Honours projects available in 2022

See the 2022 Honours projects available to potential Honours students with the Faculty of Veterinary and Agricultural Sciences at the University of Melbourne, including details of their associated research groups and supervisors.

For information on how to apply see the Honours page.

Agriculture projects

  • Agricultural big data for environmental sustainability and climate change mitigation

    The big data era has arrived for the agriculture sector. In the agriculture community, big data is often regarded as a combination of technologies and analytics that collect and collate data, generate and analyse data patterns to assist decision-making in a useful and timely way. We see the potential of using data-analytics approaches to tackle agricultural and environmental issues, in particular those revolving around nitrogen use.

    The potential project is mainly desktop-based and may involve laboratory/field experiment. Students will choose from a range of topics surrounding agricultural nutrient management and climate change, and perform a meta-analysis (a procedure of combining data from multiple studies to generate a more precise summary). Using national and international datasets on soil-plant carbon and nitrogen dynamics in agricultural systems, we have previously performed meta-analyses to assess how future CO2 climates would affect the yield and grain quality of crops and pastures, what strategies are effective for mitigating greenhouse gas emissions, whether soil carbon sequestration in cropping systems is feasible. Students will also be given opportunties to draft, revise and submit a manuscript to international journals.

    Potential supervisors: Dr Shu Kee (Raymond) Lam, Professor Deli Chen, Dr Xia Liang

    Affiliated research group: The Soils and Environment Research Group

    The Soils and Environment research group seeks to understand the impacts of agricultural management on soil processes and develop technology to improve agricultural sustainability. We carry out a range of fundamental and applied research with the aim to help farmers, policy makers and industry partners make evidence-based decisions. Current research strengths and activities include:  Nutrient cycling in agro-ecosystems; Measuring, modelling and mitigating air pollution and greenhouse gas emissions from agriculture; Novel fertiliser technologies; Agro-ecosystem modelling and decisions support tools for efficient fertilisers use; Reuse and recycling of agricultural and urban wastes; Big data (data mining): Green index, nitrogen footprint; Soil and environmental microbiomes; Transmission of antibiotic resistance genes in agro-ecosystems; Soil microbial evolution and biogeography.

  • Assessing the efficiency, agronomic and environmental impacts of newly developed nitrogen fertilisers

    Food security necessitates the use of nutrients to grow crops, with nitrogen being a key nutrient. However current nitrogen fertilisers are inefficient as nitrogen can be lost once applied to soil via gaseous and leaching pathways. This project provides the opportunity for students to test the efficiency of newly developed nitrogen fertilisers in the ARC Hub for Smart Fertilisers. Students will measure nitrogen recovery in the plant-soil system in laboratory and glasshouse trials, including, where appropriate, gaseous emissions and leaching losses, to assess the potential for the new fertilisers to improve agronomic and environmental outcomes. Students have the opportunity to work closely with our industry partners and gain industry insight, including placements.

    Skills focus: Soil science, agronomy, gaseous emissions measurement.

    Potential supervisors: Dr Helen Suter , Professor Deli Chen

    Affiliated research group: The Soils and Environment Research Group

    The Soils and Environment research group seeks to understand the impacts of agricultural management on soil processes and develop technology to improve agricultural sustainability. We carry out a range of fundamental and applied research with the aim to help farmers, policy makers and industry partners make evidence-based decisions. Current research strengths and activities include:  Nutrient cycling in agro-ecosystems; Measuring, modelling and mitigating air pollution and greenhouse gas emissions from agriculture; Novel fertiliser technologies; Agro-ecosystem modelling and decisions support tools for efficient fertilisers use; Reuse and recycling of agricultural and urban wastes; Big data (data mining): Green index, nitrogen footprint; Soil and environmental microbiomes; Transmission of antibiotic resistance genes in agro-ecosystems; Soil microbial evolution and biogeography.

  • Biodiversity and pathogenicity of foliar fungi associated with native Australian trees

    Several genera of fungi have been detected in association with native Australian trees, the taxonomy and pathogenicity of which remain little understood. This project aims to taxonomically characterise fungal species associated with foliage of native Australian trees using modern molecular approaches. The student will become familiar with fundamentals of molecular fungal taxonomy and employ molecular biology laboratory techniques and phylogenetic analyses to elucidate the taxonomy of a range of fungal strains isolated from native Australian trees and employ detached leaves bioassays to investigate their pathogenicity and biosecurity significance.

    Potential supervisors: Dr Niloofar Vaghefi, Prof Paul Taylor

  • Biodiversity, phylogeny and pathogenicity of fungi and bacteria associated with important horticultural crops

    Several Plant Pathology projects are available on phytopathogenic fungi and bacteria associated with root and foliage of important horticultural crops and native Australian plants. The projects are focused on taxonomic characterisation of pathogens using multi-gene sequencing and phylogenetic analyses as well as pathogenicity assays. The student will become familiar with fundamentals of molecular taxonomy and employ molecular biology laboratory techniques and bioinformatics analyses to elucidate the taxonomy of a range of fungal and bacterial strains and employ glasshouse and detached leaf bioassays to investigate their pathogenicity and biosecurity significance. There is potential to conduct whole genome sequencing and bioinformatics analyses (genome assembly, annotation, and characterisation of loci underlying virulence) for pathogenic isolates.

    Potential supervisors: Dr Niloofar Vaghefi, Prof Paul Taylor

  • Characterisation of SIX genes in pathogenic Fusarium oxysporum isolates causing crown and root rot in horticultural crops

    Fusarium oxysporum comprises one of the most important plant pathogenic species complexes, incurring substantial losses to Australian cropping industries. Pathogenic F. oxysporum strains secrete pathogenicity-related proteins known as ‘secreted in xylem’ (SIX), which are reported to contribute to host-specific virulence. This project aims to amplify and sequence a range of SIX genes in F. oxysporum strains isolated from different hosts and evaluate their suitability in development of molecular markers for pathogenic stains. The student will employ molecular biology laboratory techniques and phylogenetic analyses to investigate the diversity of SIX loci in F. oxysporum strains.

    Potential supervisors: Dr Niloofar Vaghefi, Prof Paul Taylor

  • Cost-Benefit Analysis for agricultural sustainability and climate change mitigation

    A cost-benefit analysis (CBA) is the process used to measure the benefits of a decision or taking action minus the costs associated with taking that action. A CBA involves measurable financial metrics, and can also include intangible benefits and costs or effects from a decision. In the agriculture community, given that many of the environmental and socioeconomical effects involved, decisions by policy makers can be supported by an integrated assessment of all societal costs and benefits of changing agricultural management, showing the trade-offs that are at stake. We see the potential of using CBA approaches to tackle agricultural and environmental issues, in particular those revolving around carbon and nitrogen cycles.

    The potential project is mainly desktop-based and may involve laboratory/field experiment. Students will choose from a range of topics surrounding agricultural nutrient management and climate change, and perform a CBA. Although there is a wide range of abatement opportunities in Australia, feasible mitigation techniques for agricultural sustainability and climate change mitigation must be economically viable, commercially applicable and technically effective. Students will also be given opportunities to draft, revise and submit a manuscript to international journals.

    Potential supervisors: Dr Alexis Pang, Professor Deli ChenDr Xia Liang, Dr Shu Kee (Raymond) Lam

    Affiliated research group: The Soils and Environment Research Group

    The Soils and Environment research group seeks to understand the impacts of agricultural management on soil processes and develop technology to improve agricultural sustainability. We carry out a range of fundamental and applied research with the aim to help farmers, policy makers and industry partners make evidence-based decisions. Current research strengths and activities include:  Nutrient cycling in agro-ecosystems; Measuring, modelling and mitigating air pollution and greenhouse gas emissions from agriculture; Novel fertiliser technologies; Agro-ecosystem modelling and decisions support tools for efficient fertilisers use; Reuse and recycling of agricultural and urban wastes; Big data (data mining), CBA, green index, nitrogen footprint; Soil and environmental microbiomes; Transmission of antibiotic resistance genes in agro-ecosystems; Soil microbial evolution and biogeography.

