Available PhD projects - agribusiness, agriculture, environment & science

Chosen a project? Find out what to do next.

Chief Investigator

Project title

Project description

Preferred educational background

Professor Stuart Phinn

s.phinn@uq.edu.au

 

Dr William Woodgate

will.woodgate@csiro.au

Scaling dynamic plant function from leaf to landscape

This broad topic could take you in many directions based on your specific interests. From leaf-level physiological and spectral measurements, to detailed 3D canopy reconstructions from laser scanning data, through to simulation models to scale the leaf signal to above-canopy sensor platforms. This research topic will involve field site visits across Australia and then recreating these sites in a computer vision environment. It will lead to a more direct link between satellite earth observation and plant productivity and health monitoring. 

This PhD is part of a collaborative project with domestic and international partners including CSIRO, The University of Western Sydney, the University of Tasmania, University of New England, CalTech, the University of Valencia, Ghent University and Oxford University. 

You will be part of the Remote Sensing Research Centre at the University of Queensland in the School of Earth and Environmental Sciences, and have access to its resources and staff support. 

For more information please email: Professor Stuart Phinn (s.phinn@uq.edu.au) or Dr William Woodgate (Will.Woodgate@csiro.au).

Desired criteria: Bachelor or Masters in biophysical remote sensing or plant physiology, with well-developed scientific programming (e.g. python), image processing, and field work experience. Ability to combine field instrument measurements with image data processing workflows.

Ideally, the candidate for this project will commence in Research Quarter 4 (October), 2019.

Associate Professor Femi Akinsanmi

o.akinsanmi@uq.edu.au

Pathogenomics of husk spot fungus in macadamia

This study will utilize genomic and metagenomics data to profile Pseudocercospora macadamiae interactions with macadamia and provide beneficial insight for disease control.

Students will enrol through the Queensland Alliance for Agriculture & Food Innovation (QAAFI).

Postgraduate studies in Agriculture, Biological Sciences

*This project is available until September 2019 unless a suitable candidate is found prior.

Professor Zhiping Xu, Professor Bernard Carroll, Professor Neena Mitter

gordonxu@uq.edu.au

Clay nanoparticle-facilitated RNAi for non-transgenic modification of crops

This project will investigate the topical delivery of large dsRNA and siRNA to plant cells using a clay nanoparticle as the vehicle to identify whether topically applied large dsRNA or small interfering RNA is more efficient in inducing silencing of plant genes. The long term aim is to induce systemic silencing of plant genes for trait modification and enhanced crop productivity.

Students will enrol through the School of Chemistry and Molecular Biosciences.


Masters in Biotechnology or Molecular Biology, experience required in Arabidopsis genetics, florescent protein imaging in plants including confocal microscopy, small RNA gel blot analysis in plants, growing Arabidopsis in soil and in axenic culture, grafting Arabidopsis, PCR genotyping of plants, construction of Agrobacterium binary vectors & transformation of Arabidopsis, sound knowledge of RNA interference (RNAi) pathways in Arabidopsis

*This project is available until September 2019 unless a suitable candidate is found prior.

Associate Professor Brett Ferguson

b.ferguson1@uq.edu.au

Characterising novel molecular components of legume nodulation regulation

Legumes form a complex beneficial symbiotic relationship with soil bacteria that is tightly controlled by the host plant through a molecular signalling pathway, called Autoregulation of Nodulation (AON). As a result of this symbiosis, legumes require less nitrogen fertiliser and will be pivotal in promoting sustainable agricultural practices. 

This project aims to use cutting-edge molecular biology techniques to characterise components of the AON pathway to increase our understanding of nodulation control and identify potential targets for selecting and/or generating superior plant varieties.  

Students will enrol through the School of Agriculture and Food Sciences.

BSc with Honours or MSc; Background in molecular biology and genetics. Experience with plants is desirable, but exceptions made for candidates with strong skills in molecular biology.

*This project is available until September 2019 unless a suitable candidate is found prior.

Dr Lee Hickey

l.hickey@uq.edu.au

New tools to develop future crops with designer root systems

The project aims to dissect the genetics of root system architecture and rapidly develop improved crops with optimised root systems. This PhD project builds on state-of-the-art developments in crop genomics tools, germplasm resources, ‘Speed Breeding’ technology, physiological and genetic breakthroughs in understanding root growth/development and high-throughput root phenotyping methods. The student will be responsible for planning and conducting large-scale field and glasshouse experiments to investigate the value of these improved root systems under different environmental contexts.

Students will enrol through the Queensland Alliance for Agriculture & Food Innovation (QAAFI).

Basic expertise and experience is required in one or more of the following areas: plant biology, plant genetics, plant physiology, quantitative genetics or plant molecular biology.

*This project is available until May 2019 unless a suitable candidate is found prior.

Professor Ben Hayes

b.hayes@uq.edu.au

FastStack - evolutionary computing to stack desirable alleles in wheat

A major emerging challenge in wheat breeding is how to stack desirable alleles for disease resistance, drought and heat tolerance, and end-use quality into new varieties with elite high yielding backgrounds in the minimum time. As the number of known desirable alleles for these traits increases every year, the number of possible crossing combinations that need to be considered increases exponentially. We will use evolutionary computing algorithms, widely used for solving highly combinatorial problems, to address this challenge. In a large scale trial with our  project partners we will evaluate the decrease in variety development time that can be achieved with this approach compared to traditional breeding approaches.

Students will enrol through the Queensland Alliance for Agriculture & Food Innovation (QAAFI).

