2014 Research Opportunities - Health


Identification of exotic bacterial and viral pathogens in imported ornamental fish and managing the disease risks posed by these fish to the Australian aquaculture industries.

Nearly 18 million ornamental fish are imported annually under a policy based on an Import Risk Analysis published in 1999. Despite the biosecurity measures in place since 2000, there have been several incidents of exotic pathogens from ornamental fish affecting wild and farmed fish populations. The study will identify species of imported ornamental fish harbouring diseases of quarantine significance and what threat the distribution of these fish pose to the wild or natural and aquaculture fish populations in Australia. The results of this study will provide information to improve current quarantine procedures and policy in the management of the biosecurity risk of imported ornamental fish. The project will start in early 2015.

The student will be based at the Camden campus of the University of Sydney. The student should have a good quantitative aptitude and willing to learn diverse range of epidemiological and laboratory methods.

The successful candidate must have completed an undergraduate degree in science, agriculture, veterinary science or equivalent, have research experience (Honours or Master’s degree), good analytical and communication skills.

The successful applicant must apply for and be awarded a scholarship (stipend):-

    Project Supervisors:

    Dr Joy Becker,


    Investigations of the application of naturally occurring or induced canine stem cells for treatment of dogs

    The application of regenerative medicine utilising adult or induced stem cells in a developing area of veterinary science and this project proposes the isolation or development and subsequent characterisation of canine stem cells for the treatment of disease and disorders in dogs.

    Project Synopsis
    Regenerative medicine is an emerging discipline in veterinary science and it is proposed that it will be utilised as an approach for the treatment of a variety of genetic, metabolic and orthopaedic diseases and injuries. Recently, reprogramming of cells to generate induced pluripotent stem cells (iPSCs) from adult differentiated cells like skin fibroblasts has gained significant interest as it would allow autologous transplantation of pluripotent cells circumventing many of the technical and ethical issues that have been of concern in human regenerative medicine. The benefit of iPS cell approaches is that differentiated cells can be harvested in reasonably non-invasive procedures (eg. skin collection) and as a resource are not encumbered with the ethical issues of embryo creation and destruction.

    The nature of pluripotent cells infers that they are capable of differentiation into many other cell types and this characteristic is under investigation for treatment of a large range of diseases.
    Mesenchymal stem cells (MSCs) are multipotent stem cells with significant therapeutic potential in veterinary medicine. These cells reside in bone marrow, adipose tissue, blood, umbilical cord blood, amniotic fluid, teeth and foetal tissues. In normal healthy animals MSCs play a role in cellular renewal processes and can differentiate into osteocytes (bone), adipocytes (fat cells), myocytes (muscle), chondrocytes (cartilage), cardiomyocytes (heart), and neurons (nervous system). As these cells can be harvested from a number of tissues and re-administered with the ability to differentiate into a range of tissue types, autologous application of MSCs has been investigated as a cell based therapeutic agent for human and animal health. While this approach has shown some promise in initial clinical trials, the conditions required for high purity culture and unambiguous identification of these stem cells have yet to be determined. This approach has already been successfully applied to a range of diseases and disorders including cartilage and bone repair, heart regeneration following cardiac infaction, neuronal regeneration following stroke or brain trauma, and wound healing. Veterinary applications in dogs may include repair of fractures, cartilage repair, relief of osteoarthritis and treatments for hip dysplasia.
    Project Objectives

    • Establish in our lab and optimize cell culture methodologies from surgical waste material (adipose tissue) based on published methods.
    • Screen cell cultures for surface markers by Fluorescence Activated Cell Sorting (FACS) to optimise cell isolation procedures and population homogeneity.
    • Characterise identified side populations by gene expression profiles of genes specific to MSCs lineages.
    • Evaluate cell labeling techniques for subsequent in vivo application.
      Establish and optimize canine iPSCs through the traditional retrovirus mediated methodology to establish the basic morphological, immunochemical and expression characteristics of these cells in vitro.
    • To investigate methodologies for formation of ‘clinic-ready’ canine iPSCs by alternate methods (non-genome integrative) and compare to retrovirus induced iPSCs.

    This project is supported by the Canine Research Foundation and is open to Masters, Honours and BScVet candidates. This project does not include student scholarship support.
    Techniques employed will include:
    Canine Primary Cell Culture
    Cell transduction (viral or other)
    Cell isolation/ FACS
    Flow cytometry
    Real-time PCR
    Fluorescence microscopy
    Cell labeling techniques

    Project Supervisors:
    A/Prof Paul Sheehy,
    Prof Rosanne Taylor,
    A/Prof Peter Williamson


    Improving fish health management and farm production in marine finfish aquaculture in Indonesia and Australia

    The project aims to identify key diseases in marine finfish aquaculture in Indonesia resulting in development of improved management protocols for hatcheries and grow-out farms.

