Biological Sciences

  1. » A forest drought experiment
  2. » Forensic analysis of pathogens and pests by eDNA analysis
  3. » Microbial community analyses of ecosystem health
  4. » Recombination and sexual conflict – testing hypotheses for sex differences in recombination in birds
  5. » What forces stabilize the retroviral capsid?
  6. » Structural analysis of viral proteins that have been captured and repurposed by the host.
  7. » Costs of exaggerated weaponry in New Zealand harvestmen
  8. » Macrophage reprogramming and chronic inflammation: exploration of the roles of plasmin system proteins in human models
  9. » Song rates and structure across breeding stage in Pīwakawaka (NZ fantails)
  10. » Revealing the hidden variation in human ribosomal RNA genes
  11. » Developing new beer yeast
  12. » How does a silver bullet work – the structure of a protein toxin
  13. » Protein biomaterials for corneal regeneration
  14. » New Protein Nanostructures for Bionanotechnology
  15. » Protein nanofibril scaffolds for wound healing
  16. » Interactions between rats & hedgehogs: does pest control mean more hedgehogs in urban reserves?
  17. » The role of plant hormones for Apple Cell differentiation
  18. » Cryopreservation of mitochondrial function in tissues: mimicking freeze tolerant animal
  19. » Turning down the pilot light for shrimp metabolism
  20. » Deciphering neuropeptide receptor signalling
  21. » Structural investigation of antibiotic biosynthesis pathways
  22. » How pathogenic bacteria sense oxidative stress?
  23. » Accelerating flowering in the reference legume Medicago
  24. » Finding a floral repressor in the reference legume Medicago
  25. » New devices to improve wound healing

A forest drought experiment


Supervisor

Cate Macinnis-Ng

Discipline

Biological Sciences

Project code: SCI001

This is a field-based project measuring the impact of drought on kauri trees at the University of Auckland’s Huapai Scientific Reserve. The student will contribute to a larger ongoing project. The work will include data management and manipulation and regular field trips. There may be an opportunity to climb the trees for canopy measurements if the weather is suitable. An interest in plant ecophysiology is essential.

Forensic analysis of pathogens and pests by eDNA analysis


Supervisor

Dr. Gavin Lear

Discipline

Biological Sciences

Project code: SCI002

Large quantities of ‘environmental DNA’ is continually excreted and shed in the environment by living organisms. For example, animals can be detected based on DNA excreted into environments from their urine, faeces, hair and skin. Similarly, plant DNA originating from roots, root exudates and litter can provide information about plant community composition. Consequently, DNA extracted from samples of soil, water or other material may simultaneously provide information about the occurrence, distribution and diversity of organisms and communities. In this project you will investigate the potential of eDNA for monitoring the presence and abundance of pests and pathogens across the New Zealand landscape. Your work may have significant implications for future biodiversity monitoring and biosecurity assessments.

Microbial community analyses of ecosystem health


Supervisor

Dr. Gavin Lear

Discipline

Biological Sciences

Project code: SCI003

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.

Recombination and sexual conflict – testing hypotheses for sex differences in recombination in birds


Supervisor

Anna Santure

Discipline

Biological Sciences

Project code: SCI004

Recombination, the exchange of DNA between maternal and paternal chromosomes during meiosis, is a fundamental biological process that is essential during meiosis, with the number of recombination events regulated to ensure accurate segregation of chromosomes. Thus, tight regulation of recombination is expected, but variable rates of recombination may be favoured in different environments or selective contexts. One of the most commonly observed patterns of variation in recombination rate is that males and females may differ in their rates of recombination across the genome, termed heterochiasmy. A number of hypotheses have been proposed to explain heterochiasmy, each with different predictions as to the direction and strength of sex differences in recombination. In this project, we will gather data from across avian species and test the support for the hypothesis that sexual conflict may lead to heterochiasmy.

