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Title of project:
Supervisor/s:
How does bacteria efflux drugs?
Supervisor 1 Alok K. Mitra Supervisor 2 Email Address: [email protected] Email Address: Phone Extension: 88162 Phone Extension:
Key Techniques: Membrane protein expression and purification; electron microscopy; 3-dimensional structural study; functional assay
Aim of Project A major challenge for the 21st century is the fight against infectious diseases. The renewal of outbreaks of tuberculosis and cholera and the pronounced resistance of these, and other common pathogenic bacteria towards most antibiotics has posed a serious threat both in the developed and developing countries. The aim of the project is to gain insight into how bacteria efflux drugs. We are focusing on the AcrB drug efflux system to understand at the molecular level how this tripartite system composed of 3 proteins AcrB, AcrA and Tolc work together to expel compounds that the bacteria considers harmful for its survival.
Prerequisites: Taken courses that have dealt with protein structure and function such as BIOSCI350 and have a strong interest in Structural Biology.
Supervisor/s:
Title of project: Bryophyte Ecology
Supervisor 1 Dr Anne Gaskett Supervisor 2 Email Address: [email protected] Email Address: Phone Extension: 89509 Phone Extension:
Key Techniques: Fieldtrip planning, fieldtrip survey techniques, moss and liverwort collection and identification skills, herbarium sample preparation, data analyses, preparing reports for publication in a local journal, and potentially some molecular skills.
Aim of Project: Bryophytes such as mosses and liverworts are charismatic but sometimes overlooked key species in NZ's native forests. What influences their distribution and diversity? Is it their unusual reproductive strategies? Or perhaps their unique relationships with other plants and insects? This project involves accompanying students and staff on fieldtrips to collect bryophytes on Little Barrier Island and mainland sites around Auckland, identifying and cataloguing the specimens for a herbarium collection, and analysing data on species diversity and abundance. You can also participate in the annual NZ Bryophyte workshop (1-7 December), build networks with other Auckland ecologists, prepare a fieldtrip report for publication, and help other students and staff with related ecological fieldwork over the summer. Depending on your skills and interests, you can also assist with some DNA barcoding and other molecular techniques. If you have the prerequisites listed here, feel free to email me for more information: [email protected]
Prerequisites: A drivers license, intention to pursue postgraduate studies in ecology or conservation topics in 2012, experience in fieldwork and plant and insect identification (e.g. completed BIOSCI320 & BIOSCI 323), very good fitness, an enjoyment of tramping and outdoor work, and the ability to work both independently and with a group.
Supervisor/s:
Title of project: Cloning and mutagenesis of sn(o)RNAs in Trichomonas vaginalis and RNA cap analysis
Supervisor 1 Augusto Barbosa Supervisor 2 Email Address: [email protected] Email Address: Phone Extension: 85087 Phone Extension:
Key Techniques: PCR, site-directed mutagenesis and DNA cloning; Transfection of eukarotic cells to introduce foreign DNA; RNA purification and analysis by Northern Blot hybridization.
Aim of Project: We have a preliminary indication that the 5'-end structure of the small nuclear and small nucleolar RNAs in T. vaginalis might result in the fate of acquiring a 5' guanosine cap. Here, we want to test this hypothesis by introducing or disrupting loops at the 5'-end of these RNAs. This will be achieved by mutagenesis and mutated RNAs can be introduced into T. vaginalis by transfection. Untransfected and transfected cells will have RNAs purified for analysis. This includes immunoprecipitation of RNAs with a guanosine cap antibody and analysis by Northern Blot hybridization.
Prerequisites: This project suits an individual with a keen interest in microbiology and molecular biology who has completed papers in related areas and is planning postgraduate research.
Supervisor/s:
Title of project: Probing the active site of AKR1C3 for anti-cancer drug design
Supervisor 1 Dr. Christopher Squire Supervisor 2 Dr. Jack Flanagan Email Address: [email protected] Email Address: [email protected] Phone Extension: 88806 Phone Extension: 86155
Key Techniques: Fragment screening by Differential Scanning Fluorimetry (drug discovery technique). Crystal soaking, X-ray diffraction, crystal structure determination and refinement
Aim of Project: We have determined 10 structures of the AKR1C3 enzyme containing a prototype mustard, currently in stage II anti-cancer trials, or a series of non-steroidal anti-inflammatory drugs (NSAIDs). We will further probe the active site by fragment screening to show how a diverse set of small molecules interacts with the protein. The project will involve the initial fragment screening by Differential Scanning Fluorimetry and then the subsequent X-ray crystallography experiments to visualize how the molecules interact at an atomic level. The details we discover will provide feedback to the chemists in the ACSRC so they can develop more selective and more powerful anticancer prodrugs.
Prerequisites: N/A but an interest in protein structure and function and/or drug discovery would be advantageous
Supervisor/s:
Title of project: Velvet proteins in fungi - structure, function and protein interactions
Supervisor 1 Damien Fleetwood Supervisor 2 Shaun Lott Email Address: [email protected] Email [email protected] Phone Extension: 83888 Phone Extension: 87074
Key Techniques: Recombinant DNA techniques; Protein expression and analysis; Protein-protein interaction analysis
Aim of Project: The fungal velvet proteins regulate sexual development and bioactive metabolite production. In the fungi we study that form agriculturally important associations with plants, these proteins also regulate the molecular communication between the plant and the fungus. While these proteins are required for important cellular and biotechnological processes, nothing is yet known about their biochemical function. In this project the structure and function of the velvet protein VelA will be probed by studying its structural properties in vitro and interactions with other proteins. The project will impart key skills in DNA and protein-based molecular biology that can be used in further study.