    Project Synopsis
    Fish diseases are a major cause of production losses in marine finfish aquaculture in Indonesia but very limited objective information is available about them. This three year project funded by the Australian Centre for International Agricultural Research (ACIAR) will first use longitudinal epidemiological studies to identify key diseases prevalent on hatcheries and grow-out farms in Bali, Indonesia and then develop and test improved protocols for managing these diseases. The ultimate aim of the project is to improve fish health management and production in marine finfish aquaculture in Indonesia and to develop capacity in fish health management in Indonesia.

    The project will start in early 2014 with a survey of hatcheries and grow-out farms. Quarterly fish sampling will then start from the enrolled hatcheries and grow-out farms using robust epidemiological sampling approaches. Samples will be tested for evidence of parasitological infestation and viral infections using microscopy, histopathology and real time PCR. This one year study will provide us information about the diseases prevalent in hatcheries and farms and enable us develop improved management and biosecurity protocols for preventing and controlling these diseases. Improved approaches will be implemented in a part of a government hatchery by keeping the other part as a control. Production and disease events in the ‘treated’ part of the hatchery will be compared with the ‘control’ part using statistical methods to demonstrate effectiveness of improved management and biosecurity approaches.

    Further Information:The project can be tailored to meet specific interests of the candidate but it would suit someone interested in making a real difference in the lives of people in developing countries and willing to work in a collaborative, multidisciplinary environment. The student will be based at the Camden campus of the University of Sydney but will be required to travel to Bali, Indonesia for conducting research. The candidate should have a good quantitative aptitude and should be willing to learn a range of epidemiological and laboratory methods.

    Eligibility:
    The successful applicant must apply for and be awarded a scholarship (stipend) for example, an Australian Postgraduate Award (APA) Scholarships for Australian and New Zealand residents.

    For International applicants, AusAid Scholarships scholarships are available for eligble students. Students must have a scholarship which covers full tuition fees and a living allowance.

    The successful candidate will have an undergraduate degree in science, veterinary science or equivalent, research experience, motivation and good communication skills

    Scholarships will commence in 2014.

    Project Supervisors:
    Dr Navneet Dhand, Dr Joy Becker, , Dr Mike Rimmer and
    Prof Richard Whittington.


    RHDV: Mechanisms of transmission

    The escape, and subsequent release of, rabbit haemorrhagic disease virus (RHDV)
    into the feral rabbit population in Australia in 1995 reduced rabbit numbers by up to
    95%. RHDV continues to persist in the Australian environment and continues to cause pathogenic infection in rabbits across the country. However, understanding of how the virus persists in the environment and how disease outbreaks are triggered remain unknown.

    The aim of this project is to develop a greater understanding of the interactions between rabbits, RHDV and the environment. Topics such as virus persistence, outbreak dynamics, and modes of transmission will all be investigated. The student should have an understanding of epidemiology, disease dynamics and ecological interactions.

    Implications of this research are far reaching: while the focus in Australia is to improve our understanding of RHDV transmission for pest animal management purposes, this research will also provide valuable information to researchers where native rabbit populations are in decline.
    Field sites will be based in the central tablelands of NSW and industry placement for the successful candidate will be offered at the Vertebrate Pest Research Unit in Orange NSW.

    Eligibility:
    Australian students will be required to be eligible for an Postgraduate Award (APA) Scholarships (which involves a tax exempt stipend of approximately $23,729 p.a. for 3 years) and there is potential for a tax exempt “top up” to $31,653 p.a. dependent on the skills and experience of the successful candidate.

    International students will need to obtain an International Postgraduate Research Scholarship through the University of Adelaide. A four year top-up scholarship (total scholarship value is $31,653 per year for four years), as well as mentorship opportunities and career-readiness training will be made available to the successful candidate.

    Interested candidates may contact the supervisors for further details
    Dr Tarnya Cox and
    Professor Michael Ward


    Using a One Health Framework to promote food and nutrition security
    One Health Framework

    The One Health framework enables human, animal and crop health professionals to work together with social scientists such as anthropologists and economists to tackle complex problems.