Background in at least one of the following fields would be preferred: quantitative genetics, statistics, plant breeding, animal breeding, human genetics, bioinformatics/computer science

*This project is available until July 2019 unless a suitable candidate is found prior.

Professor Robert Henry

robert.henry@uq.edu.au

National Tree Genomics Program – Genomics Toolbox- Macadamia Genomics

The PhD position is available to conduct genomics research in Macadamia in relation to providing the molecular basis of phenotype and gene expression or genetic variation in the genome. This will involve the establishment of high quality reference genome/s, transcriptome and re-sequencing of key tissue types and populations respectively to relate to specific industry relevant phenotypes for genetic improvement. 

Students will enrol through the Queensland Alliance for Agriculture & Food Innovation (QAAFI).

The candidate will have a master’s degree or 1st Class Honours degree or equivalent in Plant Molecular Biology, Bioinformatics, Genomics fields relevant to the above described projects and domestic applicants should be eligible for a Research Training Program (RTP) Scholarship.

Applications are invited from outstanding and enthusiastic graduates with relevant backgrounds. Applicants may be domestic or international and must be of high scholarly calibre, possessing a First Class Honours Degree, Masters Research Degree or equivalent, with at least one peer reviewed publication.   Applicants must meet the requirements for admission into the UQ PhD program.

International applicants must meet the University of Queensland's English Language Proficiency (ELP) requirements.

*This project is available until September 2019 unless a suitable candidate is found prior.

Professor Chengzhong Yu

c.yu@uq.edu.au

A Nano-platform for Affordable and Ultra-sensitive Bio-marker Detection

Lateral flow assays (LFA) are used for the rapid detection of biomarkers, however their sensitivity is relatively low.

This project aims to develop a next-generation nano-platform and LFA device for ultra-sensitive detection of
biomarkers. Innovative porous silica nanoparticles with uniform particle size and controllable structures will be
prepared.

Students will enrol through the Australian Institute for Bioengineering and Nanotechnology (AIBN).

Preferred candidate has background on biomedical or pharmacy or agriculture or nanotechnology.

*This project is available until June 2019 unless a suitable candidate is found prior.

Professor Craig Franklin

c.franklin@uq.edu.au

Environmental and physiological drivers of immune function in frogs

The environment can shape ecological processes through effects on an individuals' physiology. This project aims to investigate how ultraviolet B radiation and temperature interact during early development to influence amphibian physiology. The project utilises a combination of genetic, biochemical and physiological approaches to investigate the effects of ultraviolet B and temperature on a key fitness determinant – immune system function. Important outcomes of this research will be detailed, fundamental information on how environmental conditions experienced during development influence the growth and fitness of frogs. These data will improve our capacity to
forecast potential ecological-level effects of environmental change on amphibians.

Students will enrol through the School of Biological Sciences.

Ecological & evolutionary physiology

*This project is available until August 2019 unless a suitable candidate is found prior.

Associate Professor Daniel Ortiz-Barrientos

d.ortizbarrientos@uq.edu.au

Recombination and the genomic landscape of speciation

This project aims to evaluate how genomes become different during the origin of species by utilising an innovative system where multiple replicates of the speciation process exist. This project expects to generate knowledge in the area of speciation genetics by exploring the effects of sex, migration and selection on the diversity of hundreds of genomes from an Australian wildflower. 

Students will enrol through the School of Biological Sciences.

BSc with Honours, MSc or equivalent; Background in genetics, evolution and/or plant biology, with strong quantitative skills.

*This project is available until August 2019 unless a suitable candidate is found prior.

Dr Philip Stevenson

p.stevenson@uq.edu.au

Vaccination against herpesviruses

Herpesviruses establish persistent, systemic infections that cause considerable disease. Vaccines are needed, but have proved hard to design as the immunological correlates of protection are poorly understood. So far the only successful vaccines have been live attenuated viruses. Delivering these depends on understanding how individual viral gene products contribute to systemic infection and disease, so they can be removed from vaccine viruses to ensure safety without compromising immunogenicity. Also it is necessary to understand which steps in host colonization are amenable to immune control. Mechanisms have to be worked out in animal models. We are using Murid Herpesvirus-4 and Murine Cytomegalovirus to understand gamma-herpesvirus and beta-herpesvirus pathogenesis and immune control, and to develop new vaccine approaches that can be translated to the equivalent human pathogens.

Students will enrol through the School of Chemistry and Molecular Biosciences.

Applicants should have a BSc Hons or equivalent in virology, immunology, or a related discipline.

*This project is available until June 2019 unless a suitable candidate is found prior.

Dr Philip Stevenson

p.stevenson@uq.edu.au

Dissemination of cytomegaloviruses

Cytomegaloviruses establish chronic infections of myeloid cells. We have shown that infected myeloid cells are driven to recirculate by a viral take over of host chemokine receptor signaling. Dendritic cells infected by murine cytomegalovirus follow a novel route, entering the blood from lymph nodes via high endothelial venules before extravasating into new tissues. This has important implications for our understanding of both cytomegalovirus infections and normal innate immune function. The project will analyse targeted mutant viruses in vivo and work towards a new understanding of how chemokine receptor signals drive dendritic cell function.

Students will enrol through the School of Chemistry and Molecular Biosciences.

Applicants should have a BSc Hons or equivalent in virology, immunology, or a related discipline.

*This project is available until June 2019 unless a suitable candidate is found prior.

