Biological Sciences

Cooperative breeding and reproductive success/failure in Pūkeko

Supervisor

Dr Kristal Cain

Discipline

Biological Sciences

Project code: SCI001

Pūkeko have incredibly flexible mating systems and often multiple females will lay eggs in a single nest. However, despite large number of eggs, few chicks survive. This project will investigate cooperative breeding behaviour and seeks to determine the causes of chick mortality.
This research will require fieldwork, careful observation of birds, and locating and monitoring nests of banded individuals. Fieldwork will be undertaken alongside PhD student. No experience required, however a strong background and interest in ornithology and/or animal behaviour is highly recommended. The field site is a 25-minute drive from city campus (near airport).
Prerequisites: A drivers licence and access to a vehicle.

 

The impact of garden sugar-feeders on native birds

Supervisor

Assoc. Prof. Margaret Stanley

Dr Kristal Cain

Dr Josie Galbraith (Auckland Museum)

Discipline

Biological Sciences

Project code: SCI002

Although we know people feeding bread & seeds to birds in their backyard has negative consequences for urban bird communities, we know nothing about how sugar feeders influence bird health, social interactions and bird communities. This project will involve behavioural observations of birds at sugar feeders, with an emphasis on the competitive interactions between tui and other species. There is also an opportunity to mistnet birds and colour band them to allow behavioural observations of individuals and social hierarchies. Will be working alongside a PhD student as part of a larger project.


Pre-requisites: Must have drivers licence (preferably full) and access to a car. Must enjoy watching birds! This study will occur in householder’s backyards, therefore good communication skills and sensitivity towards volunteer households are required.

Ecological genetics of ground beetles in alpine zones

Supervisor

Thomas Buckley

Discipline

Biological Sciences

Project code: SCI003

Characterise the genetic diversity of ground beetles from alpine zones in New Zealand

Learning skills: 1) Preparing insect specimens for sequencing; 2) work in a DNA lab; 3) prepare voucher specimens for identification and storing in a taxonomic collection, and 4) DNA sequence analysis including phylogenetics.

Applicants must have a background in genetics and an interest in Entomology

Using Gene Editing to knock out a candidate flowering time gene in the reference legume Medicago

Supervisor

Dr Mauren Jaudal and Professor Jo Putterill

Discipline

Biological Sciences

Project code: SCI004

Flowering time is an important agronomic trait that affects crop yield and productivity. The aim of this project is to use the Crispr-Cas9 gene editing technique in characterising putative flowering time gene candidates in Medicago truncatula, a reference legume closely related to alfalfa, peas and chickpeas. Techniques include molecular cloning, transformation in Medicago, DNA sequencing analysis, analysis of gene expression and plant phenotyping. This project would suit someone who has a strong interest in plant molecular biology, enjoys lab work and working with plants and displays good attention to detail.

Drought impacts on kauri

Supervisor

Cate Macinnis-Ng, Ben Cranston

Discipline

Biological Sciences

Project code: SCI005

The Kauri Drought Experiment is a field-based project exploring the impacts of drought on kauri physiology. This is an opportunity for a summer student to make a contribution to this ongoing research by assisting with field and laboratory work. An interest in fieldwork and plant biology is essential.

Lens protein biomaterials

Supervisor

Dr. Laura Domigan

Discipline

Biological Sciences

Project code: SCI006

Outline:

The project is to develop a biomaterial that can perform as a scaffold for tissue engineering applications. The proteins to be used in this project are from fish lenses, and are currently a low value by-product of the New Zealand fishing industry. We propose to recycle these proteins, and use them as high value biomaterials. In this project you will design, develop and characterise the developed new biomaterial in regards to their material properties and cellular response.

Key skills:

• Able to work independently, think creatively and propose innovative solutions.
• Experience with proteins and/or cell culture would be useful but is not necessary.

