Biological Sciences

Common mynas were introduced to Australia in the 1860s, and then from Australia to New Zealand in the 1870s by local acclimatisation societies to help control grain pests. They have been incredibly successful at establishing both in Australia and New Zealand. In Australia, there is evidence of four separate successful introductions from India, but which of these locations mynas were taken from in Australia to establish the New Zealand populations is unknown. In this project, we will use genetic and morphological information to determine the number and origin of myna populations in New Zealand by comparing to the diversity across populations in Australia. This will give insight into the processes that have enabled the successful adaptation of mynas to differences in climate and diet compared to Australia.

Skills required

Student must have had experience in morphometrics.

Prerequisites

BIOSCI 202, BIOSCI 210, BIOSCI 322, BIOSCI 335

Droughts are increasing in frequency and intensity under a changing climate. Our ongoing research work is exploring the impacts of drought on plant water use and carbon uptake of kauri. The successful student will contribute to fieldwork, laboratory analysis and data processing. An interest in plants and outdoor work is essential.

Our research is interested on sexual conditions that affect women of reproductive age. We have shown that the protozoal pathogen Trichomonas vaginalis teams up with vaginal bacteria found in dysbiosis (i.e. unbalanced microbiota). Our research is describing that this unprecedented microbial relationship - protozoa and bacteria - is mutually beneficial. Your research will investigate how protozoa and bacteria cooperate on growth and antibiotic resistance, by identifying the changes on gene expression and metabolism. This investigation is funded and aligned to existing projects in our laboratory. Your work involves microbiology, cellular and molecular biology with a potential of producing publishable results that could lead you to a Hons or MSc research project.

The ecological impacts of the eight million tonnes of plastic entering our oceans each year is easy to witness, littering coastlines and clogging the guts of marine animals with plastic detritus. As the world is slowly waking up to the crisis of ocean plastic, novel solutions are needed to both stem the flow of plastic into our environment and to remove vast historic deposits of accumulated waste. Our objective is to isolate and characterise microorganisms from the New Zealand environment to explore their potential for the degradation of common environmental plastics.

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.

Skills to be developed include: trapping and animal handling, behavioural observation fieldwork skills, spatial analyses, general fieldwork HS. Students with a strong interest in ecology and/or animal behaviour are particularly encouraged to apply.

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.

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.

In this era of the Green Revolution, waste products are receiving a new life as valuable biomaterials. Proteins from fish eyes, a low value by-product of the fishing industry, are being engineered to develop scaffolds for stem cell delivery, surgical glues for sutureless ocular surgery, and hydrogels for bandaging and/or drug delivery. The protein composition in the eye of many mammals and fish changes with age. However, little is known about the Hoki fish and questions still remain as to how these changes impact the formation and performance of new biomaterials. This project will explore the protein composition in New Zealand Hoki fish lens, and map their spatial distribution. The spatial information will be used to design, develop and characterise new biomaterials with known protein compositions.

Key skills

• Ability to work independently
• think creatively
• propose innovative solutions
• Experience working with proteins would be useful, but is not necessary.
• Prior knowledge of mass spectrometry techniques is not essential, but a willingness to learn is required.
  

My lab is interested in enhancing T cells for use in adoptive immunotherapy protocols. As part of this we want to establish CRISPR/Cas9 based genome editing in primary human T cells. In this 10 week project we will use pre-validated reagents to establish the technique.

Techniques to be learnt would include

• Primary human T cell culture
• Flow cytometry
• Electroporation of T cells
• DNA isolation
• DNA sequencing

Mammalian tissue culture and flow cytometry experience would be preferential.

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.

