- » Virulence of Trichomonas vaginalis, a human urogenital pathogen
- » Why do mushrooms look the way they do?
- » Targeting the rDNA as a novel anti-cancer therapy
- » Responses of tree growth to climate
- » Geographic variation in the strength of selection in giraffe weevil weaponry
- » Sperm competition in New Zealand giraffe weevils
- » Why are there Archaea in stream biofilms?
- » Competition between birds and insects for floral resources
- » How does the Bbox domain of Trim proteins affect assembly and function?
- » Knocking out genes in the model plant Medicago
- » Insights into an Essential Enzyme from a Pathogen: Probing the Cooperative Behaviour of MenD from Mycobacterium tuberculosis (M.tb)
- » New protein nanostructures for bionanotechnology
- » Microbial community resilience to estuarine tidal fluctuations
- » New protein biomaterials for ocular surgery
- » Assessment of the effects of selected emerging micro-contaminants using the zebrafish embryo toxicity test
- » Development of a toxicity test using the New Zealand pelagic copepod Gladioferens pectinatus
- » How does feeding sugar-water to tui affect bird communities and pollination?
- » Use of urban landscapes by birds
- » Identification of magnetite-based magnetoreceptors in the olfactory epithelium of the rainbow trout
- » PAI-1: is it a novel cell-intrinsic factor regulating human T cell migration?
- » In vivo protein crystals
- » Structural analysis of viral proteins that have been captured and repurposed by the host
- » What keeps a viral polymerase on track?
- » Magnetic resonance imaging (MRI) to investigate variance in ectopic lipid ‘overspill’ in at risk populations for Type 2 diabetes (T2D)
- » Identifying metabolite profiles as novel candidate biomarkers to characterise and predict susceptibility and resilience in at risk populations for type 2 diabetes (T2D)
- » Gene expression analysis of altered Cu regulation in diabetic complications
- » Searching for new antibiotics effective against TB
- » Understanding RHS proteins as protein delivery vehicles
- » Developing greenhouse gas mitigation strategies through megasynthase enzymes
- » Expanding horizons or increasing specialisation: why do plant lineages diversify?
- » Plant reproduction and climate change: how will plants adjust?
- » Novel methods to track microbial “plant-destroyers” in New Zealand’s native forests.
- » Microbial community analyses of ecosystem health
- » Invertebrates and Entomology at Landcare Research
- » Fungi & Microbiology Collections at Landcare Research
- » Architecture of a bacterial microinjection device
- » Epigenetics and rapid adaptation to environmental change
Virulence of Trichomonas vaginalis, a human urogenital pathogen
Project code: SCI001
What is this project about?
Trichomonas vaginalis is a human urogenital pathogen. An abundant vaginal discharge, typical of trichomoniasis, may result from a ‘leaky’ vaginal mucosa. In tissue culture, T. vaginalis alters the permeability of a monolayer of vaginal cells. It is unknown how this parasitic protozoan promotes such alteration. One hypothesis is the action of secreted or membrane phosphatases as observed in other mucosal parasitic protozoans. Dephosphorylation of the surface of host cells can cause alteration of the cortical actin and disruption of cell tight junctions.
What will you do?
Your project starts with the identification of phosphatase candidates in the genome of T. vaginalis using bioinformatics. Primers for PCR targeting those genes will be designed. These primers will be used (i) to confirm expression of those genes by reverse-transcriptase PCR; (ii) Clone these genes in plasmids for expression in Escherichia coli and T. vaginalis. Expression of these proteins in a recombinant form in E. coli will be optimized. In T. vaginalis, these proteins will be overexpressed and will carry an epitope tag. Expression will be confirmed by Western blot and cytolocalization of these proteins will be observed by microscopy and immunofluorescence. If time allows, T. vaginalis overexpressing these enzymes will be used to assess gain-of-function phenotype on host cell permeability assays.
Does this suit you?
This project suits an individual with interests on Biomedical Microbiology who has knowledge on or affinity with Cellular Molecular Biology. Students who, after this training, want to take a Hons or MSc research path with the supervisor are highly encouraged to apply.