Prerequisites: Could focus on molecular biology or structural biology depending on the interests and aptitude of the student.
Supervisor/s:
Title of project: Improving wildlife forensic methodologies for field applications
Supervisor 1 Dianne Gleeson Supervisor 2 Email Address: [email protected]
Email Address:
Phone Extension: 574 4121 Phone Extension:
Key Techniques: The student would learn how to obtain DNA from a range of different field' samples (hair, scat, saliva) and gain practical skills in peR, microsateJlite genotyping, DNA sequencing. They would also learn about genetic data analysis and statistics involved inindividual identification.
Aim of Project: The use of wildlife forensics in New Zealand has recently become more common. Techniques are adapted from human forensics and used for applications such as species identification (e.g. predation detection) and detecting a specific individual. The major limiting factor in the success of these applications is the ability to obtain sufficient quality of DNA The aim of this project is to improve field sampling methodologies to increase the success of DNA analysis from these types of samples. This would include sampling from scat, hair and saliva across a variety of vertebrate species of interest e.g. deer, possums, goats, rats, cats, ferrets and stoats. Different methods of DNA recovery will be compared along with testing time dependence and environmental factors that determine success. The student will learn a range of field and laboratory methods beneficial to any future molecular ecology programmes.
Prerequisites: Preferably have completed either of the following papers Molecular Genetics, Molecular Ecology and Evolution, Genetics
Supervisor/s:
Title of project: Ecology and Behaviour of the New Zealand giraffe weevil (Lasiorhynchus barbicornis)
Supervisor 1 Gregory Holwell Supervisor 2 Chrissie Painting (PhD Student) Email Address: [email protected] Email Address: Phone Extension: 83652 Phone Extension:
Key Techniques: Setting up and conducting field experiments, behavioural observations, and precise data recording. In addition the student can develop skills in conducting lab-based staged experiments.
Aim of Project: Male giraffe weevils possess an elongated rostrum (head extension) that they can use for fighting other males, but due to extreme size variation smaller males are less likely to win during these contests due to their size disadvantage. This studentship will contribute to a larger study looking at how alternative reproductive tactics (sneaking) have evolved in the giraffe weevil. Specifically your role would be to take charge of field- based weekly surveys of giraffe weevil abundance and size, and additionally assist Chrissie Painting (PhD student) in conducting behavioural experiments which focus on 1) alternative mating tactics, 2) fighting and assessment behaviour, and 3) host tree location.
Prerequisites: Drivers license for travel to Auckland region field sites. Experience and enthusiasm for field work. Must be able to work independently. Must have taken appropriate ecology, entomology and/or behaviour papers in stage 3 and plan to continue on to do postgraduate studies in this field.
Title of project:
Supervisor/s:
The role of honeybees on Rangitoto Island
Supervisor 1 Jacqueline Beggs Supervisor 2 Sandra Anderson Email Address: [email protected] Email Address: [email protected] Phone Extension: 89823 Phone Extension: 87214
Key Techniques: pollination biology, insect and bird identification, variety of field ecology techniques, data management and analysis.
Aim of Project: Honeybees may compete with native animals for resources; nectar and pollen. They may also have an impact on the reproductive output of both exotic and native plants. The Department of Conservation (DoC) has historically granted concessions for honeybees on conservation land, but in the absence of research on their impacts. This project will be based on Rangitoto Island to address the following questions: 1. Do honeybees affect the reproductive success of pohutukawa? 2. Do honeybees significantly reduce the standing nectar crop? 3. Do honeybees displace other floral visitors from pohutukawa? 4. Are there other species of plant that the honeybees are visiting (patticularly weed species)?
Prerequisites: Some knowledge of terrestrial ecology is required. Drivers license and first aid certificate preferred. This research will involve a substantial amount of time working and living on Rangitoto Island, so willingness to work in field conditions is essential.
Supervisor/s:
Title of project: Structural Biology Studies on Isoprenyl Diphosphate Synthases from M. tuberculosis
Supervisor 1 Prof. Ted Baker Supervisor 2 Dr Jodie Johnston & Dr Genevieve Evans
Email Address: [email protected]
Email Address: [email protected] [email protected]
Phone Extension: Phone Extension: 87237
Key Techniques: In this project the student would gain experience with a wide range of experimental techniques starting from DNA based molecular biology work (PCR amplification & cloning) and progressing to protein expression, purification and protein crystallisation experiments. There is also the potential to undertake some structural studies using the technique of X-ray crystallography depending on progress.