Individuality in Banded Rails

Supervisor

Dr Thomas Bodey

Discipline

Biological Sciences

Project code: SCI007

Cryptic species such as rails are typically difficult to study, and the ecology of many species remains poorly known. Taking advantage of an abundant, accessible population on a near-predator free island, this project will investigate various aspects of the ecology of the Banded Rail/moho pereru. In particular, this study will provide a mark-recapture assessment of population size and use unique identifiers to enable study of individual variation in field assays of behaviour and territoriality.

The project will involve fieldwork on offshore islands in the Hauraki Gulf so the student will need to be able to commit to time away from Auckland. There is also the potential for nocturnal work during these trips. Work will be undertaken alongside research fellow Thomas Bodey.
Project description
Skills to be developed include: trapping and animal handling, behavioural observation fieldwork skills, spatial analyses, general fieldwork H&S, and potentially radio tracking. Students with a strong interest in ecology and/or animal behaviour are particularly encouraged to apply.

Building a global dossier of strategies and legislations related to the management of alien and invasive species

Supervisor

Shyama Pagad

Discipline

Biological Sciences

Project code: SCI007

The New Zealand office of the Invasive Species Specialist Group ISSG of the Species Survival Commission SSC of the International Union for Conservation of Nature IUCN is based within the School of Biological Sciences at the Tamaki Campus. The IUCN ISSG is the custodian of the indicator 15.8.1 linked to indicator 15.8 of Goal 15 of the 17 Sustainable Development Goals (SDG) set by the United Nations.
SDG 15.8.1 measures the proportion of countries adopting relevant national legislation and adequately resourcing the prevention and control of invasive alien species. The IUCN ISSG has completed the baseline of this indicator (see https://www.bipindicators.net/indicators/adoption-of-national-legislation-relevant-to-the-prevention-or-control-of-invasive-alien-species), and committed to complete an update by the early 2019.

This project seeks to build a dossier of national strategies and legislation related to the prevention of introduction and management of alien and invasive species, leading to the update of this indicator

Two key resources will be consulted in addition to national government resources- the ECOLEX database – the largest Environmental Law database and the legislative and policy database of the Food and Agriculture Organisation of the United Nations (FAO) FAOLEX database.

An interest in Environmental Law would be useful. Skills required Data collection, Data Analysis, Reporting.

Months available December 2018 and January 2019

Gut microbiome and metabolomic interactions in a mouse model of Autism Spectrum Disorder

Supervisor

Assoc. Prof. Mike Taylor

Discipline

Biological Sciences

Project code: SCI009

Recent evidence links the gut microbiome with various neurological conditions such as autism spectrum disorder (ASD). The gut-microbiota-brain axis describing the communication between gut microbes and the brain (and vice versa) may be involved in ASD. The gut microbiome of a mouse model of autism will be investigated used DNA-based (next generation sequencing) microbiome techniques and metabolomic analysis. This project will suit a student with a strong interest in microbiology, basic microbiology skills and with a great attention to detail.

Plant peptide hormones play important roles in coordinating plant growth and response to the environment, including responsing to nutrient demand. This project requires students to use transgenic and direct peptide application approaches to investigate the role of peptide in nutrient uptake and the impact on plant growth. Molecular biology skills are essential.

Gut microbiome of the critically endangered kākāpō

Supervisor

Assoc. Prof. Mike Taylor

Discipline

Biological Sciences

Project code: SCI010

Recent research from our lab indicates that the kākāpō gut microbiome is dominated by 1-2 bacterial species, which is unusual for a herbivore. We aim to determine the role(s) and strain-level identity of these dominant bacteria using a combination of cultivation and molecular biology (including next-generation DNA sequencing) approaches. This project will suit a student with a strong interest in microbiology, basic microbiology skills and a willingness to learn and master new techniques.

Role of peptide hormones in nutrient uptake and plant productivity

Supervisor

Nijat Imin

Discipline

Biological Sciences

Project code: SCI011

Plant peptide hormones play important roles in coordinating plant growth and response to the environment, including responsing to nutrient demand. This project requires students to use transgenic and direct peptide application approaches to investigate the role of peptide in nutrient uptake and the impact on plant growth. Molecular biology skills are essential.

