2014 Research Opportunities - PRODUCTION

Understanding the physical and chemical factors which enable sperm to pass through the cervix

Project Synopsis
Ruminant sperm are deposited in the anterior vagina and must traverse the torturous, mucus filled cervix to fertilise the oocyte. The ability of sperm to perform this task is dramatically reduced if sperm are stored in a frozen or liquid state prior to cervical insemination. One hypothesis for this is that freezing interferes with the interaction of sperm with the female tract but biophysical and biochemical study of sperm-mucus or sperm-cervical interaction is limited. The aim of this project is to combine analysis of sperm function and fertility with biochemical and biophysical analysis of cervical mucus properties and sperm membranes to delineate factors which enable sperm to pass the cervix. In the latter stage of the PhD program this information will be used to develop novel and practical solutions which improve fertility following cervical insemination of frozen-thawed ram sperm. The project will be conducted in conjunction with collaborators at INRA (Tours, France) and a PhD stipend and project costs will be provided subject to contract agreement with the funding agency.

Further Information:-
The successful candidate must have completed an undergraduate degree in the life sciences (e.g. biology, biochemistry, animal science), have research experience (Honours or Master’s degree) and excellent communication skills. Experience in biochemistry and proteomics is highly desirable. Applicants must be Australian citizens or Australian permanent residents.

Eligibility:-
A PhD stipend will be provided to successful applicant (APA equivalent rate) and commence in Semester 1, 2014. Further information can be obtained from Dr Simon de Graaf. Applications should be sent direct to and should include a curriculum vitae, a copy of an academic transcript, and the names and contact details of at least two referees


Feed allocation in automatic milking systems to optimise milking robot utilisation

Project Synopsis
There is still relatively little known about the effect of manipulating feed timing, amount and type on cow behaviour and associated voluntary cow movement (cow traffic). The timing of cow movement is important as this dictates the utilisation of the milking robots. Hence, there is a significant opportunity to improve robot utilisation on most farms, particularly in the early morning. This PhD will develop novel, feed allocation practices to increase milking robot utilisation and improve the profitability of pasture-based automatic milking systems.

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) and good analytical and communication skills.


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. 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.

Applicants may be eligible for additional support through the FutureDairy programme Future Dairy
Applications for APAs close around October 31st (for semester 1) and June 11th (for semester 2) each year.

For international applicants, the student must have a scholarship which covers full tuition fees and a living allowance. Further information can be found at International Students

Supervisor:
Dr Cameron Clark


Characterisation of oxidative stress biomarkers in exhaled breath condensate

Exhaled breath (EB) is the product of alveolar gas exchange and airway water loss, and it contains a variety of potential biomarkers originating from inflammatory reactions in the airway mucosa. Because the method of exhaled breath condensate (EBC) collection is completely non-invasive, repeatable and does not require patient cooperation, EBC analysis is increasingly used in human medicine. The detection of OS biomarkers in EB and EBC is a new field of research in veterinary medicine with the potential to provide early identification of pathologies. Early detection of ‘at risk’ animal and clarity of understanding of the relevance and significance of OS in respiratory diseases may enable the implementation of strategic measures to reduce risk of livestock developing diseases. The exact physiological origin of OS biomarkers such as H2O2, and nitric oxide has not been clearly established in farm animals; the effects of changes in respiratory rate on the concentration of exhaled compounds in livestock are unknown, and for most of the markers there are no reference ranges available for healthy or diseased animals. The study of OS biomarkers in EB and EBC will facilitate the development of methods for dealing with issues in livestock medicine that are not adequately addressed using currently available technologies

Further Information:-

The PhD candidate will be expected to undertake part of his/her research work overseas in collaboration with Prof Gabai (University of Padova, Italy).

Supervisor:-
Dr Pietro Celi
Email:pietro.celi@sydney.edu.au


Protemic measures of albumen degradation as indicators of egg freshness

Providing high quality eggs and egg products is crucial to the sustainable economic viability of the Australian egg industry. Currently, the main measures of egg freshness are based on determining physical attributes of egg albumen. These have included Haugh units (HU), albumen and yolk height, pH changes and various ratios of albumen and yolk. To a large degree most are related to the thinning of the albumen and are evident some time after lay. The thinning involves changes in the protein structure of the albumen and this begins immediately after lay. Investigating the changes in proteins found in egg albumen, also termed the egg albumen proteome should provide a more precise measure of egg freshness and at a much earlier timeframe.
The methodology to be utilised is well established (proteomic analysis utilising 2-Dimensional polyacrylamide gel electrophoresis (2D PAGE), and is an approach that can leverage published investigations of chicken egg albumen to expedite the establishment of validated biomarkers of egg freshness. Subsequent to this development phase, initial pilot experiments assessing the influence of time and temperature of storage will be undertaken to both link proteomic analysis with tradition HU measurements and also situate the methodology in the literature as a means of ensuring the developed techniques are robust and informative.