Aim of Project: The project would be focused on four Isoprenyl Diphosphate Synthase enzymes from Mycobacterium tuberculosis with the aim of over expressing and purifying at least one of these proteins for use in crystallisation experiments. Any crystals obtained during the course of the studentship would then be used for X-ray crystallographic analysis and structural biology studies. M. tuberculosis is the causative agent of Tuberculosis in humans and accounts for ~1.7 million deaths a year worldwide. Isoprenyl Diphosphate Synthases play important roles in making the building blocks of many different important compounds for M. tuberculosis including components of the cell wall, respiratory chain (menaquinone) and small molecules associated with the pathogenesis of the disease. Hence these proteins make good potential drug design targets and structural information would enable us to both understand better their mechanism of action and provide information that can be used in structure based drug design.
Prerequisites: It would be good for the student to have a strong interest in structural biology. Please forward this completed project form to Sue Skelly by Wednesday July 13th 2011
Supervisor/s:
Title of project: Auxin signalling in the plant model Arabidopsis
Supervisor 1 Karine David Supervisor 2 Email Address: [email protected] Email Address: Phone Extension: 83793 Phone Extension:
Key Techniques: in vitro tissue culture, mutant phenotyping, gene expression analysis
Aim of Project: The plant hormone auxin is one of the major plant hormone, implicated in virtually every aspect of plant development. Despite its established biological and agronomic importance, the molecular mechanisms underlying the auxin early response remain unclear. In my group we are particularly interested in the extracellular receptor ABP1 (Auxin-binding protein 1), an essential membrane-bound protein that controls early events in auxin signalling. In this project we aim to characterise candidate genes potentially involved in the ABP1 signalling pathway. This will involve the phenotypic characterisation of T-DNA mutants and expression analysis of candidate genes.
Prerequisites: Preference will be given to students with strong interest in plant sciences and willing to carry on postgraduate studies
Supervisor/s:
Title of project: Synthesis of Components for Use in Human Vaccines
Supervisor 1 Professor Margaret Brimble Supervisor 2 Professor Rod Dunbar Email Address: [email protected] Email Address: [email protected] Phone Extension: 88259 Phone Extension: 85765
Key Techniques: synthetic chemistry, peptide chemistry, immunological assays
Aim of Project: The immune system often recognises tumour cells and infectious agents from the unique peptides found on their surfaces associated bound to MHC (major histocompatibility complex) molecules. Synthetic peptides of similar structure can be used as vaccines to stimulate the immune system. In the present project, new components for human vaccines will be synthesized and tested in vitro for biological activity on human cells.
Prerequisites: Organic chemistry at second year level, Medicinal chemistry at third year level
Supervisor/s:
Title of project: Ocean acidification and developmental delay in sea urchins: a test with Evechinus chloroticus
Supervisor 1 Dr. Mary Sewell Supervisor 2 Email Address: [email protected] Email Address: Phone Extension: 83758 Phone Extension:
Key Techniques: Field collections and laboratory maintenance of adult sea urchins; spawning and fertilization of sea urchins; developmental staging via light microscopy; larval morphometrics and multivariate analysis.
Aim of Project: The reduction in pH as a result of increasing carbon dioxide in the atmosphere is generally known as ocean acidification (OA). Evidence is accumulating that many marine invertebrates are affected by OA during early development with reduced fertilization, increased mortality of embryos and smaller larval size. In this project the student will be working as part of team conducting experiments on how OA affects the development of embryos and larvae of the sea urchin Evechinus chloroticus. Sea urchins will be collected at locations in the Hauraki Gulf and maintained in the seawater facility in the Thomas Building. Laboratory cultures of sea urchins will be raised in control, medium and high CO2 conditions and the developmental stage and larval size will be monitored in all treatments throughout development. This information will be included as part of a paper to be published in 2012.
Prerequisites: Have previously taken BIOSCI 208 (Invertebrate Diversity). Ideally have experience with snorkelling (needed to collect sea urchins).
Supervisor/s:
Title of project: Can mesoplankton eat the microplastics in facial cleansers?
Supervisor 1 Dr. Mary Sewell Supervisor 2 Email Address: [email protected] Email Address: Phone Extension: 83758 Phone Extension:
Key Techniques: Field collections of plankton; collection and laboratory maintenance of adult sea urchins; spawning and fertilization of sea urchins; thinking outside the box.
Aim of Project: In a summer student project in 2008/09 we quantified the size of microplastics in four facial cleansers found in New Zealand supermarkets (Fendall & Sewell 2009, Mar. Poll. Bull. 58: 1225). A recent paper by Gouin et al. (2011) has estimated that the per capita consumption of microplastics used in personal care products for the U.S. population is approximately 2.4 mg per person per day; a total for the US population of 263 tonnes of polyethylene microplastic per year. To date we have very little understanding of the impact that microplastic in the oceans has on the plankton - will they eat microplastic ? What are the consequences of eating microplastic on biological aspects such as growth? This project requires a bit of thinking-outside-the-box in designing experiments to test for these impacts - using field collected plankton or laboratory raised sea urchin larvae.
Prerequisites: Students must have completed BIOSCI 206 or 208. The ability to snorkel for sea urchin collections would be an asset.