This project is part of a wider Marsden proposal in collaboration with Te Papa Tongarewa, which seeks to understand whether the introduction of Western honey bees (Apis mellifera) to NZ has led to measureable shifts in floral traits in native plants and what the consequences of these shifts might be. Differences in pollinator behaviour and morphology exert different selection pressures on key floral traits important for pollination. How has the introduction of a eusocial generalist bee from the northern hemisphere changed the selection pressures on NZ flowering plants? This studentship will involve the collection of datasets on variability in key floral traits from living plants in the field and herbarium specimens to assist in the initial focal species selection process, regardless of whether the Marsden bid is successful. If the bid is successful there will be opportunities to apply for related MSc and PhD projects. Candidates will have keen eye for detail, be willing to work at a fine scale in the field and in the lab, have a driver’s licences, and ideally have a good working knowledge of the NZ flora.

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.

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. ​

Tuberculosis (TB) remains one of the most significant worldwide causes of death from a communicable disease, and multidrug-resistant (MDR) TB is a growing problem. xAs 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 the structural biology of enzymes from Mycobacterium tuberculosis that are potential targets for new anti-TB drugs. This project is best suited to someone with a strong interest in protein structure and function.

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.

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.

Ribosomal DNA genes (rDNA) are present in many copies in almost all eukaryote genomes, and have been implicated in a number of diseases, most notably cancer. One consequence of the repetitive nature of the rDNA is that the number of copies can frequently change. In the last few years there has been an explosion of work looking at whether changes in rDNA copy number are associated with diseases and different cellular states. Surprisingly, though, there is no information on what the level of rDNA copy number variation is in natural populations. This project will address this gap by measuring rDNA copy number in individuals of a population of the yeast, Saccharomyces cerevisiae. We have developed three validated ways to measure the copy number, and this project will use at least two of these, including digital droplet PCR.

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.

Biological evolution can be viewed as a hill-climbing process maximizing the reproductive success (i.e. fitness) of organisms. A major problem of hill-climbing processes is that optimization gets stuck in local optima because fitness landscapes are rugged. The aim of this project is to solve this problem by combining a hill-climbing process with another evolutionary process known as Red Queen dynamics, in which organisms are constantly pitted against co-evolving parasitic or predatory agents. To this end, we will create and investigate a computer program simulating such combined evolutionary dynamics based on RNA folding. The prerequisites are programming skill (e.g. C++, C, Python, etc.) and interests in evolutionary processes.

There is no immediate measure of oxidative stress in surgical settings. I am developing a simple system to measure reactive oxygen species (ROS) from exhalant gases from animals.

This project is for students keen to play with LEGO and insects (as our model) with and without exercise. They will get to make respiration chambers, measure heart rate and attempt to measure ROS from these animals. Hopefully this equipment can then be unscaled for medical applications.

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.

Sexual conflict occurs in many species when the interests of females are at odds with those of males. In Aotearoa’s endemic seaweed flies, which live in and break down seaweed that washes onto beaches, females attempt to reject all male mating attempts. This sexual conflict should select for male characteristics that allow them to overcome female rejection.

This project will investigate sexual conflict in NZ seaweed flies along with their general ecology. It will involve laboratory rearing of multiple seaweed fly generations and observation of behavioural interactions. It will also involve a great deal of measurement of flies under the microscope from diverse species, geographic locations and beach types, to better understand their ecology and diversity in Aotearoa.

We require a talented and hard working student with a background in entomology and/or animal behaviour, and excellent attention to detail.

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, plant biology or chemistry.

The dung mosses are a unique group of moss species which make use of visual and chemical cues to draw insects to serve as vectors for spore dispersal to their preferred substrate - dung or carrion. New Zealand hosts four species of these mosses which are found primarily on carnivore dung or carrion. In this project you will be working with us to explore this fascinating relationship! This will involve collecting field samples, recording insect behaviour, measurements colour displays and odours, and insect identification. In addition, you would perform analyses of observations and write-ups of their work. Essential qualities include a love of the outdoors, an eye for detail, and patience. Desirable qualities include experience with fieldwork, entomology, botany (moss especially!), R, and scientific writing. We look forward to hearing from you and welcoming you into the lab!

