Biological Sciences

High-throughput screening of plastic-degrading microbes

Supervisor

Gavin Lear

Discipline

Biological Sciences

Project code: SCI132

Plastic pollution has become one of the most pressing environmental issues of the 21st century. Largely driven by the disposal of ‘single-use’ plastics, the fast rise in environmental plastic pollution overwhelms our current ability to deal with them. One possible solution for this problem is to use microorganisms to biodegrade plastics into carbon dioxide and water, eliminating the problem completely. We are working on isolating such microorganisms from the environment and characterizing their enzymes and biodegradation pathways. You will learn how to isolate and culture microorganisms, test their abilities to biodegrade several plastic types, and characterize their molecular arsenal. A background in microbiology and molecular biology would be useful. As an extra, some familiarity with programming and command line tools would be extremely helpful, but all you really need is enthusiasm and willingness to learn!

Birds, bugs and brains: microbiome insights into behaviour of the introduced common myna

Supervisor

Prof. Mike Taylor 
Dr Kristal Cain

Discipline

Biological Sciences

Project code: SCI133

The student working on this project will conduct microbiome analyses on gastrointestinal (faecal, gut, gizzard) samples already obtained from myna birds. Previous microbiology experience is preferred but is not essential, and the project would suit anyone with an interest in bird and/or microbial ecology. What is essential is a willingness to learn new techniques, including some bioinformatics work to analyse microbiome data.

Biodiversity on schoolgrounds

Supervisor

Margaret Stanley

Discipline

Biological Sciences

Project code: SCI136

Schools represent large areas of greenspace and can be an important place for children to connect to nature. But what sort of biodiversity 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 & bird ID skills will be useful. Need own transport. Opportunity to work within a larger, supportive research team on parallel projects.

Preventing blood clotting caused by biomedical devices

Supervisor

Jane Allison 
Chiara Neto

Discipline

Biological Sciences

Project code: SCI137

The surfaces of implanted biomedical devices can cause blood clotting (thrombosis). The first step in this process is protein adsorption and activation, whereby small proteins such as human serum albumin and factor XII adsorb on the surface of the device. These are later replaced by larger proteins such as fibrinogen, and ultimately, platelets and cells attach to form a complete blood clot. Liquid-infused surface coatings (LIS), in which a thin layer of a perfluorinated oil infused within the surface structure of the device, have been shown to significantly prevent the build-up of blood clots, but the exact mechanism by which they work is not understood.

This project involves using molecular dynamics computer simulations to reveal the interactions of blood-clotting proteins at the oil/blood interface and how these interactions differ from those at conventional solid/blood interfaces. The findings could be invaluable in helping to elucidate the anti-thrombotic mechanism(s) of liquid-infused surfaces, and improve their design. While some basic programming skills and familiarity with using the command line would be useful for this project, along with a background in chemistry, biochemistry or structural biology, we will teach you how to set up and run the computer simulations, so all you really need is enthusiasm and a willingness to learn!

Do hydrocarbons induce membrane curvature in photosynthetic organisms?

Supervisor

Jane Allison

Discipline

Biological Sciences

Project code: SCI138

Membrane curvature is essential for cellular growth, movement, division and vesicle budding/fusion, and is known
to be induced by either asymmetrical lipid packing or curvature generating proteins. However, recent breakthroughs suggest a novel mechanism of generating curvature in which long chain hydrocarbons, found in cyanobacteria and microalgae, integrate into the centre of the lipid bilayer. Supporting this hypothesis, hydrocarbons accumulate in cyanobacterial membranes in vivo, and hydrocarbon deficient mutants have significant growth, cell size and division defects and different membrane curvature.

This project is part of a large international collaboration that aims to determine whether hydrocarbons induce membrane curvature by this novel mechanism. You will learn how to set up, run and analyse large-scale, coarse-grained computer simulations of model membranes to see how they respond to different quantities of hydrocarbons. While some basic programming skills and familiarity with using the command line would be useful for this project, along with a background in chemistry, biochemistry or structural biology, all you really need is enthusiasm and a willingness to learn!

