Biological Sciences

How do antimicrobial peptides interact with cell membranes?

Supervisor

Assoc Prof. Jane Allison

Discipline

Biological Sciences

Project code: SCI085

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. The current antibiotic crisis means there is enormous interest in creating variants of these peptides that overcome their weaknesses (expensive to make, poor barrier crossing, and vulnerable to digestion). 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 (computer) simulations. Basic programming skills and familiarity with the command line would be useful, along with a background in chemistry, biochemistry or structural biology, but all you really need is enthusiasm and willingness to learn!

Allosteric regulation mechanism of Mycobacterium tuberculosis transcription factors

Supervisor

Assoc Prof. Jane Allison
Assoc Prof. Shaun Lott
Dr Stephanie Dawes

Discipline

Biological Sciences

Project code: SCI086

KstR and KstR2 are transcriptional repressors in Mycobacterium tuberculosis and are key targets for the development of new tuberculosis treatments. This project will involve using molecular dynamics simulations to investigate how these proteins bind to DNA and to their ligands, with an eye to understanding how ligand and DNA binding are allosterically communicated through the protein and whether it operates by a conformational selection or induced fit mechanism. You will learn how to set up, run, and analyse molecular dynamics (computer) simulations of proteins. There is also the possibility of using new analysis methods based on machine learning techniques. Basic programming skills and familiarity with the command line would be useful, along with a background in chemistry, biochemistry or structural biology, but all you really need is enthusiasm and willingness to learn!

Dog disturbance on West Auckland beaches

Supervisor

James Russell

Discipline

Biological Sciences

Project code: SCI087

Dogs may potentially be disturbing wildlife, especially birds, roosting and nesting on West Auckland beaches. The student will monitor West Auckland beaches over the summer recording bird and dog activity. The student will require a drivers licence and vehicle to access West Auckland beaches, must be comfortable working alone and walking along access tracks, and have proficiency in R statistics.

Drought impacts in native forest

Supervisor

Cate Macinnis-Ng
Ben Cranston

Discipline

Biological Sciences

Project code: SCI088

Droughts are predicted to increase in frequency and severity under future climates but we know very little about the impacts of droughts in native forests of Aotearoa. Our field-based drought experiment was established in 2017 in kauri forest in West Auckland. The successful candidate will undertake fieldwork, processing of samples in the lab and data management and analysis as part of this on-going project. An interest in plant ecophysiology is essential but all training will be provided.

Gene editing of flowering time genes in the model legume Medicago

Supervisor

Prof. Jo Putterill

Discipline

Biological Sciences

Project code: SCI089

Flowering time is an important trait for plants and crops because it affects plant productivity and yield. Legumes are the second most important group of crop plants after the cereals. Plants control flowering time differently so each group of plants requires analysis. Thus we study flowering time control in the model legume, Medicago.  
Skill development: You will learn plant molecular biology techniques including making gene editing constructs, designing primers, transformation of bacteria and plants and PCR. You will learn how to keep a research lab book, trouble shoot experiments and write up the project report. 
Skills required: Skills in molecular biology with an interest in plant development. BioSci papers such as 202, 351, 355 and 340 provide good background.  
Personal attributes: You need to be able to work both as part of a friendly team and independently, to be punctual, work hard and stay focused with strong attention to detail. 

Microglial TDP-43 in the post-mortem human Motor Neuron Disease brain

Supervisor

Primary: Dr Molly Swanson
Co-supervisor: Dr Emma Scotter

Discipline

Biological Sciences

Project code: SCI090

Degeneration of motor neurons causes loss of movement, speech, and eventually breathing in Motor Neuron Disease (MND). The primary pathological hallmark of MND is the cytoplasmic aggregation of TDP-43, observed in motor neurons in 97% of MND cases. TDP-43 is an RNA binding protein which, under normal physiological conditions, is found in the nucleus of all cells. The cytoplasmic aggregation of TDP-43 in motor neurons is hypothesized to cause a loss of its function, primarily driven by a corresponding loss or ‘clearing’ of TDP-43 from the nucleus. 
TDP-43 aggregation does not occur in all cells of the human MND brain and, as such, TDP-43 nuclear clearing in non-neuronal cells has not been investigated. One non-neuronal cell type of interest is microglia, the innate immune cells of the brain. Microglia alter their phenotype and function throughout MND and are hypothesized to shift from neurotrophic to neurotoxic states throughout disease. However, this change in phenotype has only been investigated relative to neuronal TDP-43 aggregates. This project will investigate whether microglial show TDP-43 nuclear clearing and how this relates to phenotype changes in post-mortem human MND brains.