Why do mushrooms look the way they do?
Project code: SCI002
Mushrooms are an iconic group of fungi, invoking fear and intrigue. Mushrooms show an enormous diversity of sizes, shapes and colours. Astonishingly, however, almost nothing is known about the ecological significance of these mushroom morphologies. This project will address this dearth of knowledge by using an unbiased statistical technique to correlate morphological features with life history characters. The project would suit someone who is organized and methodical, who is interested in fungi, and/or who enjoys working with data. There are opportunities for learning statistical programming if desired.
Targeting the rDNA as a novel anti-cancer therapy
Project code: SCI003
Despite changes in ribosome biogenesis having been associated with cancer for over 100 years, little attention has been paid to the role of the ribosomal RNA genes (rDNA) in cancer. Interestingly, recent results show dramatic changes in rDNA transcription in cancer, and, critically, inhibiting rDNA transcription kills cancer cells whilst sparing normal cells. We are interested in finding why cancer cells are so sensitive to inhibition of rDNA transcription, so that this can be targeted for future therapies. We believe that the answer lies in chromatin structure and noncoding transcription, and this project will involve investigation of the differences in the rDNA between cancer and normal cells. The project would suit someone who has a background in cellular and/or molecular biology, and who enjoys lab work.
Responses of tree growth to climate
Project code: SCI004
Tree-ring analysis has long been used as a proxy for past climate because the size of tree rings changes in response to climatic conditions. Soil water availability, temperature and evaporative demand all influence tree growth and the result is a record of climate stored in tree stems. In this study, you will analyse wood anatomy to explore the details of wood development during recent wet and dry periods. The results will be combined with fine-scale growth and sap flow data to build an understanding of the physiological mechanisms driving growth rates in kauri trees. The appropriate student will be interested in learning new techniques and will have an interest in plants. The project will include field and laboratory research.
Geographic variation in the strength of selection in giraffe weevil weaponry
Project code: SCI005
Giraffe weevil males invest into enormous extensions of their head that they use as weapons during contests over females. We previously found geographic variation in the degree of investment that males put into weapon size, but we don’t yet know if this pattern relates to variation in the strength of sexual selection. The aim of this project would be to measure the strength of sexual selection on weapon size across multiple populations of giraffe weevils throughout the North Island of NZ. This would require the student to conduct behavioural assays in the field to measure mating success and various morphological traits. The student would need to be highly independent, enjoy and be confident doing field work in remote places outside of Auckland, and have a full NZ driver’s licence.
Sperm competition in New Zealand giraffe weevils
Project code: SCI006
Many animals use weapons to increase mating opportunities. However, competition among males often continues after mating as the sperm from different males vie for access to female eggs. This project will investigate sperm competition in the New Zealand giraffe weevil, using both field and lab based experiments. A primary aim would be to set up mating experiments to look for possible differences in ejaculate allocation by sneaking versus fighting males. The student would also be required to perform dissections in the lab to observe morphological differences in male genitalia. Because of the project’s field component, the student must have a NZ driver’s license and be confident working in the forest, sometimes without assistance.
Why are there Archaea in stream biofilms?
Project code: SCI007
Prokaryotes including Bacteria and Archaea make up much of the biotic community of stream biofilms. While Bacteria dominate in stream biofilms Archaea appear relatively rare and are little studied in this environment. We have sequence data for several thousand stream biofilm samples from streams across New Zealand and would like to begin investigation of the Archaeal gene sequences contained within these datasets.
The research questions for a summer student to work on are:
What Archaeal sequences are present in the National and Auckland stream components of the data.
Are there different Archaea in different streams/regions/stream quality types.
More advanced questions lie beyond these which would add challenge for student.
Data set management and handling.
Report preparation. Note that there is an opportunity to contribute to an international publication.
An understanding of statistics would be of assistance in this project.