Supervisor/s:
Title of project: Testing for NZ Gondwanan microbes
Supervisor 1 Mat Goddard Supervisor 2 Email Address: [email protected] Email Address: Phone Extension: 89537 Phone Extension:
Key Techniques: Microbiology, PCR and sequencing and analyses of DNA sequence data
Aim of Project In collaboration with other lab members, you will build on previous work and decipher the origin of NZ’s unique S. cerevisiae by obtaining DNA sequence data (including whole genomes of ancient NZ strains) and using this to ascertain the relationship of NZ S. cerevisiae to international populations by phylogenetic inference. This will be the first study of microbial phylogeography in NZ and will not only be of significant academic merit and public value, but since portions of this natural NZ population are used by the wine industry, a deeper knowledge of their origin also adds to the story of New Zealand wine and thus the commercial value of exports
Prerequisites: enthusiasm and commitment
Supervisor/s:
Title of project: Parameterisation of a model of position determination by homing pigeons.
Supervisor 1 Michael Walker Supervisor 2 Claire Postlethwaite (Mathematics) Email Address: [email protected] Email Address: [email protected] Phone Extension: 87054 Phone Extension: 88817
Key Techniques: GPS-tracking of homing pigeons and associated field techniques; ArcGIS display and interpretation of GPS track data
Aim of Project : The student will collect GPS-tracking data to parameterise a 2011 model of magnetic position determination by homing pigeons. The model used a proposed magnetic latitude and longitude (Walker, 1998) to predict a pattern of initial orientation errors (lOEs) that is well on the way to being verified using historic data from the northern hemisphere. This project will collect GPS track data from pigeons released at at differing distances from the centres of positive and negative magnetic anomalies around Auckland. Our hypothesis is that the birds will fly down the slopes of positive anomalies to determine their position in magnetically quieter areas whereas the birds are likely to struggle to determine position when they are released near the centres of negative magnetic anomalies. The results of the work will underpin further development of the mathematical model of position determination by homing pigeons.
Prerequisites: Driver's licence; familiarity with handling animals; competent user of electronic equipment; GIS skills would be an advantage.
Supervisor/s:
Title of project: Anxiety at the molecular level: how might the serine protease inhibitor neuroserpin play a role in mood regulation?
Supervisor 1 Tet Woo Lee Supervisor 2 Nigel Birch Email Address: [email protected] Email Address: [email protected] Phone Extension: 85869 Phone Extension: 88239
Key Techniques: neuronal cell culture, immunocytochemistry, fluorescence microscopy, neuronal morphology analysis
Aim of Project: Neuroserpin is a serine protease inhibitor that is expressed in brain regions involved in learning, memory and behaviour. To directly address the system-level function of neuroserpin in the normal brain researchers generated neuroserpin-deficient mice and transgenic mice overexpressing neuroserpin. Routine neurological examination revealed these mice were hypoactive and more anxious. Complex behavioural testing indicated altered neuroserpin expression were associated with deficient exploratory behaviour and abnormal reaction to novelty. These results led researchers to suggest that neuroserpin knockout mice may constitute a model of human anxiety disorders (Madani et al., Molecular and Cellular Neuroscience 23, 473-494 (2003)). The molecular mechanisms linking changes in neuroserpin expression to the observed behavioural syndrome are unknown, although recent results from our group have found that neuroserpin can regulate biological processes associated with synaptic connectivity (Lee et al., J. Neurosci. Res. 86, 1243 – 1253 (2008); Borges et al., J. Neurosci. Res. 88, 2610 – 2617 (2010)). This summer studentship will investigate cell signalling pathways that may underlie neuroserpin’s effects on synaptic connectivity and complex behaviours including anxiety.
Prerequisites: This project would suit an individual with a keen interest in neuroscience who has completed undergraduate papers in the areas of molecular neuroscience, cell biology and/or biochemistry, and is planning postgraduate research in neuroscience in SBS.
Title of project:
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Analysis of wood cell walls
Supervisor 1 Philip Harris Supervisor 2 Email Address: [email protected] Email Address: Phone Extension: 88366 Phone Extension:
Key Techniques: Hydrolysis of wood cell walls, high performance liquid chromatography, monosaccharide analysis
Aim of Project: The mechanical properties of timber are greatly influenced by the presence of reaction wood, which is formed as a result of mechanical stresses during growth. The cell walls of this reaction wood have a different chemical composition from normal wood and can therefore be detected by chemical analysis. The aim of the project is to chemically analyze a range of wood cell wall samples and relate their compositions to the mechanical properties of the wood from which they were obtained.
Prerequisites: Prior knowledge is not essential. A positive attitude to practical work is far more important.
Title of project: Investigating how measles and mumps viruses subvert our defenses.
Supervisor/s:
Supervisor 1 Richard Kingston Supervisor 2 Email Address: [email protected] Email Address: Phone Extension: 84414 Phone Extension:
Key Techniques: DNA manipulation, cloning and mutagenesis Protein expression and protein purification
Aim of Project: The cellular interferon (IFN) response provides our most immediate defence against viral infection. As a result of the evolutionary struggle between host and pathogen, most viruses have developed mechanisms to counteract the IFN response. For example paramyxoviruses, such as measles and mumps, make proteins which interfere with the JAK-STAT signal transduction pathway, blocking IFN production. This summer project will explore the structure of the proteins from measles and mumps viruses which are responsible for interferon evasion.
