Identify your student project opportunity at QAAFI to suit your interests and contact the relevant project supervisor to discuss your role.

Soils, nutrition and weeds

Explore the range of the currently available student project opportunities in soils, nutrition and weeds. These projects will suit MSc (course work) and Honours students.

Germination ecology of summer weeds of the northern region of Australia project

Suitable for MSc (course work)/Honours students

Weeds cost the Australian grains industry a staggering $3.3 billion annually in control measures and yield loss. Although herbicides achieve satisfactory weed control, relying solely on herbicides for weed management can cause rapid evolution of resistant weed types and thereby jeopardise the initial success by herbicides. Thorough understanding on germination ecology of weeds are necessary to frame appropriate non-chemical and agronomic weed management options. Very limited information is available on the germination ecology of key summer weeds of the northern region of Australia, which makes it difficult to predict the environmental conditions that favour germination and seedling emergence. The aims of this research project are to determine the effects of environmental factors (temperature, light, salt stress, heat stress, water stress, burial depth) on germination and emergence of these weed species.

Location: Gatton
Contact supervisors: Dr Bhagirath Chauhan (b.chauhan@uq.edu.au) and Sudheesh Manalil (s.manalil@uq.edu.au)

 

Evaluation of herbicidal properties of plant extracts on major grass and broad leaf weeds project

Suitable for MSc (course work)/Honours students

Intensive use of herbicides is a major reason for the rapid evolution of herbicide resistance in many weeds. Therefore, a sustainable weed management strategy should integrate non-chemical herbicide options along with herbicides. There are reports that water extracts of certain plant residues would suppress weeds due to their allelopathy potential. The aim of this project is to examine the growth suppressive effect of allelochemicals on weeds and major crops in pot studies.

Location: Gatton
Contact supervisors: Dr Bhagirath Chauhan (b.chauhan@uq.edu.au) and Sudheesh Manalil (s.manalil@uq.edu.au)

 

Effect of environmental factors on herbicide efficacy project

Suitable for MSc (course work)/Honours students

An efficacious herbicide programme would reduce multiple herbicide applications, thereby reduce the herbicide selection pressure and resistance evolution. In addition, there would be less environmental pollution and additional economic benefits. Operational and environmental factors are crucial in deciding the level of herbicide efficacy and the level of weed control. Research indicated that temperature and light could affect the herbicide efficacy of many post-emergent herbicides. Therefore, this project would explore and identify the effect of temperature, light, and soil moisture on the efficacy of commonly used herbicides on both the susceptible and resistant weeds.

Location: Gatton
Contact supervisors: Dr Bhagirath Chauhan (b.chauhan@uq.edu.au) and Sudheesh Manalil (s.manalil@uq.edu.au)


Evaluating the weed seed sterilising effects of herbicides project

Suitable for MSc (course work)/Honours students

Post-emergent herbicides are applied during different growth phases of crop and weeds. The efficacy of these herbicides would depend on the growth stage of the weed plant. Although there would be some growth reduction in overgrown weed plants following herbicide selection, many plants may set seeds following herbicide selection. There are reports that some post-emergent herbicides have the potential to sterilise these seeds following herbicide selection. As a result, even though seeds would enrich soil seedbanks, the seeds may not be viable. Therefore, herbicides will be examined for the seed sterilising effects of weeds seeds. The dormancy and viability of these weeds will be tested.

Location: Gatton
Contact supervisors: Dr Bhagirath Chauhan (b.chauhan@uq.edu.au) and Sudheesh Manalil (s.manalil@uq.edu.au)


Weeds' response to crop interference and/or water stress project

Suitable for MSc (course work)/Honours students

How weeds respond to crop competition in terms of resource allocation? How different biotypes respond?
Do we need to increase N with crop plant density?
Water limitation is common in the northern region cropping systems. In these conditions, crops suffer but several weeds thrive.
How weeds (key winter/summer) respond to water stress and/or nutrients?

Location: Gatton
Contact supervisors: Dr Bhagirath Chauhan (b.chauhan@uq.edu.au) and Sudheesh Manalil (s.manalil@uq.edu.au)

 

Farming systems

Explore the range of the currently available student project opportunities in farming systems. These projects will suit MSc (course work) students.

High yielding sorghum for Australia’s northern grains region

Suitable for MSc (course work) students

In sorghum cropping what really matters is to understand how to match hybrids and management to the prevailing stress environment. In the Northern Grains Region farmers can choose from a large range of management practices (M) and high yielding hybrids (G) having contrasting maturity types, tillering type, yield potential, and yield stability. Though to be able to match the right hybrid and management to a growing environment, farmers need information on the site and likely seasonal conditions, and how GxM interactions modify the stress environment.  For example, recent GRDC projects have identified important differences between commercial hybrids in terms of yield potential and stability - two of the most important characteristics sought by rainfed sorghum growers. These results indicate that choosing the right hybrid for the right target yield or environment can make the differences between good yields in average sites and seasons and exceptional yields exceptional sites and seasons. Even though variability in yield potential and stability are known to exists between commercial hybrids, the physiological mechanism driving those phenotypic responses remains unknown. Understanding the physiological basis for those responses is a fundamental step in the parameterization of contrasting hybrid types in APSIM - www.apsim.info
In collaboration with a Global seed company this project will deliver:

  • A detailed physiological characterisation of hybrids having contrasting yield potential and stability characteristics;
  • An environmental characterization for both water and heat stresses around flowering, at key sorghum trial sites, and sorghum growing regions;
  • A predictive decision support tool that combines site information, outputs for APSIM and seasonal climate forecasting tools (e.g. ENSO, ACCESS-S) to quantify shifts in the likelihood of stress environments, profits and risks from alternative GxM combinations.