    Internationally, we are actively working to yield robust evidence that can be used to maximise poultry and crop health and value chain efficiency in support of sustainable household food and nutrition security. The majority of the world's rural poor rely on raising livestock for their day to day living. Livestock contribute to both poverty alleviation and food security. The majority of rural households in sub-Saharan Africa and SE Asia raise poultry. Poultry meat and eggs provide high quality protein and micronutrients that are more easily taken up by the human body than plant based nutrients. They also provide cash income to purchase food. These benefits are of notable significance to vulnerable community members such as growing children and people infected with HIV.
    Poor quality agricultural production can be detrimental to human nutrition by providing high calorie, low nutrient density food or the consumption of food contaminated by mycotoxins. These issues become especially raw in overarchingly food insecure environments.

    On the ground participation and partnership are central to our projects as are gender and ecologically sustainable production. By harnessing the strength of male and female farmers in Africa and Asia, we work with them to yield beneficial outcomes for their households and their wider communities. We actively collaborate with national Ministries of Agriculture, Health and Planning and Finance to strengthen policy environments in support of nutrition-sensitve agriculture and improved human health.

    The research seeks to answer the following questions.

    • Can deliberate and strategic linkages between family run poultry production and crop farming improve the socio-economic and biological efficiency of both operations?
    • Can family poultry production and trade be increased by supplementing the birds' feed intake with by-products from crop farming?
    • Can increased efficiency of family poultry production and trade contribute to ecologically and economically sustainable agriculture and improved food security and human nutrition?

    In Australia we are working with the Charles Perkins Centre Global Food and Nutrition Security Project Node. This project node brings together a multi-disciplinary team to focus on good nutrition and the interrelationships between farmers, traders, regulators, consumers and policy makers to determine policies and food systems that deliver appropriate, sustainable, diverse and nutritious diets.

    Supervisor: Associate Professor Robyn Alders, AO

    Synopsis
    Achieving household and community level food security is a complex issue. The One Health framework enables human, animal and crop health professionals to work together with social scientists such as anthropologists and economists to tackle such complex problems. Our projects seeks to strengthen food and nutrition security in sub-Saharan Africa and SE Asia by integrating family poultry and crop value chains in collaboration with regional and in-country partner government and research institutions.
    Village poultry production can directly increase nutritional outcomes by providing food and indirectly by providing cash income to purchase food. Poultry meat and eggs provide high quality protein and micronutrients that are more easily taken up by the human body than plant based nutrients. These benefits are of notable significance to vulnerable community members such as growing children, pregnant women and people affected by HIV and can also contribute to wildlife conservation activities. Poor quality agricultural production can be detrimental to human nutrition by providing high calorie, low nutrient density food or the consumption of food contaminated by mycotoxins.

    Additional Information
    Further Information: The research is based at the Camperdown Campus.

    Eligibility: The successful applicant must apply for and be awarded a scholarship (stipend) for example, an Australian Postgraduate Award (APA).

    For international students, Australian Award scholarships are available for eligible students. Students must have scholarship which covers full tuition fees and living allowance.

    Further Information: A/Prof Robyn Alders


    Johne’s disease in relation to MAP infection in both cattle and sheep

    We are offering two Australian Livestock Industry Biotechnology PhD Scholarships for studies to commence in 2013. The PhD scholarships are for research into Johne’s disease and will be located at the University of Sydney, Faculty of Veterinary Science, Camden, NSW. Successful candidates will have the opportunity to study several aspects of Johne’s disease in relation to MAP infection in both cattle and sheep. Working within a large multidisciplinary and supportive team, the projects will use an established experimental infection model where MAP-exposed animals can be followed throughout the course of the disease, as well as the study of natural infection on commercial farms. These studentships’ will provide successful candidates with mentorship opportunities as well as career-readiness training and there is potential for the PhD students to work with international collaborators and to attend both national and international conferences.
    There is opportunity for students to study several aspects of Johne’s disease including:

    Vaccine development: Currently there is one vaccine licensed for use in the prevention of Johne’s disease in sheep but this vaccine is not 100% effective and has significant safety issues associated with its administration. We are in the process of examining and developing new formulations for vaccines and studies in this area will enable a student to examine the process of vaccine development as well as the genetic responses of host animals to vaccine administration with a view to identifying and enhancing the optimum immune response in relation to vaccine efficacy.
    Genomic analysis of the host response to Johne’s disease: There is indication that there may be a genetic element in the host response to MAP and either resistance from or progression to clinical Johne’s disease. It is known that many immune modulations occur during mycobacterial infection, related to both the host and pathogen responses. Findings to date in cattle by our group have revealed the involvement of several immune pathways. It will be possible to study in detail these novel cellular mechanisms and how they impact upon disease outcome.
    Persistence inside cells: Currently, the cause of the lengthy sub-clinical phase of Johne’s disease is largely unknown. Within the animals, mycobacteria are localised within macrophages, where they are capable of persisting for long periods in a dormant state, ‘unseen’ by the host’s immune system. It is thought that several genes and proteins made by the MAP organisms during the process of dormancy and subsequent activation could be a bridge between sub-clinical and clinical infection. Studying these processes could aid in the development of new therapeutics or vaccines.