Skills: Human brain anatomy, fluorescent immunohistochemistry, fluorescent imaging, automated image analysis

Expression of key adhesion molecules involved in extravasation, by endothelial cell models

Supervisor

Dr Catherine (Kate) Angel
James Hucklesby
Dr E Scott Graham

Discipline

Biological Sciences

Project code: SCI091

Immune cells must be able to exit the blood vasculature (extravasate) in order to survey the tissues of the body for potential threats. This process is regulated by a variety of cell adhesion molecules. In order to study extravasation in the lab, we need an endothelial cell model that expresses the appropriate adhesion molecules.

The aim of this project is to assess adhesion molecule expression by endothelial cell models. We will then investigate how the levels of these adhesion molecules change under inflammatory conditions. Collectively these data will allow us to identify cell model/s that can be used to study how immune cells extravasate out of blood vessels. 

This project would suit a Biomedical Science student.

During this research project you will develop your scientific writing skills and learn the following techniques: 
· Cell Culture
· Immunocytochemistry
· Flow-cytometry

How do birds use resources in cities?

Supervisor

Margaret Stanley

Discipline

Biological Sciences

Project code: SCI092

This project will explore how birds use different parts of the city and different infrastructure and resources. You will become a keen observer, developing skills in study design, bird counts and behavioural observations. Would be great if you already have some bird and plant ID skills, but you will develop these over the course of the project. Need own transport. Opportunity to work within a larger, supportive research team on parallel projects.

Biodiversity in schools

Supervisor

Margaret Stanley

Discipline

Biological Sciences

Project code: SCI093

Schools represent large areas of greenspace and can be an important place for children to connect to nature. But what sort of nature do school grounds have? This project will carry out greenspace surveys on school grounds in Auckland to understand how they contribute to biodiversity. This project involves some GIS skills (via Google Earth) and some fieldwork on school grounds – so plant ID skills will be useful. Will involve interacting with school staff (permissions). Need own transport. Opportunity to work within a larger, supportive research team on parallel projects.

Enzymatic tools to produce antibiotics

Supervisor

Dr Ghader Bashiri

Discipline

Biological Sciences

Project code: SCI094

Naturally occurring antibiotics with activity against human pathogens are of medical and commercial interest. These important molecules possess complex modifications which are catalysed enzymatically, and are difficult to replicate using conventional chemical methods. This project will focus on purification of enzymes from antibiotic-producing bacteria, which catalyse these essential modifications. The purified enzymes will be used to produce mature and biologically active antibiotics in vitro. 

Students with an interest in biochemistry, molecular biology or structural biology are encouraged to apply. During this project, students will gain hands-on experience in protein expression, purification and biochemical assays.

Novel antibiotics against tuberculosis

Supervisor

Dr Ghader Bashiri

Discipline

Biological Sciences

Project code: SCI095

Cofactors are crucial component of microbial metabolism, helping to carry out a wide variety of important cellular processes. Understanding how bacteria produce and use these cofactors allows us to identify new targets for much needed novel antibiotics. We investigate the biosynthesis and use of essential cofactors in Mycobacterium tuberculosis, the bacterium that causes tuberculosis. 

This project would suit students interested in molecular biology, biochemistry and structural biology. Students will gain skills in recombinant DNA technology, protein expression and purification. 

Making random DNA to test the idea of junk DNA

Supervisor

Austen Ganley

Discipline

Biological Sciences

Project code: SCI096

New DNA sequencing technologies mean we have a wealth of genomic sequence data, yet major questions about our genome remain unanswered. One of the most fundamental is how much of our genome is important versus how much does nothing (junk). This is very hard to answer: just because we see a region doing something (eg. being transcribed), how do we know it (eg. the transcript) is doing anything? To solve this problem, we are making random DNA and introducing it into cells to see what happens. If the random DNA behaves like other parts of the genome, then the other parts of the genome are likely to be junk, but if the random DNA behaves differently it would suggest the activities in “real” DNA are there for a purpose. The project will involve molecular biology techniques to make the random DNA and introduce it into cells.

