons

Student loans and allowances SciSpace

StudyLink G16, Ground Floor, Building 303

Students' Association

AUSA, 4 Alfred Street

University Book Shop (UBS)

Kate Edger Building

+64 9 373 7599 ext 83860 +64 9 373 7513 [email protected] www.auckland.ac.nz/international +64 9 373 7599 ext 84788 www.auckland.ac.nz/recreation +64 9 373 7599 ext 87494 [email protected] www.auckland.ac.nz/scholarships +64 9 309 0789 ext [email protected] www.auckland.ac.nz/wave 0800 61 62 63 +64 9 373 7599 ext 88199 [email protected] +64 9 373 7599 ext 88850 [email protected] www.slc.auckland.ac.nz 0800 88 99 00 www.studylink.govt.nz +64 9 373 7599 ext 85510 www.science.auckland.ac.nz/scispace +64 9 309 0789 [email protected] www.ausa.auckland.ac.nz +64 9 306 2700 www.ubsbooks.co.nz

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Notes

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