    Eligibility
    These scholarships are available only to Australian or New Zealand residents who are also eligible for an APA/UPA scholarship. Application for an APA/UPA scholarship must be successful in order to receive this award Scholarships will commence in 2014.
    Scholarship terms
    The scholarship provides a tax free ‘top-up’ amount of $15,000 per annum as a stipend for three years and is in addition to the tax free APA/UPA award of $24,653 p.a. (2013 rate). The total value of the combined scholarship is $38,728 per year tax free. Separate applications are required for the APA/UCA and the Australian Livestock Industry Biotechnology Scholarships (ALIBS).
    Interested candidates may contact the supervisors for further detailsDr Auriol Purdie, Dr Douglas Begg , Dr Kumi de Silva, Dr Karren Plain and Prof Richard Whittington.

    To apply for the ALIBS, please submit a letter of application and relevant supporting documentation outlining your suitability to by the 31st October 2013.


    The development of a new rapid test for determining the serogroup and virulence of footrot affecting Merino sheep

    Current phenotypic virulence detection tests are not reliable and the agreement between the available phenotypic tests is poor. There is a need for a test for virulent footrot which offers more consistent results, or at least results that closely match the clinical potential of isolates of D. nodosus to cause disease. Genetic tests for the virulence factors of D. nodosus may overcome some of the limitations of the phenotypic tests. They may be more stable, are not likely to be influenced by the physiological state of the organism, and may be quicker and cheaper, particularly if tests can be devised that do not require prior microbial culture, and that can be applied directly to field samples like lesion swabs. In this project the whole genome sequence of D. nodosus will be examined to identify markers for virulence and serogroup, and tests devised. The tests will be applied in laboratory studies of archival samples, and in current pen and field trials. This study will also involve studying and analysing data collected from 12 farms over five years, to correlate within-flock prevalence and severity of footrot with microbial characteristics. The study is a high priority for the sheep industries in Australia.

    Eligibility
    These scholarships are available only to Australian or New Zealand residents who are also eligible for an APA/UPA scholarship. Application for an APA/UPA must be successful in order to receive this award. Scholarships will commence in 2014.

    Scholarship terms
    The scholarship provides a tax free ‘top-up’ amount of $15,000 per annum as a stipend for three years and is in addition to the tax free APA/UPA award of $24,653 p.a. (2013 rate). The total value of the combined scholarship is $38,728 per year tax free. Separate applications are required for the APA/UCA and the Ian (Peter) Wrigley Scholarship.
    Interested candidates may contact the supervisors for further details:
    Dr Om Dhungyel and Prof Richard Whittington.
    To apply for the Ian (Peter) Wrigley Scholarship, please submit a letter of application and relevant supporting documentation outlining your suitability to by the 31st October 2013.


    Marine and environmental immunology: biotic and abiotic impacts in herpesvirus epizootics in oysters

    There is a current epizootic in Pacific oysters (C. gigas) due to the herpesvirus OsHv, which had devastated commercial oyster production in France and other countries. The disease was detected in Sydney in 2010. This PhD project will investigate interactions between environmental factors and immunity in oysters in the field and also in laboratory studies.

    The goal is to devise control strategies to enable Australian oyster farmers to remain profitable. This project will seek to answer fundamental questions about how molluscs evolve through natural selection to cope with devastating diseases. The project will involve collaboration with researchers in France and throughout Australia and may require extensive travel.


    Supervisors: Dr Ika Paul-Pont / Dr Navneet Dhand
    Co-supervisor: Prof Richard Whittington

    Further Information:
    The successful candidate must have completed an undergraduate degree in science, agriculture, veterinary science or equivalent, have research experience (Honours or Master’s degree), good analytical and communication skills, and be willing to undertake marine and estuarine field studies.

    The successful applicant will be encouraged to apply for and be awarded a scholarship (stipend) for example, an Australian Postgraduate Award (APA) for Australian and New Zealand residents. Full-time award holders receive a stipend of $24,653 p.a. (2013 rate) which is currently exempt from taxation. The stipend rate is indexed on the anniversary of the commencement date of the award. Scholarships Applications for APAs close around October 31st (for semester 1) and June 11th (for semester 2) each year.