  • Facilitating transformative change in nitrogen management for agricultural and environmental sustainable

    Food security necessitates the use of nutrients to grow crops and feed animals, with nitrogen being a key nutrient. However current nitrogen fertilisers available on the market are inefficient as nitrogen can be lost once applied to soil via gaseous and leaching pathways, and growers can struggle to understand how best to manage their nitrogen. We work closely with industry and colleagues in chemistry and engineering, to develop and test new fertiliser compounds that have much greater efficiency and less environmental impact, and provide tools to assist growers, advisors and policy makers with decision making. The projects available include;

    • Smart fertilisers and biofertilisers: These projects provide the opportunity for students to test the efficiency of newly developed nitrogen and bio-fertilisers through laboratory and glasshouse trials and environmental impacts using a range of analytical techniques including 15N isotopes.
    • Decision support tools and Environmental / Societal cost assessments: These projects provide the opportunity for students to critically evaluate the agronomic and environmental implications of nitrogen use to develop tools to support growers, and metrics to identify impact.

    You will have the opportunity to work closely with our industry partners and gain industry insight. Skills focus: Soil science, agronomy, gaseous (including greenhouse gases) emissions measurement, stable isotope techniques, statistics, data interrogation.

    Potential supervisors: Dr Helen Suter, Professor Deli Chen, Dr Raymond Lam

    Affiliated research group: Soils and Environment Research Group

    The Soils and Environment Research Group seeks to understand the impacts of human management on soil processes and develop technology to improve agricultural and environmental sustainability. We work closely with industry to carry out a range of fundamental and applied research. Our aim, to help policy makers, industry partners and farmers make evidence-based decisions. Current research strengths  and activities include:  Nutrient cycling in agro-ecosystems; Measuring, modelling and mitigating air pollution and greenhouse gas emissions from agriculture, particularly intensive animal production systems; Novel fertiliser technologies; Agro-ecosystem modelling and decision support tools for efficient fertiliser use; Reuse and recycling of wastes with particular emphasis on closing nutrient loops; Big data (data mining): Green index, nitrogen footprint, decision support systems for fertiliser use; Environmental microbiomes; Transmission of antibiotic resistance genes in the environment; Soil microbial evolution and biogeography. Our research projects tackle global issues at a range of scales, from small subsistence farms in Myanmar and China to broadacre cropping enterprises in Australia.

  • How to prevent grain loss in cereals

    Plant domestication is one of the major pillars for the transition of humans from hunter-gatherer to agriculture-based societies. Loss of the natural mode of grain dispersal was perhaps the single most important event in the process of cereal domestication. We discovered two genes responsible for grain separation in wheat and barley named Brittle rachis 1 and Brittle rachis 2 (Btr1, Btr2). Based on amino acid sequences, these two genes were found independent, and their orthologue does not exist in rice, Arabidopsis or any other plant species out of the Triticeae tribe. We hypothesis that Btr1 and Btr2 raised as a result of a block duplication event from ancestral genes called Btr1-like/Btr2-like followed by functional divergence. The molecular and physiological function of ancestral Btr-like genes is completely unknown.  In the current project, you will build on these discoveries, to investigate the function of Btr1-like/Btr2-like genes using genomics and transcriptomics tools. This will be integrated into a larger effort to understand the evolution of grain dispersal mechanisms in wild cereals.  Skills focus: Plant genomics, transcriptomics, bioinformatics, and molecular biology.

    Potential supervisors: Dr Mohammad Pourkheirandish, Professor Prem Bhalla

    Affiliated research group: Plant Molecular Biology and Biotechnology

    The Plant Biotechnology group offers an exciting and stimulating world class environment for research, education and training in plant molecular biology and plant biotechnology. Programs cover the broad spectrum of research using modern techniques to genetically engineer pasture, vegetable and horticulture crops for future agricultural and environmental needs. The group is part of the Australian Research Council (ARC) Centre for Excellence for Integrative Legume Research.

  • Identification of fungi associated with pre-harvest fruit rots of processing tomato

    Victoria is the largest producer of processing tomatoes in Australia. Multiple fungal pathogens limit tomato production by causing pre-harvest fruit rots and reducing marketability. This project aims to characterise fungal strains isolated from symptomatic tomato fruits using multi-gene sequencing and phylogenetic analyses. The student will develop skills in molecular biology laboratory techniques and multi-gene phylogenetic analyses, and engage in glasshouse bioassays to investigate the pathogenicity of multiple fungal strains on tomato leaves and fruits.

    Potential supervisors: Dr Niloofar Vaghefi, Prof Paul Taylor

  • Improving subsoil properties using organic amendments

    Many subsoils across medium and high rainfall zones of south-eastern Australia contain a range of soil physical and chemical constraints that restrict the growth of crops roots by limiting the ability of the roots to efficiently extract water and nutrients from the subsoil. These constraints include poor physical structure, transient salinity and a range of specific chemical toxicities including high aluminium and nutrient deficiencies. These different constraints occur simultaneously in many subsoils which can significantly reduce crop yields and quality. Application of organic ameliorants such as biochar, green waste and lignite into clay subsoils offer the potential to overcome some of the major subsoil constraints and improve the productivity of these hostile subsoils. We are looking for enthusiastic students to join our project that are interested in improving subsoil properties using organic amendments.

    Potential supervisors: Dr Tony Weatherley, Prof Deli Chen

  • Mining of resistance genes in the wild relatives of cultivated barley

    Diseases generally result from an intimate interaction between host and pathogen. The constant conflict between plant and pathogen has shaped both organisms' genetic diversity and is referred to as co-evolution. The specificity between a host and pathogen results from the interplay of genes that have evolved in both organisms. Cultivation of modern varieties of low genetic diversity has led to increased pathogen inoculum, followed by genetic vulnerabilities. One of the primary resources of disease-resistant genes is crop wild relatives. Previously, we have discovered a rust resistance gene in cultivated barley that has been overcome by pathogen evolution. In this honours project, you will build on these discoveries to look for different resistant alleles in wild relatives. This analysis will result in mining genetic diversity to answer how many potential resistance alleles evolved to protect barley from the pathogen at a specific locus. Mining genetic diversity will identify several functional alleles with different specificities that enable us to engineer the resistance. Skills focus: Plant genomics, molecular biology, DNA sequencing and assembly, and bioinformatics.

    Supervisor: Dr Mohammad Pourkheirandish

    Affiliated research group: Plant Molecular Biology and Biotechnology

    Dr Mohammad Pourkheirandish has moved to the University of Melbourne in 2018, where he joined the School of Agriculture and Food, the laboratory of Plant Molecular Biology and Biotechnology. Mohammad is one of the world leaders in the research area of cereal evolution. Discovery of multiple resistant alleles from crop wild relatives will be an exceptional resource for diversifying the portfolio of cultivated crops and contributing to crop improvement and food security.

  • Mitigation of greenhouse gas emissions from dairy production in northern Victoria

    This project may also be completed in the Animal Science & Management Stream.

    Greenhouse gas emissions from dairy production is an major issue, as it relates to climate change/global warming. The Australian animal production industry is under pressure to meet its emission targets, in line with the Paris Agreement, through application of mitigation strategies. To support the development of mitigation strategies, this research aims to utilise existing connection with Dairy Australia’s Murray Dairy RDP in northern Victoria to:

    1. Model greenhouse gas emission from grazing vs. mixed ration dairy production systems
    2. Investigate potential mitigation strategies to reduce greenhouse gas emissions on farms

    We are looking for enthusiastic students to join our team that are interested in sustainable development of animal production. The student will need to spend time at Dookie campus and he/she should hold a valid driving licence, as travel to commercial farm to obtain sample is expected.

    Potential supervisors: Dr Paul Cheng, Dr Brendan Cullen, Professor Richard Eckard

    Affiliated research centre: Primary Industries Climate Change Challenges Centre

    Our team comprises early-, mid- and late-career researchers working in sustainable development of agricultural production. We carry out a range of laboratory and field research with the aim to help policy makers, industry partners and farmers make evidence-based decisions. The team utilises resources from the Primary Industries Climate Change Challenges Centre and Dookie campus robotic dairy farm to conduct projects.