The project is based in Toowoomba
Contact supervisors: A/Prof. Daniel Rodriguez, A./Prof. Andrew Borrell, James McLean 
Start date: Immediately after student obtains UQGSS (stipend for domestics) or UQGSS-T (tuition for domestics) scholarships. Project only covers operating cost.

The use of drone and sensing technologies in sorghum – weed interactions research

Suitable for MSc (course work) students

Crop weed interaction research requires the collection of multiple crop and weed samples over large areas during the cycle of the crop, this is a labour intensive and costly exercise. Developing fast and cost effective UAV sensing platforms to scout weed problems in large fields can help target weed control interventions, reduce costs and increase yields. This project will use drone and sensing technologies to collect and analyse detail crop reflectance information and derive relationships between reflectance indices and crop and weed properties e.g. biomass, leaf area, density.
 
The project will involve field experimentation at Gatton Research Station, and desktop data analysis. 
Contact supervisors: A/Prof. Daniel Rodriguez (d.rodriguez@uq.edu.au), James McLean (j.mclean2@uq.edu.au), Dr Bhagirath Chauhan (b.chauhan@uq.edu.au)
Start date: Immediately

Benefits and trade offs from early planting sorghum and maize

Suitable for MSc (course work) students

Early planting is being considered a an option for farmers to reduce the likelihood of heat stress damage during critical stages of crop development around flowering. However the  comparative capacity of maize and sorghum hybrids to (i) establish and yield at lower than optimal soil temperatures, (ii) withstand the effects of frost, or (iii) benefits from a longer growing season and avoidance of heat stress, is not well understood. This project will aim to answer those questions using a replicated on-farm trial with multiple planting times and maize and sorghum hybrids of contrasting cold tolerance. 
 
The project involves on farm experimentation and desktop data analysis. The project is based at Gatton Campus.
Contact supervisors: A/Prof. Daniel Rodriguez (d.rodriguez@uq.edu.au), James McLean (j.mclean2@uq.edu.au), Dr Joe Eyre (j.eyre@uq.edu.au), Peter deVoil (p.devoil@uq.edu.au)
Start date: Immediately

Tactical agronomy for uniculm and low tillering sorghum hybrids in rainfed cropping

Suitable for MSc (course work) students

Low tillering hybrids are considered to be better adapted to low rainfall environments; though they are also expected to yield, when planted at high populations in high yielding or irrigated sites. This project will quantify the role of low tillering and uniculm hybrids across three contrasting environments in Queensland, a rainfed cropping site in the Darling Downs, a rainfed and hot environment from Central Queensland, and a cool and high yielding environment from the Southern Eastern Downs.
 
The project involves on farm experimentation and desktop data analysis. The project is based at Gatton Campus.
Contact supervisors: A/Prof. Daniel Rodriguez (d.rodriguez@uq.edu.au), James McLean (j.mclean2@uq.edu.au), Dr Joe Eyre (j.eyre@uq.edu.au), Peter deVoil (p.devoil@uq.edu.au)
Start date: Immediately

 

Grain crop physiology and modelling

Explore the range of the currently available student project opportunities in grain crop physiology and modelling. These projects will suit Honours students.

Understanding approaches to model crop canopy light absorption to estimate effects of agronomical practices on crop growth

Project can be scaled to be suitable for either Honours, Masters or PhD research

Radiation from the Sun absorbed by crop canopies drives leaf photosynthesis, which in turn drives crop growth, development and yield. As the first part of this project, the student will conduct a comparative study between similar, but differing in level of detail, approaches for modelling canopy light absorption. Simpler modelling approaches are efficient and robust for field crops, such as wheat or sorghum monocultures, while more detailed approaches are deemed necessary for orchard crops, such as mango, avocado or macadamia. Agronomical practices, such as planting density and pruning, can modify canopy light absorption by opening up crop canopies to allow more light penetration through the canopy. Effects of these canopy manipulation may be estimated with detailed modelling approach, but may not be the most efficient for long-term simulations. In the second part of this project, the student will have the opportunity to develop balanced and efficient models by combining the simpler and more detailed approaches and demonstrate that the new model can be applied to both field and orchard crops. Lastly, investigate ways of how knowledge gained from this project can be used to better inform agronomical decisions for improving crop productivity. Scholarships are available from University of Queensland sources.

Skill set required: Background in either mathematics or plant science and  experience in application of mathematical models

Contact superviror: Associate Professor Jim Hanan and Dr Alex Wu
Scholarship details: graduate-school.uq.edu.au/scholarships 
Location: St Lucia, Brisbane


Characterising wheat populations selected for adaptive root traits for water-stressed environments

Suitable for Honours students

The student will learn skills in field crops research, plant physiology, new field phenotyping techniques and data analysis.

Temperatures have increased and in-crop rainfall decreased over recent decades in many parts of the Australian wheat cropping region. With these trends set to continue or intensify, improving crop adaptation in the face of climate change is particularly urgent in this, already drought-prone, cropping region.  Importantly, improved performance under water-limitation must be achieved while retaining yield potential during more favourable seasons.  
Where rain-fed wheat production is dependent on stored soil moisture, optimisation of root architecture to maximise soil moisture extraction from deep in the soil, late in the season, is important to increase crop productivity. Seminal root angle and root number of seedlings are considered as proxy traits for early selection of deep and narrow root systems, which can allow increased deep soil water extraction. 

Recently, a new high-throughput phenotyping method has been developed to screen high numbers of lines (Richard et al. 2015. Plant Methods 11:13). This method has been used to select populations with either narrow or wide seminal roots.  We would predict that the genotypes selected for narrow root angle should have a narrower overall root system with more roots at depth and extract more soil moisture from depth.  This should lead to improved yield and affect other drought adaptive traits such as green leaf area retention (stay-green).

The populations selected for either narrow or wide roots will be sown in the field in 2017 to test their performance and to measure agronomic traits such as stay-green to determine whether the narrow root types have superior adaptation to water-stress environments.