Competition between birds and insects for floral resources
Project code: SCI008
Plant-pollinator relationships are crucial for maintaining biodiversity and ecosystem function. Introduced species such as the European honey bee (Apis mellifera) may disrupt native pollinator relationships through competition for nectar and pollen. Additionally, the density of native bird pollinators on the New Zealand mainland has declined due to mammalian predators and many native plants are now pollen-limited. This study will examine interactions between native birds, insects and honey bees and compare their effect on pollination. The project will involve visiting a range of sites in the Auckland region, including offshore islands. Knowledge of terrestrial field ecology is required, and knowledge of insects is preferred. Drivers licence and first aid certificate are also preferred. This research will involve a substantial amount of time working in rural locations, so general outdoors knowledge and skills are essential. The research will require spending up to a week at a time away from Auckland city. The student will gain general skills in field ecology, including pollination biology, landscape ecology, insect identification, data management and analysis. The student needs to be available to continue this project as an MSc topic.
How does the Bbox domain of Trim proteins affect assembly and function?
Project code: SCI009
Trim proteins are important cellular proteins mediating steps in innate immune signalling, stem cell development, and genetic regulation. To carry out these diverse functions Trim use a conserved N-terminal series of domains through which they are able to self-associate. Assembly has been shown to be vital for biological activity in a number of Trim proteins. It is unknown how many Trim proteins assemble though it appears that one domain, the Bbox2, is the key to self-association. We have selected a set of Trim proteins we wish to investigate the assembly properties of. This project will involve the cloning, expression, and purification of this set of proteins. Subsequently analysis of the assembly will be undertaken using a range of techniques including AUC, SEC-MALLS, and X-ray crystallography.
Knocking out genes in the model plant Medicago
Project code: SCI010
This project aims to make and test gene constructs for knocking out genes and gene families in Medicago. Medicago is a model legume related to alfalfa, peas and clover with a completed genome sequence. Two different approaches will be tried; CRISPR-CAS gene editing and artificial microRNAs. The genes to be targeted are candidate controllers of the timing of flowering. This functional analysis will allow us to assign or reject a role for these genes in flowering time control- a critical trait for legume adaptation to their environment and crop yield.
I am looking for smart, enthusiastic, hard-working students with an aptitude for genetics and molecular biology, an ability to problem-solve and with a strong attention to detail.
Insights into an Essential Enzyme from a Pathogen: Probing the Cooperative Behaviour of MenD from Mycobacterium tuberculosis (M.tb)
Project code: SCI011
The menaquinone biosynthesis protein MenD from M. tb (Mycobacterium tuberculosis; the causative agent of Tuberculosis (TB)) is an essential enzyme and a potential drug design candidate. We have recently published the structure of this enzyme capturing key stages in its catalytic cycle and discovered the enzyme has some intriguing cooperative behaviour. Cooperativity in enzymes can be very important for their regulation and unravelling the cooperative behaviour of M.tb MenD will be vital to us understanding how menaquinone biosynthesis is regulated in the organism. During this project we will make several proposed “cooperativity mutants” of M.tb MenD and characterise their cooperative behaviour in solution to understand more about how M.tb MenD activity is regulated.
Skills obtained in this project are:
(1) DNA manpulation: Cloning and mutagensis (making mutants)
(2) Protein Expression and Purification: Expression in M.smegmatis followed by 2-step purification (purifying mutants)
(3) Protein Characterisation: Basic kinetic assays and other biophysical techniques (characterising mutants)
New protein nanostructures for bionanotechnology
Project code: SCI012
The varied surface chemistries and inherent self-assembling properties of proteins make these biological compounds ideal building blocks for creating nanodevices. Peroxiredoxins are one such protein that can be manipulated to form diverse switchable architectures from nanorings to nanotubes. Working alongside a PhD student, you will engineer proteins to assemble into new and beautiful structures. These new nanostructures have a wide range of potential applications downstream of this research, e.g. in controlled drug delivery and the design of smart new responsive materials.