This project requires the student to have completed BIOSCI 351, BIOSCI 322 and BIOINF 301.  

What forces stabilize the retroviral capsid?


Supervisor

Richard L Kingston

Discipline

Biological Sciences

Project code: SCI005

The immunologist Peter Medawar described a virus as "a piece of bad news wrapped up in a protein”. The news that is delivered by Human Immunodeficiency Virus (HIV), and other retroviruses, is uniformly terrible. A significant proportion (6-14%) of vertebrate genomes derives from retroviruses – a testament to the importance and persistence of these ancient pathogens. Consequently, the architecture of the irregularly shaped protein capsid that surrounds the retroviral genome, and acts as its delivery vehicle, has been intensively studied. The capsid enters the cytoplasm of a newly infected cell and subsequently falls apart during its journey to the nucleus, an event that is coupled with the initiation of viral replication

While capsid assembly and disassembly are central events in the viral replication cycle, the physical basis for these events is poorly understood. In this project you will develop novel in vitro assays for studying self-assembly of the Rous Sarcoma Virus Capsid Protein. This will lead to a deeper understanding of the physical forces that cause the capsid to assemble, and allow it to fall apart.

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.

Structural analysis of viral proteins that have been captured and repurposed by the host.


Supervisor

Richard L Kingston

Discipline

Biological Sciences

Project code: SCI006

Retroviruses, such as the Human Immunodeficiency Virus (HIV), cause immunological disorders and cancers in many animals. 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 have been captured and re-purposed 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 NMR spectroscopy). 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.

Costs of exaggerated weaponry in New Zealand harvestmen


Supervisor

Greg Holwell

Chrissie Painting

Discipline

Biological Sciences

Project code: SCI007

Many animals have weapons used in male-male combat to access mates. Because these weapons are costly to produce, males with larger weapons may trade-off with other traits. The New Zealand harvestmen present a unique case where three weapon morphs, including two large “major” morphs, coexist. A major aim of this project will be to set up interactions to observe the fighting style of each morph and to determine how fights are resolved. Additionally, the student will conduct experiments to test the relative stamina/speed of each male morph. 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 at night in the forest. Field and lab work will be undertaken alongside PhD student, Erin Powell. Only students with a background in ecology and/or animal behaviour and/or entomology should apply.

Macrophage reprogramming and chronic inflammation: exploration of the roles of plasmin system proteins in human models


Supervisor

Nigel Birch

Rod Dunbar

Evert Loef

Discipline

Biological Sciences

Project code: SCI008

Chronic inflammation is a major driver of disease.  It contributes to the pathogenesis of cardiovascular disease, cancer, neurodegenerative disease and many others.  These conditions reflect, in part, a failure of the mechanisms to resolve inflammatory processes.  The resolution of inflammation is complex involving multiple cellular systems and inflammatory mediators.  Very recent research in mice including a mouse model of lipopolysaccharide-induced inflammation has identified a role for the serine protease plasmin in inflammation resolution1.  Plasmin was shown to increase the influx of macrophages with an anti-inflammatory phenotype into the pleural cavity of mice.  Further research suggested plasmin, and its precursor plasminogen, induced macrophage reprogramming to an anti-inflammatory phenotype leading to the proposal that modulation of the plasmin system could represent a new therapy to resolve inflammation2

This project will investigate a role for plasmin in macrophage reprogramming in human immune cells.  Monocytes will be isolated from blood donors and conditions explored for their differentiation into M1 macrophages which play a role at the beginning of inflammation, and anti-inflammatory (M2) and proresolving (Mres) macrophages which play key roles in the progression and resolution of disease.  The different phenotypes will be characterized using fluorescent activated cell sorting (FACS) and the roles of plasmin investigated using quantitative real time PCR to monitor levels of expression, plasmin inhibitors and plasmin knockdown to reduce plasmin expression, and plasmin enzymatic assays to track plasmin activity.