How does whole genome duplication assist native plant species survival?

Supervisor

Professor Bill Lee

Discipline

Biological Sciences

Project code: SCI012

The aim of the research programme is to test whether there are any general rules that can predict successful evolutionary outcomes of whole-genome duplication in fern and angiosperm lineages. The student will assist with comparative experiments on several lineages investigating how plants with different ploidy levels cope with low light, cool temperatures and water stress. We require a student interested in ecophysiology and/or evolutionary ecology. The project is based in Dunedin but travel costs are covered.

Improving pancreas function and decreasing diabetes risk using a plant polyphenol

Supervisor

Prof. Sally Poppitt
Dr. Ivana Sequeira

Discipline

Biological Sciences

Project code: SCI013

Weight gain and the poor metabolic health, e.g. type 2 diabetes (T2D), which develops as a consequence is a global health concern. The National Science Challenge High Value Nutrition (NSC-HVN) program is focused on developing nutritional solutions to maintain optimal health across a range of platforms, including body weight and metabolic health. The HVN Peak Nutrition for Metabolic Health [PANAMAH] platform aims to identify established and novel blood markers of increased T2D risk; and to undertake nutritional interventions that target these biomarkers and so decrease T2D progression in high risk individuals. Amylin ‘misfolding’ is one of these targets.
T2D occurs when the body becomes resistant to the action of a key pancreatic hormone insulin and/or when the insulin secreting cells in the pancreas start to fail. Recent important evidence has now shown that another pancreatic hormone amylin is also important. Amylin circulating in the blood has the tendency to ‘misfold’ and then be deposited as toxic aggregates within the pancreas. This is a common occurrence, found in >90% of patients with T2D. These amylin aggregates progressively replace the insulin-producing cells and is a major cause of failure of the pancreas and so the development of T2D.
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) set up and conduct of clinical trials, (b) working with participants and adhering to good clinical practice (GCP) guidelines.

 

Costs of exaggerated weaponry in New Zealand harvestmen

Supervisor

Greg Holwell
Chrissie Painting

Discipline

Biological Sciences

Project code: SCI014

Animal weapons are structures used in male-male competition to access mates. Variation in weapon size between individuals occurs because not all males have the resources to have the biggest weapons. The New Zealand harvestmen brandish extreme weaponry with unique variation in weapon size and shape (forming discrete “morphs”) even within a single species. To help explain how this variation has evolved over time, we are exploring whether males invest in different physiological strategies. A major aim of this project will be to conduct experiments to test the relative stamina/speed of each male morph. Further, students will set up interactions to observe the fighting style of each morph and to determine how fights are resolved. This project will be conducted in Waitomo, NZ and the student should be willing to be away from Auckland for extended periods of time. Nocturnal field work will be a large component of this project so the student should be comfortable working alongside PhD student Erin Powell at night in the forest.

How do antimicrobial peptides interact with cell membranes?

Supervisor

A/Prof. Jane Allison

Discipline

Biological Sciences

Project code: SCI015

Antimicrobial peptides (AMPs) are excreted by cells to protect them from pathogens in the environment, and are part of the innate immune system of all multicellular organisms. These peptides function primarily by targeting the cell membrane, with selectivity for pathogens based on differences in the membrane lipid composition. Creating variants of these peptides that overcome their weaknesses (expensive to make, poor barrier crossing, and vulnerable to digestion) is of great interest given the current antibiotic resistance crisis. The mechanism of how they interact with and disrupt cell membranes is difficult to study experimentally, but molecular dynamics simulations allow this to be characterised at an atomic level of detail. We are working on several different types of antimicrobial peptides to determine how they affect bacterial cell membranes. You will learn how to build models of antimicrobial peptides and cell membranes, and how to set up, run, and analyse molecular dynamics simulations. Basic programming skills and familiarity with the command line would be useful, along with a background in chemistry, biochemistry or structural biology, but enthusiasm is sufficient.