Microbial community resilience to estuarine tidal fluctuations
Project code: SCI013
Estuaries are both complex ecosystems and important buffer zones between land and sea. They represent the endpoint of land watershed drainage, and are subject to cumulative waterborne contaminants. Microbial communities that inhabit sediment in the estuarine intertidal zone contribute to the removal of excess nitrogen loading that would otherwise lead to algal overgrowth, anoxic conditions and toxic sulfide production. This project aims to improve our understanding of how these microbial communities respond to repeated stress events in the form of repeated subarial exposures during successive low tides. This will allow us to model how functionally resilient these communities might be to repeated perturbation events. The student will assist in measuring microbial community responses to lab simulated stress events, including how the frequency and duration of low tide subarial exposure impacts community structure and function, and in turn estuary health and resilience. In addition to running bench-top microcosm experiments with the supervisor’s help, the student will have the opportunity to work with microbial community phylogenetic marker gene data in the form of quantitative PCR assays. The student may also have the opportunity to participate in field trips.
New protein biomaterials for ocular surgery
Project code: SCI014
We have recently created a new protein biomaterial platform that has potential applications in ocular surgery. We are developing materials that may be used for the creation of tissue engineering artificial corneas, drug delivery, and surgical adhesives.
Many naturally occurring proteins have been explored as biomaterials and in this protein you will design and construct new materials using proteins from fish eyes. You will then assess the performance of these new materials in regards to their material properties and cellular response.
Experience with proteins and/or cell culture would be useful but is not necessary.
Assessment of the effects of selected emerging micro-contaminants using the zebrafish embryo toxicity test
Project code: SCI015
Aim of Project:
To assess the effects of emerging contaminants such as pharmaceuticals and personal care products (PPCPs) using the zebrafish FET test, a more ethically acceptable method than the use of whole fish. The results generated by this research will contribute to an overarching study assessing the risks of micro-contaminants on New Zealand’s unique environments. Researching effects of chemicals produced externally and released into the natural environment is important, both nationally and globally. The intensification of industrial activities and increasing human densities lead to the release of a range of chemicals that may potentially lead to detrimental impacts on receiving ecosystems’ functions. It is important to provide information on the fate and effects of those chemicals so that appropriate management actions are triggered to minimise risks.
Key Techniques/Skills the student will learn
- Familiarise with the general husbandry of zebrafish and conducting the Fish Embryo Toxicity (FET) test;
- Use the FET assay to assess the toxicity of chloroxylenol and triclosan (two anti-microbial agents), bisphenol-A (a plasticiser with endocrine activity), and the antibiotic ciprofloxacin individually and in mixtures with 3,4-dichloroaniline as the standard positive control;
- Sewage and biosolids extract samples (from on-going research at the Cawthron Institute) containing the above contaminants will be tested and compared with the results from individual chemicals;
- A preliminary risk assessment of those micro-contaminants on the receiving environment will be estimated using the zebrafish FET data.
Development of a toxicity test using the New Zealand pelagic copepod Gladioferens pectinatus
Aim of the project:
To develop and validate a toxicity test in a pelagic copepod species based on the production of neonates. The assay will be used to characterise the impacts of pollutants on this estuarine species.
Key Techniques/Skills the student will learn
- Familiarise with the general husbandry of copepods and conducting toxicity tests;
- Basic knowledge of chemical dilutions and handling of microscope;
- Use the test to assess the toxicity of emerging contaminants: chloroxylenol and triclosan (two anti-microbial agents), bisphenol-A (a plasticiser with endocrine activity);
- A preliminary risk assessment of those micro-contaminants on the receiving environment will be estimated by deriving ANZECC water quality guideline threshold values.
How does feeding sugar-water to tui affect bird communities and pollination?
Project code: SCI017
We know that people feeding bread and seed to birds encourages exotic birds like sparrows and doves, but what are the effects of feeding sugar water in backyards? The summer student will explore issues associated with feeding sugar water to birds (primarily tui), such as changes in the bird community, and effects on pollination services performed by birds. Skills gained will include: surveys, bird observations, experimental design, analysis.
MUST have drivers licence (preferably have own car or access to a vehicle OR have full licence and be over 21yrs - to drive University vehicles).
Use of urban landscapes by birds
Project code: SCI018
Habitat for birds is highly fragmented in urban landscapes. Native birds are found primarily in small forest fragments within Auckland. But do they move out of fragments into suburbia? Or move between fragments? The summer student will explore the use of urban fragments by birds, focussed on the NorthWest Wildlink green corridor. Skills gained will include: field surveys, bird observations, behavioural ecology, analysis.
