Available PhD projects - Science, agriculture, environment & agribusiness

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Chief Investigator

Project title

Project description

Preferred educational background

Dr Thomas Sigler

t.sigler@uq.edu.au

Australia's Urban Sharing Economy

The sharing economy has evolved from a set of isolated grassroots movements into a global phenomenon driven by large corporate actors. The many digital platforms associated with the sharing economy (e.g. Uber, Airbnb) are now firmly embedded within our daily lives, and in many cases mediate the provision of our daily needs: transportation, food, lodging, etc. Perspectives on its impacts differ widely: on one hand, advocates point to efficiency gains from sharing that reduce waste and pollution; on the other hand, critics have pointed to the emergence of new forms of capitalist accumulation that exploit both labour and local regulatory powers.

This project focuses on understanding how the sharing economy has impacted Australian cities. The candidate will be working with a multi-disciplinary supervisory team from urban geography, economics, and demography. The candidate may elect to focus on one of several themes within the sharing economy, including ride-sharing, vehicle-sharing, micromobility, and/or short-term rentals. Applicants with an interest in quantitative methods are preferred, but the project will support any approach that is relevant to the candidate's chosen research topic.

This PhD opportunity is open to candidates holding an Honour's or Master's qualification in Geography, Economics, Computer Science, Sociology, Urban Planning or other related discipline. Candidates demonstrating a strong background in research and/or a strong understanding and interest in urban geography will be considered. Candidates will benefit from a strong command of quantitative methods and/or techniques, but a willingness to learn will also be deemed sufficient.

*The successful candidate must commence by Research Quarter 2, 2022. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Professor Philip Hugenholtz

p.hugenholtz@uq.edu.au

Exploring uncharacterised bacterial diversity in the rodent gut microbiome

The development of culture-independent approaches to studying microbial communities has greatly expanded our understanding of the microbial world as the majority of microorganisms remain uncultured in the laboratory. These efforts have highlighted that every environment still contains species that are insufficiently characterised or entirely unexplored. As part of an ARC Discovery Project investigating the rodent gut microbiome, the successful candidate will investigate uncharacterised bacterial species inhabiting the rodent gut using genomes recovered from metagenomic sequencing data. The candidate will develop skills in the analysis of high-throughput sequencing data and metabolic inference based on genomic annotations.

Applicants should possess a BSc Hons, MSc, or equivalent, majoring in a relevant discipline (e.g. microbiology, bioinformatics). Ideal applicants should have a strong academic record. Experience with bioinformatic techniques will be considered favourable. Excellent oral and written communication skills, motivation and the ability to work independently and as part of a team are also required.

*The successful candidate must commence by Research Quarter 1, 2021. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Dr Nicole Webster

n.webster@uq.edu.au

Quantifying the impacts of environmental stress on marine microorganisms

Microbes underpin marine ecosystem health and have the capacity to exacerbate or mitigate ecosystem changes. The Great Barrier Reef is facing unprecedented pressure from elevated sea surface temperature and declining water quality, yet the impacts of these pressures on reef microbial communities remain undefined due to the difficulty in applying stress-response data in a way that has ecological relevance. Currently there is no ecotoxicological framework to reliably quantify and predict how marine microbes and their ecologically important functions respond to environmental stress.

The PhD project will use the National SeaSimulator at the Australian Institute of Marine Science (AIMS) Townsville to perform ecotoxicological tests and use molecular tools to develop species sensitivity distributions for marine microbes to a range of environmental pressures. Outcomes from this research will enable derivation of threshold values for populations of marine bacteria to be used in environmental risk and vulnerability assessments. The successful candidate will undertake this 3 year PhD project with the Australian Centre for Ecogenomics UQ in collaboration with AIMS and University of Vienna, Austria under the direct supervision of Drs Nicole Webster, Andrew Negri, Heidi Luter and Michael Wagner. Significant periods of time will be spent running ecotoxicological assays at the AIMS Townsville site.

Masters, first class honours or equivalent with a background in microbial ecotoxicology or a related field. Previous experience with ecotoxicological assays is essential. A first authored publication and knowledge of molecular microbiological approaches such as 16S rRNA gene sequencing will be highly beneficial.