Effects of stressors on early stages of large brown algae

Supervisor

Wendy Nelson

Discipline

Biological Sciences

Project code: SCI016

Early life stages of large brown algae are poorly documented for many NZ species – yet these species form forests in the nearshore coastal zone that are critical habitat for many species and highly productive. This project builds on research into the impacts of stressors (e.g. sediment, ocean acidification, temperature) on early development stages of key species of major genera (e.g. Marginariella, Cystophora, Landsburgia, Carpophyllum).

Egg release – Landsburgia
Eggs (upper) and sperm (lower) release – Marginariella

The project involves some field work (collecting samples) and then culture studies. This involves lab work and microscopic observations on development and growth, going from the release of eggs and sperm through to development of germlings in growth chambers where temperature and daylength can be controlled and the effects of key factors can be tested experimentally.

The position is based in Wellington at NIWA, Greta Point.

Save the honeybees … or not! Honeybees, native plants and pollination

Supervisor

Dr Anne Gaskett
MSc Freya Jackson

Discipline

Biological Sciences

Project code: SCI017

Aotearoa relies on honeybees for pollinating fruit and making honey - it’s commercially important to protect bees from threats such as varroa mite and pesticides … But are bees all good? Our native plants evolved to be pollinated by native solitary bees, flies, birds and bats. Do honeybees steal nectar without pollinating flowers? Or, are the important replacements for native pollinators if they are absent? How do the colours of Aotearoa’s flowers compare with European species that evolved with honeybees?
This project involves field, lab and computer work. We will have multi-day trips to local and remote sites. You will work with us to record the behaviour of insects on flowers, identify plants and insects, and measure the colours of flowers. Back at the lab, you’ll be sorting insects for ID. At the computer, you will be organising data in excel spreadsheets and learning to analyse spectral measurements and model these into animal vision systems (using R and other software), and writing up your work.
Essential qualities: You must love the outdoors, nature, making discoveries, wrangling data, and sharing kai and working together. You will be patient and have excellent attention to detail, have great fitness and be comfortable with fieldwork in remote areas (in a team) and overnight stays in shared accommodation with others. You will be excited about the possibility of publishing our research and strongly considering postgraduate studies.
Desirable (but not essential) qualities: drivers license, fieldwork experience (e.g. in ugrad classes, tramping), familiarity with R, ecology courses e.g. BIOSCI323 Plant Diversity, BIOSCI337 Animal Behaviour, BIOSCI320 Entomology. Background in beekeeping, fruit growing, farming, conservation. Community connections with land managers (e.g. iwi, conservation groups).
We can provide field gear (e.g. raincoat, waterproof pants, gumboots etc.) and will cover fieldwork costs (e.g. transport, food, accommodation).
This project would not suit someone with a bee allergy! We welcome applications from all students with the ‘essential’ qualities. We look forward to welcoming you, your skills and knowledge to our lab group. Naku te rourou nau te rourou ka ora ai te iwi – with your basket and my basket the people will live (working cooperatively, we will do well)

Investigating a new biosynthetic pathway in the kiwifruit pathogen Psa.

Supervisor

Dr Esther Bulloch

Assoc. Prof. Matt Templeton

Discipline

Biological Sciences

Project code: SCI018

Exports of kiwifruit bring in more than $1.5 billion to the New Zealand economy each year. The kiwifruit pathogen Pseudomonas syringae pv. actinidiae (Psa) was first discovered in New Zealand in 2010 and over the subsequent years caused major disruption of the industry. We have discovered a new biosynthetic pathway in particularly devastating variants of Psa. This pathway appears to make a small molecule that Psa may use to control interactions with the kiwifruit host plant. You will help us identify this small molecule by studying enzymes along the pathway. This project would be particularly suited for someone with an interest in biochemistry, molecular biology or chemistry.