MUST have drivers licence (preferably have own car or access to a vehicle OR have full licence and be over 21yrs - to drive University vehicles).
Identification of magnetite-based magnetoreceptors in the olfactory epithelium of the rainbow trout
Project code: SCI019
A. (Left) Whole cells of magnetotactic bacteria stained with Prussian Blue
B. (Right, above and below) Cells containing magnetite in sections from the olfactory epithelium (arrows)
We have been able to identify cells in rainbow trout that contain magnetite crystals organised as multiple braided chains that are tightly bound to the cell membrane. We hypothesise that these cells are magnetoreceptor cells and that they have afferent nerves with synapses that carry magnetic field information to the brain. We seek to identify the cells by using alternate serial sections in which we (i) stain sections with Prussian blue under alkaline conditions to identify the magnetite chains in the cells; and (ii) seek to identify afferent synapses on the cells. In earlier work, we have been able to stain both magnetotactic bacteria and magnetoreceptor cells by using the Prussian Blue stain under alkaline conditions. We now seek to develop a method that will also enable us to identify afferent synapses on the cells. This will require testing of different markers for synapses. We expect this part of the work to be challenging because the afferent nerve fibres are not myelinated, which means the afferent synapses will be hard to find.
PAI-1: is it a novel cell-intrinsic factor regulating human T cell migration?
Project code: SCI020
T cells migration is essential for T cell responses. Movement of T cells is initially required to allow scanning of antigen presenting cells (APCs) for presention of their cognate antigen. This usually happens in secondary lymphoid organs, including lymph nodes. Activated T cells then leave the lymph node and migrate to peripheral tissues to find their antigen leading to killing of infected host cells by effector T cells. In tumours, effector immune cell responses are suppressed with T lymphocytes unable to access the core of tumours probably because of the physical tumour microenvironment and possibly because of effects on chemokines that may restrict the migration patterns of T lymphocytes.
This project will investigate the role of plasminogen activator inhibitor-1 (PAI-1), a member of the serpin superfamily of serine protease inhibitors, in T cell migration. We have recently found that PAI-1 is synthesized by human T cells and is regulated by T cell activation and that another, closely related serpin, can inhibit chemokine-mediated T cell migration. The student will work closely with Evert Jan Loef, a Postdoctoral Research Fellow working in the Birch and Dunbar laboratories, to explore PAI-1 expression using quantitative real time PCR and western blot analysis, and the effects of PAI-1 on chemokine-mediated migration using a range of cell biological and biochemical assays.
This project would suit an individual with a keen interest in immunology who has completed undergraduate papers in the areas of cell biology, biochemistry and/or molecular immunology, and is planning postgraduate research in the School of Biological Sciences. If you are passionate about biomedical science, this is the summer project for you.
In vivo protein crystals
Project code: SCI021
The student will be investigating possibilities for making protein crystals using GM bacteria. This is a very demanding project suitable for a committed student.
Structural analysis of viral proteins that have been captured and repurposed by the host
Project code: SCI022
Retroviruses, such as the Human Immunodeficiency Virus (HIV), cause immunological disorders and cancers in many animal species. Because these viruses are extremely ancient, and integrate their genetic material with that of the host, animal genomes contain rich evidence of past retroviral infection. In some cases, proteins derived from retroviruses appear to have been captured and repurposed by the host, so that normal cellular activity now depends on them.
The objective of this project is to investigate some of these co-opted retroviral proteins using structural techniques (X-ray crystallography and electron microscopy). This will give us more insight into their evolutionary origin, and help us understand if they have retained any of the functions of their viral counterparts.
The project is suitable for someone with a good background in protein science, and a strong interest in structural analysis of biological molecules.
What keeps a viral polymerase on track?
Project code: SCI023
Many disease-causing human viruses have RNA genomes that are packaged into helical protein-nucleic acid complexes. These structures - termed nucleocapsids - act as the track along which the viral RNA polymerase runs when it transcribes and copies the viral genome.