  • Nutrient (re)cycling and agricultural waste management

    Nutrient use-efficiency of agricultural production systems are sub-optimal. A large proportion of the protein which is consumed by animals is lost to the atmosphere as ammonia gas. In addition, animal manures and other agricultural by-products are regarded as wastes but are valuable co-products which are high in nutrients (especially nitrogen and phosphorus). Our research looks at mitigating reactive nitrogen losses from intensive animal industries, retaining the nutrients in these ‘waste’ materials during subsequent composting/processing and ultimately producing stable, pathogen-free, bio-fertilisers and soil amendments. We are interested in studies that investigate nutrient dynamics during animal production, nutrient (re)cycling of agricultural products and the use of bio-products to overcome chemical, physical and biological constraints to productivity (eg, soil acidity, compaction, sodlcity, soil-borne pathogens). We are looking for enthusiastic students to join our lab that are interested in nutrient (re)cycling, re-use and agricultural waste management, with a passion for agricultural sustainability and food security.

    Potential supervisors: Dr Clayton Butterly, Dr Tony Weatherley, Professor Deli Chen

  • Origin of grain dispersal in cereals

    Grain dispersal in the wild progenitor of wheat and barley differs from other cereal crops such as rice. In barley and other members of the Triticeace tribe, including wheat and rye, grain progressively breaks off along the floral axis (or rachis) and scatters on the ground as the plant senesces and dries. This functional trait of grain dispersal is called the brittle rachis. The grain separation unit in barley includes a section of the rachis that is absent in grain shattering types found in rice and Arabidopsis. This specialised characteristic is controlled by two major genes, Btr1 and Btr2, which affect the thickness of cell walls around the separation zone. The unique separation mechanism (brittle rachis) and exclusive sequences suggest that the Btr1 and Btr2 genes evolved within Triticeae, which ultimately developed a new dispersal mechanism. Previously, we demonstrated that brittle rachis genes resulted from a block duplication event from ancestral genes called Btr1-like/Btr2-like followed by functional divergence. We have also shown that Btr-like genes are exclusively expressed during anther development. However, where exactly within the anther is still unknown. In the current project, you will build on these discoveries to investigate the molecular and biological function of Btr1-like/Btr2-like genes using genomics and transcriptomics tools, including in situ hybridisation. This will be integrated into a more considerable effort to understand the evolution of grain dispersal mechanisms in wild cereals.  Skills focus: Plant genomics, transcriptomics, bioinformatics, and molecular biology.

    Potential Supervisors: Dr Mohammad Pourkheirandish Dr John Golz

    Affiliated research groups: Plant Molecular Biology and Biotechnology, Plant Developmental Genetics

  • Pasture intake and grazing pattern of dairy cows selected for ‘Feed Saved’ Australian breeding value

    This project may also be completed in the Animal Science & Management Stream.

    A major challenge in selecting more efficient grazing cows is the difficulty in measuring an individual’s feed intake, especially of pasture. ‘Feed saved’ is a new Australian breeding value (ABV) released recently in Australia that is an indicator for predicting feed intake, which may provide an idea about how efficient a cow is in converting feed (pasture) into milk. However, this ABV requires validation in the grazing system. The project aims to evaluate the differences of pasture intake, grazing behaviour, rumination time and production parameters between cows selected for feed saved ABV.

    The project activities are Parkville based, however, for field experimentation student may need to travel to Dookie Dairy.

    Potential supervisors: Dr Saranika Talukder, Dr Brendan Cullen, Dr Ellen Jongman, Dr Paul Cheng

  • Precision agriculture and soil nitrogen management

    Nitrogen is essential for crop production, yet its mismanagement has caused a cascade of environmental problems. Precision nitrogen management is an important area of precision agriculture for solving problems in food and environmental security for sustainable agricultural and social development. Rapidly advancing sensor systems on ground, air and space-borne platforms delivering hyperspectral and thermal remote sensing imagery at high spatio-temporal resolutions provide massive volumes of data to be analysed in novel ways to unveil detailed insights into crop performance and their variability across large areas. Students will have the opportunity to conduct research on proximal and remote sensing, crop growth modelling, spatial statistics, agronomy, and greenhouse gas emission mitigation.

    Potential supervisors: Dr Alexis Pang, Dr Shu Kee (Raymond) Lam

    We work within a multidisciplinary group of researchers with backgrounds in Soil and Crop sciences, Geographic Information Systems, Remote Sensing, Engineering and computer-based modelling. Working in collaboration with various local and international research institutions and industry partners, we develop new scientific insights as well as industry-relevant solutions in an agricultural production environment that is technology and data rich. We don’t just ask “why”; we also ask “why not?”

  • Precision dairy: understanding grazing behaviour of dairy cows in automatic milking systems

    This project may also be completed in the Animal Science & Management Stream.

    Managing the nutrition of dairy cows requires advances in knowledge of cows grazing behaviour and pasture intake.  New precision dairy tools are available to measure grazing behaviour of dairy cows but the need to be tested and applied under Australian conditions.  In this project the RumiWatch noseband sensors will be applied to dairy cows at the Dookie dairy to understand individual animal grazing behaviour in an automatic milking system.

    This project will involve field work based at Dookie at times throughout the year.

    Potential supervisors: Brendan Cullen, Saranika Talukder, Paul Cheng

  • Rural Innovation Studies

    Rural Innovation Studies

    Innovation in agriculture involves new technology and practices, but it is also fundamentally a social process. Innovation requires people to change the way they do things, and this requires supportive advisory services, learning opportunities and institutional arrangements. The FVAS Rural Innovation Research Group (RIRG) carries out applied social science research to understand and improve innovation processes in agriculture and natural and cultural resource management. Through this research, we aim to improve the resilience of farms, rural industries and rural communities. We welcome students interested to pursue Honours research on the social dimensions of innovation and change. We work with students to develop research topics that connect to their interests and our current projects. Current topics and potential research questions include:

    • Social dimensions of digital agriculture
    • Farm employment relationships, job quality and agricultural workforce development
    • Farm succession and social change in agriculture
    • Climate change and drought policy and farming system adaptation
    • Agricultural extension and advisory systems

    During your honours program you will complete a subject in social research methods, you will complete a human ethics application for conducting research involving human participants and, through completing your research, you will develop skills in social research and community and industry engagement. These skills are highly desired by industry and social research experience is important if you are considering a Masters by research or PhD in the future.

    Potential supervisors: Please contact Dr Michael Santhanam-Martin to discuss your interests. Other potential supervisors include Prof Ruth Nettle and Dr Margaret Ayre

    Affiliated research group: Rural Innovation Research Group (RIRG)

  • The effect of fertilisers on the capacity of soil bacteria to scavenge atmospheric hydrogen

    Soil microorganisms are key players in biogeochemical nutrient cycles, with recent studies highlighting soil microbial mediators are capable of oxidising atmospheric trace gases such as hydrogen. Moreover, research has indicated that both exogenous H2 and hydrogen-oxidising bacteria have a net positive effect on plants. This research project aims to characterise effect of fertiliser addition on hydrogen scavenging by plant-associated microorganisms using microbiological, molecular and biochemical techniques. In addition, the project aims to determine whether this process can benefit the broader agricultural industry, potentially as a probiotic supplement to biofertilisers.

    During your honours program you will complete a subject in social research methods and complete a human ethics application for conducting research involving human participants.  You will develop skills in social research and community and industry engagement. These skills are highly desired by industry and are important if you are considering a Masters by research or PhD in the future.