The influence of the human vaqinal microbiota on the virulence of Trichomonas vaginalis

Supervisor

Dr Augusto Simoes-Barbosa

Discipline

Biological Sciences

Project code: SCI019

Our laboratory examines the influence of the vaginal commensal bacteria on the virulence of the human pathogen Trichomonas vaginalis. This parasitic protozoan is the causative agent of the most common sexually transmitted infection worldwide known as trichomoniasis. You research aims to continue an investigation on the interactions of the protozoan with the biofilm produced by a vaginal bacterium. The biofilm is a potential substrate that the parasite might take advantage of, such as for nutrition and adhesion. Our preliminary investigation suggests that this biofilm helps the parasite with migration and adhesion and it might increase resistance to drug treatment. Your research aims to describe and understand the consequences of the biofilm produced by the vaginal commensal bacteria on facilitating the virulence of T. vaginalis. Your work will involve microbiology and cell biology with methodologies that may comprise of culture of microorganisms, spectrophotometry, fluorescence microscopy, flow cytometry among others. You will work close with a PhD student in our laboratory during the summer.

There is a potential of producing results that are publishable. Also, there is potential for a subsequent investigation which could lead to a Hons or MSc research project.

Making an interventional radiological procedure more efficient

Supervisor

A/Prof Anthony Phillips
Mr Bruce Stokes
Prof John Windsor

Discipline

Biological Sciences

Project code: SCI020

This studentship relates to development of a device for improving outcomes from a particular interventional radiological procedure (minimally invasive procedure in patients). The project will involve literature searching and bench device prototyping work of a new device. An interest or experience in biomedical devices and health related interventions is an advantage. An interest in making simple mechanical devices is also an advantage. This would be a good project for a biomedical or biotechnology student but that is not an absolute pre-requisite.

Optimising a new endoscopic procedure

Supervisor

A/Prof Anthony Phillips
Prof John Windsor
Mr Bruce Stokes

Discipline

Biological Sciences

Project code: SCI021

This studentship relates to development of a device for enabling a new intervention to be performed using an endoscope (fibre-optic device used to look inside body cavities). The project will involve literature searching and bench device prototyping work of a new device. An interest or experience in biomedical devices and health related interventions is an advantage. An interest in making simple mechanical devices is also an advantage. This would be a good project for a biomedical or biotechnology student but that is not an absolute pre-requisite.

Designing peptide ligands to Erp44, a potential drug target

Supervisor

Alok K. Mitra
Henry Tang

Discipline

Biological Sciences

Project code: SCI022

We are interested in understanding the important role that Erp44, an endoplasmic reticulum chaperone, plays at the structural/functional level to regulate oligomerization of adiponectin. Adiponectin is a critical player in insulin sensitization and therefore in the obesity related disorders such as type 2 diabetes. The correct oligomeric assembly of adiponectin is critical for its function and our goal is to progressively improve peptide ligands that enhance the secretion of high-molecular-weight adiponectin by interfering with the Erp44-adiponectin interaction. For this purpose, rationally designed peptides will be synthesized and their binding to Erp44 revealed by x-ray crystallography to iteratively lead to structure-based drug design.
Student with noted interest in Structural biology and expertise in biochemical/biophysical techniques will be most appropriate.

Cryopreservation of mitochondrial function in tissues: mimicking freeze tolerant animal

Supervisor

A/P Anthony Hickey

Discipline

Biological Sciences

Project code: SCI023

Mitochondria appear to play ever increasing roles in disease states, so we measure mitochondrial function to test function in various tissues such as brain, heart, liver muscle…However, tissues currently must be assessed almost immediately, as mitochondria appear to be very labile.
We have some ideas on how we can preserve mitochondrial function so we can test tissues another day, and therefore bank tissues from studies.
The student will learn how to measure various functions of mitochondria test different approaches to cryopreservation.