Professor David Jordan

david.jordan@uq.edu.au

Next generation plant breeding: integrating genomic selection and high throughput phenotyping to enhance genetic gain in sorghum and mungbeans

This project aims to develop approaches that will integrate genomic selection and high throughput field and platform based phenotyping to generate step change in the rate of genetic gain in the sorghum and mungbean breeding programs.

Students will enrol through the Queensland Alliance for Agriculture & Food Innovation (QAAFI).

Masters or Honours in:
•    Quantitative Genetics
•    Genomic prediction 
•    Bioinformatics
•    Plant Breeding

*This project is available until June 2019 unless a suitable candidate is found prior.

Dr Cheong Xin Chan

c.chan1@uq.edu.au

Genomics and evolution of symbiont transmission in coral reefs

This Project aims to understand how genomes of differently acquired microalgae have evolved to support symbiosis with corals, through sequencing of algal genomes of Symbiodiniaceae from Australia’s Great Barrier Reef, and free‐living relatives. Genes that have been gained or lost, or are under adaptive selection will be identified. These genes, systems and functions are potential targets for new management strategies for protecting Australian coral reefs in the face of climate change.

Students will enrol through the Institute for Molecular Bioscience.

Molecular biology, genomics, bioinformatics, computer science, evolution

*This project is available until June 2019 unless a suitable candidate is found prior.

Associate Professor Jack Clegg

j.clegg@uq.edu.au

Flexible Molecular Crystals: Single Crystals that Bend, Stretch and Twist

Single crystals are typically brittle, inelastic materials that crack, shatter or deform irreversibly when they are struck or bent. Such mechanical responses limit the use of these materials in new applications like flexible electronics and optical devices. Crystals that can be reversibly and repeatedly bent - characteristics normally associated with soft matter - would be extremely attractive for a host of engineering applications that require materials with properties that can be tuned through external stimuli. We have recently discovered a series of materials that possess the characteristics of both crystallinity and significant flexibility including single crystals of a metal-organic complex that exhibit sufficient elastic flexibility that they can be tied in a knot. This project will develop and apply molecular design principles to produce new metal-organic crystals that display elastic flexibility and use this flexibility to tune the physical properties of these materials. The project will involve a mixture of coordination chemistry, crystallography and materials science.

Students will enrol through the School of Chemistry and Molecular Biosciences.

Hons Class 1 in Inorganic Chemistry and/or Materials Science

*This project is available until June 2019 unless a suitable candidate is found prior.

Professor Liz Gillam

e.gillam@uq.edu.au

 

Professor Ben Hankamer

b.hankamer@imb.uq.edu.au

Solar-Driven Biocatalysis: Development of Cytochrome P450 Enzyme Systems for Pharmaceutical Synthesis in Microalgae’

The project will involve the development of microalgal systems for using cytochrome P450 enzymes as biocatalysts in the pharmaceutical industry. The research is aimed at gaining a fundamental understanding of the way in which P450 catalysis can be supported by photosynthesis as well as how such systems can be customised for industrial application. The research is supported by an industry-funded collaboration and will involve frequent interactions with the industry partner.

Students will enrol through the School of Chemistry and Molecular Biosciences.

Candidates should have an Honours or Masters degree in Biochemistry, Chemistry, Biotechnology or Plant Molecular Biology. Advanced undergraduate training in biological chemistry and/or enzymology is strongly preferred. Skills in HPLC analysis of small molecules, demonstrated expertise in working with redox biochemistry, cytochrome P450 enzymes and/or microalgae, and industrial research experience are highly desirable

*This project is available until June 2019 unless a suitable candidate is found prior.

Professor Michael Monteiro

m.monteiro@uq.edu.au

Precision-built dynamic and functional polymer vesicles

The research in this project will provide significant new knowledge in the fundamental chemical synthesis of polymer vesicles, their physical and functional capabilities, and the ability to manipulate the fine structure on the nanoscale to mimic some key dynamic features used by the cell. The proposed new artificial polymer vesicles will impact the field of chemistry through the synthesis of new dynamic and responsive polymer nano-vesicles.

Students will enrol through the School of Chemistry and Molecular Biosciences.

Candidates should have a first class BSc Hons (or equivalent), majoring in chemistry, materials science, or related discipline.

*This project is available until June 2019 unless a suitable candidate is found prior.

Professor Paul Bernhardt

p.bernhardt@uq.edu.au

Molybdenum enzyme electrochemical communication

This project aims to understand the activity of three novel, but related, molybdenum enzymes, human mARC and its bacterial homologs YcbX and YiiM. The role of mARC in humans remains unknown twelve years after its discovery. All three enzymes catalyse the reduction of potentially harmful N-hydroxylated compounds and there is interest in this area from the perspective of drug design. This project will apply an electrochemical methodology to rapidly identify enzyme substrates and inhibitors. Molybdenum enzymes pervade all life forms and the outcomes of this research include a unified understanding of an emerging enzyme class involved in drug metabolism.

Students will enrol through the School of Chemistry and Molecular Biosciences.

Should possess a BSc Hons, or equivalent, majoring in chemistry. Experience in electrochemical methods and evidence of peer reviewed publications will be an advantage.

*This project is available until June 2019 unless a suitable candidate is found prior.

Associate Professor Shih-Chun Lo

s.lo@uq.edu.au

Development of functional organic materials for opto-electronics

To develop (synthesise and characterize) functional organic materials (including organometallics) for opto-electronics (e.g., organic light-emitting diodes and photodetectors).

Students will enrol through the School of Chemistry and Molecular Biosciences.

Should possess a BSc Hons (1st class or equivalent in chemistry) or MSc, or equivalent, majoring in a relevant discipline (e.g. chemistry or materials chemistry).