    Skills Focus: Soil biology, microbial ecology, molecular biology and bioinformatics

    Potential supervisors: Dr Zahra Islam, Dr Hangwei Hu,

    Affiliated research group: The Soils and Environment Research Group

    The Soils and Environment research group seeks to understand the impacts of agricultural management on soil processes and develop technology to improve agricultural sustainability. We carry out a range of fundamental and applied research with the aim to help farmers, policy makers and industry partners make evidence-based decisions. Current research strengths and activities include: Nutrient cycling in agro-ecosystems; Measuring, modelling and mitigating air pollution and greenhouse gas emissions from agriculture; Novel fertiliser technologies; Agro-ecosystem modelling and decisions support tools for efficient fertilisers use; Reuse and recycling of agricultural and urban wastes; Big data (data mining): Green index, nitrogen footprint; Soil and environmental microbiomes; Transmission of antibiotic resistance genes in agro-ecosystems; Soil microbial evolution and biogeography.

  • Transcriptional reprogramming during pollen development

    Analogous to animal systems, in most land plants sexual reproduction requires pollination involving transfer of the male sperm carried in the pollen to the female part of a flower, the stigma. In flowering plants, pollen is produced within anthers, the male reproductive organs of flowers, and its formation is a culmination of a highly specialized and tightly regulated developmental program. From economic perspective, sexual reproduction results in formation of edible fruit and grains, underpinning crop yield and global food security. Although indispensable to sexual reproduction pollen formation has been identified as developmatal stage most vulnerable to heat stress, which commonly results in significant yield losses especially due to climate change. This project will use available genomics resources and in-house RNA sequencing data to help understand the biological processes involved in pollen formation and identify target genes conferring pollen heat stress-tolerance. (Supervisors; Dr Agnieszka Golicz and Prof Mohan Singh).
    Skills gained: Bioinformatics, Transcriptomics, RNA-Seq data analysis, differential gene expression analysis, Linux command line.

    Potential supervisors: Professor Prem Bhalla, Professor Mohan Singh

    Affiliated research group: Plant Molecular Biology and Biotechnology

    The Plant Biotechnology group offers an exciting and stimulating world class environment for research, education and training in plant molecular biology and plant biotechnology. Programs cover the broad spectrum of research using modern techniques to genetically engineer pasture, vegetable and horticulture crops for future agricultural and environmental needs. The group is part of the Australian Research Council (ARC) Centre for Excellence for Integrative Legume Research.

  • Understanding plant meiosis across 500 million years of evolution

    Sexually reproducing eukaryotes, including plants, generate gametes using a specialised cell division called meiosis which serves both to halve the number of chromosomes and to reshuffle genetic variation present in the parent. Although the core processes of meiosis remain the same, changes arose in the course of evolution including diversification and neo-functionalisation of meiosis related genes. Better understanding of the context, initiation, and progression of meiosis in diverse plant groups will help harness the existing variation and fuel improvement of key plant breeding programs. With over 250 plant genome sequences available to date, this project will use integrative analysis, comparative genomics and transcriptomics to identify homologues of known meiotic genes in diverse plant species and novel plant-specific genes which arose during evolution.
    Skills gained: Bioinformatics, comparative genomics, genome annotation, nucleotide and protein sequence comparative analysis, phylogenetic analysis, Linux command line.

    Potential supervisors: Professor Prem Bhalla, Professor Mohan Singh

    Affiliated research group: Plant Molecular Biology and Biotechnology

    The Plant Biotechnology group offers an exciting and stimulating world class environment for research, education and training in plant molecular biology and plant biotechnology. Programs cover the broad spectrum of research using modern techniques to genetically engineer pasture, vegetable and horticulture crops for future agricultural and environmental needs. The group is part of the Australian Research Council (ARC) Centre for Excellence for Integrative Legume Research.

Animal science projects

  • How could animals ‘communicate' through data?

    Dairy cows are complex biological systems that need to maintain long- (homeorhesis) and short- (homeostasis) metabolic balances in order to produce the highest possible quality milk in relation to their genetic potential. They are subject to a range of metabolic and infectious diseases, as well as herd dynamics that impinge on wellbeing and productivity. Recent technological advances in remote sensing and wireless systems, combined with new methods of data management and processing, provide new and exciting opportunities to explore and exploit the potential for significant animal health gains whilst improving productivity. Compared with traditional livestock management (eg, gathering auditory, olfactory and visual information from animals to evaluate health, welfare and productivity), technologies and sensors can monitor, manage, and control many aspects of livestock production, both simultaneously and automatically with the added benefit of being ‘real-time’. The project will validate the automated captured behavioural data of Dookie dairy in a more meaningful way.

    The project activities are Parkville based, occasionally the student needs to travel to Dookie Dairy.

    Potential supervisors: Dr Saranika Talukder, Dr Brendan Cullen

  • Mitigation against heat stress in livestock

    With increasing severity of severity and incidence of cyclic heat events as well as an increase in livestock production in sub-tropical and tropical areas, the management of heat stress (HS) is paramount. Livestock reared under high heat load conditions exhibit a reduced growth rate and increased respiration rate and body temperature. There is also some limited evidence that skeletal muscle from animals exposed to high environmental heat has reduced rates of protein synthesis and proteolysis which may impact on subsequent meat quality. The aims of research is investigate dietary additives or manipulations that may mitigate against the effects of heat Stress in livestock and maintain product quality and animal welfare. Studies may be based at Parkville or Dookie campus.

    Potential supervisors: Professor Frank Dunshea, Dr Jeremy Cottrell, Dr Surinder Chauhan, Dr Hafiz Suleria, Professor Brian Leury, Dr Kristy DiGiacomo

    Our research team works on the effects of thermal stress on the physiology, endocrinology and metabolism of livestock. We have already developed a range of dietary strategies to protect against some aspects of Heat Stress and we are now shifting our focus towards plant derived bioactives and polyphenols. We are also interested in the quality of meat, wool and milk produced from animals exposed to thermal stress.

Food science projects

  • Assessing sustainability of meat and meat analogue products

    This project may also be completed in the Agriculture/Agricultural Science stream.

    There is an increasing consumer interest in reducing meat consumption due to concerns of its environmental impacts. While extensive scientific literature has focused on meat production, little is known about consumer perception and sustainability of retail-ready products, some of which require extensive processing. This project aims to compare greenhouse gas emission and water scarcity of several meat and meat analogue products. The project will be closely linked to another project examining nutritional values of these products. Results from these projects will inform consumers, manufacturers and policy makers nutritional and sustainability issues in replacing meat with alternative proteins.

    Potential supervisors: Dr Natalie Doran-Browne, Dr Anita Lawrence, Dr Minh Ha, Dr Brad Ridoutt (CSIRO) , Professor Robyn Warner

    This is an interdisciplinary project leveraging expertise of multiple research groups at The University of Melbourne and the CSIRO. Our expertise include food, human nutrition and environmental sciences.

  • Barriers and opportunities to a circular food economy for Melbourne: A policy analysis

    This project may also be completed in the Agriculture/Agricultural Science stream.

    There is an increasing international focus on circular food systems and circular food economies that minimise food waste, make the most of natural resources and regenerate natural ecosystems. With rapid urbanisation, cities are likely to play an important role in creating circular food economies. This project will investigate the policy barriers and opportunities to creating a circular food economy in Melbourne. You will undertake a review of the relevant literature on circular food economies at city region level and undertake a small number of interviews with waste, policy and other food system stakeholders in Melbourne and elsewhere in Victoria. This research will contribute to an understanding of the policies needed to promote circular food systems in rapidly growing cities.

    This is a social science research project that uses qualitative methods. You will complete a subject in social research methods and develop a human ethics application to conduct research interviews. You will develop skills in qualitative research, interviewing and policy analysis.

    Potential supervisors: Dr Rachel Carey

    Affiliated research group: Foodprint Melbourne

    Dr Rachel Carey leads the Foodprint Melbourne research team, which is based at the Parkville campus. The Foodprint Melbourne team conducts research to inform the development of a resilient and sustainable food system for Melbourne and has a particular focus on research for policy impact. The team partners with a wide range of stakeholders, including the City of Melbourne.

  • Bioactive compounds from food processing waste and their bioactivities

    This project may also be completed in the Agriculture/Agricultural Science stream.

