Postgraduate courses

(15 points) (City) Semester One

An overview of the methods and applications of bioinformatics with specifi c reference to: Internet-accessible database technology, database mining, applications for gene and protein sequence analysis, phylogenetic analyses, three-dimensional protein prediction methods, and genome sequence analysis. The course involves basic programming using the Perl scripting language.

Prerequisite: 30 points from Stage II in Biological Sciences
Restriction: BIOSCI 359, BIOSCI 742
Assessment: 30% Examination, 70% Coursework
Format: Assignments 5 x 10% (50%), Project (20%)
Coordinator: Associate Professor Nicole Cloonan
Phone: +64 9 373 7599 ext 83441
Email: n.cloonan@auckland.ac.nz

(15 points) (City) Semester One

Much knowledge of biological systems is acquired by making comparisons with known systems. Several computational methods, including Markov models, HMMs and dynamic programming can be used in making these comparisons. Technical aspects of these methods and their application to biological problems will be discussed.

Prerequisite: BIOINF 701 or equivalent
Assessment: 40% Examination, 60% Coursework
Format: Assignments 5 x 10% (50%), In-course test (10%)
Coordinator: Dr Simone Linz, Department of Computer Science
Phone: +64 9 373 7599 ext 81983
Email: s.linz@auckland.ac.nz

(15 points) (City) Semester Two

Advances in genetic sequencing technologies are rapidly changing our ability to determine the genome sequence and to explore the gene expression profiles of organisms. Relevant computational methods, including graph theory, string comparison and pattern matching will be discussed, along with their application to genome assembly, metagenomics, gene-gene interaction and systems biology.

Prerequisite: BIOINF 701 or equivalent
Assessment: 40% Examination, 60% Coursework
Format: Assignments 6 x 10% (60%)
Coordinator: Professor Ant Poole
Phone: +64 9 373 7599 ext 86160
Email: a.poole@auckland.ac.nz
 

(15 points) (City) Semester Two

IBIOINF 704 provides (1) a detailed description of the statistical techniques required to analyse modern human genetic data (80%) and (2) an introduction to the analysis of gene-expression data (20%). The methods used to locate genomic regions involved in genetic diseases through the analysis of pedigree data are introduced. Central concepts in population genetics are also presented and a thorough description of genome-wide association studies (GWAS) is given. The limitations and ethical implications of GWAS are also discussed. The second part of the course focuses on the statistical analysis of microarray data and the methods that are used to make sense of the expression levels of thousands of genes measured in various experimental conditions.

BIOINF 704 is mainly aimed at statisticians, medical school students, computer scientists and biologists with a desire to understand the challenges brought by the deluge of genetic data available nowadays. It will provide them with the statistical techniques required to make sense of this type of information.

Restriction: BIOSCI 744 and STATS 771
Assessment: 40% Examination 60% Coursework
Format: Assignments 4 x 15% (60%)
Coordinator: Dr Simone Linz, Department of Computer Science
Phone: +64 9 373 7599 ext 81983
Email: s.linz@auckland.ac.nz

(15 points) (City) Semester One

Current topics in marine ecology at the population, community, and ecosystem level. One focus is on ecology and evolution in a life-history context, including topics on fertilisation, larval development and population connectivity. At the community/ecosystem level we also consider the role of macroalgae, keystone species, the influence of climate change, terrestrial/marine comparisons and marine biosecurity. A sound understanding of BIOSCI 333 or equivalent is assumed.

Assessment: 40% Examination, 60% Coursework
Format: 2 Short Essay/Assignments 30%, 10 Seminar Synopses 30%
Class Limit: 24
Coordinator: Dr Richard Taylor
Phone: +64 9 373 7599 ext 83607
Email: rb.taylor@auckland.ac.nz

(15 points) (City) Semester One

Physiological and biochemical processes enable animals to occupy diverse habitats. Highly variable and extreme environments provide an opportunity to study the functional attributes of animals, particularly ectotherms, with respect to their metabolic, respiratory, and nutritional adaptations. A sound understanding of physiological and biochemical principles is required for this seminar series. A knowledge of BIOSCI 335 or equivalent is assumed.