The student will work closely with Evert Jan Loef, a Postdoctoral Research Fellow working in the Birch and Dunbar laboratories.  It 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.

References

  1. Plasmin and plasminogen induce macrophage reprogramming and regulate key steps of inflammation resolution via annexin A1. Sugimoto. MA et al., Blood (25 May, 2017) 129, 2896 – 2907
  2. Reprogramming macrophages by plasmin. Pelegrin, P.  Blood (25 May, 2017) 129, 2823

Song rates and structure across breeding stage in Pīwakawaka (NZ fantails)


Supervisor

Dr. Kristal E Cain

Discipline

Biological Sciences

Project code: SCI009

This project will examine how song rates and structure change across the breeding season. Data from this research will be used to test for sexual and non-sexual functions of different songs types in pīwakawaka (NZ fantail). This research will require, careful observations of birds, locating and monitoring nests, recording songs and analysing song using software. No experience is required, however, a strong interest in animal behaviour and patience when observing free-living birds is critical. 

Revealing the hidden variation in human ribosomal RNA genes


Supervisor

Dr. Austen Ganley

Discipline

Biological Sciences

Project code: SCI010

Variation is the cornerstone of genetics, and is critical for understanding human disease. A key change in many cancers is an increase in expression of the ribosomal RNA genes (rDNA). Despite this, virtually nothing is known about variation in the rDNA in humans, and how this might influence these rDNA expression changes. This project will characterize human rDNA variation using the wealth of available human genome sequence data. The project is strictly computational in nature. While a computational background is not required, you will need to be willing to learn how to perform computational analyses. Therefore, the project would suit someone who enjoys data analysis.

Developing new beer yeast


Supervisor

Dr. Austen Ganley

Discipline

Biological Sciences

Project code: SCI011

Yeast are a critical contributor to beer. However, the ability to improve the properties of yeast for beer fermentation is limited, as almost all beer yeast strains have lost the ability to go through the sexual cycle. To overcome this hurdle, this project will involve isolating wild yeast from the environment that still retain the sexual cycle, and using strategies to make these wild yeast suitable for beer fermentation. This would suit a student interested in microbiology, evolution, and/or biotechnology.

How does a silver bullet work – the structure of a protein toxin


Supervisor

A/P Alok K. Mitra

Dr. Paul Young

Discipline

Biological Sciences

Project code: SCI012

Coded by a plasmid of a soil bacterium Serratia entomophila, antifeeding prophage (Afp) is a multi-protein complex pathogenic to a New Zealand insect pest that destroys grass pastures. The pathogenicity arises due to the ability of Afp to deliver a protein toxin Afp18 into the pest. Due to the fact that unlike for other related systems, Afp’s host is eukaryotic, it has raised the possibility that apart from the benefit of using Afp as a chemical-free biological pesticide, Afp may be tailored for targeted delivery in anti-tumour immunotherapy. This requires an elucidation of a high-resolution 3D structure of Afp18, a multi-domain 200kD protein with limited known homology to any other protein. We are pursuing this research in collaboration with Dr. Mark Hurst of Ag Research. In this study, Afp18 will be over expressed and purified and subjected to cryo-EM and X-ray crystallographic studies. Strong interest in Structural Biology is a primary requisite.Yeast are a critical contributor to beer. However, the ability to improve the properties of yeast for beer fermentation is limited, as almost all beer yeast strains have lost the ability to go through the sexual cycle. To overcome this hurdle, this project will involve isolating wild yeast from the environment that still retain the sexual cycle, and using strategies to make these wild yeast suitable for beer fermentation. This would suit a student interested in microbiology, evolution, and/or biotechnology.