Evolution of reproductive division of labour in eusocial colonies

Supervisor

Nobuto Takeuchi

Discipline

Biological Sciences

Project code: SCI139

Many biological systems display a division of labour between the transmission and utilization of genetic information. For example, multicellular organisms display a division of labour between germline and soma cells, and eusocial animals display a division of labour between queens and workers. This project will explore whether this division of labour in eusocial animals is a consequence of multilevel selection. The project involves comparative sociobiology of relevant eusocial species, from naked mole rats to bees, and it requires a comprehensive search and reading of literature. This project is best suited to a student with interests in evolution and animal biology. You will be working alongside a PhD student.

Investigating the genetic cause of rare neurodevelopmental disorders

Supervisor

Jessie Jacobsen 
Whitney Whitford

Discipline

Biological Sciences

Project code: SCI140

Many disorders of neurodevelopment have a genetic basis, however for several families, the molecular basis of their child’s condition remains elusive to current diagnostic screening approaches. This summer studentship will help identify the underlying genetic cause for individuals who have a neurodevelopmental disorder but no clear candidate gene to explain their condition. The research project will evaluate called variants from whole genome and/or whole exome sequence reads and use bioinformatic tools to prioritise candidate variants. Where appropriate, variants will be validated using PCR and Sanger sequencing.

How flexible is spider web building behaviour?

Supervisor

Greg Holwell

Discipline

Biological Sciences

Project code: SCI141

The webs of pūngāwerewere | spiders offer amazing opportunities to study variation in behaviour. Webs can vary greatly in their dimensions between species, between individuals and from night to night for the same individual as many spiders reconstruct new webs each night. This project will investigate the ability of spiders to respond flexibly to changes in prey interceptions and modify their web structure. The project will involve both field and laboratory experiments and I look forward to applications from motivated students who are currently studying relevant courses in zoology, behaviour and evolution. A drivers licence is an advantage. Our lab is an inclusive, supportive and fun place to gain some experience exploring the fascinating natural history of Tāmaki Makaurau.

Do longer legs mean longer escape jumps in cave wētā?

Supervisor

Greg Holwell

Discipline

Biological Sciences

Project code: SCI142

Wētā and their relatives (grasshoppers, crickets) have exaggerated hindlegs, modified to help them jump away from predators. Cave wētā have particularly long hindlegs, but do longer legs necessarily lead to longer or faster escape jumps? This projects will explore the escape behaviour and biomechanics of both small and large species of cave wētā and test hypotheses about the adaptive significance of leg length. The project will involve both field and laboratory experiments and I look forward to applications from motivated students who are currently studying relevant courses in zoology, behaviour and evolution. A drivers licence is an advantage. Our lab is an inclusive, supportive and fun place to gain some experience exploring the fascinating natural history of Tāmaki Makaurau.

The vaginal microbiome and infections

Supervisor

Dr Augusto Simoes-Barbosa

Discipline

Biological Sciences

Project code: SCI143

Our research is interested on two of the most common infectious conditions of woman’s reproductive tract: trichomoniasis and bacterial vaginosis. We want to understand how the vaginal microbiome changes, either protecting the host against or facilitating the infection by the protozoan parasite Trichomonas vaginalis. Your research will investigate how protozoa and bacteria interact at metabolic, cellular and molecular levels. This investigation is aligned to existing projects in our laboratory. Your work will involve microbiology, cellular and molecular biology and molecular genetics with a potential of producing results that could lead you to a postgraduate research project.

Join the single molecule revolution

Supervisor

Dr Richard Kingston
Dr Adrian Turner

Discipline

Biological Sciences

Project code: SCI144

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 molecules; investigate molecular interactions; and track molecular movement - both inside and outside the cell.

SBS has recently acquired 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.

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

Supervisor

Dr Richard Kingston

Discipline

Biological Sciences

Project code: SCI145

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.

Investigating NZ food products to increase thermogenesis and promote fat oxidation

Supervisor

Ivana Sequeira (09 630 1162)
Jennifer Miles-Chan

Discipline

Biological Sciences

Project code: SCI146

This project is part of a clinical trial at the Human Nutrition Unit, which will investigate NZ food/beverage product(s) that may elicit beneficial metabolic effects, in the context of diabetes prevention.

Your role: screening and recruitment, assist in postprandial metabolic measurements. You will be part of a dynamic team and will gain hands-on experience in various aspects of conducting a clinical trial, including participant interaction, data collection, management and analysis.

Key skills required: ability to work well as part of a team and with a wide variety of population groups; attention to detail; availability for early morning starts (~7am); interest in human nutrition and metabolism.