Other Information
This project is funded by the Poultry CRC. The student will be encouraged to apply for a tax exempt scholarship (APAI) currently ($24,653 pa). Students who may not be successful in obtaining an APA are still encouraged to apply. Applicants for CRC scholarships need to be Australian citizens or have permanent residency. Ideally, the student would enroll in semester 2 of 2013 as the starting date for their studies.

Supervisor:
Dr Jeff Downing
A/Prof Paul Sheehy


Timing, nature, extent and impact of diseases on dairy goat health and production in Australia

The dairy goat industry in Australia is rapidly changing as a consequence of the increased popularity of goat cheeses and the unprecedented demand for goat’s milk. The dairy goat industry is predominantly pasture based and is therefore confined to the high rainfall, agricultural areas of the country. While this offers cost of production advantages, it represents a potential threat to the industry as it increases the susceptibility of goats to intestinal parasites and footrot. Diseases like internal parasites, mycoplasmosis, clostridial diseases, CAE, CLA and Salmonellosis are known to affect goats however the impact of these or other conditions has not been qualified or quantified in the Australian dairy goat industry. The intensification of the dairy goat industry coupled with climate change (floods and drought) might result in an increased incidence of these conditions. This project will monitor the incidence, timing, impact and nature of diseases in Australian dairy goat farms: this will be correlated with the changes in environmental and climatic conditions to generate models and predict future trends. This project will focus on epidemiological studies on dairy goat diseases and how different regional/state environmental conditions, husbandry calendar of events and management techniques influence the incidence, prevalence, susceptibility and impact of diseases of different dairy goat breeds. Particular attention will be given to the increased parasite infection risks due to global changes, in particular climate change, which poses new challenges to traditional methods of dairy goat husbandry and the need for new solutions to ensure sustainable livestock production in future years.

Other 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 must 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.
For international applicants, the student must have a scholarship which covers full tuition fees and a living allowance. In addition, a ‘top-up’ of the living allowance may be negotiated with the successful student. Further information can be found at International Students

This project is supported by the Dairy Goat Society of Australia (DGSA) Research Foundation.

Supervisors:-
Dr Pietro Celi
Dr Peter White


Associations between stress, egg quality and other welfare measures in laying hens maintained in different housing systems

Our group has developed a non-invasive means of measuring the extent of stress experienced by laying hens. This is done by measuring corticosterone concentrations in egg albumen. In recent work the concentrations of corticosterone in albumen was determined in eggs collected from different housing systems. Early in the production cycle there were found to be differences between farms, with flocks showing distinct patterns of stress during this time. These early differences were linked to differences in egg production and mortality rate with production decreased and mortality increased when the corticosterone concentrations increased. The project objectives are to evaluate the link between stress in laying hens and other welfare measures but also to determine if there are effects on egg quality.

Further Information:
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.

Supervisor:
Dr Jeff Downing

Students would be encouraged to apply for a Poultry CRC scholarship.


Nutrient distribution on farms with Automatic Milking Systems (AMS)

Opportunity exists for a student project to investigate the impact of AMS and more specifically voluntary cow traffic on the distribution of nutrients within the farm system. Effluent deposited on laneways is of concern since it cannot be captured, stored and distributed on paddocks and it can pose environmental management challenges. With an AMS the cows voluntarily traffic around the farm system. To date there has been no known work conducted on the impact of this voluntary traffic on nutrient distribution. It is possible that the volume of effluent deposited on laneways is reduced since the cows are not being herded to the dairy as a group. On the other hand the volume may be increased as cows have the opportunity to loiter on laneways as they move through the system at ‘cow pace’.

Supervisor:
Dr Kendra Kerrisk
Co-supervisor:
A/Prof Sergio (Yani) Garcia

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


Grazing of forage crops and different pasture species in automatic milking systems

This PhD project will investigate the interactions at the animal-plant interface when cows moving voluntarily in an automatic milking system are given access to grazable forage crops and different pasture species. The ultimate goal of the project is to develop grazing management guidelines for some key forage crops that may be used in AMS systems in Australia in different seasons. The project may involve direct collaboration with researchers at Michigan State University in USA and may require spending at least one Australian autumn-winter in USA.

Supervisor:
A/Prof Sergio (Yani) Garcia
Co-supervisor: Dr Kendra Kerrisk
Dr Santiago Utsumi (Michigan State University)

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


Using forage crops to enhance cow traffic in automatic milking systems

This PhD project will investigate the use of different forage crops to enhance cow traffic of cows moving voluntarily in automatic milking systems (AMS). The successful candidate will develop a program to understand the interactions between time of the day and distance to the paddocks for different grazable forage options across all 4 seasons.