Protein biomaterials for corneal regeneration


Supervisor

Laura Domigan

Discipline

Biological Sciences

Project code: SCI013

Corneal replacement is becoming increasingly common as the age of the population increases and there is an insufficient supply of donor corneas – around 10 million people suffer corneal blindness worldwide but only 100,000 replacements are performed per annum because of the lack of donors. This has lead to research into the creation of corneal analogs. One way this is done is through tissue engineering; where a substrate (either synthetic or biological) is used to guide cell growth and tissue regeneration.  The larger goal of this project is to create new protein biomaterials, suitable for corneal regeneration. In this project you will design and construct new protein based materials. 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.

New Protein Nanostructures for Bionanotechnology


Supervisor

Juliet Gerrard

Discipline

Biological Sciences

Project code: SCI014

Nanotechnology or nanoscience involves the study and manipulation of matter at the molecular level leading to the formation of materials, structures or devices ranging from 1 to 100 nanometers in size.  Proteins are attractive raw materials as building blocks of nanostructures due to their ease of preparation and wide choice found in nature that are known to self-assemble.  Self-assembly is an ideal method of assembling nanostructures and our research group is exploiting the natural tendency of self-assembling proteins to build new components for bionanotechnology.  This project involves the use of protein called peroxiredoxin that can be manipulated through an external initiator to self-assemble into ordered nanorings and nanotubes.  The ultimate goal is to create various types and sizes of components that can self-assemble into nanodevices upon exposure to specific environmental triggers.  In this project you will explore the use of peroxiredoxin to create new components for bionanotechnology and manipulate the nanoscale architecture by altering the protein’s concentration, surrounding pH, metal content and temperature.  You will engineer proteins so that they can 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.

Protein nanofibril scaffolds for wound healing


Supervisor

Juliet Gerrard

Laura Domigan

Discipline

Biological Sciences

Project code: SCI015

Protein nanofibrils are a protein material with recognised applications in personal care, cosmetics, and wound care. They can be formed from a number of naturally occurring proteins, and have a high surface-to-volume ratio, with dimensions in the range of 2-10 nm wide and 1000-10,000 nm long.

In this project, you will create scaffolds capable of binding and releasing active ingredients, such as antimicrobials and growth factors, for future use in wound care.

Interactions between rats & hedgehogs: does pest control mean more hedgehogs in urban reserves?


Supervisor

Margaret Stanley

Discipline

Biological Sciences

Project code: SCI016

With more and more community and council pest control in urban reserves, rat numbers are declining. However, hedgehogs are not being targeted with trapping even though the impacts of hedgehogs on invertebrate communities are likely to be significant. This project will investigate whether rat control in urban reserves in resulting in high hedgehog abundances.

The project will involve field work (primarily tracking tunnels). Will develop skills in: footprint ID, analysis, fieldwork and H&S, hedgehog capture. Some evening work may be required – although not alone.

Prerequisites: A drivers licence and access to a vehicle.

The role of plant hormones for Apple Cell differentiation


Supervisor

Dr Karine David

Discipline

Biological Sciences

Project code: SCI017

Fruit are an essential part of our diet and understanding what control their development is an important area of plant biology. Plant hormones are essential for proper fruit development and ripening. The aim of the project is to assess the role of selected plant hormones on apple fruit cells grown in suspension. This will involve in vitro cultures, hormone treatments and analyses at the cell level (cell size/cell division) and molecular level (gene expression).

Preference will be given to students with a strong interest in plant biology and willing to carry on postgraduate studies in Plant Science.

Cryopreservation of mitochondrial function in tissues: mimicking freeze tolerant animal


Supervisor

A/P Anthony Hickey

Discipline

Biological Sciences

Project code: SCI018

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: SCI019

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. 

Deciphering neuropeptide receptor signalling


Supervisor

Dr. Christopher Walker

Discipline

Biological Sciences

Project code: SCI020

Pain is controlled by receptors on the surface of sensory neurons. The major class of cell surface receptors are G protein-coupled receptors (GPCR). Several GPCRs that are as file name.

