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  • 1. 700 LEVEL PROGRAMME 2009 PLANT BIOLOGY, MICROBIOLOGY, GENETICS AND BIOCHEMISTRY All full-time 700 level programmes offered within the College of Sciences must have a 120 credit value per annum. A standard programme within the Institute of Molecular BioSciences will consist of the following: Biochemistry Plant Biology Genetics Microbiology 162.760 162.760 162.760 162.760 122.703 120.798 122.703 162.704 122.704* 203.762 162.798 122.798* 203.798 162.703 *For Plant Biology, substitution with an appropriate paper may be possible. General enquiries concerning the post-graduate programme offered within the Institute of Molecular BioSciences should be directed to the IMBS Director of Postgraduate Studies (Dr Kathryn Stowell, ScD3.08A, x7517). Specific subject enquiries should be directed to the relevant Postgraduate Subject Leader: Dr Kathryn Stowell (Biochemistry), Professor Barry Scott (Genetics), Professor Bernd Rehm (Microbiology) Professor Michael McManus (Plant Biology). All students must have their course approved by the Director of Postgraduate Studies (Dr Kathryn Stowell, ScD3.08A, x7517) The following papers will be offered in 2009: Credits Semester 120.713 Advanced Topics in Plant Biology 30 Double 120.714 Botanical Evolution 15 Double 120.791 Special topics in Evolution 30 Double 122.703 Gene Expression 30 Double 122.704 Molecular Cell Biology 30 Double 122.712 Advanced Topics in Molecular Biology 30 Double 122.713 Advanced Topics in Biochemistry 15 Double 162.703 Advanced Topics in Microbiology 30 Double 162.704 Current Topics in Microbiology 30 Double 162.760 Research Methods in Molecular BioSciences 30 Double 203.711 Advanced Topics in Molecular Genetics 30 Double 203.752 Computational Biology 15 Double 203.761 Molecular Evolution 15 Double 203.762 Genetic Analysis 30 Double 203.763 Phylogenetics 15 Double xxx.798 Research Report 30 Double xxx.897 Thesis (Year 1) 60 1, 2 and Double xxx.898 Thesis (Year 2) 60 1, 2 and Double xxx.899 Thesis 120 Double 1
  • 2. 120.706 PLANT DEVELOPMENTAL BIOLOGY (30 credits) (co-ordinator: Associate Professor Al Rowland) This paper considers the nature of developmental and physiological processes in plants. The paper offers a wide-ranging survey of the current literature ranging from the morphological to the molecular and includes the use of genetic approaches to understand plant development and function, including the interactions of plants with the environment. Not offered in 2009 120.713 ADVANCED TOPICS IN PLANT BIOLOGY (30 credits) (co-ordinator: Professor Michael McManus) This paper will involve the use of the current literature to critically examine the experimental systems used to advance knowledge in Plant Biology. Topics will include: • Senescence programmes in higher plants Dr Paul Dijkwel The process of senescence is divided into three stages: induction, mobilisation and cell death. The physiological, biochemical and molecular changes that occur in plant cells at each stage are described and discussed. • Abscission processes in higher plants Professor Michael McManus The physiological, biochemical and molecular changes that occur in plant cells under-going cell separation are described. Aspects of the control of the differentiation of specific abscission cells, and the precise cellular location of the process in various plant tissues will be discussed. • Hormone Target Cells in Plants Professor Michael McManus A discussion on how the chemically simple compounds that comprise the plant hormones are able to exert specific effects in differentiated tissues. The topic will examine the evidence for plant hormone receptors and for signal transduction. • DNA recombination in plants Dr Paul Dijkwel DNA damage in plant cells can be repaired by homologous recombination or in a non-homologous fashion. The two repair pathways are described and the consequence of the repair pathways on genetically modifying DNA for the improvement of crops will be discussed. Assessment • Written Assignments (30%) • Contribution to class discussions (20%) • Final interpretative examination (30%) • Final oral examination (20%) 120.714 BOTANICAL EVOLUTION (15 credits) (co-ordinator: Professor Peter Lockhart) This paper covers current research issues and research topics in Evolution and Molecular Ecology. Students read primary literature and prepare discussions on 3 topics. These may include, but are not limited to the following: • island syndromes and adaptive radiation • biodiversity mapping and LENZ • angiosperm origins Assessment • Research paper critique (10%) • Research Essay (50%) • Two hour final examination (40%) 120.791 SPECIAL TOPICS IN EVOLUTION (30 credits) (co-ordinator: Dr. Vaughan Symonds) This paper is designed to stimulate discussion and further understanding of modern evolutionary research with special focus on the processes that lead to the origin, maintenance, and demise of species. Topics may include: * Species: realities and concepts * Studying speciation * Ecological and genetic bases of reproductive isolation * Speciation and macroevolution and will include contributions from Professor Peter Lockhart, Dr. Jennifer Tate and Dr. Steve Trewick. 2