    The project is based at the Camden campus.


    Immune modulation during mycobacterial infection:host and pathogen processes

    M.paratuberculosis causes chronic intestinal disease in animals. Recently, this mycobacterium has been found to infect humans and may be linked to Crohn’s disease, a debilitating inflammation of the bowel. The pathology and immune response to M.paratuberculosis infection closely resembles what occurs in other diseases caused by mycobacteria, including tuberculosis (M. tuberculosis) and leprosy (M. leprae) in humans. This makes Johne’s disease, the disease caused by M.paratuberculosis in cattle and sheep, an excellent animal model for mycobacterial infections.

    Immune modulation occurs during mycobacterial infection, both related to the host and the pathogen responses. Findings from microarray analysis of early exposure of cattle to M.Paratuberculosis have revealed the involvement of immune pathways. This PhD project will study in detail the implications of these findings with particular emphasis on novel cellular mechanisms that may be altered in response to M.paratuberculosis and how these changes impact upon the pathogenesis of Johne’s disease, both from the point of view of the pathogen and the host.

    Working within a large multidisciplinary and supportive team with access to ongoing field trials, this project will use an established experimental infection model in cattle and sheep. Animals can be followed throughout the course of the disease. Pathology of the lesions and expression of cytokines and chemokines throughout disease will be compared. The role of regulatory cells and molecules in M.paratuberculosis infection will also be examined. The study will incorporate molecular techniques such as cell culture, immunohistochemistry, quantitative RT-PCR, flow cytometry and genome array analysis to monitor changes in host cellular responses.

    Supervisor: Dr Auriol Purdie / Dr Karren Plain
    Co-supervisor: [Prof Richard Whittington

    Further Information:
    The project is based at the Camden campus. The successful candidate must have completed an undergraduate degree in science, agriculture, veterinary science or equivalent, have research experience (Honours or Master’s degree), good analytical and communication skills, and be willing to perform laboratory and field based studies.

    The successful applicant will be encouraged to apply for and be awarded a scholarship (stipend) for example, an Australian Postgraduate Award (APA) for Australian and New Zealand residents. Full-time award holders receive a stipend of $24,653 p.a. (2013 rate) which is currently exempt from taxation. The stipend rate is indexed on the anniversary of the commencement date of the award. Scholarships Applications for APAs close around October 31st (for semester 1) and June 11th (for semester 2) each year. In addition, a ‘top-up’ of the living allowance may be negotiated with the successful student.


    Vaccines for Johne’s disease: defining protection

    Johne’s disease is an infection of ruminants that results in wasting and the eventual death of the affected animal. The infection is caused by the bacterium Mycobacterium avium subspecies paratuberculosis. While there is a currently available vaccine for sheep, this does not stop infections and can result in severe injection site lesions. A safe and effective vaccine for Johne’s disease is an imperative for disease control in the agricultural industry in Australia. This project will examine alternative formulations that could be used for new vaccines to control Mycobacterium avium subspecies paratuberculosis infections primarily in sheep. Working within a large multidisciplinary and supportive team with access to ongoing field trials, this project will examine the immunity developed by various vaccine formulations to determine why the vaccines do or do not provide protection. This project will enable the candidate to develop a range of skills including animal handling, cellular and humoral immunology and molecular biology. The successful candidate will be exposed to state of the art immunology and vaccine technology. After graduation the candidate will be well placed to enter the vaccine development, commercial or research fields.

    Supervisor: Dr Douglas Begg / Dr Kumi de Silva
    Co-supervisor: Prof Richard Whittington

    Further Information:
    The successful candidate must have completed an undergraduate degree in science, agriculture, veterinary science or equivalent, have research experience (Honours or Master’s degree), good analytical and communication skills, and be willing to participate in laboratory and field based studies.

    The successful applicant will be encouraged to apply for and be awarded a scholarship (stipend) for example, an Australian Postgraduate Award (APA) for Australian and New Zealand residents. Full-time award holders receive a stipend of $24,653 p.a. (2013 rate) which is currently exempt from taxation. The stipend rate is indexed on the anniversary of the commencement date of the award. Scholarships Applications for APAs close around October 31st (for semester 1) and June 11th (for semester 2) each year. Dependant on experience, a ‘top-up’ of the living allowance may be negotiated with the successful candidate.

    The project is based at the Camden campus.