    Food processing (fruit, vegetables and marine) industries produce large amounts of processing waste, are discarded as by-products. This food processing waste is enriched with bioactive compounds especially polyphenols that provide a variety of health benefits and could potentially be used as ingredients in functional foods and nutraceuticals and provide candidates for drug discovery and pharmaceutical development. The aim of our project is to establish high-throughput screening of bioactive molecules (polyphenols) from food processing waste, elucidate the relationship between their structure and molecular mechanism involved and to determine their potentially useful bioactivities. By identifying and enhancing the health-promoting compounds from food processing waste can be used to develop further innovative functional food and nutraceuticals on large scale.

    Potential supervisors: Dr Hafiz Suleria, Professor Frank Dunshea

    Affiliated research group: Sustainability

    Our research team works on isolation and characterization of bioactive compounds from different food waste streams. Our main objectives are (1) extraction of bioactive compounds from different food materials especially food waste stream using different solvent extraction systems (2) purification and characterization of bioactive compounds using high pressure liquid chromatography and mass spectrometry (HPLC and LCMS) (3) to screen bioactivities of targeted compounds by adopting our previously developed high-throughput screening assays including 96-well plate reader, spectrophotometric and chromatography methods.

  • Microbial diversity and ecology in sourdough bread

    This project may also be completed in the Agriculture/Agricultural Science stream.

    Sourdough bread is made with a mixture of yeast and bacteria in a starter. The identity, diversity and interactions of the microbes dramatically affect the composition and health benefits of bread. This project will use a range of emerging and traditional microbiological and genomic techniques, together with small molecule analysis to understand the extent and degree of interactions. Understanding the metabolic capabilities of the novel yeasts and bacteria and their interactions during an extended dough fermentation will lead to bread with enhanced health and functional properties.

    Potential supervisors: Dr Kate Howell

    Affiliated research group: The Howell Lab

    The food and nutritional sciences research group at the Parkville campus is an extensive and interdisciplinary group which works closely with industry to achieve real impact.

  • Novel wine making by incorporation of teas

    This project may also be completed in the Agriculture/Agricultural Science stream.

    Wine is a very popular alcoholic beverage globally. Traditionally, wine is made by different grape cultivars and their flavour/taste are varied accordingly. Grape polyphenols are a group of important chemical compounds significantly contributed to the flavour/taste of the resultant wine. It is also well-known that the polyphenols in teas contribute to the tea taste/flavour. In this project, we plan to make a series of innovative wines by incorporating of different type of teas during the wine making process. The flavour/taste related compounds will be analysed by LC-MS and GC-MS, and further the sensory properties of the wine will be evaluated in our FVAS state-of-art sensory facilities. Skills focus: analytical chemistry, microbiology, fermentation, winemaking, LC-MS, GC-MS, sensory evaluation.

    Potential supervisors: Dr Zhongxiang Fang, Dr Pangzhen Zhang

  • Optimising an in vitro digestion technique to estimate protein digestibility of novel protein sources in different regions of the gastrointestinal tract

    This project may also be completed in the Agriculture/Agricultural Science stream. There will be increasing reliance on non-invasive techniques to estimate the nutrient availability of novel plant products and by-products for ruminants. The Ankom gas fermentation system has the potential to be used to estimate fast and slow rumen fermentation of protein as well as rumen bypass protein of feedstuffs. This project will focus on feed with the potential to be used in the both Australia and some developing countries.

    Potential supervisors: Professor Frank Dunshea, Professor Brian Leury, Dr Kristy DiGiacomo

    Our research team has a strong background in ruminant nutrition and conduct research with sheep, cattle and goats. We have extensive experience in using the Ankom system to determine fermentation patterns of a variety of grains, conserved fodder and dietary protein sources. This research will extend these capabilities to better characterise the sites of digestion.

  • Probiotics, prebiotics and healthy food design

    This project may also be completed in the Agriculture/Agricultural Science stream.

    The growing preference for functional foods favours the probiotic and prebiotic market growth and is expected to reach over USD 66 billion by 2024. There is an obvious potential for a synergetic effect when combining probiotics and prebiotics appropriately, because prebiotics promote the growth and activities of probiotics.

    Research topics available for Honours projects cover the various aspects of probiotic and prebiotic technology from new product development to analysis of functional efficacy of probiotics/ prebiotics using in vitro gastrointestinal and colonic fermentation, probiotic adhesion to gut epithelium and some specific bio marker analysis including basic molecular biological applications.

    Potential supervisors: Dr Senaka Ranadheera, Associate Professor Said Ajlouni

    Affiliated research group: Food Science

    We mainly focus on functional efficacy of probiotic microorganisms using in vitro techniques. Probiotics are associated with maintaining optimum microbial balance in the digestive tract with a number of well-documented health benefits. Therefore, these organisms such as lactobacilli and bifidobacteria have been extensively incorporated into various food products over the last decade. We are aiming to maximise the potential health benefits of probiotics through various strategies related to food processing and preservation and offer an exciting and stimulating research environment.

Human nutrition projects

  • Are general level health claims promoting healthy food choices or are they just providing a ‘health halo’ for unhealthy foods?

    General level health claims link consumption of a food or a component of food to health.  The intention of the standard regulating their use is to protect and improve the health of the population and to promote healthy food choices.

    The aim of this research project is to use the FSANZ health claims register to identify the types of foods using self-substantiated general level health claims and to assess if the use of these claims is: 1) likely to protect and improve the health of the population and; 2) likely to promote healthy food choices.

    Potential supervisor: Dr Anita Lawrence

    Associated research group: Human Nutrition

    The strategic goal of the Human Nutrition team’s research is to improve knowledge of the relationships between human nutrition and health.

  • Development and validation of a photographic method to estimate usual intakes for use in a semi-quantitative food frequency questionnaire

    Methods of self-reported dietary intake, including food frequency questionnaires, have several limitations in terms of their accuracy to assess usual intakes of nutrients. One of the main errors to occur is the assessment of portion sizes. Food photographs, depicting portions of different sizes, can aid in estimating usual intakes of individuals, and for reducing the respondent burden associated with completing food records. This honour’s project aims to develop and validate the use of digital food photographs as a tool to aid in the quantitative assessment of usual intakes in a semi-quantitative food frequency questionnaire.

    Potential supervisors: Dr Robyn Larsen, Shirley Poon

    Associated research group: Human Nutrition

    The strategic goal of Human Nutrition research group is to improve knowledge of the relationships between human nutrition and health by providing capacity to measure and

  • Food and daytime sleepiness – ultra-processed or minimally processed lunch?

    Sleepiness in the afternoon can adversely impact on work and learning, particularly activities such as long-distance driving. The amount and type of food consumed at lunchtime is known to influence feelings of sleepiness and mood in the afternoon. There is also a growing body of research evidence suggesting that consumption of ultra-processed food adversely impacts on many aspects of health. However, little is known about its impact on daytime sleepiness and mood. This honours project aims to compare the effects of an ultra-processed lunch on daytime sleepiness and mood with those of a minimally processed lunch.

    Potential supervisor: Dr Anita Lawrence

    Associated research groups: Human Nutrition. The strategic goal of Human Nutrition research group is to improve knowledge of the relationships between human nutrition and health by providing capacity to measure and interpret, biochemical, functional and dietary indicators of nutritional status and health.

  • Investigating the association between energy-adjusted protein intake and blood pressure in type 2 diabetes

    Short-term intervention trials suggest a blood-pressure lowering effect of increasing dietary protein intake, however the long-term effects are unclear. High protein diets are also a popular choice for weight loss and weight management due to their satiating effect and effects on preserving lean body mass. However, because weight loss plays a mediating role in improving blood pressure, it is often difficult to isolate the effects of dietary protein intake from that of the energy deficit in weight loss trials.  This honours project will examine data collected from a 12-month weight loss trial conducted at Baker Heart and Diabetes institute. This project will investigate associations between macronutrient intake and blood pressure after controlling for the confounding effect of reduced energy intake.