Assessment: 50% Examination, 50% Coursework
Format: 2 assignments 15% each, Seminar 5%, Synopsis 15%
Class Limit: 24
Coordinator: Associate Professor Tony Hickey
Phone: +64 9 373 7599 ext 82615
Email: a.hickey@auckland.ac.nz

(15 Points) (City) Semester Two

Current assessment of the national and global status of aquaculture, including consideration of future potential and prospects. Examples of invertebrate and fish aquaculture, and a review of general environmental and biological problems and the role of scientific knowledge in aquaculture management. Coverage of factors include analysis of significant New Zealand aquaculture industries, the role of hatchery technology, stock improvement via genetic programmes and issues surrounding the productivity, quality and welfare of fish. A sound understanding of BIOSCI 328 or equivalent is assumed.

Assessment: 40% Examination, 60% Coursework
Format: 2 short reports 40% each, Seminars 20%
Class Limit: 24
Coordinator: Professor Andrew Jeffs (School of Biological Sciences and Institute of Marine Science)
Phone: +64 9 373 7599 ext 87638
Email: a.jeffs@auckland.ac.nz

(15 points) (City) Semester Two

A contemporary approach to central issues in evolutionary biology. Topics covered include natural selection, speciation, macroevolution, sexual conflict and kin selection. A sound understanding of general evolutionary concepts (eg BIOSCI 322 or equivalent) is assumed.

Assessment: 70% Examination, 30% Coursework
Format: 2x essays 15%
Coordinator: Professor Kendall Clements
Phone: +64 9 373 7599 ext 87223
Email: k.clements@auckland.ac.nz

(15 points) (City) Semester Two

More than half of all described species are insects, and there are many times more species awaiting discovery and description. Insects at every trophic level above plants dominate terrestrial and freshwater food chains. This course will examine the evolution of insects, the importance of their role in terrestrial ecosystems, and the problems posed by insects as biosecurity invaders in non-native environments.

This course assumes a prior knowledge of entomology at Stage 3. Students are strongly recommended to have completed BIOSCI 320.

Assessment: 100% Coursework
Format: 15% Seminar, 20% Seminar, 40% Review, 15% Poster, 10% Review Outline
Coordinator: Associate Professor Jacqueline Beggs
Phone: +64 9 373 7599 ext 86823
Email: j.beggs@auckland.ac.nz

(15 points) (City) Semester Two

This course examines the patterns of ecology and evolution at landscape scale, and the processes that infl uence these patterns. Topics covered include species diversity, species abundance, ecology and evolution in the community and speciation. A sound understanding of BIOSCI 395 or equivalent is assumed.

Assessment: 70% Examination, 30% Coursework
Format: Essay 20%, Seminar 10%
Class Limit: 24
Coordinator: Dr Shane Wright
Phone: +64 9 373 7599 ext 87294
Email: sd.wright@auckland.ac.nz

(15 points) (City) Semester Two

A powerful and increasingly important way to address many ecological and evolutionary questions is by using the information stored in the molecular archive. This course provides a broad theoretical and practical basis for undertaking such studies in fi elds ranging from conservation genetics and connectivity, to phylogenetics and molecular evolution. Topics may include the neutral theory of molecular evolution, inbreeding depression, gene fl ow and population structure, coalescent analyses, molecular identifi cation of species, phylogenetic analysis, selection at the molecular level, and the estimation of kinship. A sound understanding of BIOSCI 322 or equivalent is assumed. Three labs may be held on consecutive Mondays after mid semester break.

Assessment: 40% Examination, 60% Coursework
Format: Project 20%, Essay 20% & Seminar 20%
Class limit: 24
Coordinator: Dr Shane Lavery
Phone: +64 9 373 7599 ext 83764
Email: s.lavery@auckland.ac.nz

(15 points) (City) Semester Two

Plants form the autotrophic basis of terrestrial food chains and their distribution, diversity and abundance is a critical determinant of ecosystem functioning. Topics covered include both plant population ecology - including population growth and structure, seed and seedling dynamics, and life history strategies - and community ecology - including vegetation structure, dynamics, and species interactions. Methods to survey, analyze, and model plant populations and communities will also be discussed. A sound understanding of BIOSCI 396 or equivalent is assumed. There will be a 2-3 day field trip with dates TBA.

Assessment: 100% Coursework
Format: Essay 40%, Seminar 20%, Field Trip Report 30%, Participation 10%
Coordinators: Dr Bruce Burns and Professor George Perry
Phone: +64 9 373 7599 ext 83135 or 84599
Email: b.burns@auckland.ac.nz
Email: george.perry@auckland.ac.nz

(15 points) (City) Semester One

Behavioural ecology explores the dynamic interplay between evolution, ecology and behaviour, focusing on proximate and ultimate mechanisms. This course develops professional skills in reading, researching, discussing, presenting, and writing about contemporary topics in behavioural ecology. We focus on critical analyses of concepts, research methods and publication styles, and assignments are tailored to student-directed inquiry. A sound understanding of BIOSCI 337 or equivalent is assumed. You are advised to consult the course co-ordinator regarding your academic preparation for this course.