*This project is available until June 2019 unless a suitable candidate is found prior.

Principal advisor: Dr William Harrison

w.harrison@uq.edu.au

Associate advisor: Professor Jason Mattingley

j.mattingley@uq.edu.au

 

The influence of naturalistic context on visual perception and memory

Human perceptual systems evolved and continue to develop in highly complex environments. The aim of this project is to understand how complex naturalistic context may influence neural processing of visual information. To address this question, the student will be trained to use a variety of methods, such as psychophysics, computational image processing, and statistical models. The student will use these tools to investigate how low-level (e.g. image statistics) and high-level (e.g. semantic content) image features influence the fundamental neural computations involved in visual processing.

Students will enrol through the Queensland Brain Institute.

This project is suited to anyone who wants to understand human cognition and perception, and who has an Honours or Masters degree in a field related to the following:  Cognitive Science, Psychology, Cognitive Neuroscience, Engineering, Maths. 

Although prior experience is not required, the project may appeal particularly to those interested in psychophysics, computational modelling, and programming in languages such as R and MATLAB.

*This project is available until June 2019 unless a suitable candidate is found prior.

Dr Rochelle Soo

r.soo@uq.edu.au

Exploring the evolution and ecology of non-photosynthetic Cyanobacteria

The dogma that all Cyanobacteria are photosynthetic has recently been challenged by the discovery of non-photosynthetic lineages. This project should expand our rudimentary understanding of non-photosynthetic Cyanobacteria by obtaining representative genome sequences using metagenomics and culturing. Predicted surface structures will be visualised using immuno-DNA labelling and electron microscopy. The proposed research should provide insights into the function and evolution of non-photosynthetic Cyanobacteria and their viruses, and pure or enriched cultures to enable future studies.

Students will enrol through the School of Chemistry and Molecular Biosciences.

Honours in Microbiology, Biochemistry or related disciplines.

*This project is available until June 2019 unless a suitable candidate is found prior.

Associate Professor Yao-Zhong Zhang

yzz@maths.uq.edu.au

From superintegrability to quasi-exact solvability; theory and application

This project is in the area of integrability and exact solvability. Quantum integrable systems and exact solvable models are of central importance for understanding the correct behaviours of complex quantum problems without approximation. This project aims to  develop mathematical frameworks and novel techniques to solve important questions across a variety of models such as superintegrable systems, quantum spin chains and spin-boson systems.

Prospective PhD students will work on specific aspects of the project, e.g. (1) the design and exploration of computational experiments to support the theoretical developments of new techniques for solving Rabi type spin-boson models, and (2) the exploration of specific applications of polynomial algebras and orthogonal polynomials, in the context of specific models.

Students will enrol through the School of Mathematics and Physics.

Honours or Master’s degree or equivalent in Theoretical or Mathematical physics

*This project is available until September 2019 unless a suitable candidate is found prior.

Associate Professor Ulrike Kappler

u.kappler@uq.edu.au

Responses of respiratory pathogens to host-generated antimicrobial compounds

The human innate immune response to infection leads to the generation of a variety of highly reactive antimicrobial agents which include hypochlorite (HOCl). HOCl causes oxidative damage to sulfur-containing molecules such as amino acids, as well as lipids and DNA, and can also give rise to derivative antimicrobials such as N-Chlorotaurine that can cause further damage.

This project will target mechanisms by which respiratory pathogens such as Haemophilus influenzae are able to evade the effects of HOCl and derivative antimicrobials by exploring HOCL-induced changes in cellular physiology as part of a larger research program exploring interactions between H. influenzae and the human host.

Students will enrol through the School of Chemistry and Molecular Biosciences.

Applicants must hold a 1st class Honours or Masters degree (or equivalent) in microbiology or biochemistry

*This project is available until July 2019 unless a suitable candidate is found prior.

Dr Ramiro Lafuente

r.lafuente@uq.edu.au

Geometric flows and symmetry in Hermitian geometry

The search for the analogous of the Ricci flow in non-Kähler Hermitian geometry has produced a number of interesting evolution equations. The main aim of this project is to study the geometric and dynamical properties of some of them under additional symmetry assumptions.

Students will enrol through the School of Mathematics and Physics.

BSc/MSc in Pure Mathematics.
The candidate will have a solid background in complex differential geometry, Lie groups and geometric analysis


*This project is available until April 2019 unless a suitable candidate is found prior.

Dr Simon Quigley

s.quigley@uq.edu.au

Nutritional requirements and rumen function in Rangeland goats

This project will conduct experiments to understand the nutritional requirements of Rangeland goats at different stages of maturity. Basic research on rumen function and urea recycling in goats will also be  undertaken.  

Students will enrol through the School of Agriculture and Food Sciences.

Masters degree in Agriculture / Science / Animal Science essential. Research experience with ruminant livestock species is essential. Experience in the conduct of relevant animal experimentation and laboratory skills desirable.

*This project is available until April 2019 unless a suitable candidate is found prior.

Professor Jonathan Aitchison

sees.hos@uq.edu.au

Diamonds in ophiolite: Recycling deep mantle into supra-subduction zones

Investigation of mantle components of ophiolitic assemblages in eastern Australia, New Zealand and New Caledonia to unravel the petrogenesis of microdiamonds which occur in associated chromite deposits.

Students will enrol through the School of Earth and Environmental Sciences.

BSc/MSc in Geology with experience in field geology, tectonics, petrology, geochemistry, metamorphic and structural geology

*This project is available until December 2019 unless a suitable candidate is found prior.