    Potential supervisor: Dr Robyn Larsen, Professor Jonathan Shaw (external supervisor)

    Associated research group: Clinical Diabetes Group, Baker Heart and Diabetes Institute

    The strategic goal of Human Nutrition research group is to improve knowledge of the relationships between human nutrition and health by providing capacity to measure and interpret, biochemical, functional and dietary indicators of nutritional status and health

  • Investigating the relationship between poor sleep and glucose tolerance in pregnant women

    Little is known on the impact of poor sleep on pregnancy outcomes. Decreases in both duration and sleep quality are common in pregnant women due to changes in hormonal and physical factors. In non-pregnant populations, poor sleep is associated with an increased risk of glucose intolerance and type 2 diabetes. This observational study, which was conducted in collaboration with Baker Heart and Diabetes Institute, involves the analysis of objective measurements of sleep from 100 pregnant women recruited through obstetric services at a Victorian public hospital. This honour’s project will investigate the relationship between objective assessments of sleep and glucose metabolism during pregnancy.

    Potential supervisor: Dr Robyn Larsen, Professor David Dunstan (external supervisor); Assoc Professor Martha Lappas (external supervisor)

    Associated research group: Physical Activity and Behavioural Epidemiology Laboratory, Baker Heart and Diabetes Institute; The Mercy Hospital for Women

    The strategic goal of Human Nutrition research group is to improve knowledge of the relationships between human nutrition and health by providing capacity to measure and interpret, biochemical, functional and dietary indicators of nutritional status and health

  • Nutritional genomics

    We share most of our genetic materials with the members of our species, yet the small differences that make each of us a unique individual, determine not only the colour of our eyes and how tall we will grow, but also our risk to developing chronic pathologies and our metabolic responses to food. The deeper understanding of human genetics is giving us insights into the mechanisms behind individual response to food and diet.

    New genetic platforms that include targeted single nucleotide polymorphism (SNP) and gene expression analysis dataset (GEO) are arguably some of the most transformative technologies in biomedical science in the last 50 years. Even over the past decade, the ability to interrogate large data sets for genetic anomalies has continued to undergo revolutionary innovations that now allows the complexities of chronic diseases to be unravelled.

    It is currently thought that over 30% of all long-term chronic illnesses have a dietary or nutritional contribution. This Honours project seeks to investigate this burgeoning public health emergency. Specifically, we will perform bioinformatic analysis on large data sets of genetic variants and gene expression to find new biomarkers, therapeutic targets and future diagnostics for long long-term chronic diseases associated with diet and lifestyle.

    This project will give students the opportunity to be involved in clinical that seeks to translate research findings into clinical practice in the short- to medium-terms. Students will gain experience in a range of laboratory and in silico techniques and technologies.

    Potential supervisor: Dr Chiara Murgia

    Associated research group: Human Nutrition

    The strategic goal of Human Nutrition research group is to improve knowledge of the relationships between human nutrition and health by providing capacity to measure and interpret, biochemical, functional and dietary indicators of nutritional status and health

Veterinary bioscience projects

  • Anthelmintic resistance in parasites of Australian Thoroughbred horses

    Various parasites can affect the health, performance and welfare of horses. Currently, drugs (anthelmintics) are used to control important intestinal parasites of horses. However, owing to the frequent and indiscriminate use of anthelmintics, anecdotal reports suggest the emergence of resistance in intestinal nematodes of Australian horses.

    This project will involve the testing of various anthelmintic drugs on various Thoroughbred horse farms across Australia to assess the status of anthelmintic resistance in parasitic nematodes. The project activities will involve the visit to Australian Thoroughbred farms, administration of drugs to horses under supervision, collection and testing of horse faeces for parasites and use of molecular methods to identify nematodes.

    Potential supervisor: Prof Abdul Jabbar

    Associated research group: Veterinary Parasitology

    Associate Professor Abdul Jabbar’s research is focussed on molecular diagnosis and epidemiology of parasites of veterinary and medical significance and the discovery of antiparasitic drugs. Our work has led to the improved understanding of various parasitic diseases of domestic animals and the establishment of novel diagnostic methods.

    Currently, we are improving the diagnosis of parasites as well as exploring various novel non-chemical methods to control parasites of livestock.

  • Assessment of two sheep breeds for their natural resistance to a parasitic nematode, Haemonchus contortus

    A variety of gastrointestinal nematodes can infect sheep, resulting in significant economic losses due to reduced production and mortality. Owing to the development of drug resistance in nematodes, alternative methods are needed to control worms in sheep. This project aims to evaluate the two sheep breeds for their natural resistance to a parasitic nematode, Haemonchus contortus. The project activities will involve the experimental infection of sheep, collection of sheep blood, blood and serum analysis, and histological examination of various tissues.

    Potential supervisor: Prof Abdul Jabbar

    Associated research group: Veterinary Parasitology

    Associate Professor Abdul Jabbar’s research is focussed on molecular diagnosis and epidemiology of parasites of veterinary and medical significance and the discovery of antiparasitic drugs. Our work has led to the improved understanding of various parasitic diseases of domestic animals and the establishment of novel diagnostic methods.

    Currently, we are improving the diagnosis of parasites as well as exploring various novel non-chemical methods to control parasites of livestock.

  • Arbovirus vector study

    Arbovirus diseases such as African horse sickness pose a serious threat to the international movement of horses. This project will monitor insect vector populations at the Werribee quarantine centre to determine whether possible vectors of arbovirus diseases can be found. insect traps will be set and the insects collected will be identified. Genomic sequencing techniques will be used to determine if these insects are infected with arboviruses, and to determine what animal species they have been biting.

    Potential supervisors: Prof James Gilkerson, A/Prof Carol Hartley, Dr Charlie El-Hage

    Affiliated research group: Centre for Equine Infectious Disease

    The Centre for Equine Infectious Disease is a major national resource for the study of equine diseases in Australia.  We conduct research into the major viral and bacterial pathogens infecting horses. Our research has led to the development of diagnostic tests, the development of vaccines and our staff are engaged in providing advice to various level of government. We provide diagnostic testing for serious endemic pathogens of horses including strangles and equine herpesviruses.  We are actively involved in providing advice to industry on the management of infectious disease outbreaks.

  • Bone structure in BawBaw frogs determined by histomorphometry and microCT scanning

    Metabolic bone disease is a common problem in captive frog populations world-wide and often leads to pathological fractures and significant subsequent mortality.  Little is known about the development of bones in frogs as they morph from tadpoles to subadults, or the influence of environmental, nutritional or regulatory processes that affect bone structure and function. In collaboration with scientists at RMIT, Dr Liz Dobson (a wildlife specialist pathologist) and Dr Michael Lynch at The Royal Melbourne Zoo, we have collected specimens of BawBaw frogs after tetracycline labelling of bones.  The project involves high resolution CT scanning of frog skeletons to determine bone morphology and density, as well as documenting appositional bone growth rates (from tetracycline labelling) and microscopic descriptions of bone structure in animals that were considered clinically normal. This study is fundamental to determination of normal values for BawBaw frogs and will enable improved understanding, detection and monitoring of captive frog populations faced with the high risk of developing osteoporosis.

    Skills focus: Microanatomy and histopathology, 2D and 3D modelling and diagnostic imaging techniques.

    Potential supervisors: Prof Ron Slocombe, Dr Reza Sanaei

    Frog populations are considered key indicators of environmental health and worldwide, wild populations are in serious decline.  For some species, only captive populations remain, and these captive collections often develop metabolic bone disease.  Collectively, our group has specific expertise in the structural evaluation of calcified tissues and has waited for years for an opportunity to turn this expertise to this important work, the study of frog skeletal development.  Our group has expertise in wildlife pathology, imaging, bone histomorphometry and clinical management of captive animal populations at zoos, including frog populations.