Prerequisites: BioSci350
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Mild strain cross protection of Tamarillo mosaic virus
Supervisor 1 Robin MacDiarmid Supervisor 2 Email Address: [email protected]
Email Address:
Phone Extension: 09 9257163 Phone Extension:
Key Techniques: Sequencing of virus strains and analysis of suppressors of RNA silencing; Virus inoculation and titre analysis by ELISA and RT-PCR; Virus symptom assessment and correlation with virus strain accumulation
Aim of Project: Non-transgenic approaches are required in New Zealand to manage virus infections as genetically modification (GM) of crops does not have public support. Tamarillo mosaic virus has been a major pathogen of tamarillo in New Zealand for several decades and despite a successful field trial of GM plants no acceptable management strategy has been identified. A mild strain of Tamarillo mosaic virus has recently been identified from field collected samples. The ability of the mild strain to confer cross-protection to severe strains has not been fully characterised. In addition, the field isolate is composed of several sequence variants which may have distinct characteristics. This project will characterise the cross-protection of the mild strain of Tamarillo mosaic virus and determine the sequence of the virus that gives mild symptoms and can confer cross-protection, if any.
Prerequisites: Enthusiasm for plant virology is required and experience is preferable
Supervisor/s:
Title of project: Whale food: From pooh to plankton
Supervisor 1 Rochelle Constantine Supervisor 2 Mary Sewell Email Address: [email protected] Email Address: [email protected] Phone Extension: 85093 Phone Extension: 83758
Key Techniques: Field data collection; plankton sample sorting; basic DNA extraction skills; database management; ecosystem level thinking
Aim of Project: The critically endangered Bryde's whales are found year-round in the Hauraki Gulf as there appears to be an abundant source of prey for these large whales. However, their diet varies throughout the year from fishes to krill. This project has two aims: (1) to determine if seasonal diet variation can be detected via field observations of diet and using genetic techniques to analyse scat (pooh) samples, and (2) to determine whether water samples collected throughout the year show variation in the composition of zooplankton. We will use a variety of techniques to answer this question, including plankton sample sorting and DNA methods. This project is part of a long-term study on how Bryde's whales use the Hauraki Gulf and why they are vulnerable to vessel-strike mortality. The student will conduct field data collection, no doubt see whales and then contribute to an ecosystem-level understanding of the Hauraki Gulf from plankton to whales.
Prerequisites: Attention to detail, basic lab skills (DNA extraction), Excel database skills
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Assessment of Novel Human Disease Gene Mutations in C elegans
Supervisor 1 Russell Snell Supervisor 2 Kristen Henty Email Address: [email protected] Email Address: [email protected] Phone Extension: 85059 Phone Extension: 86182
Key Techniques: literature review and assessment of the ability of a C.elegans model to answer a specific question cloning, molecular biology techniques, mutagenesis, c elegans handling, phenotypic assay development
Aim of Project: Clinicians who have identified novel human variations within patients not yet described as disease causing, are unable to provide a clear diagnosis, which hinders genetic counselling as well as the lack of certainty for the patients and their families. In collaboration with these clinicians we have identified some novel mutations which may be assessed for functional affect in a C elegans system. For example, a variation in a gene known to cause a common neurological disease; autosomal dominant spastic paraplegia (SPG6) can be assessed in a worm. The student will generate worm expression vectors for selected disease mutations to allow the generation of transgenic worms, and would assist in the development of the appropriate phenotypic assays.
Prerequisites: N/A
Supervisor/s:
Title of project: Assessment of Novel Human Disease Gene Mutations in Mammalian Cell Culture
Supervisor 1 Russell Snell Supervisor 2 Suzanne Reid Email Address: [email protected] Email Address: [email protected] Phone Extension: 85059 Phone Extension: 86182
Key Techniques: literature review and assessment of the ability of a cell cuture systems to answer a specific question cloning,molecular biology techniques, mutagenesis, tissue culture, techniques assessment of gene expression, phenotypic assay development
Aim of Project: Clinicians who have identified novel human variations within patients not yet described as disease causing, are unable to provide a clear diagnosis, which hinders genetic counselling as well as the lack of certainty for the patients and their families. In collaboration with these clinicians we have identified some novel mutations which may be assessed for functional affect in a simple cell culture system. For example, novel variations have been found for Ryanodine receptor 1 (RYR-1), a gene that is associated with Central core disease and Malignant hypothermia. Assessment of these variations for the likelihood of causing disease is possible using mammalian cell culture systems. The student would generate expression vectors for selected disease mutations to allow expression in an appropriate human cell line, and develop the appropriate phenotypic assays.
Prerequisites: N/A
Title of project:
Appetite studies in human volunteers – what controls food choice and weight gain?
Supervisor/s:
Supervisor 1 A/P SD Poppitt Supervisor 2 Email Address: [email protected] Email Address: Phone Extension: Phone Extension:
Key Techniques: Clinical studies with focus on appetite regulation, weight gain & obesity; Intervention trial protocol & ethics development; Recruitment, screening & day-day supervision of participants undertaking human studies; Diet design and preparation; Data entry
Aim of Project: An inability to regulate appetite and control food intake is believed to be one of the major causes of weight gain and obesity. Interestingly, some (many!) individuals have a much greater susceptibility to obesity than their lean counterparts, despite comparable environmental pressure of today’s world which encourages overeating and inactive behaviour. These individuals are most at risk of gaining weight and being unable to lose weight long term. We are interested in studying the physiological regulation of appetite in order to understand whether feelings of hunger, fullness and satiety may direct eating behaviour, and also whether factors such as timing and size of meals may further confuse the appetite regulation system and induce over eating. See the Human Nutrition Unit website at www.humannutritionunit.auckland.ac.nz
Prerequisites: The student who participates in this project will work as part of a team of researchers running these clinical studies. Preferably they should have an interest in nutrition, as well as a desire to work with volunteer participants in a human study.