Flowering time is an important agronomic trait that affects crop yield and productivity. The aim of this project is to use plant molecular biology techniques to analyse/identify flowering time gene candidates in Medicago truncatula, a reference legume closely related to alfalfa, peas and chickpeas. Techniques include quantitative real-time PCR, molecular cloning, DNA sequencing analysis, and plant phenotyping. 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.

Summary: We are seeking a student who would like to help us research the origins of the most ancient system that helps organisms move: the bacterial flagellum.

The bacterial flagellum is a tiny spinning motor that bacteria use to swim. It is made of over 20 different kinds of proteins that self-assemble to produce a “tail” that is powered by the flow of protons or sodium ions through the bacterial membrane. It is often described as an amazing piece of nanotechnology.

The evolutionary origins of the bacterial flagellum have been a subject of scientific and public controversy (see Google) – how can evolution produce such a complex system? We believe we can make progress on the issue by updating old phylogenetic work with new datasets and improved models, and combining this with experimental evolution work being done with collaborators at the University of New South Wales.

The task for a summer student will be to help us assemble a well-organized database of flagellar proteins. Exploring sequenced bacterial genomes with genome browsers and sequence-similarity searches, the student will identify flagellar proteins and their evolutionary relatives, including recording their position in the genome. The student will also participate in discussions and planning of the phylogenetic analyses between UoA and UNSW, and begin conducting analyses if time allows. We plan for this work to lead to publication and to involve the student in this as well if they are interested.

Skills

The main skill is enthusiasm for the topic (evolution and/or biochemistry) and a decent general background in biology and evolution. We can teach the key skills regarding use of Genbank, sequence searches, genome browsers, and use of Excel/databases. Prior experience or coursework in these or other related areas of bioinformatics would be useful, but is not required.

An important class of models in Phylogenetic Comparative Methods are called “State-dependent Speciation/Extinction” (SSE) models. These models allow scientists to study the relationships between traits (e.g. flying vs. nonflying, geographic location, body size, etc.) and macroevolutionary dynamics (the rates of speciation and extinction over millions of years). SSE models allow calculation of the likelihood (the probability of the data under the model), which is the key step in conducting Maximum Likelihood or Bayesian inference.

The main problem with these models is that they are slow to run, as they require two Ordinary Differential Equations (ODEs) per trait state. It is easy to generate problems that contain hundreds of interacting equations.

Sophisticated methods for solving these kinds of large ODE problems exist in the open-source computing language Julia. I have made substantial progress in finding much faster solvers for SSE problems, so I have confidence there is an interesting result here. A summer student is sought to do formal speed tests of (a) different-sized SSE models under (b) the various traditional and new solvers available in Julia. This work will lead to a co-authored publication with the student.

Skills

Julia is designed to be relatively easy to learn and use (like R), but is also optimized for compilation and high speed (like Java and C++). An ideal student would have a high interest in learning about Julia and working on this speed optimization problem. It would be very helpful to have some prior experience in programming of some sort, and some coursework involving phylogenetics, but prior experience with Julia or ODEs is not required.

Two students requested.

Work with taxonomists on the diversity of terrestrial invertebrate species in New Zealand and Sub Antarctic Islands.

Learning skills to work in a taxonomic collection or natural history museum, including:

1. fieldwork and sorting field samples
2. curation and identification of insect groups
3. DNA extraction of insect specimens
4. databasing and geo-referencing specimens for biodiversity and biosecurity research project

Ability to work in a group or independently, position requires dexterity, care and attention to detail, patience, data entry, and read small labels. Applicants must have an interest in Entomology.

The Landcare Research fungal systematics group maintains the largest collections of both dried and living fungi in New Zealand, and also delivers data associated with the collections through the NZFungi website. The successful applicants (X2) will provide assistance adding data to the NZFungi database and maintaining, tracking, and storing fungal specimens and cultures and associated DNA sequence data.

You will gain an understanding of the day to day running of a mycological research laboratory and key techniques you will learn include handling fungal cultures, data capture and management and microscopy. In addition, you will be expected to assist with an ongoing project on myrtle rust in the mycology labs at Landcare Research, Tamaki. These could potentially involve culturing and identification of fungi from field samples, analysis of taxonomic or eDNA data from nanopore sequencing, etc.