So what prevents the viral polymerase from derailing? For human mumps virus and its closest relatives, the polymerase has flexible leg-like elements that repeatedly bind and release the nucleocapsid as the polymerase moves. In this project you will help us understand how these extremely dynamic regions of the polymerase can flex and reconfigure, by analyzing Nuclear Magnetic Resonance (NMR) spectroscopy data.
The project is suitable for someone with a good background in protein science, and a strong interest in applying physical techniques to understand how molecular machinery works.
Magnetic resonance imaging (MRI) to investigate variance in ectopic lipid ‘overspill’ in at risk populations for Type 2 diabetes (T2D)
The Peak Nutrition for Metabolic Health ‘PANaMAH’ study is part of the National Science High Value Nutrition program. PANaMAH is focussed on investigating the susceptibility of the Asian population to poor metabolic health and diabetes and to study the association and risk related to the storage of body fat.
Hitherto, body mass index (BMI) and total adipose mass, associated with dysglycemia, were considered adequate predictors of T2D and associated metabolic risk. However latterly, the underpinning susceptibility and resilience to adverse metabolic health has been shown to be the site at which lipids are deposited. Known as ‘TOFI - Thin on the Outside and Fat on the Inside’, seemingly slim individuals are reported to be more susceptible to developing diabetes compared with morbidly obese ‘resilient’ individuals due to lipid ‘over spill’ into ectopic sites such as liver, pancreas and muscle. Asian populations, characterised by the TOFI profile, are at a greater risk of poor metabolic health compared to their European, Maori or Pacific counterparts.
We will determine if lipid overspill matters and is an early event in developing diabetes (n = 100), using state of the art MRI methodology by investigating differences in ‘at risk’ populations, i.e. overweight/obese, healthy/prediabetic Asian Chinese and Caucasian European individuals.
An interest in nutrition, anatomy and/or physiology would be advantageous along with an enthusiasm to work in clinical trials. You will pick up key skills in (a) MRI methodologies, (b) set up and conduct of clinical trials, (c) working with participants and adhering to good clinical practice (GCP) guidelines.
Identifying metabolite profiles as novel candidate biomarkers to characterise and predict susceptibility and resilience in at risk populations for type 2 diabetes (T2D)
Project code: SCI025
- School of Biological Sciences
- AgResearch, Palmerston North*
The Peak Nutrition for Metabolic Health ‘PANaMAH’ study is part of the National Science High Value Nutrition program. As part of the overall focus of the PANaMAH project we be investigating novel candidate biomarkers in blood and tissue using metabolomics.
Diagnosis of T2D is typically determined by fasting blood glucose, the oral glucose tolerance test (OGTT) and glycated haemoglobin (HbA1c). Despite these measures, it is reported that 60 % of T2D cases go undiagnosed. The reason being the inability of these assays to predict pre-diabetic and diabetic threshold values. Early diagnosis is key to the prevention of progression and/or management of the disease. Clinical risk factors appear to cluster in certain individuals and are often independent of the known risk factors such as body mass index (BMI) and total adipose mass. Using a Metabolomics approach a comprehensive characterisation of metabolites that are involved in the disease process can be identified. Previous published work have investigated the role of metabolites (such as amino acids) as predictors of developing diabetes. Hence identified metabolites could serve as biomarkers along with the known risk factors for T2D.
We will identify early blood and tissue biomarkers to characterise and predict susceptibility and resilience to T2D in overweight/obese, healthy/prediabetic Asian Chinese (n = 200) and Caucasian European (n = 200) individuals. An interest in nutrition and/or chemistry would be advantageous. You will benefit with hands on experience in learning state of art Metabolomic techniques, data interpretation and analysis (based in Palmerston North). Also, you will be introduced to the clinical aspects of data collection, i.e. set up and conduct of trials.