Title of project: Appetite studies in human volunteers – predisposition to weight gain and obesity: a study of lean and overweight men and women
Supervisor/s:
Supervisor 1 A/P SD Poppitt Supervisor 2 Email Address: [email protected] Email Address: Phone Extension: Phone Extension:
Key Techniques: Clinical studies with focus on appetite regulation, weight gain & obesity; Intervention trial protocol & ethics development; Recruitment, screening & day-day supervision of participants undertaking human studies; Diet design and preparation; Data entry
Aim of Project: An inability to regulate appetite and control food intake is believed to be one of the major causes of weight gain and obesity. Interestingly, some (many!) individuals have a much greater susceptibility to obesity than their lean counterparts, despite comparable environmental pressure of today’s world which encourages overeating and inactive behaviour. These individuals are most at risk of gaining weight and being unable to lose weight long term. We are interested in studying how physiological appetite control may differ between lean and overweight individuals using a range of screening methods, including giving daily challenges of high and low fat foods to assess feelings of hunger, fullness and the amount of food that is eaten when a set menu is presented. See the Human Nutrition Unit website at
www.humannutritionunit.auckland.ac.nz
Prerequisites: The student who participates in this project will work as part of a team of researchers running these clinical studies. Preferably they should have an interest in nutrition, as well as a desire to work with volunteer participants in a human study.
Supervisor/s:
Title of project: Phylogeography of New Zealand Coastal Marine Invertebrates
Supervisor 1 Shane Lavery Supervisor 2 Email Address: [email protected] Email Address: Phone Extension: 83764 Phone Extension:
Key Techniques: DNA bioinformatics, phylogeographic analysis, DNA extraction, PCR, DNA sequence analysis
Aim of Project: Although some individual studies have been undertaken examining the molecular phylogeography of NZ marine organisms, there is still very little understanding of the overall patterns of population fragmentation and genetic connectivity in coastal marine species around the country. This project aims to re-analyse data from existing studies in a consistent and comparable manner to determine locations of common barriers to gene flow and dispersal. Depending on progress and student interest, the student may also be able to participate in new laboratory genetic analysis of additional species using PCR and DNA sequencing.
Prerequisites: Helpful skills: Good computer skills (e.g., spreadsheet, statistical analysis packages); bioinformatic skills such as GenBank searching and DNA sequence alignment; depending on progress, laboratory experience of DNA extraction and PCR .
Title of project: Tuberculosis drug development
Supervisor/s:
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Supervisor 1 Shaun Lott Supervisor 2 Email Address: [email protected] Email Address: Phone Extension: 87074 Phone Extension:
Key Techniques: Protein purification and crystallisation, X-ray crystallography, computational analysis and modelling.
Aim of Project: Mycobacterium tuberculosis is the causitive agent of TB, and still causes over 1.5M deaths per annum worldwide. M. tuberculosis requires an intact tryptophan biosynthesis pathway in order to be able to cause disease. Hence, we have commenced an inhibitor development program aimed at TrpD, the enzyme that catalyses the second step of tryptophan biosynthesis. This project aims to use X-ray crystallography to visualise how our most potent inhibitors bind to the enzyme, an important stepin structure-aided drug discovery.
Prerequisites: A strong interest in structural and/or computational biology is essential. A good grade in BIOSCI.203 and/or BIOSCI.350 is a strong advantage.
Title of project:
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Culturing the unculturable: strategies to isolate and culture the iconic New Zealand blue mushroom
Supervisor 1 Silas G. Villas-Boas Supervisor 2 Email Address: [email protected] Email Address: Phone Extension: 83762 Phone Extension:
Key Techniques: Fungal isolation and growth, preparation of culture media, flow cytometry, fungal tissue microdissection, microscopy, DNA extraction, PCR, fungal identification.
Aim of Project: The aims of this project are to use flow cytometry to isolate sexual spores of the deep sky-blue mushroom of New Zealand, Entoloma hochstetteri and microdissection of the mushroom mycelial tissue to eliminate superficial soil contaminants. The isolated spores and dissected mushroom tissues will be then cultured on agar plates using different media. Growing cultures will be examined by microscopy and ribosomal DNA sequence to confirm fungal identification.
Prerequisites: Passed microbiology paper(s)
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Molecular Phylogenetics of New Zealand Mecodema Ground Beetles (Carabidae)
Supervisor 1 Thomas Buckley Supervisor 2 David Seldon Email Address: [email protected] Email Address: [email protected] Phone Extension: 574 4116 Phone Extension: 84929
Key Techniques: Collecting techniques and identification of Mecodema species. Molecular analysis techniques.