Assessment: Coursework 100%
Format: Weekly Synopses 30%, Presentation 20%, 1 Literature review 30%, Group Debate 10%, Class Participation 10%
Class limit: 24
Coordinator: Associate Professor Rochelle Constantine
Phone: +64 9 373 7599 ext 85093
Email: r.constantine@auckland.ac.nz

Coordinator: Dr Kristal Cain
Phone: +64 9 373 7599 ext 85815
Email: k.cain@auckland.ac.nz

(15 points) (City) Semester Two

Cross-disciplinary issues involved in the understanding of microbial genome structure, gene regulation and metabolism. Topics may include: the genetic basis of microbial interactions and horizontal gene transfer, genomics-proteomics-metabolomics of microorganisms, the effect of the environment on microbial gene expression, metabolism and evolution and modern approaches used to link gene sequence to biological function and phenotypes. A sound understanding of BIOSCI 348 or equivalent is assumed.

Assessment: 40% Examination, 60% Coursework
Format: 3x Essay/Seminar modules 20% each
Class Limit: 24
Coordinator: Associate Professor Silas Villas-Boas
Phone: +64 9 373 7599 ext 85087
Email: s.villas-boas@auckland.ac.nz

(15 points) (City) Semester One

X-ray crystallography and electron microscopy are two of the principal techniques used by biologists to determine molecular structures. Taken together, their applicability extends over many orders of size – being capable of visualizing individual amino acids as well as the gigantic molecular complexes found within the cell. This course addresses the theory and practice of these two disciplines, and includes a laboratory component, where 3D structures are determined from experimental data. The course is designed to be accessible to students with a variety of backgrounds, including Biology, BioEngineering, Chemistry, Physics, Mathematics and Computer Science.

A sound understanding of BIOSCI 350 or equivalent is assumed. This course complements CHEM 738 and BIOSCI 757.

Assessment: 100% Coursework
Format: 35% Practical assignment, 30% Test, 35% coursework assignment
Coordinator: Associate Professor Alok Mitra
Phone: +64 9 373 7599 ext 88162
Email: a.mitra@auckland.ac.nz

(15 points) (City) Semester One

Advanced biological data analysis, including analysis of variance with nested and random effects, analysis of covariance, cluster analysis, principal components analysis, multidimensional scaling, and randomization methods. There will be a practical component to this course involving the use of the R statistical software.

Prerequisite: 15 points from BIOSCI 209, STATS 201, 207, 208 or equivalent.
Assessment: 40% Examination, 60% Coursework
Format: Six fortnightly assignments at 10% each. Workshop/Tutorial: Must attend 5 out of 6 to pass the course overall.
Coordinator: Dr Kathy Ruggiero
Phone: +64 9 373 7599 ext 89938
Email: k.ruggiero@auckland.ac.nz

(15 points) (City) Semester One

Cross-disciplinary issues in biology will be debated and explored including ethical and commercial issues underpinning science; scientific publishing and advocacy; medical and agricultural biotechnology; animal and environmental ethics, conservation and biodiversity, the history and philosophy of science.

Assessment: 40% Examination 60% Coursework
Format: 3 Essays (20% each)
Class Limit: 24

(15 points) (City) Semester One

This course covers the role of microbes in wastewater management, food products and bioremediation. We also consider microbial diversity as a rich source of novel enzymes which have wide-ranging applications in industry and biotechnology. As case studies of biotechnological applications, synthetic blood products and viral vaccine development are also covered. A sound understanding of BIOSCI 347 and/or 348 or equivalent is assumed.

Assessment: 60% Examination, 40% Coursework
Format: 2 essays
Class Limit: 24
Coordinator: Associate Professor Silas Villas-Boas
Phone: +64 9 373 7599 ext 83762
Email: s.villas-boas@auckland.ac.nz

(15 points) (City) Semester Two

The experimental investigation and modelling of protein behaviour at the molecular level, in order to explain cellular biology and facilitate protein engineering. Topics addressed may include binding, transport, catalysis, chemical modification, and dynamics. A sound understanding of BIOSCI 350 or equivalent is assumed.