Professor Kevin Thomas

kevin.thomas@uq.edu.au

advisory team will also include

Dr Sarit Kaserzon and Dr Jake O'Brien

High resolution mass spectrometric characterisation of archived environmental and human biomonitoring samples

A key challenge in the environmental and exposure sciences is to establish experimental evidence of the role of chemical exposure in human and environmental systems. Non-target analysis employing high-resolution mass spectrometry (HRMS) has been established over the past years as one of the key approaches for tackling this complexity and allows for the retrospective screening of previously archived HRMS data.

This PhD project will focus on the HRMS characterisation of environmental and human biomonitoring samples for newly identified and novel contaminants of emerging concern. The student will work on the target, suspect and non-target analysis of samples from the Australian Environmental Specimen Bank and other opportunistic sample collections, generating data for a newly created ARC funded Australian Environmental Data Bank. The PhD student will receive all necessary training in HRMS analysis.   

Students will enrol through the School of Pharmacy.

Applicants must hold a 1st Class Honours or Masters degree (or equivalent) in environmental analytical chemistry or related fields.

A background in mass spectrometry would be advantageous

*This project is available until August 2019 unless a suitable candidate is found prior.

Dr Michael Taylor

m.taylor@sbs.uq.edu.au

Brillouin microscopy to study cell biomechanics

A Brillouin microscope measures sample stiffness and viscosity using only light, and thereby allows detailed mechanical studies with high resolution in inaccessible regions such as the cell interior. This project implements new techniques and data analysis in Brillouin microscopy to improve sensitivity and speed, for use in cellular biomechanics.

Students will enrol through the Australian Institute for Bioengineering and Nanotechnology (AIBN).

Physics or Engineering. Experience and interest in optics, signal processing, or biomechanics is an advantage

*This project is available until December 2019 unless a suitable candidate is found prior.

Dr John Dwyer

j.dwyer2@uq.edu.au

 

Professor Margie Mayfield

m.mayfield@uq.edu.au

Diversity maintenance in patchy environments

Plant diversity and composition is well known to vary across patchy environments, but the mechanistic drivers of these patterns remain poorly understood. Using data from threatened Western Australian wildflower communities and novel ecological models of species coexistence, this project aims to deliver a mechanistic understanding of biological diversity, and provide fundamental knowledge needed to improve ecosystem management and restoration outcomes.

Students will enrol through the School of Biological Sciences.

Bachelor of Science majoring in ecology

Australia: First class Honours thesis on topic related to the project

Elsewhere: Masters thesis on topic related to the project
 

*This project is available until September 2019 unless a suitable candidate is found prior.

Professor Neal Menzies

n.menzies@uq.edu.au

Economics of ameliorating soil constraints in the Northern Region: Project D:  Program co-ordination – communication, extension and evaluation

GRDC project will develop coordination and communication strategy to increase awareness, facilitate learning and help growers and advisers implement strategies to manage their soil constraints.  

A number of questions are relevant and important to improve our understanding on how growers and advisors learn and make decisions to implement strategies to manage soil constraints. The PhD project will evaluate growers’ and advisors’ existing Knowledge, Attitude, Skills, Aspiration and Practice to identify gaps. This will ensure clear and consistent messages are developed and delivered across the soil constraints program to increase the adoption of strategies to identify and manage soil constraints. 

Students will enrol through the School of Agriculture and Food Sciences.

BSc or MSc with knowledge and skills in agriculture, rural science, extension and communication

*This project is available until July 2019 unless a suitable candidate is found prior.

Associate Professor Ethan Scott

ethan.scott@uq.edu.au

Optical Physics in Neuroscience

We seek PhD students who are ready to contribute to our program in integrative circuits neuroscience.  Neuroscientists are welcome to apply, and we are also very eager to recruit optical physicists interested in applying their skills to problems in neuroscience. Such work might include design and optimisation of light sheet microscopes, optical trapping in vivo, targeted illumination in vivo, and sculpted light for optogenetics.  Our publications and details of the exciting interdisciplinary projects available in the group can be found at the Scott Lab’s website at   https://biomedical-sciences.uq.edu.au/research/labs/neural-circuits

Students will enrol through the School of Biomedical Sciences.

Bachelor with Honours or Masters

*This project is available until July 2019 unless a suitable candidate is found prior.

Associate Professor Ethan Scott

ethan.scott@uq.edu.au

Quantitative analysis of whole-brain neural activity during sensory processing 

Our group uses calcium indicators and light sheet microscopes to perform whole-brain functional imaging at cellular resolution in larval zebrafish.  This work produces vast activity datasets encompassing millions of neurons and billions of timepoints. We seek new PhD students with expertise in mathematics, coding, and high-performance computing to contribute to our analyses of these data.  Supervision will be provided both by neuroscientists and mathematicians. Details of our current analytical methods can be found in our recent publications, and details of the exciting interdisciplinary projects available in the group can be found at the Scott Lab’s website at   https://biomedical-sciences.uq.edu.au/research/labs/neural-circuits 

Students will enrol through the School of Biomedical Sciences.

Bachelor with Honours or Masters

*This project is available until July 2019 unless a suitable candidate is found prior.

Dr Jan Engelstaedter

j.engelstaedter@uq.edu.au

Predicting the evolutionary dynamics of adaptation

The successful candidate will work on a project investigating the evolutionary genetics of multidrug resistance in bacteria, aiming to gain a better understanding of distributions of fitness effects of resistance mutations and their epistatic interactions, as well as the repeatability and predictability of resistance evolution. Methods to be employed include high-throughput fitness assays, whole genome sequencing, experimental evolution and mathematical modelling. This is a joint project with and will be co-supervised by Dr Isabel Gordo (Gulbenkian Institute, Portugal). For more information about our research, please visit www.engelstaedterlab.org and www.igc.gulbenkian.pt/igordo.