Prevention of Diabetes in an Asian Chinese, European Caucasian and Polynesian Cohort resident in New Zealand: PiCUP_NZ

Supervisor

Louise Lu  (09 630 1162)
Jennifer Miles-Chan

Discipline

Human Nutrition Unit, School of Biological Sciences

Project code: SCI147

This project is part of a large clinical trial at the Human Nutrition Unit, which will investigate the effects of acute weight loss on glycaemia and biomarkers of diabetes risk.

The student will be part of a dynamic team and will gain hands-on experience in various aspects of conducting a large community-based nutritional study, including interaction with participants from different backgrounds, data collection, management and analysis.

Key skill required: ability to work well as part of a team and with a wide variety of population groups; comfortable at multi-tasking; interest in human nutrition and metabolism.

The NZ Synergy Residential Study: Diabetes prevention in Asian Chinese and Caucasian cohorts

Supervisor

Ivana Sequeira (09 630 1162)
Jennifer Miles-Chan

Discipline

Human Nutrition Unit, School of Biological Sciences

Project code: SCI149

This project is part of a clinical trial at the Human Nutrition Unit, which will investigate the effects of a tightly controlled diet on glycaemia and biomarkers of diabetes risk. This is a residential study, with study participant living on-site at our Unit, with all food items provided to them and compliance carefully monitored.

The student will be part of a dynamic team based study and will gain hands-on experience in various aspects of conducting a residential nutritional study, including interaction with participants from a wide variety of backgrounds, and data collection, management and analysis.

Key skill required: ability to work well as part of a team; excellent communication and people skills; comfortable at multi-tasking; interest in human nutrition and metabolism.

Understanding peptide hormone effects to target obesity

Supervisor

Dr Christopher Walker

Discipline

Biological Sciences

Project code: SCI150

Several neuropeptides and neuroendocrine hormones (peptide) represent excellent targets for the treatment of obesity and metabolic disorders. These peptides activate G protein-coupled receptors (GPCR) at the surface of the cell leading to specific biological outcomes. This project will investigate the cellular consequences of peptide receptor activation using plate-based technologies (eg. Alphascreen, HTRF, Elisa) in cell culture models.

Marine biodiversity of Rangitāhua (Based in Auckland)

Supervisor

Prof Mary A. Sewell

Discipline

Biological Sciences

Project code: SCI151

Marine biological collections housed at Auckland Museum hold critical information for understanding the marine biodiversity of Rangitahua/Kermadec Islands. An MBIE-funded research programme Te Mana o Rangitāhua has just begun, co-led by Ngāti Kuri and Auckland Museum with involvement from University of Auckland as a key research partner. Rangitāhua (Kermadec Islands) hosts one of Aotearoa’s largest marine reserves – scientifically identified as one of the most pristine marine ecosystems on Earth. This summer project will involve working with the collections at the Auckland Museum and helping with their documentation. Applicants should be interested in marine biodiversity, taxonomy and the care of biological collections. Skills required: attention to detail; interest in taxonomy and biodiversity.

Marine biodiversity of Rangitāhua (Based in Wellington)

Supervisor

Prof Wendy Nelson

Discipline

Biological Sciences

Project code: SCI152

Marine biological collections housed at NIWA (Wellington) hold critical information for understanding the marine biodiversity of Rangitahua/Kermadec Islands. An MBIE-funded research programme Te Mana o Rangitāhua has just begun, co-led by Ngāti Kuri and Auckland Museum with involvement from University of Auckland as a key research partner. Rangitāhua (Kermadec Islands) hosts one of Aotearoa’s largest marine reserves – scientifically identified as one of the most pristine marine ecosystems on Earth. This summer project will involve working with the collections at NIWA and helping with their documentation. Applicants should be interested in marine biodiversity, taxonomy and the care of biological collections.

Behaviour and song complexity of common mynas

Supervisor

Kristal Cain

Discipline

Biological Sciences - EEB

Project code: SCI153

Common mynas (Acridotheres tristis) are widely distributed birds that are adapted to a range of environments and conditions. However, there is still a lot that we don’t know about their songs and behaviour. In this project, you will annotate and analyse video/audio data collected from captive mynas in order to identify individual differences. You will learn how to work with software like Raven, BORIS, and R, which are commonly used in animal behaviour research. Note: this study is entirely computer-based but there will be limteid opportunities for some fieldwork if interested.