There is an exciting opportunity for an honours student to participate in this experiment.

Location: UQ Gatton campus/Toowoomba

Contact supervisors: Dr Jack Christopher (j.christopher@uq.edu.au; tel: +61 7 45291413), Dr Karine Chenu (k.chenu1@uq.edu.au; tel: +61 7 4688 1357)

Prior to applying: If you are interested in this project, please contact the project supervisors  to discuss the project.

Agricultural nanotechnology

Explore the range of the currently available student project opportunities in agricultural nanotechnology. These projects will suit Honours, MSc or PhD students.

Optimisation of a tissue-culture pipeline for commercial avocado propagation 

Suitable for Honours, or MSc or PhD applying for own scholarship.

Clonal propagation of genetically identical plantlets is intrinsic to the production and propagation of elite genotypes of horticultural and woody species including avocado. However, the horticultural and forestry industries can lose millions of dollars every year due to lack of elite rootstock cultivars. The Mitter lab has developed a working pipeline for clonal avocado propagation in tissue culture, as a viable solution to this problem. This project aims to take this project forward to real-world outcomes, by translating our current tissue culture pipeline to new industry-relevant rootstock cultivars. There may also be opportunity to profile molecular and histological factors involved with shoot and root induction. The student will work closely with other members of the Mitter laboratory and with industry partners to aim to develop a viable commercial system for avocado propagation. It is expected that the student will learn valuable techniques in project design, plant tissue-culture/in vitro techniques, plant molecular, histological and physiological work (including hormonal response assays, microscopy, RNA extractions and qRTPCR).

Location: Mitter Laboratory, QAAFI Centre for Plant Science, Queensland Bioscience Precinct, UQ St Lucia campus, Brisbane
Contact supervisors: A/Prof. Neena Mitter (n. mitter@uq.edu.au) and Dr Alice Hayward (a.hayward @uq.edu.au)

Cryopreservation of avocado

Suitable for Honours, or MSc or PhD applying for own scholarship

Avocado (Persea Americana Mill) is a high value horticultural crop for Queensland. Currently, avocado genetic resources are maintained in the form of field repositories at great cost and risk of natural disasters, pest and diseases. Cryopreservation is the long-term storage of live tissues at ultra-low temperatures, and offers a necessary, complimentary method that is safe, cost-effective and long-term. This project will further develop our cryopreservation protocol for avocado, and translate this to a number of Persea spp cultivars/diverse germplasm. The student will work closely with collaborators in California, USA, and will have opportunity to work in California for a part of their project. The student may also have opportunity to undertake some next-generation molecular work in order to help elucidate Persea evolution and diversity with the goal to inform cryopreservation priorities. This project could be transformational for genetic preservation of avocado and other important tree species. 

Location: Mitter Laboratory, QAAFI Centre for Plant Science, Queensland Bioscience Precinct, UQ St Lucia campus, Brisbane. In collaboration with The Huntington Library, Art Collection, and Botanical Gardens, California, USA.
Contact supervisors: A/Prof. Neena Mitter (n. mitter@uq.edu.au) and Dr Alice Hayward (a.hayward @uq.edu.au)

Application of BioClay to viruses of importance to the Australian horticultural industries

Suitable for Honours, or MSc or PhD applying for own scholarship

Viral infection in economically important food and fibre crops is a major concern to Australian horticultural industries due to crop loses, yield-reductions and unmarketable fruit. The Mitter lab has developed ‘BioClay’, a world leading spray-on RNAi delivery platform that is able to protect plants from viral infection. This project aims to further explore the utility of the BioClay platform against viruses of economic importance to the Australian horticultural industry. This project will result in real-world outcomes, by translating and expanding our current virus targeting range to an industry-ready, world leading crop protection technology. It is expected that the student will learn valuable techniques and strong skills in experimental design, molecular biology (cloning, PCR, qRT-PCR, sequencing, RNA/DNA extractions), plant virology, plant-virus interaction, bioinformatics, material science and the application of RNAi to crop protection. There may also be opportunity to delineate fundamental molecular factors involved in plant RNAi induction mechanisms. The student will work closely with other members of the Mitter laboratory and industry partners to produce high value science and develop a highly productive research career. 

Location: Mitter Laboratory, QAAFI Centre for Plant Science, Queensland Bioscience Precinct, UQ St Lucia campus, Brisbane
Contact supervisors: A/Prof. Neena Mitter (n.mitter@uq.edu.au) and Dr Karl Robinson (k.robinson2@uq.edu.au)

Application of BioClay to insect of importance to the Australian horticultural industries. 

Suitable for Honours, or MSc or PhD applying for own scholarship

Insects cause significant physical damage to plants and are primarily responsible for the transmission of viruses that results in significant economic losses every year due to crop losses, yield-reductions and unmarketable fruit in Australian agricultural industries. In this project we aim to further explore the utility of our world leading RNAi delivery platform ‘BioClay’, to protect plants from vector mediated viral infection and insect feeding induced damage. This project will result in real-world outcomes, by translating and expanding on our current virus and insect target range to an industry-ready, world leading crop protection technology. It is expected that the student will learn valuable techniques and strong skills in experimental design, molecular biology (cloning, PCR, qRTPCR, sequencing, RNA/DNA extractions), plant virology, plant-virus and virus-insect interactions, bioinformatics, material science and the application of RNAi in crop protection. There may also be opportunity to delineate fundamental molecular factors involved in plant/insect RNAi induction mechanisms. The student will work closely with other members of the Mitter laboratory and industry partners to develop high value scientific outcomes and a highly productive research career.