Turning down the pilot light for shrimp metabolism

Supervisor

A/P Anthony Hickey

Discipline

Biological Sciences

Project code: SCI024

We have a potential method to sedate aquatic animals using tricks of hibernators. This is useful for supressing metabolism in animals they we may want to ship. This is a simple project that will involve the student imaging transparent glass shrimps exposed to various natural sedatives.

A global assessment of the impacts of invasive alien species on marine turtles

Supervisor

Souyad Boudjelas

Discipline

Biological Sciences

Project code: SCI025

Nearly all species of marine turtle populations are endangered. Poaching and over exploitation for their meat, skin, shell and eggs are key threats.

Turtles are also at risk from invasive alien species especially in their nesting/breeding sites. The three main impact mechanisms are predation (eggs and hatchlings), habitat alteration due to invasive alien plant species, resulting in decline in population numbers and loss of habitat and physical disturbance.

Eight turtle species are listed on the Convention on Migratory Species (CMS) Appendix I & II- Green turtle (Chelonia mydas), Loggerhead turtle (Caretta caretta), Hawksbill turtle (Eretmochelys imbricata), Kemp's Ridley turtle (Lepidochelys kempii), Olive Ridley turtle (Lepidochelys olivacea), Leatherback (Dermochelys coriacea), Podocnemis expansa (only Upper Amazon populations and Appendix II - other populations of P. expansa) and the Flatback turtle Natator depressus. Hawksbill turtle, Kemp’s Ridley turtle are classified as ‘Critically Endangered (CR)’ in the IUCN Red List of Threatened Species. Green turtle is classified as ‘Endangered (EN)’, Leatherback, Loggerhead and Olive Ridley turtle as ‘Vulnerable (VU)’. The South American River turtle is classified as at ‘Least Concern (LC), however the Upper Amazon populations are at a greater risk than the other populations. Flatback turtle is listed as Data Deficient.

This project will undertake a global assessment of invasive alien species impacts on the nesting and breeding sites of marine turtles and assess the extent of this risk. A peer-reviewed publication of the results is planned.

Data/information on nesting sites and breeding grounds across the world are available from the SWOT Database (The State of the World's Sea Turtles). Contact for data, information and peer-review is planned with global experts of the Marine Turtle Specialist Group of the International Union of Conservation of Nature IUCN.

An interest in Endangered species would be useful. Skills required Data collection, Data Analysis, Reporting.

Months available December 2018 and January 2019

What drives colony growth rates and the production of reproductive castes in bumble bee colonies?

Supervisor

David Pattemore

Discipline

Biological Sciences

Project code: SCI026

Based at Plant & Food Research’s Ruakura campus, this project will involve running experiments on observation colonies of the bumble bee Bombus terrestris. Bumble bee colonies only survive for a few months, and vary significantly in their rate of growth, peak size, and the time at which they start to produce males and new queens. By experimentally manipulating the flow of food resources into the colonies and other potential factors, the aim of this project is to further our understanding of the drivers of this variation. We’re looking for a student with a keen eye for observing animal behaviour, an interest in the evolution of eusociality in insects, and a willingness to work hands-on with stinging insects.

Supercharging mitochondria to maintain brain function

Supervisor

Mr Jin Ng (Year 3 PhD student)
A/P Nigel Birch
A/P Tony Hickey

Discipline

Biological Sciences

Project code: SCI027

Mitochondria play an important role in maintaining neuronal cell health. Dysfunctional mitochondria are a hallmark of the aging brain and are implicated in the onset of neurodegenerative diseases such as Alzheimer’s and Parkinson’s disease1. Healthy neuron function is dependent on mitochondrial processes, which include the maintenance of mitochondrial redox state, networks, control of superoxide production and cellular bioenergetics. Therapeutics that target and improve these processes may impede the progression of aging-associated mitochondrial dysfunction. One source of therapeutics that targets brain health appears to come from dietary phytochemicals2.