  • 3. Assessment * Lead discussion for one topic (15%) * Written assignment (Paper Critique) (15%) * Contribution to class discussions (20%) * Written final exam (30%) * Oral final exam (20%) 122.703 GENE EXPRESSION (30 credits) (co-ordinator: Dr Kathryn Stowell) With a focus on eukaryotic systems, this paper presents an integrated approach to the study of the molecular mechanisms involved in modulating gene expression. There is a strong emphasis on protein:protein and protein:nucleic acid interactions from chromatin through to the gene products themselves. • Dosage compensation in Drosophila Associate Professor Max Scott The MSL protein-RNA complex is required for the precise 2-fold increase in gene expression of most X-linked genes in male Drosophila. We will discuss the current knowledge of how this is achieved and the wider relevance to epigenetic mechanisms of gene regulation. • Epigenetics and gene expression Dr Kathryn Stowell Methylation of DNA and histone modifications and their relevance to mammalian gene expression. Specific topics may cover aging, circadian rhythms or cancer. • Gene silencing in plants and fungi Professor Barry Scott Post-transcriptional regulation of gene expression by miRNAs MicroRNAs are emerging as key players in the control of a range of biological processes. Recent studies have revealed that miRNAs repress gene expression by targeting both mRNAs levels and translation. The topic will discuss the role of miRNAs in regulating gene expression and developmental processes in plants and animals. • The changing face of DNA: links between DNA topology and the regulation of gene expression Dr Justin O’Sullivan This topic will cover exciting new literature which is linking the topology and 3-dimensional organisation of DNA with the regulation of gene expression. As such it will include studies into the effect of the DNA's position within the nucleus and the positions of similarly transcribed genes, both within the nucleus and the chromosome itself. • Translational control Dr Evelyn Sattlegger All cells or organisms are exposed to various stress conditions. Signal transduction pathways allow cells to sense and appropriately cope with these stresses. This topic will focus on the regulation of protein synthesis, which is a common mechanism in the cellular response to stress. Assessment • Essay and oral presentation (10%) • Two hour interpretative examination (20%) • Written report (5%) • Contribution to class discussions throughout the course (5%) • Three hour final examination – three questions from a choice of five (60%) 122.704 MOLECULAR CELL BIOLOGY (30 credits) (co-ordinator: Dr Andrew Sutherland-Smith) An advanced course on selected topics in protein function at the molecular level and inter- and intra-cellular communication and transport. • Molecular recognition Dr Gill Norris Antigen presentation and recognition of antigens by the mammalian immune system. • Molecular Motors Dr Andrew Sutherland-Smith Myosin motor proteins convert chemical energy into mechanical force and motion, essential for many cellular events: the structure and function of the 'reverse-geared' myosin VI will be examined. • Protein Engineering Dr Wayne Patrick Modern molecular biology gives us the tools to alter the structure and function of proteins by rational and/or random means. We will discuss these methods, and the sorts of questions that they can be used to address • Host-pathogen interactions Dr Jasna Rakonjac Bacteria are able to invade eukaryotic cells and manipulate the host signal transduction. In this topic we will discuss sophisticated bacterial systems that mediate interactions with the host cell. • Bacteriocins Dr Mark Patchett Bacteriocins have been described as ‘the microbial weapons of choice’ (Riley and Wertz, 2002). This topic investigates bacteriocin molecular biology: regulation, production, structure-function, immunity, and evolution. 3
  • 4. Assessment • Essay and oral presentation (10%) • Two hour interpretative examination (20%) • Written report (5%) • Contribution to class discussions throughout the course (5%) • Three hour final examination – three questions from a choice of five (60%) 122.712 ADVANCED TOPICS IN MOLECULAR BIOLOGY (30 credits) (coordinator: Dr Kathryn Stowell) Three topics selected from those listed for 122.703 and three topics from those listed for 122.704 Assessment • Internal (40%) • Final examination (60%) Assessment will be tailored according to topics chosen 122.713 ADVANCED TOPICS IN BIOCHEMISTRY (15 credits) (coordinator: Dr Kathryn Stowell) Three topics selected from those listed for either 122.703 or 122.704 Assessment • Internal (40%) • Final examination (60%) Assessment will be tailored according to topics chosen. 