Students will enrol through the School of Biological Sciences.

BSc with Honours, MSc or equivalent; Background in genetics, evolution and/or microbiology, with strong quantitative skills.

*This project is available until July 2019 unless a suitable candidate is found prior.

Dr Nicholas J. Hudson

n.hudson@uq.edu.au

The Gateway to selecting for nutrient efficient livestock – ‘Better doers’

This project explores various aspects of mitochondrial function as it applies to ruminant farm animals. The aim is to better understand the basis of variation in feed efficiency and other metabolic traits.

Students will enrol through the School of Agriculture and Food Sciences.

Molecular biology; metabolism; biochemistry

*This project is available until July 2019 unless a suitable candidate is found prior.

Associate Professor Sandie Degnan

s.degnan@uq.edu.au

Marine sponge-microbe interactions and the origin of animal innate immunity

Two PhD positions are available on an ARC-funded project that explores the role of the innate immune system in animal-bacterial symbiosis. Specifically, we will use advanced genomic, molecular and cellular approaches to understand how the coral reef sponge Amphimedon queenslandica interacts with symbiotic and foreign bacteria throughout its life cycle. Because the Amphimedon genome encodes the same innate immune gene families as humans, the project will shed light more generally on the co-evolution of innate immunity and animal-microbe interactions. Because marine sponge holobionts are amazing ecosystem engineers that filter-purify large volumes of sea water daily, the project also will provide a foundation for advanced marine bioremediation and biomanufacturing technologies.

Students will enrol through the School of Biological Sciences.

Research-intensive honours or equivalent in the biological sciences is required. Some experience in molecular biology or immunology would be an advantage, but is not necessary.

*Applcations for these two positions are open until 31 January, 2019 for commencement in Research Quarter 2 (April) 2019.

Professor Sassan Asgari

s.asgari@uq.edu.au

A novel approach in understanding regulation of development in mosquitoes

Development of novel approaches in mosquito control or inhibition of transmission are urgently required to combat against mosquito-borne pathogens. One such approach is to interrupt the reproduction or reduce the fitness of mosquitoes. This project aims to explore the role of microRNAs in regulation of the synthesis of a key
hormone, juvenile hormone, involved in mosquito development and reproductive maturation.

Students will enrol through the School of Biological Sciences.

Molecular biology, familiarity with insects is preferable

*This project is available until July 2019 unless a suitable candidate is found prior.

Associate Professor Robbie Wilson

r.wilson@uq.edu.au

Predicting the survivial of native mammals using studies of performance

This study aims to provide a model of predator-prey interactions and test these using wild animals and human performances. These will be used to predict the long-term impacts of invasive predators on native animals.

Students will enrol through the School of Biological Sciences.

Bachelor of Science or Sports Sciences with Honours (or equivalent).

*This project is available until February 2019 unless a suitable candidate is found prior.

Professor Neal Menzies

n.menzies@uq.edu.au

Economics of ameliorating soil constraints in the Northern Region: Project A: Spatial soil constraint diagnoses in the Northern Region

GRDC project will use a global archive of Landsat satelite imagery to produce paddock scale yield maps. 

A number of drivers of primary biological productivity need to be better defined to improve our understanding of the variation in crop yields at different spatial scales in order to achieve better crop management. The PhD project will improve our abiity to accurately (i) detect where and when a wheat crop has been grown, (ii) map past wheat past wheat yields at broad and local scales.

The candidate will develop and investigate the potential of data-analytic methods (geo-statisitical methods combined with machine learning and mechanistic model predictions) to improve upon existing methods to reliably account for differences in yield maps at spatial scale.

Students will enrol through the School of Agriculture and Food Sciences.

BSc or MSc with knowledge and skills in agriculture, remote sensing, GIS and geo-statistics

*This project is available until December 2019 unless a suitable candidate is found prior.

Dr Philip Bond

phil.bond@uq.edu.au

Understanding the  microbial coupling of the anaerobic oxidation of ammonium to Fe(III) reduction (Feammox)

We are undertaking research of the recently discovered microbial activity of anaerobic ammonium oxidation coupled to Fe(III) reduction (Feammox). We aim to discover the molecular mechanisms by which microbes can couple electron transfer from water soluble ammonium to insoluble Fe minerals. The student will work with state-of-the-art facilities with a multidisciplinary team, utilising their expertise in microbial physiology, microbial ecology, bioinformatics and bio-engineering. The key role will be to undertake research on the microbial coupling of the anaerobic oxidation of ammonium to Fe(III) reduction and evaluating its importance in biogeochemical nitrogen and iron cycles.

Students will enrol through the School of Chemical Engineering.

Hons 1st Class, or Masters level in Microbiology, Environmental Microbiology or related field. Background or interest in Bioreactor operation and Bioinformatics is would be beneficial.

*This project is available until February 2019 unless a suitable candidate is found prior.

Dr Jaquie Mitchell

jaquie,mitchell@uq.edu.au

Traits of importance for aerobic 'DryRice' varieties for the southern Australian rice industry

This rice pre-breeding project will combine physiology with genomics to gain an understanding of the genetic basis for traits contributing to adaptation to aerobic conditions for the southern Australian production environment. The main aim of this project is the development of sound screening methods to identify donor varieties and traits/QTL that are associated with well-watered aerobic conditions.