Gene expression analysis of altered Cu regulation in diabetic complications
Project code: SCI026
The chronic hyperglycemia of diabetes is associated with long-term complications such as damage, dysfunction and failure of various organs including heart, kidneys, eyes, liver and blood vessels etc. Previous works from our group have shown that acquired Cu imbalance is a key mechanism of diabetic organ damage that can be ameliorated by chronic treatment with triethylenetetramine (TETA), a divalent Cu(II)-selective chelator. The aim of this project is to investigate the changes of gene expression associated with impaired Cu homeostasis (cellular Cu uptake and transport) in diabetes-affected tissues such as brain, muscle and gut, by RT-qPCR and western blotting using a streptozotocin (STZ)-diabetic rat model. This study will provide important data concerning the role of Cu dysregulation in diabetic organ damage, and it is part of our ongoing research programme on preclinical investigation of Cu(II)-chelation treatment for diabetic complications.
Collection of tissue samples, Tissue/cellular RNA extraction, RNA gel electrophoresis, RNA/protein quantification assay, RT-qPCR, real-time PCR data analysis, Western Blotting.
Searching for new antibiotics effective against TB
Project code: SCI027
Tuberculosis (TB) remains one of the most significant worldwide causes of death from a communicable disease: in 2014, ~1.5 million people died from TB, almost half a million people developed multidrug-resistant (MDR) TB, and over 40,000 people developed extensively drug-resistant (XDR) disease. As population mobility from Asian countries with a high burden of drug-resistant TB such as India and China continues to increase, so the exposure of the New Zealand population will also increase. This project will focus on enzymes from Mycobacterium tuberculosis that are potential targets for new anti-TB drugs. Enzyme structures will be determined in complex with chemical inhibitors, using standard crystallographic methods, to inform a structure-guided optimisation of inhibitor potency by subsequent medicinal chemistry.
Understanding RHS proteins as protein delivery vehicles
Project code: SCI028
RHS repeat proteins are found in both bacteria and some eukaryotes, suggesting that they have a fundamental biological function. Based on our previous work published in Nature in 2013, our hypothesis is that they sequester and deliver cargo proteins to particular cells or cellular locations. The proposed research will test this idea, using a combination of functional and structural analyses, providing fundamental biological insight into the mechanism of action of these poorly understood proteins.
Developing greenhouse gas mitigation strategies through megasynthase enzymes
Project code: SCI029
This project is a chance for the student to join a team of researchers investigating novel molecular solutions to agricultural greenhouse gas mitigation. Over 30% of New Zealand’s total greenhouse gas emissions are made up of methane produced by microbial methanogens that live in the rumens of livestock. This research is focusing on “megasynthase” enzymes from the methanogens. Megasynthases are large molecular assembly lines that synthesise diverse bioactive secondary metabolites. It is known that secondary metabolites play important biological roles in signalling, nutrient acquisition and defence in many organisms. However, almost nothing is known about the secondary metabolites made by methanogens. In this project we aim to use the purified megasynthase enzymes to produce their secondary metabolite products in vitro in order to identify and characterise them. This will allow us to understand the role they play in methanogen biology and to develop compounds based on these secondary metabolites that will inhibit methanogen growth. The techniques used will include protein expression and purification, protein crystallisation and biochemical assays.
Expanding horizons or increasing specialisation: why do plant lineages diversify?
Project code: SCI030
New Zealand has a number of spectacular plant radiations but we know little about the ecological processes involved. The project will gather trait and environmental information on all taxa within several woody groups and integrate with existing phylogenetic and eco-physiological information. The research involves a combination of data-collection and analysis and collaborative work with postgraduate students. The project is located in Dunedin and funds for a return airfare from AK are available.
Plant reproduction and climate change: how will plants adjust?
Project code: SCI031
The aim is to use a 45 year data set of flowering in six alpine Chionochloa (tussock grasses) species in Fiordland, coupled with associated climate data. We want to investigate any climate shifts during the critical floral induction period and explore how the plants have responded through changes in flowering frequency and intensity. Mainly analysis of time-series data integrated with existing environmental information. The project is located in Dunedin and funds for a return airfare from AK are available.
Novel methods to track microbial “plant-destroyers” in New Zealand’s native forests.