Requirements

• Attention to detail
• ability to keyboard accurately
• a general interest in fungi
• bacteriology or plant pathology

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 desired.

Plant hormones and growth regulators play important roles in controlling source (production of sugars) to sink (use of assimilates) relationship including fruit setting, grain filling and even nodulation. These are important processes for plant production. However, how hormones and hormone-related compounds control source to sink relationship is not understood. In this project students will use transgenic and direct hormone application approaches to investigate the role of phytohormones and growth regulators in the control of source-sink relationships. Molecular biology skills are desired.

An important question in plant biology is how plants distinguish beneficial microbes from pathogens? Imin lab has identified critical transcription factors and receptor kinases that are crucial for this decision-making process. This project requires students to use transgenic approaches to investigate this conundrum. Molecular biology skills are essential.

The project will entail working with a team to survey epiphyte communities in large native trees from the ground using both binoculars and a drone to determine the accuracy of drones as a tool for these kinds of surveys. An ideal candidate will be comfortable in the field, a strong work ethic and have experience with flying drones. The work will also entail reviewing footage and creating a database out of this. We will be looking to write up this project in a paper comparing methodologies.

Pūkeko are joint-laying cooperative breeders and appear to lack individual egg recognition, which may be a reason this reproductive strategy persists. Eggs of varying size and/or colour will be experimentally added to nests to test at what point (if any) egg rejection occurs in this species. This research will involve a lot of patience to locate and monitor nests and birds. The field site is a 25 minute drive from city campus (access to a car required) and the research will be carried out alongside a PhD researcher on a known population of pūkeko. No experienced required, however a strong interest in ornithology and/or animal behaviour is highly recommended.

Rifleman (Tītipounamu -Acanthisitta chloris) are a small native and endemic bird species that lives in forested areas throughout New Zealand. Rifleman produces diverse types of calls like contact calls, alarm calls, distress calls, and nest calls. The vocal interactions between rifleman parents, rifleman helpers and nestlings, is of particular interest to scientists.

This project will investigate vocal interactions in rifleman. at our field sites roughly 1h away from Napier (Mohi Bush and Boundary Stream Mainland Island). Field work will be will focus on finding rifleman nests, and recording rifleman, especially helper-nestling behaviours. The project will also use acoustic analysis software to analyse these recordings.

The summer student will acquire experience in bioacoustics field techniques and equipment, avian monitoring techniques, and bioacoustics analysis. You will live at the field site with accommodation and transport supplied (DOC cabins or camping).

Skills required

Field work:

• Ability to work in unfavorable outdoor conditions for long period of time (e.g. wet, cold)
• Attention to detail
• Critical thinking
• Team spirit and positive attitude

Computer work:

• Documentation skills and computer literacy
• Ability to work long hours annotating sound
  
• Knowledge of R (although not required)
• Consistency

Science is often said to be a self-correcting discipline, because even if dodgy science slips through the peer-review process, other scientists will fail to replicate that study and publish their results. In practice, this rarely happens because replication work is generally not funded. In a pilot study on reproducibility of RNASeq analyses, we found that at least 40% of published studies could not be replicated, using the authors own data and best-practice analysis. In this project, you will perform more comprehensive analyses of published RNAseq data sets, and contribute these to the Reanalyze Science website. Confidence with computers is required, but experience in RNAseq data analysis is not. Familiarity with R is preferred, but not mandatory.

Long after mutations render the relationships between DNA and protein sequences senseless, the three-dimensional shape of a protein continues to be preserved. This project uses comparisons of protein structures, combined with molecular simulations of whole proteins to look deep into evolutionary time. By doing so we can learn new clues about how early life evolved and how the earliest branches in the tree of life developed.

This is a computational project. A basic familiarity with the Linux terminal environment is strongly recommended. Experience with any scripting languages, such as Perl, Python, R etc., is preferable.