Location: Mitter Laboratory, QAAFI, CPS, Queensland Bioscience Precinct, UQ St Lucia campus. 
Contact supervisors: A/Prof. Neena Mitter (n.mitter@uq.edu.au) and Dr Karl Robinson (k.robinson2@uq.edu.au)
 

Grain crop improvement

Explore the range of the currently available student project opportunities in grain crop improvement. These projects will suit Honours students.

Understanding the genetics of roots to improve drought adaptation of wheat and barley

Suitable for Honours students

Modern crop varieties are subject to unprecedented climatic fluctuations, particularly in the frequency and severity of drought. A genetic predisposition for deep rooting can enable the plant to access more stored soil moisture during the grain-filling period. However, knowledge about the genetic controls of root growth habit in wheat and barley is limited.

This project will involve experiments investigating root growth behavior for a series of wheat and barley genotypes performed under controlled conditions at St Lucia, plus data collection for above-ground water-use traits from field experiments located at Warwick and Toowoomba. 
Outcomes from this project will assist plant breeders to assemble wheat and barley varieties that are better adapted to drought and will represent a step toward customization of root systems that are tailored for local environments. We anticipate this will stabilize crop yields across years despite fluctuations in rainfall. 

The student will gain hands-on experience in crop physiology, plant breeding and genetics, and will join a diverse lab comprising 17 members who collectively speak 13 languages. 

Location: Hartley Teakle Building, St Lucia campus, Brisbane
Contact supervisor: Dr Lee Hickey, l.hickey@uq.edu.au, +61 7 3365 4805

Animal science: pests and diseases

Characterisation of the transcriptional units of bovine herpesvirus 1

Suitable for Honours students

Bovine herpesvirus 1 (BoHV-1) is an important viral pathogen of cattle worldwide. BoHV-1 is strongly associated with bovine respiratory disease which causes annual losses in excess of $US2 billion. The virus has a large double stranded genome which encodes approximately 70 genes. This project will characterise selected transcription units of BoHV-1 genes using an infectious clone of the virus. The project will utilised mammalian cell culture, western blotting, quantitative real-time PCR, and fluorescence microscopy. The resulting information will be used improve our understanding viral gene expression and to inform the construction of improved vaccines to reduce the impacts of BoHV-1 on cattle production.

Cells infected with bovine herpesvirus 1 expressing green fluorescent protein

Location: Queensland Bioscience Precinct, Building 80, St Lucia UQ Campus, Brisbane
Contact supervisor: A/Prof. Tim Mahony
Candidates with their own project ideas that fit within the research activities described at this website are also encourage to contact A/Prof. Mahony.


Determining the role of virally encoded microRNA during infection

Suitable for Honours students

Non-coding RNA species, such as microRNA (miRNA) play important roles in regulating gene expression of many complex biological pathways such as cellular differentiation and the immune response. Not surprisingly viruses also use miRNA to control the expression of viral genes and manipulate host gene expression. Bovine herpesvirus 1 (BoHV-1) encodes multiple miRNA species. This project will utilise mammalian cell culture, cloning, transfection, site directed mutagenesis, quantitative real-time PCR to identify genes regulated by BoHV-1 encoded miRNAs during the infection processes. 

Location: Queensland Bioscience Precinct, Building 80, St Lucia UQ Campus, Brisbane
Contact supervisor: A/Prof. Tim Mahony
Candidates with their own project ideas that fit within the research activities described at this website are also encourage to contact A/Prof. Mahony.


Conferring viral resistance to bovine cells with genome editing

Suitable for Honours students

Viral infections are important limiters of animal production. Conventional approaches to control of viral infections have depended on the development of safe and efficacious vaccines. While this approach has been effective for some viruses, it is costly and time consuming process. For optimal vaccine performance, the animal must be in good to condition to ensure it can mount an effective immune response on challenge in the field. This project will utilise mammalian cell culture, western blotting, quantitative real-time PCR, and genome editing (CRISPR/Cas9) to construct bovine cell-lines that are resistant to infection with important cattle viruses. The project results will underpin the future development of cattle that are no longer susceptible to important viruses.

Location: Queensland Bioscience Precinct, Building 80, St Lucia UQ Campus, Brisbane
Contact supervisor: A/Prof. Tim Mahony
Candidates with their own project ideas that fit within the research activities described at this website are also encourage to contact A/Prof. Mahony.


Antimicrobial sensitivity testing method for Avibacterium paragallinarum

Suitable for Honours students

Avibacterium paragallinarum is the causative agent of infectious coryza; which is a significant problem throughout the world for the intensive chicken industry. Antimicrobial therapy still remains an essential tool for the control of this pathogen, which brings with it the risk of antimicrobial resistance. There are no standard guidelines for antimicrobial testing for this bacterial species and hence antimicrobial resistance can’t be routinely monitored. A. paragallinarum is a fastidious organism which does not grow in standard media recommended for other bacterial species as it requires V-factor (nicotinamide adenine dinucleotide or NAD) for its growth. Hence, the aim of this project is develop a new method for antimicrobial testing, starting off with developing suitable media – agar as well as broth – for antimicrobial sensitivity testing and then evaluating the media with field strains, reference strains and antimicrobials. The final outcome will be a method for antimicrobial sensitivity testing for A. paragallinarum.

Location: EcoSciences Precinct, Dutton Park, Brisbane
Contact supervisor: A/Prof. Pat Blackall, Dr Conny Turni 


The underlying genetic causes of antimicrobial sensitivity in Avibacterium paragallinarum

Suitable for Honours students

Avibacterium paragallinarum is the agent for a highly contagious disease in chicken called infectious coryza. In 1985 there has been some work done on defining the antimicrobial sensitivity of pathogens from birds among the A. paragallinarum and resistance was found to tetracycline, sulphonamides, streptomycin and sulpamethoxazole-trimethoprim. Resistance genes for some of these phenotypical resistances against some antimicrobials have been found in other countries.  Resistance genes to streptomycin, tetracycline and sulphamethoxazole have been reported. There also has been a plasmid reported encoding streptomycin, sulfonamide, kanamycin and neomycin resistance genes. It is the first multidrug resistance plasmit reported in A. paragallinarum and might facilitate the spread of antibmicrobial resistant genes. This study will explore if any of the genes and plasmids found overseas are the cause for resistance found in Australia. A large culture collection of A. paragallinarum exists at the Microbiology Research group and this collection will be used to screen the bacteria for resistance genes. This knowledge of resistance genes will be the building block for development of new technologies to screen for antimicrobial resistance for routine monitoring of farms.