Supervisor:
A/Prof Sergio (Yani) Garcia
Co-supervisor:
Dr Kendra Kerrisk

Further Information:
The successful candidate must have completed an undergraduate degree in agriculture or veterinary science, have research experience (Honours or Master’s degree), good analytical and communication skills, and be willing to work with data analysis and undertake 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. A possibility exists for outstanding Australian or NZ candidates to apply for a FutureDairy scholarship (AU$30,000).


Dynamic simulation of cow traffic in Automatic Milking Systems

This PhD project will develop a dynamic model capable of representing the basic aspects of cow traffic system in a pasture-based automatic milking system (AMS). The successful candidate will work with dynamic simulation platforms to develop an ad hoc model and/or investigate the potential adaptation of existing models.

Supervisor:
A/Prof Sergio (Yani) Garcia
Co-supervisor:
A/Prof. Kendra Kerrisk

Further Information:
The successful candidate must have completed an undergraduate degree in agriculture, veterinary or IT/computer science, have research experience (Honours or Master’s degree), good analytical and communication skills, and be willing to work with simulation modelling but also undertake 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.

For international applicants, the student must have a scholarship which covers full tuition fees and a living allowance. In addition, a ‘top-up’ of the living allowance may be negotiated with the successful student. Further information can be found at International Students


The use of n-alkanes and other internal markers to estimate intake of dairy cows fed complex mixes of pasture and forage diets

Plant wax markers can be used to estimate pasture/forage intake and diet composition based on the faecal recovery of these markers. This PhD project will develop techniques to better estimate actual faecal recovery of n-alkanes and other long-chain carbon compounds in cows fed complex diets comprised of pasture and forage crops and grains. The project will be largely based on analytical procedures related to the n-alkane technique, although controlled studies will be carried out to test different techniques/hypothesis.

Supervisor:
Dr Ravneet Kaur Jhajj -
Co Supervisor:
A/Prof Sergio (Yani) Garcia

Further Information:
The successful candidate must have completed an undergraduate degree in agriculture, veterinary or chemistry, have research experience (Honours or Master’s degree), good analytical and communication skills, and be prepared to work in a laboratory but also undertake 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.

For international applicants, the student must have a scholarship which covers full tuition fees and a living allowance. In addition, a ‘top-up’ of the living allowance may be negotiated with the successful student. Further information can be found at International Students


Application of NIR in the nutritive evaluation of dairy cow diets

Near Infrared Reflectance Spectroscopy (NIRS) analysis is commonly used to determine nutritive value of feed-stuffs in recent years. Commercially, it is important that farmers on individual farms have accurate and reliable results. This project will develop techniques to improve the application of NIR systems to assess the nutritive value of dairy cow diets. The project is laboratory based.

Supervisor:
Dr Ajantha Horadagoda -
Co-supervisor: Dr Ravneet Kaur Jhajj - / A.Prof Yani Garcia

Further Information:
The successful candidate must have completed an undergraduate degree in agriculture, veterinary or chemistry, have research experience (Honours or Master’s degree), good analytical and communication skills, and be prepared to work in a laboratory but also undertake 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.

For international applicants, the student must have a scholarship which covers full tuition fees and a living allowance. In addition, a ‘top-up’ of the living allowance may be negotiated with the successful student. Further information can be found at International Students


Carbon sequestration of high yielding complementary forage rotations (CFR)

This PhD project will investigate aspects of carbon sequestration and carbon balance in high yielding CFR systems. The CFR comprise double or triple crop rotations capable of producing over 40 t DM/ha per year.

Supervisor:
Dr Rafiq Islam
Co-supervisor:
A/Prof Sergio (Yani) Garcia

Further Information:
The successful candidate must have completed an undergraduate degree in agriculture, veterinary or chemistry, have research experience (Honours or Master’s degree), good analytical and communication skills, and be prepared to work in a laboratory but also undertake 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.

For international applicants, the student must have a scholarship which covers full tuition fees and a living allowance. In addition, a ‘top-up’ of the living allowance may be negotiated with the successful student. Further information can be found at International Students


Improvement of nutritive value of maize silage for dairy cows

Maize silage is a major component of complementary forage rotation (CFR) system which yielded over 25 t DM/ha out of a total of 40 t DM/ha from CFR. This PhD project will investigate aspects of improving nutritive value particularly metabolizable energy content of maize silage without compromising yield of maize.

Supervisor:
Dr Rafiq Islam
Co-supervisor:
A/Prof Sergio (Yani) Garcia

Further Information:
The successful candidate must have completed an undergraduate degree in agriculture, veterinary or chemistry, have research experience (Honours or Master’s degree), good analytical and communication skills, and be prepared to work in a laboratory but also undertake 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.

For international applicants, the student must have a scholarship which covers full tuition fees and a living allowance. In addition, a ‘top-up’ of the living allowance may be negotiated with the successful student. Further information can be found at International Students