Biological Sciences

Project

Following in the footsteps of ‘climate emergency’ declarations, some conservationists have declared a ‘biodiversity emergency’. Yet ‘emergency’ framing can have complex implications, with critics noting that ‘crisisification’ (e.g., around climate change) could be used to justify overriding rights, particularly of Indigenous peoples. Little work has examined debates about crisis framing in conservation. This project will make a first step towards understanding crisis debates in Aotearoa New Zealand.

The project will involve desk-based research into how crisis framing has been used in discussions around NZ conservation to date. It may also (ethics approval permitting) involve conducting initial interviews with conservation researchers and activists to understand their views on the use of crisis/emergency framing.

Ideal candidate

The candidate must have demonstrated some experience in social science research, ideally qualitative. This could mean successful completion of at minimum one course in social science (e.g., human geography, anthropology, sociology).

Project

Recombination is the exchange of DNA between maternally- and paternally-inherited chromosomes during meiosis, effectively ‘mixing’ genetic information before it is passed to the next generation. It is a fundamental biological process, and the number of recombination events must be regulated to ensure accurate segregation of chromosomes. Despite this regulation, recombination rates can vary between individuals depending on factors such as their sex, environment and genetic background. Further, in mammals recombination rate has been found to vary with age, and altered rates of recombination may contribute to chromosomal abnormalities and age-related declines in fertility.

In this project, we will analyse recombination data from a large collection of dairy bulls to test whether recombination rates vary across the lifetime of these individuals, whether this change in recombination rate is heritable, and determine whether any genetic variants are associated with lifetime recombination rate changes. Knowledge of how recombination rate varies with age can improve our understanding of how male fertility changes with age and how age influences this fundamental evolutionary parameter.

Ideal student

This project requires the student to have completed BIOSCI 351 and at least one COMPSCI or STATS course at 200-level or above.

Project

Myrtle rust (Austropuccinia psidii) is a virulent plant pathogen of the family Myrtaceae, with the rust now having spread globally and infecting >500 plant species. It arrived in New Zealand in 2017 and is still spreading. Because it is a recent arrival, our understanding of host susceptibility and disease progression is also still developing, both within and amongst species. For pōhutukawa within Auckland, infections of individuals seem to vary by infection date, location, plant size, proximity to roads, and whether the plant was planted or wild grown. Sometimes infected plants and healthy plants occur in proximity. This proposed project would build on an initial survey of pōhutukawa within Auckland carried out last summer to score the infection status of trees and a range of potential factors (e.g., size, proximity to roads, and likely origin) that may describe susceptibility to infection. These data would then be analysed for infection patterns. The goal would be to determine correlative evidence for factors that might facilitate myrtle rust infection to better understand the infection process.

Project

Myrtle rust (Austropuccinia psidii) is a virulent plant pathogen of the family Myrtaceae, with the rust now having spread globally and infecting >500 plant species. It arrived in New Zealand in 2017 and is still spreading. Susceptibility to myrtle rust is highly variable amongst species and it is not clear which plant traits facilitate infection. Myrtle rust infections are usually initiated on the newly expanding and soft tissue of leaves, flowers, or stems, but differences in traits associated with these processes of expansion and hardening off amongst species are not documented. This project would stringently follow leaf expansion processes on several Myrtaceae species over time and record traits relevant to infection susceptibility, e.g., leaf SLA, cuticle development, phenology, etc. Relating these traits against known infection susceptibilities may lead to greater understanding of variation in infection susceptibility. The student will also contribute to other myrtle rust related research (e.g., estimating the age of planted and naturally regenerating mānuka trees using tree ring dating).

Project

Many Gram-positive bacteria use long narrow adhesin molecules to stick to host cells and to each other in forming biofilms. We want to investigate a potential novel antibiotic mechanism that would interfere with the function of these sticky adhesin molecules.

The adhesins are made up of many small protein domains that are secreted from the bacterial cell membrane and then must fold up into their proper 3D shape. In the figure to the right, you can see a blue-coloured peptide – this is the last part of the protein to be completed in folding. We will investigate whether a synthetic peptide can function as an antibiotic to replace the blue section of the protein, disrupt proper folding, and thus make the lifestyle of the bacterium untenable – it won’t be sticky anymore!