Location: EcoSciences Precinct, Dutton Park, Brisbane
Contact supervisor: A/Prof. Pat Blackall, Dr Conny Turni 


Understanding the sequence variation that defines the LPS structure in P. multocida

Suitable for Honours students

Pasteurella multocida is a major pathogen in the chicken industry causing fowl cholera. The disease results in considerable losses to layer and breeder flocks in the poultry industry worldwide. Vaccines to control the disease are both killed and live-attenuated vaccine. The protection of a killed vaccine is only against the same serovars as are in the vaccine, while a live vaccine is supposed to give heterologous protection. It was found recently that the protection of the killed vaccine will not protect against strains producing an LPS structure different to that produced by the strains included in the vaccine. The live vaccine is largely independent of the LPS structure. However, the live vaccine is an aroA mutant and is not available everywhere. This means that there are many producers that rely on autogenous vaccine and for them the knowledge of the LPS structure is imperative to achieve vaccine protections. Only recently did we start to understand the region of the gene that is responsible for the LPS structure and its transport to the outer surface. This project seeks to understand the variability, mutations and deletions in this structure that lead to different structures of LPS, from very truncated LPS to the full expressed form with all the sugars intact. This will be done in two ways, one being to harness the full genomes available on line and the second is to look at a well-defined set of strains and do full genome sequencing of these strains to determine the underlying genetic variation that leads to these differences.

Location: EcoSciences Precinct, Dutton Park, Brisbane
Contact supervisor: A/Prof. Pat Blackall, Dr Conny Turni 


On-farm detection of antimicrobial resistance genes

Suitable for Honours students

Antimicrobial resistance is a key issue that the pig industry is neeeking to address. The impact of antimicrobial resistance is in two key areas – pig health (an inabilkity to treat a disease outbreak) and food safety (presence of both antimicrobial agents and the associated resistance genes). In this proposal, we are seeking to develop novel rapid molecular based tools that can be applied on-farm to detect key antimicrobial resistance genes.  The work is a proof of concept approach.  A novel molecular technique will be established first using pure cultures in the laboratory.  The validated technique will then be used on pig faeces. The development of a novel rapid assay suitable for use on the famr would be a major step foreward in the capacity of the pig industry to control the spread of antimicrobial resistance. Both the pig industry sand the broader Australian community will benefit from an improved ability to detect and monitor antimicrobial resistance.

Typical phenotypic detection of antimicrobial resistance in a bacterial. The discs are soaked in different antimivcrobial agents. Those discs surrounded by a clear zone indicate that the bacterium is sensitive. Those discs that have no clear surroiunding zone indicate that the bacterium is resistant to the agent.

Location: EcoSciences Precinct, Dutton Park, Brisbane
Contact supervisor: A/Prof. Pat Blackall, Dr Conny Turni 


Development of a bead-based molecular assay to identify and serotype Haemophilus parasuis

Suitable for Honours students

Haemophilus parasuis is the causative agent of Glasser’s disease in pigs. The disease mainly occurs as infection of the joints, serosal surfaces and/or the brain. The disease is an economic problem wherever pigds are raised. Our laboratory is a national and international reference centre for H. parasuisi As part of our reference services, we identify H. parasuis isiolates at the serovar level (there are 16 serovars). The typing is sued to guide vaccination programs as all vaccines are serovar specific. Currently, the serovars are determined by several standard conventional multiplex PCR assays. In this work, the PCR will be re-designed to be used in a bead-based approach. The bead-based approach allows a single reaction to determine all 16 serovars. In addition, further assays such as those for key resistance genes could be added to the single reaction approach. The use of bead-based approach would be a considerable improvement in speed and accuracy of the assays that guide the vaccination programs for this key disease.

Typical colponies of Haemophilus parasuis. They grow as satellites to the nurse colony of Staphylococcus.
Severe pleuritis (yellow sheets overlaying lungs – white arrow) in pig infected with Haemophilus parasuis.

Location: EcoSciences Precinct, Dutton Park, Brisbane
Contact supervisor: A/Prof. Pat Blackall, Dr Conny Turni 


Bovine campylobacteriosis diagnosis

Suitable for Honours students

Bovine venereal diseases affect cattle in northern Australia causing decreased calf output and thus a reduction in breeding efficiencies. As the causative agent of bovine campylobacteriosis, our laboratory is developing novel diagnostic methods to differentiate Campylobacter fetus subspecies venerealis from other organisms. Genomic sequencing has identified potential new diagnostic targets to separate this subspecies from the closely related species C. fetus subspecies fetus. These subspecies are currently indistiguishable using available molecular and phenotypic methods which has perplexed researchers world-wide. Research in our laboratory is investigating molecular and microbial culture options in order to improve the identification and isolation of C. fetus subsp. venerealis. We have undertaken genomic sequencing as well as biolog phenotypic array analysis of several C. fetus subsp. venerealis strains, in order to identify markers for both molecular and improved culture methods. Opportunities for genomics, molecular and culture method development for research are available in our laboratory – the angle of the project can be negotiated to suit the candidate.