Coordinator: Dr Richard Kingston
Phone: +64 9 737 7599 ext 84414
Email: rl.kingston@auckland.ac.nz

(15 points) (Tamaki) Semester One

The science of invasion biology, including stages of the invasion process and ecological interactions between species. The impacts of invasive alien species in different ecosystems. Population and community ecology, in relation to biosecurity.

NB. If you are interested in enrolling in BIOSCI 747 and its companion course BIOSCI 748 you should be considering taking the PGDipSci in Biosecurity & Conservation.

Assessment: 100% Coursework
Format: Distribution modelling exercise 10%, Policy submission 35%, Species risk assessment 55%
Class Limit: 24
Coordinator: Dr Margaret Stanley
Phone: +64 9 373 7599 ext 86819
Email: mc.stanley@auckland.ac.nz

(15 points) (Tamaki) Semester Two

Techniques for the management of invasive plants and animals (vertebrates and invertebrates) in different ecosystem types, including terrestrial and aquatic ecosystems, approaches to the prevention, control and eradication of invasive species in different situations.

NB. If you are interested in enrolling in BIOSCI 747 and its companion course BIOSCI 748 you should be considering taking the PGDipSci in Biosecurity & Conservation.

Assessment: 100% Coursework
Format: Management Recommendations Report 50%, Research Proposal 50%
Class Limit: 24
Coordinator: Dr Margaret Stanley
Phone: +64 9 373 7599 ext 86819
Email: mc.stanley@auckland.ac.nz

(15 points) (City) Semester Two

Microorganisms are intimately associated with their immediate environment. This course considers those associations. Topics to be discussed will include microbial communities and their survival strategies in natural and artificial systems. A sound understanding of BIOSCI 347 or equivalent is assumed.

Assessment: 60% Examination, 40% Coursework
Format: Seminars 2x 5%, Assignments 3x 10%
Class Limit: 24
Coordinator: Associate Professor Mike Taylor
Phone: +64 9 373 7599 ext 82280
Email: mw.taylor@auckland.ac.nz

(15 points) (City) Semester Two

This course addresses selected topics in plant microbial interactions. Modern research on issues relating to plant pathogens and biosecurity, plant disease spread (epidemiology) and plant microbial interactions (both pathogenic and mutualistic) will be investigated and discussed. A basic understanding of microbiology and molecular biology is assumed.

Prerequisite: BIOSCI 321 preferred but not essential
Assessment: 100% Coursework
Format: 2 or 3 Seminars 40%, 3 Written Assignments 60%
Coordinators: Associate Professor Matt Templeton
Phone: +64 9 373 7599 ext 86631
Email: Matt.Templeton@plantandfood.co.nz

(15 points) (City) Semester One

How genomics and gene transfer technologies could be used to achieve improved plant growth and to develop food with new traits. Topics may include: plant genomics methods, engineering fruit color, control of fruit ripening and texture, biotechnology project design. A sound understanding of BIOSCI 354 or BIOSCI 340 or equivalent is assumed.

Assessment: 50% Examination, 50% Coursework
Format: Essay 20%, 2x seminars 30% total
Coordinator: Dr Karine David
Phone: +64 9 373 7599 ext 83793
Email: k.david@auckland.ac.nz

(15 points) (City) Semester Two

Aspects of the biosynthesis of plant products and foods: the biosynthesis of selected plant cell-wall components important in dietary fibre or biomass for the production of biofuels, including lignins, cellulose or non-cellulosic polysaccharides; the biosynthesis of antioxidant pigments in food plants and their possible impacts on human health; the manipulation of nitrogen assimilation in plants to increase the yield and quality of agricultural and horticultural plant products. A sound understanding of BIOSCI 340 or equivalent is assumed.

Assessment: 50% Examination, 50% Coursework
Format: 3x essays (15% each), 3x seminars 5% total
Coordinator: Professor Philip Harris
Phone: +64 9 373 7599 ext 88366
Email: p.harris@auckland.ac.nz

(15 points) (City) Semester Two

This course focuses on regulation of gene expression in plants and how genes modulate plant responses. Original journal papers and research techniques common in plant molecular biology are analysed in detail. Topics include transcription factors, RNAi, epigenetics and post translational controls in the regulation of flowering time genes and genes regulated by plant hormones. The course consists of a mix of lectures, round table discussion groups and student seminars. A sound understanding of BioSci 354 and/or 340 is assumed.