Students will enrol through the School of Agriculture and Food Sciences.

UQ Honours, UQ Masters coursework or equivalent or MPhil 

*This project is available until July 2019 unless a suitable candidate is found prior.

Professor Debra Bernhardt

d.bernhardt@uq.edu.au

Improving nanostructured supercapacitors through computational insight

Nanostructured supercapacitors offer the potential to provide improved storage of renewable energy resources and to power portable devices. This project aims to enhance the understanding of the mechanism of charge and discharge in these systems to guide in the development of better energy storage systems.  This will be achieved using molecular computations of the structure and diffusion coefficients.

Students will enrol through the Australian Institute for Bioengineering and Nanotechnology (AIBN).

Chemistry, physics, applied maths, chemical engineering or related disciplines

*This project is available until December 2018 unless a suitable candidate is found prior.

Professor Alan Rowan
alan.rowan@uq.edu.au

Dr Jan Lauko
j.lauko@uq.edu.au

Characterisation of Cytoskeleton information transfer

This project studies the intracellular mechanisms that allow the transfer of mechanical force imposed by the ECM to the cell nucleus as a result of an internal cell signalling reaction cascade. For this study, biomimetic synthetic materials will be employed, and the cellular events studied using microfluidic devices.

Students will enrol through the Australian Institute for Bioengineering and Nanotechnology (AIBN).

MSc or honours in cell biology, biochemistry, material science or bioengineering.

*This project is available until December 2019 unless a suitable candidate is found prior.

Professor Alan Rowan
alan.rowan@uq.edu.au

Dr Jan Lauko
j.lauko@uq.edu.au

Synthesis of biomimetic materials

For this project, in a synthetic/rheological approach, the candidate will examine material changes as a function of chemical modification of semiflexible polymers. By modifying the monomer structure, the stiffness and helical pitch of the polymers can be altered and the effect upon bundling studied. Ultimately, the project aim is to characterise what the structural parameters are that control the onset and gradient of the strain stiffening – the two key parameters of biomimetic hydrogels.

Students will enrol through the Australian Institute for Bioengineering and Nanotechnology (AIBN).

MSc or honours in physical organic and/or polymer chemistry, with experience in structural and material characterisation.

*This project is available until December 2019 unless a suitable candidate is found prior.

Professor Alan Rowan
alan.rowan@uq.edu.au

Dr Jan Lauko
j.lauko@uq.edu.au

Controlling hybrid systems

The candidate will examine the properties of synthetic/biopolymer interpenetrating networks as a function of polymer binding density and investigate the dependence in stiffness and strain-stiffening on crosslinking density, interpenetration and altered pore size. The project will also study how these hybrid extracellular matrix materials interact with the cell cytoskeleton, and study these interactions from a mechanistic perspective employing high resolution spectroscopy.

Students will enrol through the Australian Institute for Bioengineering and Nanotechnology (AIBN).

MSc or honours in polymer/materials chemistry or bioengineering. Previous experience with live cells and tissue culture will be a plus.

*This project is available until December 2019 unless a suitable candidate is found prior.

Dr Elizabeth Dann

e.dann@uq.edu.au

Investigating fungi causing fruit stem end rot and branch dieback in avacado

Avocado is affected by fruit and orchard diseases caused by several different fungi. Stem end rot of fruit and branch canker and dieback are diseases associated with Botryosphaeria fungi (eg. Fusicoccum, Neofusicoccum and Lasiodiplodia), Phomopsis, Pestalotiopsis and others, yet we don't really know if fungi are specific to either fruit disease or branch dieback, or whether they are generalists and can infect all plant parts. Firstly, a survey of fruit and orchards from all growing regions across Australia will establish an isolate collection. These will be accurately identified, and molecular phylogeny studies undertaken. Pathogenicity tests will check for ability of different species or isolates within a species to cause disease in different plant tissues. The student will evaluate factors exacerbating severity and potential management strategies.

Students will enrol through the Queensland Alliance for Agriculture & Food Innovation (QAAFI).

MSc or Honours in Plant Sciences, with experience in plant pathology

*This project is available until December 2018 unless a suitable candidate is found prior.

Associate Professor Daniel Rodriguez

d.rodriguez@uq.edu.au

Optimising sorghum yield through agronomic management

In the Northern Grains Region, managing heat and moisture stresses around critical growth stages remains the focus for sorghum adaptation and systems agronomy.  The overall aim of this project is to answer How do combinations of hybrid and crop managements positively modify stress environments and yield distributions in early sown sorghum; and how the practice positively influences the cropping system, increases farm profits and reduces risks?

Students will enrol through the School of Agriculture and Food Sciences.

Agriculture

*This project is available until December 2019 unless a suitable candidate is found prior.

Professor Paul Burn

paul.burn@uq.edu.au

Poly(dendrimer)
Organic light-
Emitting diodes

In this multidisciplinary project we aim to create innovative semiconductor materials and diode architectures that optimise each step in light generation; from charge injection, transport and capture, to light emission, the project aims to deliver transformative OLEDs that can be used in lighting.

Students will enrol through the School of Chemistry and Molecular Biosciences.

An Honours or Masters degree in the physical sciences, preferably in the area of synthetic chemistry or physical chemistry or physics.

*This project is available until December 2018 unless a suitable candidate is found prior.

Professor Paul Burn

paul.burn@uq.edu.au

Transformational
lighting: changing the way we live

The Fellowship project aims to advance the science of ultrathin efficient lighting technologies based on low embedded energy organic light-emitting diodes (OLEDs). The intended outcomes of the project are design rules for OLED componentry, including thin, flexible architectures and demonstrating a large-area lighting module with power efficiency of 150 lm/W.