Project code: SCI032
Phytophthora is a genus of soil, air or water borne plant pathogens that poses major challenges to global biosecurity and affects a broad range of hosts worldwide. Translating literally as “plant destroyer” various species of Phytophthora currently impact New Zealand’s natural and plantation forests, horticultural, agricultural and amenity plants with the most notable being Phytophthora taxon Agathis, the cause of Kauri dieback. In partnership with Scion (New Zealand Forest Research Institute) the successful candidate will gain expertise in a variety of modern molecular techniques to develop novel methods to track the presence and abundance of Phytophora in a wide range of NZ forest soils. The data provided by your study, and its interpretation, may have significant implications for the way in which we continue to monitor, protect and manage New Zealand’s iconic Kauri forests.
Microbial community analyses of ecosystem health
Project code: SCI033
Degradation of the health and fertility of soil is a widespread problem in New Zealand. For this reason an easy, rapid, and universally-applicable method for monitoring soil quality is needed. Using an expansive collection of soils taken from horticulture (i.e. orchards, viticulture, arable and market gardening), plantation forestry, dairy pasture and dry-stock pasture land uses, you will used advanced DNA-based methods to map the distribution of soil microbial genes of direct relevance to soil health and productivity. Specifically, this project aims to identify locations within NZ with reduced production potential by i) mapping the distribution of functional (e.g., N and P-cycling) genes that are relevant to soil health and performance, and ii) designating threshold values for desired abundance of these genes in various NZ soils. The data provided by your study, and its interpretation, may have significant implications for the way in which we continue to monitor, protect and manage New Zealand’s natural soil resource in the future.
This project will be undertaken in partnership with Land and Soil Scientists at Auckland Council.
Invertebrates and Entomology at Landcare Research
Project code: SCI034
THREE STUDENTS REQUESTED
Work with taxonomists on the diversity of terrestrial invertebrate species in New Zealand.
Assist with management of the invertebrate collection by sorting and transferring specimens into new cabinets, and by databasing specimens for biodiversity and biosecurity research projects.
Ability to work in a group or independently, position requires dexterity, care and attention to detail, patience, data entry, and read small labels.
Applicants must have an interest in Entomology.
Students from Entomology 320 or 730 courses preferred.
Fungi & Microbiology Collections at Landcare Research
Project code: SCI035
TWO STUDENTS REQUESTED
Work with taxonomists on the diversity of terrestrial fungi & microbe species in New Zealand.
Assist with management of the fungi & microbiology collections for biodiversity and biosecurity research projects.
Ability to work in a group or independently, position requires dexterity, care and attention to detail, patience, and data entry.
Applicants must have an interest in Fungi and/or Microbiology.
Architecture of a bacterial microinjection device
Project code: SCI239
Nature has evolved sophisticated molecular machinery for specific biology. One such example is the multi-protein secretion systems (type I –VII) that bacteria utilize to transfer effector molecules to confer survival advantage that can lead to pathogenicity towards other bacteria or eukaryotic hosts. The subject of our research, the anti-feeding prophage (Afp), is a mobile microinjection device produced by Serratia entomophila) comprised of 18 different proteins. The objective is to determine near atomic resolution 3-D structures of the component proteins and reveal the structural dynamics responsible for the toxic activity of Afp.
Epigenetics and rapid adaptation to environmental change
Project code: SCI243
Aim of the project
This project will use the highly invasive marine invertebrate, Didemnum vexillum, as an experimental organism to determine the epigenetic mechanisms associated with adaptation to environmental stressors.
This project is based at the Cawthron Institute in Nelson. The student will spend time at the town premises and at the Cawthron Aquaculture Park. Transport to the Aquaculture Park can be arranged if the student doesn’t have a car.
Key techniques/skills the student will learn
- General husbandry of colonial ascidians and transferable skills applicable for the wet lab culture of marine invertebrates for manipulative marine ecology experiments and aquaculture;
- Emerging and cutting edge field of ecological epigenetics;
- Become familiar with highly transferable molecular techniques such as DNA and RNA extraction, PCR, gel electrophoresis, and epigenetic techniques such as MS AFLP;
- Set up and maintenance of laboratory experiments manipulating environmental variables such as temperature, pH and salinity and measure response variables as indicators of physiological stress.
- Field skills if trips to collect Didemnum are required