Function of the novel gene TAR1

Supervisor

Austen Ganley

Discipline

Biological Sciences

Project code: SCI097

The TAR1 gene is a highly unusual gene located antisense to the essential ribosomal RNA gene (rDNA). Currently the role of TAR1 is unclear, but by virtue of being encoded in the highly repetitive rDNA, the number of TAR1 gene copies can vary dynamically. Based on this and work showing an association between Tar1 protein and mitochondria, we previously proposed that TAR1 acts to prevent spread of selfish mitochondrial genomes in the yeast, Saccharomyces cerevisiae. This project will involve experimentally testing this hypothesis. The basis of the work will be testing to see if Tar1p knockdown and overexpression modify the inheritance of selfish mitochondrial genomes in yeast. This will involve genetic work to construct the appropriate strains to test, and microbiological work to test mitochondrial genome inheritance.

Fixing the nitrogen problem by boosting the plant productivity – a molecular approach

Supervisor

Nijat Imin

Discipline

Biological Sciences

Project code: SCI098

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 peptides and molecular networks involved in nitrogen uptake and utilisation. Molecular biology skills are desired. You will be working alongside with a PhD student.

Cracking the symbiosis code: Unravelling how nodule formation and biological nitrogen fixation is controlled

Supervisor

Nijat Imin

Discipline

Biological Sciences

Project code: SCI099

We have identified master regulators that control nodulation and biological nitrogen fixation. This project requires students to use reverse genetic approaches to investigate the role key regulators that control nodulation. Molecular biology skills are desired. You will be working alongside with a PhD student.

Unique features in the genome of the threatened New Zealand hihi

Supervisor

Annabel Whibley
Anna Santure

Discipline

Biological Sciences

Project code: SCI100

The hihi (Notiomystis cincta) is an endangered native bird once widespread across the North Island but now limited to a remnant population on Te Hauturu-o-Toi and a handful of managed sanctuary populations. This project will set the recently assembled and annotated draft genome of the hihi alongside other published avian genome assemblies to explore features of the gene repertoire of hihi, which is the sole sequenced representative of an interesting branch of the avian phylogenetic tree. The project will involve gene family analysis to assess whether particular gene families have expanded or contracted, along with genome scans for signatures of selection and will provide a solid grounding in contemporary bioinformatics approaches to genome analysis. 

Although not required, it is desirable to have a background in genetics, computer science and/or statistics, and an interest or experience in bioinformatics / genome biology. 

The introduction history of invasive common starling birds to Aotearoa New Zealand

Supervisor

Annabel Whibley
Anna Santure
Dr Heather Battles

Discipline

Biological Sciences

Project code: SCI101

Common starlings (Sturnus vulgaris) were introduced from ports in the United Kingdom (UK) to Aotearoa New Zealand in the 1870s by local acclimatisation societies to help control grain pests. They have been incredibly successful at establishing in Aotearoa and globally, and are classified as one of the ‘top 100’ global invasive species due to their impacts on native ecosystems. This summer scholarship project will track the introduction and establishment of common starlings in Aotearoa, using literature searches of published journal articles and theses, historical newspaper content, and searching archives, with a particular focus on uncovering the minutes of the acclimatisation societies that introduced these birds. The project will aim to determine whether starlings were introduced once or repeatedly from the UK, and from which likely UK ports, and whether these introductions were successful. The research will provide context for a broader study that is analysing the levels of genetic similarity in starling populations across Aotearoa in order to determine if there are signals of local adaptation as starlings established in new habitats.

Although not required, desirable skills for the project include: experience using scientific / scholarly databases to find academic literature, experience using qualitative software such as NVivo, and experience in conducting systematic literature reviews.

Larval development in local marine invertebrates

Supervisor

Prof. Mary A. Sewell
Ph (09) 923-3758

Discipline

Biological Sciences

Project code: SCI102

The larval development of New Zealand’s invertebrate fauna is poorly described. This project will focus on development of local species of echinoderms and polychaetes and use field collected adults to produce larval cultures in the laboratory. Detailed descriptions and photographs of the embryo and larval stages will be used to develop a photo-identification guide for the Hauraki Gulf plankton. Ideally have previously taken BIOSCI 208 (Invertebrate Diversity).