Biomarkers for resistance to cattle ticks

Cattle ticks cost $22-30b worldwide in losses with 80% of the world’s cattle populations at risk across tropical and sub-tropical regions. Research has focused on vaccine development which is progressing well, however the development of predictive markers would assist breeders to select cattle which may be more tick resistant. Previous studies from this group using skin immunohistochemistry have shown that certain cattle are primed with T cells in the skin before a tick challenge. New investigations using Next Generation Sequencing and proteomic methods will be used to study these phenomena further. Opportunities for molecular biology, RNA seq, proteomics and bioinformatics analysis for research are available in our laboratory – the angle of the project can be negotiated to suit the candidate.

Location: Queensland Bioscience Precinct, Building 80, St Lucia UQ Campus, Brisbane
Contact supervisor: Prof. Ala Tabor
Associate advisors:  A/Prof. Pat Blackall, Dr Conny Turni, Dr Peter James


 

Horticultural crop improvement

Understanding approaches to model crop canopy light absorption to estimate effects of agronomical practices on crop growth

Project can be scaled to be suitable for either Honours, Masters or PhD research

Radiation from the Sun absorbed by crop canopies drives leaf photosynthesis, which in turn drives crop growth, development and yield. As the first part of this project, the student will conduct a comparative study between similar, but differing in level of detail, approaches for modelling canopy light absorption. Simpler modelling approaches are efficient and robust for field crops, such as wheat or sorghum monocultures, while more detailed approaches are deemed necessary for orchard crops, such as mango, avocado or macadamia. Agronomical practices, such as planting density and pruning, can modify canopy light absorption by opening up crop canopies to allow more light penetration through the canopy. Effects of these canopy manipulation may be estimated with detailed modelling approach, but may not be the most efficient for long-term simulations. In the second part of this project, the student will have the opportunity to develop balanced and efficient models by combining the simpler and more detailed approaches and demonstrate that the new model can be applied to both field and orchard crops. Lastly, investigate ways of how knowledge gained from this project can be used to better inform agronomical decisions for improving crop productivity. Scholarships are available from University of Queensland sources.

Skill set required: Background in either mathematics or plant science and  experience in application of mathematical models

Contact superviror: Associate Professor Jim Hanan and Dr Alex Wu
Scholarship details: graduate-school.uq.edu.au/scholarships 
Location: St Lucia, Brisbane


Understanding avocado, mango or macadamia growth and development through field studies and functional-structural plant modelling

The complexity of the phenology, physiology and canopy development of tropical and sub-tropical orchard trees make it a challenging area of study. This project will provide the opportunity to apply the latest in functional structural plant modelling techniques to integrate existing hypotheses, use the resulting models to discover where our understanding is incomplete, then to investigate the system in field studies. This research will form the basis for future systems that can be applied to the broader tropical fruit and nut industry. Areas of particular interest in these studies include:

  • Physiology, phenology and consistency of flowering;
  • Carbon allocation, including aspects of carbon storage;
  • Responses to planting density and pruning, including impact on the light environment.

These studies could involve the student in work with the fruit and nut industry from northern New South Wales to far north Queensland, and will be supported by expertise in horticulture and plant physiology from the Queensland DAF and the NSW DPI. The research will be undertaken within a group involved in the Small Trees High Productivity Initiative of Queensland DAF and QAAFI at The University of Queensland.

Contact superviror: Associate Professor Jim Hanan
Scholarship details: graduate-school.uq.edu.au/scholarships 
This project can be scaled to be suitable for either Honours, Masters or PhD research.

Computational plant science

Computational plant science postgraduate projects

We are always interested to hear from prospective post-graduates wishing to pursue research using mathematics and computer models to understand the processes underlying plant growth and development. Scholarships are available from University of Queensland sources.

Scholarship details: graduate-school.uq.edu.au/scholarships 
These projects can be scaled to be suitable for either Honours, Masters or PhD research.


Understanding genetic regulatory networks in plants

The development of plant structure in response to environment is controlled by complex molecular systems that can be described as networks. This project will apply mathematical and computational tools and techniques to help piece together the puzzle of how genetic regulatory networks in different parts of the plant, connected by long-distance signals, are integrated to control plant development.

Contact superviror: Associate Professor Jim Hanan


Understanding avocado, mango or macadamia growth and development through field studies and functional-structural plant modelling

The complexity of the phenology, physiology and canopy development of tropical and sub-tropical orchard trees make it a challenging area of study. This project will provide the opportunity to apply the latest in functional structural plant modelling techniques to integrate existing hypotheses, use the resulting models to discover where our understanding is incomplete, then to investigate the system in field studies. This research will form the basis for future systems that can be applied to the broader tropical fruit and nut industry. Areas of particular interest in these studies include:

  • Physiology, phenology and consistency of flowering;
  • Carbon allocation, including aspects of carbon storage;
  • Responses to planting density and pruning, including impact on the light environment.

These studies could involve the student in work with the fruit and nut industry from northern New South Wales to far north Queensland, and will be supported by expertise in horticulture and plant physiology from the Queensland DAF and the NSW DPI. The research will be undertaken within a group involved in the Small Trees High Productivity Initiative of Queensland DAF and QAAFI at The University of Queensland.

Contact superviror: Associate Professor Jim Hanan

2017-2018 QAAFI Summer Research Program projects

Super early crops to avoid heat stress and dry spells around flowering

Suitable for the applications from students with a background in cereal agronomy and crop physiology. Student can be based at either QAAFI Gatton or Toowoomba Campuses.

Project duration: 10 weeks

Initial results from a single year of trials sown in Jimbour on the 2nd of August 2016 (10°C soil temperature at planting depth), showed unexpected high cold tolerance both among maize and sorghum hybrids with potential to (i) avoid periods of stress around flowering, (ii) improved crop competition with spring weeds, (iii) increased farm profits from an increased cropping intensity and longer summer fallows. These potential benefits will be assessed using a combination of field trial and modelling (APSIM) approaches to answer:

  • How early is too early to sow sorghum and maize?
  • What are the implications on subsequent crops and the cropping system (e.g. more efficient fallows and increased cropping intensity)? 
  • How do the heat and water stress environments change for ‘super’ early crops?