This project will involve protein expression, purification, and characterisation. Ideally, you will also synthesise a simple fluorescent peptide. No specific skills are required, simply a “can do” attitude and willingness to learn new things.

Project

There is a prevalent assumption that all molecular complexes have been crafted by natural selection to maximise performance with minimal components. However, it has been proposed that ‘unnecessary’ molecular complexity can emerge under the conditions of genetic drift via a process known as Constructive Neutral Evolution (CNE).

CNE has been offered as an explanation to describe the complexity of diverse biological phenomena, such as the seemingly gratuitous number of components of the spliceosome. However, there is a lack of clear experimental evidence for this theory. This project aims to test the validity of CNE by looking for the emergence and fixation of unnecessary protein-protein interactions in E. coli under the conditions of genetic drift. The successful candidate will develop skills in the areas of molecular cloning, protein expression and purificaton, and experimental evolution.

Ideal candidate

The ideal candidate would have a keen interest in molecular evolution, and a desire to grow their wet lab skill set.

Project

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 and in kiwifruit (with Plant and Food Research). 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 326 provide good background.

Personal attributes: A sense of curiosity. 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.

Project

Viruses can be propagated in the lab by infection of human or animal cell lines. Infecting cells with viruses like influenza, measles, herpes simplex-1, dengue or rotavirus allows measurement of virus replication. This is turn allows quantification of the antiviral effects of synthetic compounds, naturally occurring plant or marine extracts or serum-derived antibodies.

This project will introduce students to working with animal cell cultures for the propagation of infectious viruses leading to a screen of antiviral activity.

The student will be trained to work with one or more viruses using classical tools for measuring infectivity like plaque assays or immunofluorescent focus assay.

Ideally, project work will get underway in December, prior to a 3-week shut-down, over Christmas then resume in January.

Project

Invasive species are a global concern due to their negative impacts on the economy and local ecosystems. However, well documented invasions provide a useful system in which to pose interesting questions regarding how a species may become established and spread in a new environment. The globally invasive European starling (Sturnus vulgaris) was introduced at numerous locations across New Zealand/Aotearoa in the 1860’s. Previous research identified genetic structure across the country, however used alloenzyme markers which do not have high resolution or genomic representation. We will be using next generation sequencing data (DArT-seq) to update the picture of starling genetic diversity, giving us important information about which historical introductions were most successful. We can then explore this data further, looking for signals that indicate, for example, dispersal, inbreeding, and selection.

This project will involve working with genomic data on the command line. You will learn some fundamental population genetics analysis and interpret findings alongside the starlings’ introduction story told by existing historical records. Command line/bioinformatics experience is not a prerequisite for this project as you will receive training, but a willingness to troubleshoot using google is essential.

It would be useful to have completed BIOSCI 202, BIOSCI 355, and BIOSCI 322, though this project is open to all second- third- and fourth-year students.

Project

Cancer cells bypass normal cellular checkpoints in order to proliferate. Our laboratory is studying an enzyme, called malic enzyme, which helps cancer cells maintain a proliferative state. We are currently undertaking structural studies on malic enzyme isoforms to identify ways to inhibit its activity as a potential anticancer therapy.

This summer project aligns with these goals and will involve the expression of human malic enzyme isoforms in a bacterial expression system.Once expressed and purified, studies will be undertaken to identify binding interactions of small molecule inhibitors.

Ideal student: Skills in protein expression and SDS/PAGE are preferred.

Project

This project is Nelson based as part of the Cawthron-UoA Joint Graduate School. The project will involve:

• A better understanding and characterisation of potassium to modulate thallium toxicity
• Completion of a peer-reviewed scientific manuscript summarising results to date and submission to a peer-reviewed

Techniques/Skills taught

• General culture maintenance of freshwater green algae
• General planning of ecotoxicity testing and binary mixturesBecome familiar with the standard green algae, P subcapitata toxicity testing method from Environment Canada (Environment Canada 2007) and derived from the ASTM International Standards (ASTM 2004)
• Analysis of toxicity data and contribution to the writing of a scientific manuscript

Project

Plankton samples that have been previously collected at different locations in Rangitāhua will be examined in the laboratory using a microscope, with a focus on quantifying the meroplankton (larval stages of marine invertebrates and fish). Photographic images of rare and abundant meroplankton will be used to start an identification guide for future research at Rangitāhua in an MBIE project (Te Mana o Rangitāhua) with Ngati Kuri and Auckland Museum.