*The successful candidate must commence by Research Quarter 3, 2021. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Professor Matthew Davis

mdavis@physics.uq.edu.au

Spin vortices in an ultracold quantum gas

This experimental project will be based in the Bose-Einstein condensate (BEC) laboratory at the School of Mathematics and Physics, a state-of-the-art facility for creating and manipulating quantum gases. The project aims to create and manipulate spin vortices in a magnetic quantum fluid by using optical and magnetic fields. It expects to advance the manipulation, control, and measurement of spin vortices in a magnetic ultracold quantum gas. Magnetic spin vortices are potentially fundamental elements of future electronic technologies based on spin for advanced storage and logic. Magnetic quantum fluids are also exquisitely sensitive to magnetic fields and have the potential to be used for high precision magnetometry.

This experimental project will allow for the development of diverse and transferable skills, including electronic and optical design, experimental system design and implementation, software design, and data analysis. This project will also allow for attendance of related international workshops and conferences.  There will also be the opportunity to interact with other projects within the ARC Centre of Excellence for Engineered Quantum Systems (EQUS), as well as the theoretical quantum atom optics group at the University of Queensland.

Students will enrol through the School of Mathematics and Physics.

The candidate should have a masters, honours-equivalent, or 4 year degree (with a substantial research project component), in Physics/Optics or related fields. Previous coursework in quantum optics and condensed matter, and prior laboratory experience would be advantageous.

*The successful candidate must commence by Research Quarter 2, 2021. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Dr Andries Potgieter

a.potgieter@uq.edu.au

Determining crop phenology and/or crop type discrimination metrics using hyperspectral sensing technologies and machine learning algorithms for major winter crops in Australia.

The primary focus of this PhD position is to undertake functional research in the exploration and analysis of multi-temporal and -spatial hyperspectral sensing data. Developing and application of current and novel data fusion approaches to integrate climate, sensing and biophysical data for detecting of crop type and phenological stages for main winter crops across Australia. This PhD is part of the four year project funded and supported the GRDC funded  “CropPhen: Remote mapping of grain crop phenology and crop type prediction” project lead by UQ QAAFI (Project : UoQ2002-010RTX).

Essential:

  • MASTERS degree in the area of Remote Sensing and/or Machine Learning (ML) or artificial intelligence with a background in crop physiology or environmental sciences or closely related sciences.

Preferable

  • Background and experience in the area of design and application of multi-modal data fusion algorithms to support systems modelling.
  • Working knowledge of ML software and libraries such as TensorFlow and/or Pytorch.

*The successful candidate must commence by Research Quarter 1, 2022. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Dr Pat Scott

pat.scott@uq.edu.au

The world as a neutrino telescope

Dark matter interacts extremely weakly with regular matter, but it does still interact enough to scatter off nuclei occasionally in many models. The Sun sits in bath of dark matter particles, with many of them passing through it every day. Some dark matter particles scatter off a nucleus in the Sun, and lose enough energy to become gravitationally bound to it. They then return on bound orbits, scatter again and again, losing more energy and sinking down to the core of the Sun. They then annihilate with each other, producing a shower of energetic particles. Those particles include neutrinos, which travel straight through the Sun, and can be detected here on Earth using neutrino telescopes such as IceCube, Super-Kamiokande and ANTARES.

The first part of the project is to combine the results of these three neutrino telescopes, to produce one of the strongest probes of interactions between dark matter and nuclei to date. The second part is to determine the projected sensitivity of the next generation of neutrino telescopes (KM3NeT, IceCube Gen2/Pingu, Hyper-Kamiokande), in order to build an analysis framework that will allow all three experiments to combine their results, and collaborators involved in the GAMBIT project to combine the results with those from all other experiments.

Starting point: arxiv:1601.00653

Strong Hons/MSc thesis research results in astroparticle physics or adjacent fields (particle physics, astrophysics, general relativity, mathematical physics, computational physics, etc).

*The successful candidate must commence by Research Quarter 2, 2022. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Associate Professor Shih-Chun Lo

s.lo@uq.edu.au

Organic light-emitting devices

Positions are available for PhD students to work on the Australia Research Council supported project in developing a new class of lighting technology based on organic light emitting devices for augmented realities. The research is interdisciplinary and the candidates will work closely with world-class researchers in physics and chemistry and gain a first class postgraduate education at the state-of-the-art research centre.