162.703 ADVANCED TOPICS IN MICROBIOLOGY (30 credits) (coordinator: Dr Zoe Jordens) Five selected topics from approved papers (122.704, 122.703, 203.762 or 203.761) by arrangement. Assessment Assessment will be tailored according to topics chosen 162.704 CURRENT TOPICS IN MICROBIOLOGY (30 credits) (coordinator: Dr Zoe Jordens) An advanced course on current topics in microbiology with a strong emphasis on the importance of microorganisms in industry and in the environment. • Pathogenicity of Neisseria spp. Dr Zoe Jordens This topic will explore what makes some members of the genus Neisseria cause life-threatening infections, others cause irritating infections and others just harmless commensals, through critical analyses of journal articles. • Candida albicans virulence Dr Jan Schmid In this section students will learn about extracting information from scientific papers, with emphasis on distinguishing between factual evidence and author's interpretation of this evidence, using journal articles on Candida albicans virulence. • Microbial Biofilms Prof. Bernd Rehm Microbial biofilms represent a growth mode of bacteria responding to environmental stimuli such as nutrient starvation and desiccation. The development of differentiated microbial biofilms represents a complex differentiation process involving cell-to-cell communication, phenotypic changes and the production of exopolymers impacting on the architecture of the biofilm. • Molecular Ecology and Microbial Genomics of the Rumen Dr Graeme Attwood This topic will explore the molecular ecology of the complex microbial community that inhabits the rumen and will investigate the genomes of cultivated rumen microorganisms to gain an insight into the mechanisms they use to digest plant material. The topic will also touch on the exciting new field of rumen metagenomics that is beginning to retrieve DNA sequence information from uncultured microbes that make up the majority of the rumen's inhabitants. • Probiotics Dr James Dekker The concept of probiotic bacteria, or microbes beneficial to human health, has been around for quite some time, although the level of proof supporting health claims offered by probiotic bacteria can be highly variable to say the least. This topic will cover a science-based appreciation of issues around the selection, efficacy and application of 4
  • 5. probiotic bacterial strains, including investigation into how technological advances have impacted on the probiotics industry. Assessment 100% internally assessed • Research paper critique and oral presentation (10%) • Three minireviews and oral presentations – 20% each (60%) • Interpretive exam (20%) • Contribution to discussion (10%) 162.760 RESEARCH METHODS IN MOLECULAR BIOSCIENCES (30 credits) (co-ordinator: Dr Zoe Jordens) Compulsory for all students majoring in Biochemistry, Genetics, Microbiology, and Plant Biology and will be 100% internally assessed. • Hypothesis testing (25%) Professor Peter Lockhart An interactive exercise based on case studies. Focused on formulating an hypothesis, the principles of testing predictions by observation and inference including data management and analysis. • Research proposal (25%) Dr Kathryn Stowell Three to five pages excluding references outlining the research project to be undertaken. It should take the form of a short abstract followed by background information, aims, methodology, budget and references. Includes production and presentation of a poster. Full guidelines will be provided. • Research review (25%) Dr Zoe Jordens Twelve to sixteen pages (excluding references and figures) to form the basis of the introduction to the thesis or project report. It should take the form of a comprehensive literature review of the subject area, aims and references. Full guidelines will be provided. • Oral presentation (25%) Dr Jasna Rakonjac A 15 minute oral presentation describing your research project and preliminary results. Full guidelines will be provided. This will be held early in Semester 2. 203.711 ADVANCED TOPICS IN MOLECULAR GENETICS (30 credits) (co-ordinator: Professor Barry Scott) Three topics from those listed for 122.703 and three topics from those listed for 203.762 Assessment • Internal (40%) • 3 hour final examination, 3 questions from a choice of 6 (1 from 203.702, 1 from 122.703, 1 from remaining topics) (60%) Assessment will be tailored according to topics chosen 203.752 COMPUTATIONAL BIOLOGY (15 credits) (co-ordinator: Professor David Penny) Lectures selected from computational complexity, heuristics, simulations and search strategies, particularly as they apply to biological applications. Monte Carlo Markov Chains, Hidden Markov models, motif searching, alignment and BLAST searches. Maximum Likelihood computation. Parallel computation. Splits, clustering, trees and networks. Assessment • Project (100%) Assessment will be tailored according to topics chosen. 203.761 MOLECULAR EVOLUTION (15 credits) (co-ordinator: Professor David Penny) The course is a synthesis of evolutionary theory and the study of macromolecules. It integrates basic biological questions with molecular and genetic knowledge to understand (rather than just describe) long-term biological processes. There is a blending of theoretical and experimental approaches to molecular biology. • Principles of molecular evolution 5