Expected outcomes: The applicant will work alongside QAAFI research scientists to gain experience in field, laboratory and modelling techniques used to quantify the effect of sowing date on the yield and performance of maize and sorghum crops. The applicant will help to translate this research into an agronomic package for climate smart farming in Australia’s Northern Grains Region.

Contact supervisor: Associate Professor Daniel Rodriguez


Low-tillering sorghum phenotypes produced by matching genetics and management to the cropping environment

Suitable for the applications from students with a background in cereal agronomy and crop physiology. Student can be based at either QAAFI Gatton or Toowoomba Campuses.

Project duration: 10 weeks

In Australia, most commercial sorghum hybrids are medium to high tillering. However, there is a trend, and farmer interest in having access to low tillering sorghum hybrids. Preliminary results from field experimentation conducted by the QAAFI farming systems research group indicate that sorghum hybrids having a low propensity to tiller are higher yielding in poorer seasons and environments. Also, unlike high tillering hybrids, low tillering hybrids tend to respond to increases in plant density. However, there is little information on how to manage low tillering hybrids in poor and high yielding situations or the opportunity cost of planting low tillering hybrids in highly variable climates. This project will combine field trials and modelling (APSIM) to address the following questions:

  • Under what type of seasonal conditions will low tillering hybrids allow farmers to achieve high and stable yields?
  • Are low tillering hybrids able to compensate yield in high yielding sites and good seasons?
  • What are the benefits and risks associated with growing non-tillering hybrids in highly variable climates?

Expected outcomes: The applicant will work alongside QAAFI research scientists to gain experience in field, laboratory and modelling techniques used to quantify the effect of management, genotype and environment interactions on crop yield. The applicant will help to translate this research into an agronomic package for low tillering sorghum across environments of contrasting yield potential.

Contact supervisor: Associate Professor Daniel Rodriguez


Design and implementation of a software user interface for the GECKO proximal sensing platform

Suitable for an 3rd or 4th year undergraduate student, honours, or masters coursework student with a background in human-computer interaction and software development. Previous experience with Python is necessary. Experience with Linux and ROS (Robot Operating System) would be preferred but is not required.

Project duration: 4-6 weeks

The GECKO platform is a tractor equipped with a range of sensors for measuring crop characteristics. These sensors produce hyperspectral, thermal, sonar, & lidar readings, and are used to regularly scan wheat and sorghum crops at the Hermitage research station near Warwick (south-west of Brisbane).

The driver of the GECKO controls the sensors via a simple touch-screen user interface implemented using Python and PySide. This interface has buttons to start/stop each sensor, and coloured boxes to indicate sensor states (e.g., capturing, error, not capturing).

This project is seeking a motivated HCI student to improve (or redesign) this user interface, so that it can (1) provide more relevant information to the driver, and (2) be more intuitive and easy to use in the field. A required outcome of this project is a working GUI, so the ability to implement user interface designs in Python is a prerequisite.

The scholar will have the opportunity to visit the Hermitage Research Station to see the GECKO in action, and to assess the user interface needs of the project. They will be contributing to a world-leading effort in agricultural proximal sensing.

Expected outcome of this project is a functional graphical user interface for the GECKO sensing platform, and a report outlining the design principles and procedures followed to arrive at the final solution. The scholar will gain valuable experience of in-the-field user interface design in the face of competing hardware constraints, and in elucidating requirements from users unfamiliar with HCI. They will also gain experience working in a research project comprised of scientists from many different technical backgrounds.

Contact supervisor: Dr James Watson

Click to read an article about the GEKO platform


Functional-structural models to improve management of fruit trees

Suitable for the applications from 3-4 year students with a background in Plant Science. Students might have previous programing knowledge or not.

Project duration: 6 weeks

The Small Trees – High Productivity Initiative is focused on improving the understanding of growth and development in avocado, macadamia and mango. Our final aim is to improve management practices, e.g. pruning, thinning or bending, that will allow more efficient use of light and improved yields in small trees planted at high density. The project focuses on four areas: tree architecture, vegetative vigour, crop load and light interception. 

We employ functional-structural models to simulate and understand the interactions between management practices, environmental factors, plant carbon balance and growth. Our simulations require data collected from field trials and/or previous literature. In our ‘Plant systems’ trials we compare various rootstock, training system and plant density combinations. Computer simulations are used to interpret the results of field trials, as well as to generate new hypothesis and experiments.

Expected outcomes: Scholars may gain skills in data collection, data analysis, fruit tree management and use of models. Scholars with previous knowledge in programing can learn to develop their own models. Students will have an opportunity to generate publications from their research, and may also be asked to produce a report or oral presentation at the end of their project.

Contact supervisor: Dr Inigo Auzmendi


Assessing the quality of Australian oats for domestic and Chinese foods

Suitable for the applications from 3-4 year UQ enrolled students with a background in food science or food chemistry

Project duration: 10 weeks

The demand for food of all types in China is increasing at an exponential rate. This includes all types of grains to be used as raw materials. Australian oats have also been identified as one of these important grains and China could easily purchase the whole Australian oat crop each year. However, it is important to understand the quality requirements of the oats and how the oat quality connects specifically to the functional properties for different food types. The project will profile in-depth quality parameters. 

Expected outcomes: The summer scholar will gain significant laboratory skills in testing oat grain quality as well as the functional properties of specific Chinese oat food products.  In addition the scholar will gain in-sight into the importance of the Chinese market for Australian agriculture and global food security. 