Aim of Project: Mecodema are the most diverse of the seven endemic Broscini genera found in New Zealand, with 70 described species and subspecies found throughout NZ. We believe the Mecodema ancestor arrived through dispersal via New Caledonia after NZ separated from Gondwana. Recently described species from Northland suggest a strong connection to New Caledonia, therefore we would like to test this hypothesis through molecular analyses at species level. This project will involve the collection of Mecodema beetles from native forest, sorting of specimens, including previously collected DNA-grade material in the New Zealand Arthropod Collection, Landcare Research. Select specimens will then be sequenced for mitochondrial and nuclear genes. The project will also involve editing and alignment of DNA sequences, and downstream phylogenetic analysis.
Prerequisites: An interest in entomology and genetics would be useful (or at least an interest in either one). A driver's license would be appreciated. Field work in rugged forest areas.
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Title of project: Dispersal patterns of juvenile whio: what do we need to know to stop population decline?
Supervisor 1 Todd Dennis Supervisor 2 Email Address: [email protected] Email Address: Phone Extension: 87288 Phone Extension:
Key Techniques: point pattern analysis; geographic information systems; satellite telemetry
Aim of Project: The whio (Hymenolaimus malacorhynchos), New Zealand's endemic blue duck, is under continual threat to significant population decline due to increasing rates of depredation by introduced mammalian pests and loss of habitat to hydroelectric schemes. Post-fledging juveniles are thought to be particularly vulnerable, running a literal gauntlet of hazards as they disperse from natal territories. This project will analyse location data of juvenile whio obtained by ARGOS satellite telemetry in a Geographic Information System to quantify patterns of natal dispersal and model the minimum area of predator-free areas necessary to stop population decline. Model outputs will provide a means of ranking the importance of threats and estimating rates of population decline. Research findings will be disseminated to DOC staff to inform mitigation strategies.
Prerequisites: N/A
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Agent based models of animal movement: toward a mechanistic concept of individual space use
Supervisor 1 Todd Dennis Supervisor 2 Claire Postlethwaite Email Address: [email protected] Email Address: [email protected] Phone Extension: 87288 Phone Extension:
Key Techniques: Agent based modelling; geographic information systems (GIS); time series analysis
Aim of Project: Animal movement is a complex spatio-temporal phenomenon that has important implications for many biological sub-disciplines. Interactions amongst animals and between animals and their environments play important roles in the ecological and social systems in which they are embedded. 'Agent-based' models have been increasingly employed to investigate animal movements across diverse land- and seascapes. In this project we will develop simple agent-based movement models of a number of terrestrial and marine species that mimic their real-world patterns of behaviour. We will then use information extracted from these trajectories to compare descriptions of individual space-use derived from point data with a newer paradigm based on geospatial lifelines.
Prerequisites: computer literacy; no programming experience necessary
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Title of project: Substrate specificity of a yeast beta-lyase enzyme
Supervisor 1 Richard Gardner Supervisor 2 Email Address: [email protected] Email Address: Phone Extension: 87234 Phone Extension:
Key Techniques: Basic biochemistry and enzymology; monitoring of protein expression in E. coli.
Aim of Project: Three volatile thiol compounds contribute passionfruit, grapefruit and blackcurrant notes that are an key component of the distinctive aroma of New Zealand Sauvignon Blanc wines. The thiol compounds are produced by yeast during fermentation from carbon- and sulphur-containing derivatives in grape juice. The project will examine the substrate specificity of the key yeast gene involved in the conversion of the grape precursors to the thiol compound, using an in vitro biochemical assay. The work will also involve monitoring protein expression in E. coli.
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Title of project: Lactose utilisation by yeast
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Supervisor 1 Richard Gardner Supervisor 2 Email Address: [email protected] Email Address: Phone Extension: 87234 Phone Extension:
Key Techniques: Basic microbiology; PCR and DNA sequencing; construction of gene knockouts; sugar uptake assays
Aim of Project: Currently in New Zealand, Gull generates bioethanol from the lactose in milk whey using the yeast Kluyveromyces marxianus. The bakers yeast, Saccharomyces cerevisiae, is unable to utilise lactose as a carbon source, in part because it is unable to transport lactose into the cell. Recently a gene that is homologous to a lactose transporter was discovered in the sequence of a Brazilian bioethanol strain of yeast. The goal of this project is to examine the distribution of this lactose permease gene in other S. cerevisiae strains, and to test whether the presence of the gene allows yeast to take up lactose and/or to metabolise it.
Prerequisites: Some background in genetics would be helpful.
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Title of project: Stacking of multiple traits in wine yeasts
Supervisor 1 Richard Gardner Supervisor 2 Email Address: [email protected] Email Address: Phone Extension: 87234 Phone Extension:
Key Techniques: Basic microbiology and yeast genetics; PCR and DNA sequencing
Aim of Project: The Gardner lab is using breeding methods to develop improved strains of wine yeast. This project will utilise yeast genetic approaches to try to introduce multiple traits into new varieties by hybridization. In particular, the use of haploid strains will be investigated to speed up generations and mulitplexed PCR will be tested alongside microbiological screens to monitor gene inheritance of useful traits for winemaking.
Prerequisites: A good background in genetics is required.