Searching for new antibiotics

Supervisor

A/Prof Shaun Lott (Ext 87074)

Discipline

Biological Sciences

Project code: SCI154

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.

Improving enzymes for plastic degradation

Supervisor

Assoc Prof. Shaun Lott (ext 87074)

Discipline

Biological Sciences

Project code: SCI155

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.

Investigating the Kaupapa of voyaging waka pedagogy to provide insights into teaching Mātauranga Māori in the School of Biological Sciences

Supervisor

James Brock 
Te Kahuratai Painting

Discipline

Biological Sciences

Project code: SCI156

The aim of this project is to establish Kaupapa Māori practices that can be implemented in SBS for teaching students about Mātauranga Māori. To achieve this the student researcher will explore differences in pedagogical practice and praxis between Te Toki Voyaging Trust and the Faculty of Science when considering Mātauranga Māori.

This research project will build on the experiences of students in departments of the Faculty of Science at the University of Auckland who are also trainees with Te Toki Voyaging Trust where they will be learning voyaging skills.

The student researcher will undertake a literature review on Kaupapa Māori pedgogy, will facilitate discussions with student voyaging trainees, and (using abstraction as the method for recordings) collate reflections and autoethnographies comparing learning experiences between the University and Te Toki Voyaging Trust.

A potential outcome of this project are recommendations for implementation of teaching practice at the University.

Molecular analysis of gene-edited plants

Supervisor

Prof Jo Putterill

Discipline

Biological Sciences

Project code: SCI157

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. We are using gene editing to knock out candidate flowering time control genes.

Skill development: You will learn plant molecular biology techniques including how to make 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 and genetics with an interest in plant development. BioSci papers such as 202, 351, 355 and 340/326 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.

Motor neuron disease: Why motor neurons?

Supervisor

Emma Scotter
Molly Swanson

Discipline

Biological Sciences

Project code: SCI158

Motor neuron disease is a fatal and incurable movement disorder affecting ~1 in 15,000 New Zealanders. Most people with motor neuron disease harbour aggregates (clumps) of the protein TDP-43 in the motor neurons that degenerate. Other cell types such as oligodendrocytes, astrocytes, and microglia harbour occasional TDP-43 aggregates but certainly less frequently than do neurons. This project aims to use publicly available single cell data to compare the RNA expression of TDP-43 between human brain cell types, and correlate these findings to immunostaining of TDP-43 protein in human brain. The RNA expression of TDP-43 interactors and proteins that degrade TDP-43 will also be examined. If the burden of TDP-43 aggregates in different cell types relates to their RNA and protein load of TDP-43, and/or to the expression of TDP-43 degrading proteins, this would rationalise therapeutic approaches that reduce TDP-43 levels.

Techniques:

  • Database analysis/ basic bioinformatics
  • Multiplexed human brain immunohistochemistry
  • Multiplexed tissue imaging
  • Automated image analysis
  • Scientific writing

The student will be based at the School of Biological Sciences, University of Auckland. This pilot project is part of a larger program of research and there is potential for a successful candidate to continue into a Masters or PhD project. The Scotter lab is a diverse and safe lab- we welcome applications from all students.

Prion-like propagation of pathology: tracing the transmission of protein aggregates in brain tissue in motor neuron disease

Supervisor

Emma Scotter
Molly Swanson

Discipline

Biological Sciences

Project code: SCI159

Motor neuron disease is a fatal and incurable movement disorder affecting ~1 in 15,000 New Zealanders. Most people with motor neuron disease harbour aggregates (clumps) of the protein TDP-43 in the motor neurons that degenerate, many also harbour TDP-43 aggregates in the frontal cortex, while few also harbour TDP-43 aggregates in the hippocampus. Is TDP-43 spread in a prion-like fashion from region to region along connected neuronal circuits? This project will use spatial analysis to determine whether the pattern of TDP-43 aggregation in a range of brain areas is best predicted by aggregate formation within individual neurons or by prion-like propagation between neurons.

Techniques:

  • Basic bioinformatics/ R software
  • Multiplexed human brain immunohistochemistry
  • Multiplexed tissue imaging
  • Automated image analysis
  • Scientific writing

The student will be based at the School of Biological Sciences, University of Auckland. This pilot project is part of a larger program of research and there is potential for a successful candidate to continue into a Masters or PhD project. The Scotter lab is a diverse and safe lab- we welcome applications from all students.