Contact supervisor Dr Glen Fox 


Rapid screening of maize and sorghum population density response

Suitable for the students with a background in cereal agronomy and crop physiology. Student can be based at either QAAFI Gatton or Toowoomba Campuses. Consideration will be given to students with an excellent academic record and interest in undertaking a research higher degree.

Project duration: 10 weeks

Single stem maize and sorghum hybrids are required for Australias’ dryland cropping regions so farmers can better manage canopy size and crop water use for prevailing and expected seasonal conditions.  Genetic variability exists in the propensity to tiller and the effect of population density on final tiller number is genotype specific.  Artificially manipulating light quality also influences tillering in maize and sorghum (Casal et al 1985; Maddoni et al 2002) and could be used to screen for single stemmed germplasm. This project will:

  • Develop an experimental protocol for evaluating the effect of light quality on maize and sorghum seedling tillering dynamics;
  • Manage a pot trial evaluating tillering;
  • Analyse data and report results for peer review.

Expected outcomes:The applicant will work alongside QAAFI research scientists to gain experience in field, laboratory and modelling techniques used to quantify the effect of population density on the yield and performance of maize and sorghum crops. The applicant will help to translate this research into an agronomic package for climate smart farming in Australia’s Northern Grains Region.

Contact supervisor Dr Joseph Eyre


Taking crop design to the farm

Suitable for the students with a background in agricultural engineering, mechanical engineering and agronomy. Student can be based at either QAAFI St Lucia, Gatton or Toowoomba Campuses.

Project duration: 10 weeks

Optimal management of broadly adapted maize and sorghum hybrids to prevailing and expected environmental conditions increased yields by 48 to 60% for Australian maize and sorghum hybrids, respectively (Clarke, Eyre and Rodriguez Unpublished).  However, high plant-to-plant variability is negatively correlated with yield even with optimal crop design (Martin et al 2005; Tokatlidis et al. 2010). This variability is associated with uneven plant establishment that is mostly due to seeding error rather than population densities or genetic variability in the Australian context (Pommel and Bonhomme 1998).  Farmers need advanced sowing equipment and known crop establishment potential to realise the benefits of crop design.  This project will:

  • Develop a gearbox for rapid seed rate changes with industry standard planting equipment;
  • Evaluate the effect of gear ratios and planter configuration on theoretical seed distribution;
  • Quantify maize seed distribution and plant-to-plant variability in field trials.

Expected outcomes: The applicant will work alongside QAAFI research scientists to gain experience in field trials and machinery design (with a commercial partner) used to quantify the effect of population density on the yield and performance of maize and sorghum crops. The applicant will help to translate this research into an agronomic package for climate smart farming in Australia’s Northern Grains Region.

Contact supervisor Dr Joseph Eyre


Development of live viral vaccines against Necrotic Enteritis and Mareks Disease for Australian poultry industries

Suitable for the UQ enrolled 3-4th year students with a background in microbiology, molecular biology, biotechnology or animal science with interest in veterinary virology and recombinant vaccine systems.

Project duration: 8 weeks

Clostridium perfringens, causing necrotic enteritis, is major concern to poultry industries worldwide. The Mahony lab located within the Centre for Animal Studies (CAS) at QAAFI has developed world’s first herpesvirus based live-viral vaccines for poultry and beef production systems. 

This project aims to further explore the utility of turkey herpesvirus (HVT), maintained as an artificial chromosome in bacteria, as a bi-valent live viral vaccine platform for vaccination of chickens against Mareks disease and necrotic enteritis. 

Expected outcomes: This project will result in real-world outcomes, and translate cutting edge vaccine research into an industry-ready, world leading vaccine technology.

The student will learn valuable techniques and develop strong skills in experimental design, molecular biology (cloning, PCR, sequencing, DNA extractions), cell culture, protein expression and detection.  

Students are expected to gain a deep understanding of the context and value of vaccination in intensive animal production systems, to submit lab books, a final report and oral presentation of research findings at the completion of the project.

Contact supervisor Dr Karl Robinson
 


Characterisation of the promoter elements of the Bovine herpesvirus 1 microRNA genes

Suitable for the 3rd or 4th year students with a background in virology, molecular biology or biotechnology with interests in animal diseases. Students completing 2nd year with an exceptional academic record in relevant areas may also be considered.

Project duration: 10 weeks

Bovine herpesvirus 1 (BoHV-1) is a ubiquitous cattle pathogen, that is associated with respiratory and reproductive diseases. There are three recognised subtypes of BoHV-1 which are loosely associated with disease severity. The genetic basis for this variable capacity to cause disease is poorly understood. MircoRNAs (miRNA) are small non-coding RNA molecules that play crucial roles in the regulation of many complex biological pathways. As with other herpesviruses, BoHV-1 encodes and expresses miRNAs. However, few studies have investigated the role of miRNA in BoHV-1 biology. The aim of this project is to characterise the promoter elements for selected miRNA genes encoded by BoHV-1. To address this aim selected, BoHV-1 microRNA genes and associated upstream genetic elements will be PCR amplified from the viral genome and cloned into a eukaryotic expression system. The DNA constructs will be transfected in to cultured mammalian cells and miRNA expression confirmed. The upstream genetic material of the miRNA gene will then be sequentially truncated and the impact on miRNA expression determined. This process will identify the minimal viral sequences required for miRNA expression.

Expected outcomes: Student’s will develop skills in experimental design, scientific record keeping and the practical application of these skills in molecular biology (DNA cloning, conventional and quantitative real-time PCR, DNA sequencing), mammalian cell-culture and the growth and characterisation of herpesviruses.

Students will be expected to develop insight into the biology of herpesviruses and their importance in intensive animal production systems. Students will be required, to complete and submit laboratory notebooks, a final report (in scientific manuscript format) and give an oral presentation at the completion of the project.

Contact supervisor A/Professor Tim Mahony