Ideal student

An understanding of marine invertebrate diversity would be a distinct advantage (e.g., completion of BIOSCI 208 or similar Invertebrate Diversity course), but on-the-job training will be provided during the project.

Ideally suited for a student with interests in biodiversity, identification of small organisms, and in gaining skills in scientific photography and illustration.

Project

Plankton samples have been collected with a multiple opening-closing net (MOCNESS) in the deep water off Rangitāhua. This divides the water column into 50-m depth strata from 300m to the surface. Samples will be examined in the laboratory using a microscope, to look at differences between locations and day/night samples to detect vertical migration.

Ideal student

An understanding of marine invertebrate diversity would be a distinct advantage (e.g., completion of BIOSCI 208 or similar Invertebrate Diversity course), but on-the-job training will be provided during the project.

Ideally suited for a student with interests in biodiversity, identification of small organisms, and in gaining skills in scientific photography and illustration.

Project

Antibiotics are a special category of drug that underpin modern medicine as we know it. Resistance to antibiotics is a growing global problem. Without action, this is estimated to place 10 million lives per year at risk by 2050. This project will focus on identifying an inhibitor, the enzyme RNase HI that is a potential target for new antibiotics against tuberculosis and gonorrhoea.

Ideal student

This project is best suited to someone with a strong interest in protein structure and function, medicinal chemistry and/or medical microbiology.

Project

Our previous work published in Nature showed that bacterial RHS/YD repeat sequences encapsulate toxic proteins prior to delivery. However, in the eukaryotic teneurin proteins, the same repeat sequences help form intercellular connections. The bacterial homologues of teneurins are uncharacterised: Do they encapsulate toxins or form cellular interactions? Or do they do both? This project will use cryo-EM to determine the currently unknown structure of a bacterial teneurin-like protein.

Ideal student

This project is best suited to someone with a strong interest in protein structure and function.

Project

Languages evolve over time just like species do, but there is massive variation in just how fast languages evolve: some languages are highly stable over hundreds of years, while others have radically reorganised themselves.

This project will use phylogenetic methods to infer and quantify the rates of language evolution across the world’s major languages families. Which languages are evolving the fastest and which are the most stable over time, and how might we explain this variation?

Ideal student

Applicants for this project should have some background knowledge of computational phylogenetic methods and an interest in languages.

Project

Methods to specifically target cytotoxic drugs to tumour cells are a successful way to treat cancers exemplified by the antibody drug conjugates, such as Kadcyla. However, as a biological agent, there are difficulties with its production, potency and side effects. Using small molecules dyes that are selective only for cancer cells are an alternative way to target drugs directly and as a non-biological are easier to synthesise, handle and can be conjugated to virtually any anti-cancer drug with an appropriate chemical linker. This project will involve chemical synthesis of both the dye and peptide and explore methods to conjugate both moieties into suitable construct.

Ideal student

A background in synthetic chemistry is mandatory and an interest in biological assays would be beneficial.

See: Jose et al Bioconjugate Chem. 2020, 31, 7, 1724–1739

Project

Antibiotic resistance has been recognised by the WHO as one of the greatest threats to humanity and infectious diseases rank as the second most common cause of death worldwide. New antibiotics are desperately needed and if nothing is done by 2050 it is estimated > 10M people will die per annum, which is more that cancer and diabetes.
Cyclic lipopeptides are an emerging subset of peptide-based antibiotics (e.g., FDA-approved daptomycin and polymyxin) containing a lipid or fatty acid. They have been shown to possess clinical efficacy and are used as the “last line of defence” against otherwise untreatable bacterial infections. Despite their promise, undesired toxicity is a significant drawback
We are developing novel, non-toxic derivatives of naturally occurring lipopeptide antibiotics (e.g., Fig. 1) by modifying the chemistry of the lipid tail. Novel antibiotic analogues will undergo biological testing against multi-drug resistant (MRD) strains of bacteria and evaluation of potential toxicity.