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Title of project: Secondary metabolite biosynthesis by agriculturally important fungi
Supervisor 1 Verne Lee Supervisor 2 Shaun Lott Email Address: [email protected] Email Address: [email protected] Phone Extension: 83888 Phone Extension: 87074
Key Techniques: Standard molecular biology techniques, protein expression and purification, protein crystallisation
Aim of Project: The synthesis of bioactive secondary metabolites by modular megaenzymes such as non-ribosomal peptide synthetases plays a vital role in the biology of bacteria and fungi. In this project we are investigating non-ribosomal peptide synthetases from the symbiotic fungi of grass, Epichloe festucae, and the cereal pathogen, Fusarium graminearum. This project aims to determine the structures of functional domains from non-ribosomal synthetases of these fungi and characterise their biochemical activity. This research will aid in the search for novel secondary metabolites with agricultural or medical relevance and will lead to better understanding of the biology of these fungi.
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Targeting secondary metabolite biosynthesis for new antibacterial drugs
Supervisor 1 Verne Lee Supervisor 2 Shaun Lott Email Address: [email protected] Email Address: [email protected] Phone Extension: 83888 Phone Extension: 87074
Key Techniques: Standard molecular biology techniques, protein expression and purification, protein crystallisation
Aim of Project: In bacteria, the small MbtH-like proteins have recently been shown to bind to the secondary metabolite-synthesising megaenzymes known as non-ribosomal peptide synthetases. The formation of this protein complex is necessary for the activity of many of these megaenzymes. This project aims to characterise the interaction between the MbtH-like proteins and non-ribosomal synthetases. As MbtH-like proteins are unique to bacteria and the secondary metabolites synthesised by the megaenzymes are often important virulence factors, this interaction represents an attractive target for novel antibacterial drugs.
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A review of publications and availability of information on ways of quantifying the impact of invasive species on ecosystems and ecosystem services
Supervisor 1 Shyama Pagad Supervisor 2 Email Address: [email protected] Email Address: Phone Extension: 88624 Phone Extension:
Key Techniques: Literature search and review
Aim of Project: It has been recently proposed to develop IUCN Red List Categories and Criteria for Ecosystems, as part of a global effort to systematize ecosystem risk assessment and conservation priority setting. The Invasive Species Specialist Group of the Species Survival Commission of the International Union for Conservation of Nature -IUCN/SSC ISSG would like to review the availability of information (in addition to presence/absence of invasive species) on % area invaded by each species, or relative abundance of invaders, or other ways of measuring impact of invasive species on ecosystems to assist and inform this process.
Prerequisites : An interest in the impact of invasive species on ecosystems and ecosystem services
Invasive Species Specialist Group (ISSG) is a global network of scientific and policy experts on invasive species, organized under the auspices of the Species Survival Commission (SSC) of the International Union for Conservation of Nature (IUCN). The ISSG aims to reduce threats to natural ecosystems and the native species they contain by increasing awareness of invasive alien species, and of ways to prevent, control or eradicate them. The ISSG Regional Pacific Office is based at the Tamaki Campus and is tasked with managing the information resources of the ISSG. Website: www.issg.org/
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Collation and analysis of data and information on the impacts of invasive species on threatened species listed on the IUCN Red List of Threatened Species
Supervisor 1 Shyama Pagad Supervisor 2 Email Address: [email protected] Email Address: Phone Extension: 88624 Phone Extension:
Key Techniques: Data mining and analysis
Aim of Project: The Invasive Species Specialist Group of the Species Survival Commission of the International Union for Conservation of Nature -IUCN/SSC ISSG is working on preparing data and information in its two main databases- the Global Invasive Species Database- GISD and the thematic Island Biodiversity and Invasive Species database -IBIS for the forthcoming linkage with the IUCN Red List of Threatened Species. The focus is on data and information on the impact of invasive species on threatened species (Red List category Critically Endangered (CR), Endangered (EN) and Vulnerable (VU)) across all taxa.
Prerequisites: A deep interest in the conservation of biodiversity.
Invasive Species Specialist Group (ISSG) is a global network of scientific and policy experts on invasive species, organized under the auspices of the Species Survival Commission (SSC) of the International Union for Conservation of Nature (IUCN). The ISSG aims to reduce threats to natural ecosystems and the native species they contain by increasing awareness of invasive alien species, and of ways to prevent, control or eradicate them. The ISSG Regional Pacific Office is based at the Tamaki Campus and is tasked with managing the information resources of the ISSG. Website: www.issg.org/
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Review of inter-linkages between climate change and invasive species management in the Pacific
Supervisor 1 Souad Boudjelas Supervisor 2 Bill Nagle Email Address: [email protected] Email Address: [email protected] Phone Extension: 86805 Phone Extension: 86822
Key Techniques: Literature searches and information analysis
Aim of ProjectTo demonstrate that there are inter-linkages between climate change and invasive species, and their combined impacts on island biodiversity, as well as the role of invasive alien species management in mitigating the effects of climate change by enhancing ecosystem resilience and adaptation.
Prerequisites: Interest in biodiversity conservation.
Invasive Species Specialist Group (ISSG) is a global network of scientific and policy experts on invasive species, organized under the auspices of the Species Survival Commission (SSC) of the International Union for Conservation of Nature (IUCN). The ISSG aims to reduce threats to natural ecosystems and the native species they contain by increasing awareness of invasive alien species, and of ways to prevent, control or eradicate them. The ISSG Regional Pacific Office is based at the Tamaki Campus and is tasked with managing the information resources of the ISSG. Website: www.issg.org/