Salinity tolerances of local echinoderms

Supervisor

Prof. Mary A. Sewell
Ph (09) 923-3758

Discipline

Biological Sciences

Project code: SCI103

Recent research has indicated that the salinity tolerances of some echinoderms are far greater than expected, with survival in <5 o/oo seawater (starfish: Barker and Russell 2008). Sea urchins are commonly preserved in the fossil record and the habitat in which they were found is then assumed to have been fully marine. In these experiments we will use laboratory experiments to measure the behavioural and physiological response of sea urchins to low salinity environments to aid future interpretation of the fossil record. Ideally have previously taken BIOSCI 208 (Invertebrate Diversity). 

Effect of biological membranes on amyloid inhibitory activity of natural polyphenols

Supervisor

Tina Nie
Garth Cooper

Discipline

Biological Sciences

Project code: SCI104

Amylin is one of several amyloidogenic proteins of which misfolding of the protein is implicated in disease, in this case Type 2 diabetes. Amyloid formation may be enhanced by interaction with cell membranes. Many natural polyphenolic compounds have been shown to inhibit the aggregation process. However, their activity in a lipid membrane environment is unclear. 
This project will involve:
• developing an in vitro membrane model system
• fluorometric assays 
• potentially some cell culture work
The student should have general lab skills such as pipetting and problem solving skills.

Determining why toxic and non-toxic cyanobacteria are so different

Supervisor

Dr Kim Handley
Dr Susanna Wood

Discipline

Biological Sciences

Project code: SCI229

This project will experimentally investigate the physiological differences between closely related toxic and non-toxic groups of cyanobacteria that form summertime blooms along riverbeds rivers globally, including in New Zealand. These two related groups of cyanobacterial species often co-occur in nature, and recent genomic analysis of these bacteria in our laboratory, show that the toxic group are smaller and less metabolically flexible then their non-toxic relatives. From this we predict that toxic members may co-habit with larger non-toxic species in order to steal resources. 

Skills required: Have successfully studied microbiology at stage 2 and/or 3. 

Travel: Will require spending time in Nelson to work at the Cawthron Institute for microbial cultivation experiments.

For more information on these cyanobacteria see our recent Nature blog post. 

Genomic analysis of methanotrophy in groundwater

Supervisor

Dr Kim Handley

Discipline

Biological Sciences

Project code: SCI230

Methanotrophs consume C1 compounds, such as methane. Our recently constructed dataset of hundreds of groundwater microbial genomes suggest methanotrophs might be common place in aquifers. This project will involve analysing these genomes to identify mechanisms indicative of methanotrophy.

Skills required: Have successfully studied microbiology at stage 2 and/or 3 AND/OR have a keen interest/skills in computational biology.

For more information on our laboratories work on aquifers see the following UoA news story

Searching for new antibiotics

Supervisor

Assoc Prof. Shaun Lott (ext 87074)

Discipline

Biological Sciences

Project code: SCI231

Antibiotics are a special category of drug that underpin modern medicine as we know it. Resistance to antibiotics is a growing global problem, which is estimated will place 10 million lives per year at risk by 2050 without action. This project will focus on understanding enzymes that are potential targets for new antibiotics. This project is best suited to someone with a strong interest in protein structure and function and/or microbiology.

The role of RhsA in bacterial competition

Supervisor

Assoc Prof. Shaun Lott (ext 87074)

Discipline

Biological Sciences

Project code: SCI232

RhsA is a conserved bacterial protein thought to be involved in bacterial competition. Based on our previous work published in Nature, our hypothesis is that RhsA delivers a toxic cargo protein to adjacent cells via the Type VI secretion system. 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 this poorly understood protein. This project is best suited to someone with a strong interest in protein structure and function.

Improving enzymes for plastic degradation

Supervisor

Assoc Prof. Shaun Lott (ext 87074)

Discipline

Biological Sciences

Project code: SCI233

Plastic waste is a world-wide problem. In New Zealand, more than 25,000 kg of plastic waste is discarded every day and only 7% of PET (polyethylene terephthalate ♳) plastic waste is fully recycled. This project will focus on engineering a more effective way to break PET down into its environmentally benign components, terephthatlic acid (TPA) and ethylene glycol (EG), by linking thermostable enzymes onto a novel, patented bio-scaffold. This will bring plastic waste into the circular economy - ōhanga āmiomio. This project is best suited to someone with a strong interest in the structure and engineering of proteins.