1st class Honours degree or equivalent degree in Physics or Engineering or Chemistry with skills and experiences in condense matter physics/semiconductors/optics/spectroscopy

Mandatory requirements:

  1. Excellent academic performance to Honours/Masters level, evidenced by a high Grade Point Average (GPA); and
  2. International applicants must meet the University of Queensland's English Language Proficiency (ELP) requirements.

*The successful candidate must commence by Research Quarter 2, 2021. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Dr April Hastwell

a.hastwell@uq.edu.au

Characterisation of peptides in legume root and nodule development

Legumes are an important agricultural commodity not only for their yield but for a beneficial microbial symbiosis which decreases the need for synthetic nitrogen fertiliser application. Plants facilitate the symbiosis by producing novel root organs called nodules and using unique signalling pathways. Understanding these pathways at molecular level is critical to optimising legume growth.

The PhD project will investigate novel signalling peptides and their associated pathways in legume root and nodule development. Outcomes will increase our fundamental understanding of peptides and legume growth which may underpin future crop development efforts. The successful candidate will undertake this project in the Integrative Legume Research Group under the direct supervision of Dr April Hastwell and Associate Professor Brett Ferguson.

Masters, first class honours or equivalent with a background in molecular biology, genetics, biotechnology or a related field. Previous molecular experience is essential, including cloning, qRT-PCR and plant transformation. Knowledge of legume and/or root development will be beneficial.

*The successful candidate must commence by Research Quarter 1, 2021. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Associate Professor Gideon Rosenbaum

g.rosenbaum@uq.edu.au

Magmatic response to slab tearing

Spatially and geochemically anomalous arc magmas (SGAM) provide unique records of complexities in the subduction process and are commonly associated with ore mineralisation (e.g., gold and copper). By linking SGAMs to independent geophysical constraints on the dynamics and geometry of the subducting slab, this project aims to explicitly resolve how changes in the shape/form/geometry of the slab through time are expressed in the geochemical and metallogenic record.

The PhD project will involve the following research activities (depending on the research interests, skills, and qualifications of the selected candidate):

  1. Three-dimensional visualisation of slab structures;
  2. Geodynamic reconstructions;
  3. Structural geology/geophysics in supra-subduction zones;
  4. Geochemical investigation of arc magmas;
  5. Petrological investigation of magmatic plumbing systems in arc settings.
  • BSc (Honours) and/or MSc in geological sciences;
  • Demonstrated knowledge and skills in at least one of the following sub-disciplines: structural geology, tectonics, geodynamics, geophysics, igneous petrology, geochemistry and/or volcanology;
  • Proof of English language proficiency.

*The successful candidate must commence by Research Quarter 2, 2021. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Dr Chun-Yu Lai

chunyu.lai@uq.edu.au

Simultaneous biogas upgrading and biofuel production

Biogas is an important alternative to fossil fuels as a clean and renewable energy. However, the low methane (50-70%) and high carbon dioxide (30−50%) contents in biogas has limited its value as a fuel. This project aims to develop an innovative biotechnology to convert carbon dioxide in biogas to valuable liquid biofuels at ambient conditions without the use expensive catalysts, and simultaneously update biogas to more valuable biomethane. By adopting a multi-disciplinary approach, the project will also reveal the fundamental science underpinning the innovative technological solutions. By creating a much stronger economic driver for biogas production and utilization, this project will contribute to the development of a circular economy.

Bachelor and/or Masters in Energy Science, Environmental Engineering or Environmental Biotechnology. This project is available until December 2020 unless a suitable candidate is found prior.

*The successful candidate must commence by Research Quarter 1, 2021. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Professor Dirk Kroese

kroese@maths.uq.edu.au

Partially Observable MDPs, Monte Carlo Methods, and Sustainable Fisheries

Reinforcement learning is an learning paradigm that is widely believed to play an important role for enabling machines to behave in an intelligent way. While significant advances have been made in the last few years, most works focus on fully observable environments, and there are still many challenges associated with dealing with partially observable environments. In particular, large and complex environments often demand lot of computation and large number of samples. This project aims to develop computationally and sample efficient reinforcement algorithms under Partially Observable Markov Decision Processes, a general framework for decision making under uncertainties (including partial observability). In particular, several ideas will be explored, implemented and tested - these includes integrating planning and reinforcement learning, and leveraging recent advances in sample efficient reinforcement learning for Markov Decision Processes.