  • Development of diagnostic tools for elephant endotheliotropic herpesvirus

    Elephant endotheliotropic herpesvirus (EEHV) can cause severe and fatal disease in elephants. In Victoria, Australia there is a lack of diagnostic tests for EEHV that can be performed locally. This laboratory-based project aims to develop and validate diagnostic tools to detect exposure or infection with EEHV, such as an enzyme linked immunosorbent assay (ELISA) to detect antibodies to EEHV in elephant serum, PCR-based diagnostics to detect viral DNA in clinical samples, and/or a rapid diagnostic test (i.e. LAMP assay) that could be performed on site. This project will be conducted in collaboration with veterinarians at Melbourne Zoo. The ELISA will be used to help manage the health of elephants in Australia.

    Potential supervisors: Prof Joanne Devlin, A/Prof Carol Hartley, Dr Alistair Legione, Dr Michael Lynch (Melbourne Zoo)

  • Development of novel diagnostic methods for the detection and quantification of horse parasites

    Various parasites can affect the health, performance and welfare of horses. Currently, various conventional methods are used to detect, quantify and differentiate horse parasites. This project would involve the development of novel molecular and artificial intelligence methods to improve the diagnostics of parasites of horses. The project activities will involve the visit to Australian Thoroughbred farms, collection and testing of horse faeces for parasites, use of molecular methods and artificial intelligence tools.

    Potential supervisor: A/Prof Abdul Jabbar

    Associated research group: Veterinary Parasitology

    Associate Professor Abdul Jabbar’s research is focussed on molecular diagnosis and epidemiology of parasites of veterinary and medical significance and the discovery of antiparasitic drugs. Our work has led to the improved understanding of various parasitic diseases of domestic animals and the establishment of novel diagnostic methods.

    Currently, we are improving the diagnosis of parasites as well as exploring various novel non-chemical methods to control parasites of livestock.

  • Epidemiology of coccidiosis in Australian dairy goats

    Various unicellular protozoan parasites (coccidia) can affect the young dairy goats, leading to a disease, coccidiosis resulting in significant economic losses to the industry. Very little is known about the disease in Australian dairy goats. This project will involve the visit to various goat farms in Victoria, collection of faeces from goats, testing of faeces for the presence of coccidian parasites, use of DNA-based tests to identify the parasites.

    Potential supervisor: A/Prof Abdul Jabbar

    Associated research group: Veterinary Parasitology

    Associate Professor Abdul Jabbar’s research is focussed on molecular diagnosis and epidemiology of parasites of veterinary and medical significance and the discovery of antiparasitic drugs. Our work has led to the improved understanding of various parasitic diseases of domestic animals and the establishment of novel diagnostic methods.

    Currently, we are improving the diagnosis of parasites as well as exploring various novel non-chemical methods to control parasites of livestock.

  • Equine orthopaedic research

    The Equine Orthopaedic Research Group is a multidisciplinary team that works closely with the racing industry, and has a strong collaborative relationship with Racing Victoria. We welcome honours project enquiries from students interested in working with big data, diagnostic imaging, pathology, and behavioural methods for identifying orthopaedic pain.

    Potential supervisors: Prof Chris Whitton, Dr Peta Hitchens

    Associated research group: Equine Orthopaedic Research Group

    The Equine Orthopaedic Research Group conducts research aimed at the prevention of musculoskeletal injury in athletic horses. We are a multidisciplinary group using detailed investigation of bone microstructure, bone biomechanical properties, computational modelling of limb loads and epidemiological studies of injury to investigate the causes of bone and joint injury in horses and to develop preventative strategies that can be implemented by the equine industry.

  • Genomic tools to characterise molecular variation in parasites

    Reference genomes for many parasitic worms are now available. These genomes are now the foundation of molecular research that aims to understand the biology of these parasites and their host-pathogen interactions. To explore genetic variation in parasite populations, genome sequence surveys are being used to construct phylogenies using nuclear genomic data sets and assess genetic variation in genes between populations. These data are also being used to verify intraspecific conservation in vaccine or drug target candidates as an important first step toward developing effective vaccines and chemotherapies against these parasites. You will help refine an established bioinformatic approach developed in our lab to explore genetic variation in parasite populations using Illumina sequence reads. The results of your study will be used to prioritise the search for new drug candidates to treat a broad range of parasitic infections. Skills focus: Parasitology, population genetics and genomics.

    Potential supervisors: Dr Neil Young, Prof Robin Gasser

    Affiliated research group: Parasitology

    Our team works mainly on socio-economically important parasites. Parasitic diseases cause millions of deaths and enormous suffering in people and animals around the world. Our main goal is to understand parasites and the diseases that they cause, so that we can develop effective treatments, vaccines, diagnostic tests and strategies for effective control.

  • Identifying novel targets to improve diagnostic assays for mycoplasmas

    Currently available immunoassays for the diagnosis of mycoplasma infections detect antibodies produced against a single antigen. Detecting antibodies against multiple antigens will lead to improved sensitivity and specificity of diagnoses using a range of sample types. In this project you will assess novel targets for their application as immunogenic antigens to be incorporated into diagnostic assays. This will involve the expression and purification of recombinant GST proteins in E. coli and determining their immunogenicity by Western blot and ELISA. Immunogenicity will be assessed in different sample types from both uninfected and infected animals at various stages of infection.

    Potential supervisors: Dr Kelly Tivendale, Dr Nadeeka Wawegama, Prof Glenn Browning

    Affiliated research group:The Asia Pacific Centre for Animal Health (APCAH) is an internationally focused research and research training centre that aims to optimise animal health, production and product quality through improved control of infectious agents.

  • Infectious respiratory disease of foals

    Strangles is an important bacterial disease of horses. This project will complement an existing PhD project investigating the epidemiology of Streptococcus equi infection on a Victorian stud farm. Serial blood samples will be collected from foals after weaning to determine whether outbreaks of respiratory disease are associated with infection with common respiratory bacteria and viruses.

    Potential supervisors: Prof James Gilkerson, A/Prof Carol Hartley, Dr Charlie El-Hage

    Affiliated research group: Centre for Equine Infectious Disease

    The Centre for Equine Infectious Disease is a major national resource for the study of equine diseases in Australia.  We conduct research into the major viral and bacterial pathogens infecting horses. Our research has led to the development of diagnostic tests, the development of vaccines and our staff are engaged in providing advice to various level of government. We provide diagnostic testing for serious endemic pathogens of horses including strangles and equine herpesviruses.  We are actively involved in providing advice to industry on the management of infectious disease outbreaks.

  • Investigation of mycoplasma virulent genes responsible for host pathogen interactions

    In our laboratory we work exclusively on developing vaccines against some of the major pathogenic mycoplasmas in production animals. We investigate the interactions between the mycoplasmas and their hosts to identify the virulent genes involved in pathogenicity of the bacteria, which would ultimately help to develop better vaccine candidates to control the diseases. This project will investigate how mycoplasma virulent genes help pathogenic Mycoplasmas to interact with its hosts through in-vitro cell culture studies. You will be involved in mycoplasma culture, different cell culture assays such as co-culture, adhesion, invasion and transcytosis and molecular detection methods.

    Supervisors: Dr Nadeeka Wawegama, Prof Glenn Browning, Dr Paola Vaz

    Affiliated research group: The Asia Pacific Centre for Animal Health (APCAH) is an internationally focused research and research training centre that aims to optimise animal production and product quality through improved control of infectious agents.

  • Molecular detection and characterisation of avian coronaviruses circulating in poultry farms in Australia

    Avian coronavirus or infectious bronchitis virus (IBV) causes a highly contagious respiratory tract disease in chickens leading to major economic losses. Over recent decades IBV has re-emerged in Australian flocks as a result of recombination between existing strains in chickens and distinct IBVs of unknown origin (possibly from wild birds) (2-4). Investigating the characteristics of current circulating IBV strains would help to better understand the origin, spread and evolution of IBVs in Australia. The proposed project will investigate respiratory disease outbreaks in commercial poultry flocks, providing highly valuable and much needed IBV genomic information for vaccine development and disease control.