Skills developed

Successful candidates will use organic synthesis and modern methods of solid phase peptide synthesis. Candidates will also have the opportunity to undertake and learn biological assays if they desire.

References

See: Harris et al. ACS Infect. Dis. 2022, 8, 2413
See: Sarojini et al. J. Med. Chem. 2015, 58, 2, 625

Project

One emerging field of natural products being evaluated for anti-cancer activity are the naturally occurring peptaibols (8-20 amino acid residues) which display a variety of biological functions due to the occurrence of voltage-dependant ion channels in lipid bilayer cell membranes that these peptaibols influence, leading to their inherent cytotoxicity.

In 2015, Lin et. al. reported the isolation of peptaibols Microbacterin A and B extracted from the deep sea actinomycete Microbacterium sediminis sp. nov. YLB-01. These novel compounds exhibited antitumour activity against a variety of human cancer cell lines ranging from A2780 (human ovarian cancer cell), A549 (human lung cancer cell), Bel-7402 (human hepatoma cell), BGC-823 (human gastric cancer cell) and HCT-8 (human intestinal adenocarcinoma cell) with IC50 values ranging from 1.03-5.93 µM.

In this project we will prepare the unique amino acid (R,S)-3-amino-2-hydroxy-3-methylbutanoic acid (AHV) as a racemate and employ advanced methods to separate and characterise the two enantiomers. The correct (R) enantiomer will be equipped with suitable protecting groups for solid phase peptide synthesis and the first total chemical synthesis will be performed to afford the natural product. Comparison of the spectroscopic data of the synthetic Microbacterin with that published will confirm the structure and allow subsequent structure activity studies to identify more potent leads.

Requirement: An interest in organic synthesis and modern methods of solid phase peptide synthesis will be required.

References: See: Org. Lett. 2015, 17 (5), 1220–1223

Project

There is still an unmet need to effectively treat metabolic disease. This research addresses a new strategy to combat obesity and its associated metabolic diseases such as type-2 diabetes mellitus and cardiovascular disease. This therapeutic approach focuses on enhancing mitochondrial capacity to counteract insulin resistance and enhance muscle mass.

Strong evidence suggests that decreased mitochondrial function contributes to fatty acid dysregulation that contributes to insulin resistance. We will develop peptide antagonists from a 56 amino acid venom peptide, HCRG21, derived from the sea anemone H. crispa (left) HCRG21 is a known peptide neurotoxin that can act at a specific receptor to exert its beneficial metabolic effects. It contains three disulphide bonds that create a 3-D architecture, and this project will undertake a chemical synthesis of HCRG21 that precisely installs the correct disulphide configuration using peptide chemistry, protein folding and bioconjugation. An interest in peptide and protein chemistry is needed but assumes no prior experimental techniques in this area.
See: Marine Drugs. 2016; 14(12):229

Project

Telomerase is an enzyme involved in DNA replication and has been implicated in malignant cancers. Telomestatin (above) is a cyclic peptide-based inhibitor of telomerase with nanomolar potency in vitro but translation to the clinic has been hampered by limited availability of material as chemical synthesis has proven to be difficult. Detailed structure activity relationships are therefore unable to be undertaken. Telomestatin is essentially a cyclic peptide consisting of threonine, serine and cysteine amino acids that have been dehydrated to form the corresponding oxazoles (serine/threonine) and thiazoles (cysteine). This project will embark on a new total synthesis of Telomestatin from an all-amino acid cyclic precursor, prepared via solid phase peptide synthesis followed by examination of chemical dehydration conditions to form the oxazoles and thiozoles in a one-pot manner.

Requirements

Students will need to have a solid background in synthetic organic chemistry and an interest in assembly of cyclic peptides by solid phase peptide synthesis.

References

See: J. Am. Chem. Soc. 2011, 133, 4, 1044–1051