This project will investigate the effect of several plant metabolites, at human physiological concentrations, on neuronal mitochondrial function. The selection of plant metabolites is driven by previously published results of our collaborators3. Promising plant metabolites will then be screen in an in vitro model of Alzheimer’s and Parkinson’s using differentiated SH-SY5Y human neuroblastoma cells. The student will use several medium through-put assays to measure metabolic activity (MTT assay), cellular necrosis (LDH assay), and cellular respiration (in collaboration with Associate Professor Tony Hickey). Other techniques used may include high-content screening to measure different parameters of mitochondrial networks and superoxide production.

The ideal student will have an interest in molecular cellular neuroscience and completed undergraduate courses in cell biology, molecular biology and/or biochemistry. This project will suit someone with a passion for biomedical science, in particular, cellular and molecular aspects of neurodegeneration.


1. Lin, M. T., & Beal, M. F. (2006). Mitochondrial dysfunction and oxidative stress in neurodegenerative diseases. Nature, 443(7113), 787–795. https://doi.org/10.1038/nature05292

2. Murugaiyah, V., & Mattson, M. P. (2015). Neurohormetic phytochemicals: An evolutionary-bioenergetic perspective. Neurochemistry International. https://doi.org/10.1016/j.neuint.2015.03.009

3. Tang, J. S., Vissers, M. C. M., Anderson, R. F., Sreebhavan, S., Bozonet, S. M., Scheepens, A., & Melton, L. D. (2018). Bioavailable Blueberry-Derived Phenolic Acids at Physiological Concentrations Enhance Nrf2-Regulated Antioxidant Responses in Human Vascular Endothelial Cells. Molecular Nutrition & Food Research, 62(5), 1700647. https://doi.org/10.1002/mnfr.201700647

Searching for new antibiotics effective against TB

Supervisor

A/Prof Shaun Lott

Discipline

Biological Sciences

Project code: SCI028

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

Supervisor

A/Prof Shaun Lott

Discipline

Biological Sciences

Project code: SCI029

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.

Cows unplugged: molecular mechanisms of the rumen’s response to extra dietary protein

Supervisor

Dr Mallory Crookenden
Prof Russell Snell
Dr John Roche

Discipline

Landcare Research

Project code: SCI126

This project provides an opportunity to conduct research aligned with New Zealand’s dairy industry. The rumen is the largest compartment of a cows’ stomach. It is here that feed (i.e., pasture) ferments, with the help of microbes, before being absorbed for post-digestive metabolism. Small, finger-like projections called papillae increase the surface area of the stomach wall for nutrient absorption. Changes in feed composition alter rumen papillae physiology and microbial populations. We can use gene expression to investigate these physiological changes in rumen tissue.

We have collected rumen papillae tissue samples from dairy cows before and after an increase in dietary crude protein. This project will investigate the effect of dietary crude protein on molecular changes in rumen papillae compared with control animals. This project will provide valuable insight into rumen physiology and potentially help reduce dairying’s environmental footprint through cow genetics.

This project is suitable for someone with a molecular biology and/or physiology background. It will involve molecular techniques including RNA extraction, target gene selection, primer design, and gene expression analysis using RT-qPCR.
 

Join the single molecule revolution

Supervisor

Dr Richard Kingston

Discipline

Biological Sciences

Project code: SCI225

The ability to image single molecules with a light microscope is revolutionizing molecular and cellular biology. Using single molecule techniques, developed over the past decade, it is now possible to monitor conformational changes in individual biological molecules; investigate molecular interactions; and track molecular movement - both inside and outside the cell.

This year SBS will acquire the equipment to perform Total Internal Reflection Fluorescence Microscopy (TIRFM). This technique allows single molecule observation of fluorescently-labeled proteins and nucleic acids. In this project, you will help develop protocols for using the new equipment, and hopefully make our first single molecule observations.
The project is suitable for someone with a background in protein science, and an interest in applying physical techniques to understand how molecular machinery works.