Activated by neuropeptides and expressed on sensory neurons are emerging targets to treat chronic pain. Our research programme explores the mechanisms of how neuropeptide hormones activate their receptors and how these receptors regulate intracellular signalling. We employ a wide range of techniques to study intracellular signalling, histology and molecular pharmacology in cell culture models.

Structural investigation of antibiotic biosynthesis pathways


Supervisor

Dr Ghader Bashiri

Discipline

Biological Sciences

Project code: SCI021

We investigate biosynthesis pathways for novel secondary metabolites and antibiotics. In this project, we aim to study the structural details of proteins involved in the biosynthesis of two novel antibiotics. We have already identified proteins in these pathways and are interested in molecular understanding of these processes. These proteins will be expressed and purified, followed by crystallisation and functional characterisation. 

How pathogenic bacteria sense oxidative stress?


Supervisor

Dr Ghader Bashiri

Discipline

Biological Sciences

Project code: SCI022

In this project, we aim to investigate the biogenesis of iron-sulfur (Fe-S) clusters. Fe-S clusters are required in many critical functions within cells and could act as a molecular “redox sensors” to detect environmental and intracellular redox signals. Inhibiting Fe-S biosynthesis could therefore be a promising strategy towards development of novel anti­bacterial agents. We will clone the open reading frames that encode proteins in the Fe-S cluster biogenesis. The proteins will subsequently be expressed and purified to study their function using various biochemical and biophysical tools. 

Accelerating flowering in the reference legume Medicago


Supervisor

Dr Mauren Jaudal

Professor Jo Putterill

Discipline

Biological Sciences

Project code: SCI023

In Medicago truncatula, a reference legume plant closely related to alfalfa and chickpeas, winter cold is an important inductive condition that promotes flowering in spring. The aim of this project is to analyse vernalisation process by identifying genes in the pathway. Thus candidate flowering time genes will be over expressed in Arabidopsis and Medicago and transformed plants tested for their ability to flower early. Techniques include molecular cloning, transformation experiments, analysis of transgene expression and plant flowering time. This project would suit someone who has a strong interest in plant molecular biology, enjoys lab work, working with plants and displays good attention to detail. 

Finding a floral repressor in the reference legume Medicago


Supervisor

Dr Mauren Jaudal

Professor Jo Putterill

Discipline

Biological Sciences

Project code: SCI024

We have been using the powerful genomic and genetic resources of Medicago  truncatula, a reference legume plant, to identify controllers of flowering time, an important agronomic trait that affects plant productivity. By forward genetics, we found a mutated line that shows recessive early flowering. Thus, a potential repressor of flowering is mutated in that line.  The aim of this project is to identify the candidate repressor using a variety of techniques that include transposon display, sequencing, genotyping and linkage analysis. Students that enjoy genetics and molecular biology and are hard working with good attention to detail are encouraged to apply.  

New devices to improve wound healing


Supervisor

Assoc. Prof. Anthony Phillips (School of Biological Sciences; Department of Surgery)

Assoc. Prof. Greg O’Grady (Auckland Bioengineering Institute; Department of Surgery)

Mr Bruce Stokes (Auckland Bioengineering Institute; Department of Surgery)

Discipline

Biological Sciences

Project code: SCI025

Scope: This project will involve prototyping some new devices aimed at improving surgical and chronic wound healing. The project will involve some initial background literature research and then progress to prototyping and bench testing the new device ideas.

Requirements: Interest and background in bioengineering or applied biomedical engineering. However applicants do not have to specifically be an engineering student in these fields but a reasonable grasp of general physics, and a keen interest in practical construction of equipment or devices is an advantage.  Basic biological knowledge is also an advantage. You will also need to be comfortable with cross-disciplinary supervision by Scientists, Engineers and Surgeons!

Location: work will be undertaken between two locations. The Applied Surgery and Metabolism Laboratory in the School of Biological Sciences, and the Surgical Engineering Lab in Auckland Bioengineering Institute.