Students will enrol through the School of Chemistry and Molecular Biosciences.

An Honours or Masters degree in the physical sciences, preferably in the area of synthetic chemistry or physical chemistry or physics.

*This project is available until December 2019 unless a suitable candidate is found prior.

Professor Paul Burn

paul.burn@uq.edu.au

Australian Centre for Advanced
Photovoltaics

The project will develop new materials and device architectures for thin film photovoltaics.

Students will enrol through the School of Chemistry and Molecular Biosciences.

Honours or Masters chemistry or physics graduate.

*This project is available until December 2018 unless a suitable candidate is found prior.

Dr Elizabeth Krenske

e.krenske@uq.edu.au

Computational Tools for Organic Synthesis

This Project aims to develop new computer modelling techniques with the ability to rapidly identify efficient synthetic routes to target molecules. This technology will have the potential to increase the speed, efficiency, and environmental sustainability of chemical synthesis, an enterprise which underpins innovations in the fields of manufacturing, energy, agriculture, and medicine.

Students will enrol through the School of Chemistry and Molecular Biosciences.

First class Honours degree or equivalent in Chemistry, including a significant component of organic chemistry. Prior experience in molecular modelling (computational chemistry) is valuable, but not essential.

*This project is available until March 2019 unless a suitable candidate is found prior.

Dr Jacinda Ginges

j.ginges@uq.edu.au

Heavy atoms and ions and precision tests of fundamental physics

Precision studies of atomic properties provide powerful probes of fundamental physics. Studies of violations of fundamental symmetries, in particular atomic parity violation and atomic electric dipole moments (parity and time-reversal violation), complement the searches for new physics performed at the Large Hadron Collider and in some cases exceed its energy reach. A PhD project is available in the development of high-precision atomic many-body methods and codes, and their application to fundamental and applied problems including violations of fundamental symmetries, superheavy elements, and atomic clocks. 

Students will enrol through the School of Mathematics and Physics.

High-level achievement in theoretical physics undergraduate courses, particularly in quantum mechanics. Ideally, the candidate should be able to demonstrate high-level research ability or capacity through  successful completion of an Honours or Masters research project.

*This project is available until December 2019 unless a suitable candidate is found prior.

Professor Andrew Whittaker

a.whittaker@uq.edu.au

Next-generation Lithography - Photo-directing Assembly of Block Copolymers

This project aims to develop photo-reactive materials for directing self-assembly of polymers on surfaces. The application is new device for memory storage.

Students will enrol through the Australian Institute for Bioengineering and Nanotechnology (AIBN).

Chemistry, preferable polymer chemistry or organic synthesis

*This project is available until December 2018 unless a suitable candidate is found prior.

Professor Warwick Bowen

wbowen@physics.uq.edu.au

Nanomechanical Computing

Background: Computers based on the flow of electrical currents are ubiquitous in modern technology. However, they have limitations: they cannot be forever miniaturised with Moore’s Law already starting to saturate, their energy efficiency is fundamentally constrained by the laws of physics, and they cannot operate when exposed to high radiation levels such those found in some space environments and caused by space weather. An alternative approach to computation that can evade these constrains is to use vibrations confined on a silicon chip, rather than electrons, to perform logic. In our laboratory, we are developing nanoscale logical processors based on mechanical vibrations in collaboration with Lockheed Martin, and for ultimate applications in aerospace and satellite technologies. Projects are available to lead the development of this new form of computing.

Students will enrol through the School of Mathematics and Physics.

Experience/interest in micro-/nanofabrication and/or technology translation would be an advantage.

*This project is available until December 2018 unless a suitable candidate is found prior.

Professor Christine Beveridge

c.beveridge@uq.edu.au

A new signalling component in shoot architecture: trehalose 6-phosphate

Shoot branching in plants is regulated by a balance between auxin and sucrose. Auxin inhibits the outgrowth of axillary buds into branches by controlling the synthesis of cytokinins and strigolactones. However, how sucrose interacts with the two other signals is not fully understood. This project aims to highlight the sugar signalling pathways involved during shoot branching and to investigate how sucrose interacts with cytokinins and strigolactones at the molecular level. This PhD will give to the student a good background in plant physiology and molecular biology.

Students will enrol through the School of Biological Sciences.

Plant biology; molecular biology, physiology

*This project is available until July 2019 unless a suitable candidate is found prior.

Associate Professor Bhagirath Chauhan

b.chauhan@uq.edu.au

Innovative crop weed control for northern region cropping systems

Over the last two decades northern region crop production has changed dramatically from systems dominated by cultivation and residue removal to those with little or no soil disturbance and complete residue retention.  These dramatic changes in production practices will likely have also impacted on the biology of weed species infesting these production systems. For example, it is now evident that the effectiveness of harvest weed seed control is improved through crop competition increasing the height of retained seed. Additionally as we move towards the development of site specific weed control technologies the efficacy of these systems will rely on a thorough understanding of the biology of the weeds being targeted. 

The general approach for this area of research is to investigate key biological attributes (dormancy, seedbank viability, seed dispersal, phenological development etc.) of northern region problematic weed as they occur in crop and fallow situations with the aim of identifying control opportunities.  

Students will enrol through the Queensland Alliance for Agriculture & Food Innovation (QAAFI).

Masters in Agronomy 

*This project is available until 30 June 2019 unless a suitable candidate is found prior.