  • 6. Including Kimura's neutral theory, Muller's ratchet, levels of selection, duplication and divergence. RNA viruses as models of evolution, quasi-species, overlapping genes, prisoner's dilemma, and HIV origins. • From the origin of life to prokaryotes and eukaryotes The RNA-world, origins of coding and protein synthesis. Nucleus, RNA-world as an outgroup, thermoreduction hypothesis, horizontal transfer. • General molecular evolution Ancient DNA, experimental (in vitro) evolution, hypermutation. Human evolution and migration from DNA sequences. Assessment • Report (25%) • Weekly write-ups (10%) • Oral contributions (5%) • Two hour final examination - either one question (pre-circulated) or three questions from a choice of six (60%) 203.762 GENETIC ANALYSIS (30 credits) (co-ordinator: Associate Professor Max Scott) This paper will cover a selection of topics where genetic approaches have been used to address key biological questions. • X chromosome inactivation Dr Neville Honey X chromosome inactivation (XCI) is a complex process that depends on a number of epigenetic events. This topic examines the mechanisms responsible for the initiation, spread and maintenance of XCI. DNA and histone methylation plays a central role in XCI. The process also involves chromosome counting and the choice of which X chromosome is to be inactivated. The roles of XIST and TSIX in XCI will be examined. • Plant Microbe Symbiosis Professor Barry Scott This topic will explore the molecular basis for the interaction between rhizobia and legumes and in particular the host signal transduction pathways that lead to nodule morphogenesis and development. • Plant-Fungal Gene Interactions Dr Rosie Bradshaw The molecular basis for interactions between fungal pathogens and their plant hosts will be studied. The interaction of fungal invasion tactics and plant defence systems will be explored, with an emphasis on the gene-for-gene system of pathogen recognition. • The genetic basis of learning and memory Dr Max Scott The vinegar fly Drosophila melanogaster has both short and long-term memory. This topic will discuss how genetic and other experimental approaches have been used to identify the genes that are important in memory formation. We will also discuss how the gene products likely contribute to memory formation/retrieval. • Plant Development To be announced All flowers have the same basic ground plan: they are composed of sepals, petal, stamens and carpels. The ABC model of floral organ identity provides the molecular and genetic basis for the basic floral ground plan and is conserved across the angiosperms even though there is a vast array of floral morphologies. This topic will discuss the ABC model, particularly the B class genes and investigate how the ABC model has been used to address questions of homology and gene evolution. Assessment The course is a selection of topics on chromosomes (sessions 1 & 2), plant-microbe interactions (sessions 3-6), and plant and insect development (sessions 7-10). Internal assessment is outline below and will comprise 40% of the total course. Final examination – four questions from a choice of six - 60% of the total course. Assessment for 2009 Contribution to discussion (5%) Paper critique (10%) Oral presentation (10%) Interpretative exam (15%) Final Exam (60%) 203.763 PHYLOGENETICS (15 credits) (co-ordinator: Professor David Penny) 6
  • 7. This paper is a block course taught over two weeks. It includes the important biological questions being considered, a strong theoretical background, and computer experience in advanced packages. The course is suitable for those with a biological, mathematical or computer science background, and the assessment will allow students to select questions relevant to their backgrounds. 7
  • 8. xxx.798 RESEARCH PROJECT FOR PGDipSci, BSc (Hons) or MSc A wide range of research projects will be offered (outlined in "Research Projects within the Institute of Molecular BioSciences"). Students should read this document and discuss possible projects with the associated staff members. It is important to consider several different options before making a final choice. Laboratory work associated with the research project in the first year will be carried out between February and August for an average of 22 hours per week. The period of work shall include at least six weeks in addition to sixteen weeks of semester time, ie the mid-semester break of the first semester, and the mid-year break. Students are recommended to commence their work on the Monday before enrolment, if not before. (A written report detailing progress throughout year one and intended research plan for year two will be submitted in December of year one for the MSc). The final grade given for the PGDipSci or BSc (Hons) research project will be made up from assessment of the year's practical work and a written report. The assessors will consist of the primary supervisor and one additional staff member not directly associated with the project. Guidelines for preparation of research reports will be provided at the beginning of the academic year. For the MSc, project work should be recommenced as soon as practicable after the examination period in October/November and be continued throughout the following year on a full-time basis of at least 50 hours per week. The MSc thesis will be assessed by the primary supervisor and one additional staff member not directly associated with the project. An external examiner from another New Zealand University or Research Institute will also assess the thesis. Guidelines for preparation of theses will be provided at the beginning of the academic year. Kathryn Stowell, Graduate Studies Coordinator, IMBS August 2008 8