    Supervisor: Dr Karim Mardani

  • Modulating immunity by herpesvirus infection

    Herpesviruses survive a lifetime with their hosts because they have evolved many varied mechanisms to avoid immune-mediated destruction. Horses can be infected with more than 5 different types of herpesviruses that can cause a range of clinical disease signs. This project aims to compare infection by two different equine gammaherpesviruses in horses and will investigate how infection can alter the population of immune cells resident in respiratory sites. The student will gain a range of skills including cell and virus culture, PCR and molecular biology, and FACS analysis.

    Potential supervisors: A/Prof Carol Hartley, Dr Charlie El-Hage, Prof James Gilkerson

    Affiliated research group: Centre for Equine Infectious Disease

    The Centre for Equine Infectious Disease is a major national resource for the study of equine diseases in Australia.  We conduct research into the major viral and bacterial pathogens infecting horses. Our research has led to the development of diagnostic tests, the development of vaccines and our staff are engaged in providing advice to various level of government. We provide diagnostic testing for serious endemic pathogens of horses including strangles and equine herpesviruses.  We are actively involved in providing advice to industry on the management of infectious disease outbreaks.

  • Molecular detection and characterisation of avian coronaviruses circulating in poultry farms in Australia

    Filarial worm parasites of canines, such as Dirofilaria immitis (heartworm) can exert a huge toll on canines with respect to morbidity and mortality, whilst genera such as Brugia are zoonotic, posing a risk of lymphatic filariasis to human populations as well. Most canine filaroids are transmitted by mosquitoes and hence in tropical regions transmission can occur year-round. Despite limited research into the distribution of canine-infecting filarial worms in Southeast Asia their occurrence has been found to be high and widely distributed, with species such as Dirofilaria immitis found in countries across Southeast Asia reaching prevalence up to 16% in some regions. Moreover, zoonotic filaroids including Brugia pahangi and Brugia malayi have also been detected in Malaysia and Thailand, respectively. The Knott’s test used alongside morphological identification is typically used to diagnose the presence of microfilaria in dog blood, however such characterisation is prone to microscopist error and is less sensitive than molecular methods. This project will involve the employment of molecular techniques, including PCR and Sanger sequencing, to elucidate the epidemiology of canine filarial worms from across Cambodia, including the detection of zoonotic species. The lack of prior country-wide data means that the possibility of identifying species never previously detected in Cambodia is great. Additionally, there is evidence that non-mosquito vectors may act as novel vectors of filaroids, and hence there is scope within this project for molecular testing of ticks, lice and fleas as well.

    Skills focus: DNA extraction, conventional PCR & Sanger sequencing, epidemiological analysis

    Supervisors: Dr Lucas Huggins, Prof Rebecca Traub

    Affiliated research group: Traub Lab, Veterinary Bioscience, Parkville

    The Traub Lab focuses on the field of veterinary public health, with an emphasis on the epidemiology and control of parasitic zoonoses, human geo-helminthiasis and vector-borne pathogens. Much of the Traub Lab’s research involves the development and application of molecular-based diagnostic techniques, including harnessing the power of novel next-generation sequencing based technologies to facilitate new discoveries into pathogens, parasite epidemiology and their zoonotic potential.

  • Prediction and classification of novel protein families in parasitic worms

    Our lab has generated a wealth of genomic, transcriptomic and proteomic data sets for a range of parasitic worms responsible for human and livestock disease. We have identified a range of conserved and species-specific protein families and are beginning to unravel their involvement in biological and developmental processes. In most cases, there is no detailed characterisation of these proteins. You will use bioinformatics to identify, classify and investigate protein families in a range of parasitic worms. You will assess their potential for parasite-specific proteins to become the next drug target candidate, and explore their role in host interactions and pathogenesis at the molecular level. Skills focus: Parasitology, genomics, pattern searching and modelling.

    Potential supervisors: Dr Neil Young, Professor Robin Gasser

    Affiliated research group: Parasitology

    Our team works mainly on socio-economically important parasites. Parasitic diseases cause millions of deaths and enormous suffering in people and animals around the world. Our main goal is to understand parasites and the diseases that they cause, so that we can develop effective treatments, vaccines, diagnostic tests and strategies for effective control.

  • Role of dopamine in insulin regulation in ponies and horses

    Equine pituitary pars intermedia dysfunction (PPID; formerly known as Cushing’s disease) is a fairly common condition in older horses and ponies, associated with an overactive pituitary gland due to low dopamine levels. This may cause insulin dysregulation and lead to a foot condition called laminitis.

    This project is part of a larger study and will involve validating some blood hormone assays and measuring biomarkers of dopamine in insulin-resistant and control ponies.

    Potential supervisors: Prof Simon Bailey, Dr. Nick Bamford

    Affiliated research group: Veterinary Inflammation and Metabolism

    Our Research group investigates the causes of laminitis in equines, which is a common and debilitating condition of their feet, where the hoof attachments weaken, stretch and/or separate. The most common form of this condition is associated with two endocrine conditions - equine metabolic syndrome (EMS) and pituitary gland dysfunction (PPID; formerly known as Cushing’s disease). Our group investigates why ponies and certain horse breeds are prone to endocrine laminitis and the metabolic differences between different breeds and types of equids. We are also investigating the mechanisms of how the disease occurs and are currently developing novel treatments

  • Survival of bacterial and viral animal pathogens in the environment

    Survival of pathogens in the environment has important implications for disease control in animal populations. This project will study the survival of an important viral pathogen of chickens (infectious laryngotracheitis virus, ILTV) and an important bacterial pathogen of cattle (Mycoplasma bovis) under different environmental conditions, including survival of a novel vaccine strain of ILTV in water and other substrates used for vaccine administration. The project will involve a number of traditional laboratory techniques including bacterial culture, cell culture and viral propagation.

    Potential supervisors: Prof Joanne Devlin, Prof Glenn Browning

  • Unravelling the basis of virulence in mycoplasmas using a live vaccine model

    Mycoplasma synoviae is an economically important poultry pathogen causing respiratory disease, lameness, reduced egg production and downgrade of egg quality. A Live attenuated vaccine (MS-H) developed in our laboratory is used to control M. synoviae infections. This project is to address the molecular basis of attenuation of the MS-H vaccine by using targeted mutagenesis followed by gene expression and protein analyses, and metabolomics. It is also anticipated that this project will result in development of a protocol for expression of foreign genes in M. synoviae leading to development of recombinant poultry vaccines against diseases that target the upper respiratory system.

    Potential supervisors: Prof Amir Noormohammadi, Dr Marc Marenda, Dr Sara Klose

    Affiliated research group: Asia-Pacific Centre for Animal Health (APCAH)

    The Asia Pacific Centre for Animal (APCAH) is an internationally focused research and research training centre that aims to optimise animal production and product quality through improved control of infectious agents. Previous work at APCAH has resulted in the development and registration of a number of commercial animal vaccines.

  • Viral-bacterial coinfection dynamics of respiratory pathogens in cells

    In the natural world, respiratory pathogens coexist within their hosts, but their dynamics and interactions remain poorly understood. Many significant acute and chronic respiratory diseases of animals are polymicrobial, with disease being a consequence of coinfections with multiple viruses, bacteria, fungi or parasites. Increasingly, the importance of studying multi-pathogen interactions has been recognised as crucial for understanding the pathogenesis of infectious disease in a ‘real-world’ context.

    This project will investigate how viral and bacterial respiratory pathogens of animals interact within its host through in vitro cell culture studies. You will learn how to culture herpesviruses, mycoplasmas and/or chlamydias and apply them in different cell culture assays such as co-culture, invasion and co-infection. You would investigate their dynamics through various molecular, metabolic, culture and microscopic techniques.

    Potential supervisors: Dr Paola Vaz, Dr Nadeeka Wawegama

    Affiliated research group: Asia-Pacific Centre for Animal Health (APCAH)

    The Asia Pacific Centre for Animal (APCAH) is an internationally focused research and research training centre that aims to optimise animal production and product quality through improved control of infectious agents. Previous work at APCAH has resulted in the development and registration of a number of commercial animal vaccines.