Assessment: 50% Examination, 50% Coursework
Format: 1 Essay 25%, 1 seminar and hand-in (25%)
Coordinator: Professor Joanna Putterill
Phone: +64 9 373 7599 ext 87233
Email: j.putterill@auckland.ac.nz

(15 points) (City) Semester One

This course will address the analysis of genomes and gene expression as a means of understanding biological processes. Aspects of functional and chemical genomics will be presented, as well as gene expression profiling using microarray technology. In terms of the latter, features of experimental design and data analysis will be discussed in the context of disease and developmental processes. A sound understanding of BIOSCI 351 or equivalent is assumed.

Assessment: 70% Examination, 30% Coursework
Format: Essay 15%, Seminar 15%
Class limit: 24
Coordinator: Dr Austen Ganley
Phone: +64 9 373 7599 ext 82906
Email: a.ganley@auckland.ac.nz

(15 points) (City) Semester Two

Reviews recent studies of biological systems that highlight molecular structure, and its ability to explain cellular biology. Topics may include: protein folding and targeting in the cell, motor proteins, pathogen and immune system molecules, and the inference of protein structure and function from genomic data. A sound understanding of BIOSCI 350 or equivalent is assumed.

Assessment: 100% Coursework
Format: 1x Essay 34%, 2x Seminars @ 20% each, Class Participation 26%
Class limit: 24
Coordinator: Associate Professor Christopher Squire
Phone: +64 9 373 7599 ext 84810
Email: c.squire@auckland.ac.nz

(15 points) (City) Semester Two

Examples of normal and perturbed gene expression from selected model organisms and humans will be used to develop understanding of biological pathways that may span development, ageing, genetic diseases and cancer. A sound understanding of BIOSCI 356 or equivalent is assumed.

Assessment: 60% Examination, 40% Coursework
Format: 2 Essays (17.5% each), 1 Seminar 5%
Class limit: 24
Coordinator: Dr Jessie Jacobsen
Phone: +64 9 373 7599 ext 84781
Email: j.jacobsen@auckland.ac.nz

(15 points) (City) Semester One

This course will explore recent advances in cell biology that have led to a greater understanding of a variety of cellular processes at the molecular level. Emphasis will be placed on biochemical and genetic approaches to understanding disease mechanisms at the cellular level. A sound understanding of one or more of BIOSCI 349, 353 or MEDSCI 314 or equivalent is assumed.

Assessment: 70% Examination, 30% Coursework
Format: Essay 15%, Seminar 15%
Class limit: 24
Coordinator: Dr John Taylor (Semester One)
Phone: +64 9 373 7599 ext 82854
Email: ja.taylor@auckland.ac.nz

(15 points) (City) Semester Two

This course will provide students with insight into several areas of current biomedical research with particular focus on immunology and molecular biology. We will examine some of the molecular events that regulate disease mechanisms and explore how we can exploit molecular and cellular processes for the treatment of disease. During this course you will learn how to critically evaluate the scientific literature and develop skills in researching, discussing and writing about biomedical science. A sound understanding of one or more of BIOSCI 349, 350, 353 or MEDSCI 314 or equivalent is assumed.

Assessment: 55% Examination, 45% Coursework
Format: Essay 15%, Seminar 15%, Research Paper Synopsis 10%, Class Participation 5%
Class limit: 24
Coordinator: Dr Catherine Angel (Semester Two)
Phone: +64 9 373 7599 ext 81235
Email: c.angel@auckland.ac.nz

(15 points) (City) Semester One, Semester Two

A detailed outline of the proposed thesis research and experimental design. The proposal must review current scientific literature and emphasise the relevance of the proposed study. Students will also be required to present their proposal as a seminar.

Restriction: BIOINF 761, ENVSCI 701, MEDSCI 701
Assessment: 100% Coursework
Format: Seminar Report 10%, Seminar 20%, Proposal Report 70%
Class Limit: (BIOSCI 761 FC + SC) 50
Coordinators: Dr Monica Kam
Phone: +64 9 373 7599 ext 81234
Email: monica.kam@auckland.ac.nz

(15 points)

A review of the literature associated with the dissertation topic and an outline of your proposed research and its significance to the research field. The dissertation proposal is to be completed in Semester One.

Assessment: 100% Coursework
Format: Dissertation Proposal 80%, Seminar Presentation 20%
Coordinator: Dr Kathryn Jones
Phone: +64 9 373 7599 ext 88703
Email: ks.jones@auckland.ac.nz

(45 points) (City) Semester One, Semester Two

(45 points) (City) Semester One, Semester Two

(120 points) (City) Semester One, Semester Two

(120 points) (Tamaki) Semester One, Semester Two

(120 points) (City) Semester One, Semester Two