  • Highly motivated with effective communication skills
  • Strong foundation in mathematics, statistics, and programming, as evidenced by a relevant degree and course grades
  • Knowledge and experience in machine learning / deep learning is highly desirable
  • Prior research experience in a related field is desirable

*The successful candidate must commence by Research Quarter 1, 2021. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Dr Jean-Paul Hobbs

jp.hobbs@uq.edu.au

Climate change and the genetic consequences of hybridisation in clownfishes

Coral reefs are the world’s most biodiverse marine ecosystem. However, this biodiversity is threatened by escalating human impacts. Theoretical models predict biodiversity loss due to impacts on evolutionary processes, including hybridisation, but this threat remains untested and unmanaged. Using clownfishes as a model group, the PhD student will investigate: 1. whether climate change increases hybridisation; and 2, the genetic consequences of hybridisation.

The PhD student will lead a global project on clownfishes with access to international collaborators and an extensive collection of samples. There will be opportunities for the student to develop their own research agenda and join research expeditions. The student will work in a leading molecular laboratory and join a multidisciplinary team that studies behaviour, sensory neurobiology and ecology.

The successful applicant will enrol through the School of Biological Sciences.

Masters, first class honours or equivalent with a background in evolutionary biology and/or molecular ecology, especially population genomics. Experience in statistics and bioinformatics (e.g. R, Python, bash) is preferred. Experience with fishes or marine organisms is not required.

*The successful candidate must commence by Research Quarter 1, 2021. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Dr Peter Crisp

p.crisp@uq.edu.au

Using epigenomics to discover hidden genetic control elements for crop improvement

Sustainable, productive agricultural processes are essential for tackling the challenges of tomorrow’s world. The ability to optimise beneficial agricultural traits depends on the precise control of genes in a crop plant’s enormous genome. Yet, identifying valuable gene control regions – also known as cis-regulatory elements – is like looking for needles in a haystack. The location of these regions is often not obvious and current detection technologies are impractically expensive and intensive. This PhD project aims to refine and implement a new technology, based on epigenomic profiling, that is expected to facilitate rapid and cost-effective discovery of all the control regions in a genome, enhancing our understanding of crop genomes and unlocking new avenues for agricultural improvement.

In this PhD project, the successful candidate will create and analyse genome-wide maps of candidate gene control regions (cis-regulatory elements) using epigenome profiling and next generation sequencing in cereal crops; for instance, barley, sorghum, wheat, rice, and maize. The functionality of select regulatory elements will be tested using traditional reporter assays in combination with massively parallel reporter assays (eg STARR-seq). This project will test our ability to utilise these regulatory maps to create new traits, by gene editing select regulatory elements using CRISPR. There will be opportunities to work in model species such as Nicotiana benthamiana as well as translational work in crops.

Candidates should have an Honours degree, Masters by research, Masters by coursework or equivalent in Plant Biology or Plant Genetics, Biotechnology, Molecular Biology or a related field. Experience in cloning or plant transformation will be highly regarded. Candidates interested in learning and performing bioinformatic analyses are encouraged to apply; prior computational experience not required. Please contact the Dr Peter Crisp to check on this project's availability.

*The successful candidate must commence by Research Quarter 1, 2021. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Dr Karishma Mody

k.mody@uq.edu.au

Topical RNAi for Sustainable Animal Health

The aim of the project is to develop a sustainable solution using clay particles to deliver RNA to protect Queensland’s sheep from flystrike and lice infestation. Current control measures mainly rely on vaccination or chemical control, causing issues of residue and toxicity. Both of these pathogens have developed resistance to nearly all control chemicals used in the past. This project will deliver a clean-green formulation to counter chemical resistance, improve animal welfare, reduce residues in products, allowing better responses to market demands.

BSc with Honours Class I or Masters in a relevant field. Previous experience in molecular biology, insect pathogen, animal or veterinary science, and sound knowledge of RNA interference (RNAi) pathways in insects is highly desirable.

*The successful candidate must commence by Research Quarter 2, 2021. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Associate Professor Jon Links

jrl@maths.uq.edu.au

Quantum control designed from broken integrability

This project aims to open avenues in the mathematical design quantum devices based on cold atom systems. This will be achieved through the use of methodologies developed around the notion of quantum integrability, and the breaking of that integrability. The classic techniques of quantum integrability, centred around the Quantum Inverse Scattering Method and the Bethe Ansatz, will form the foundations for the theory. Potential applications will be developed for the field of atomtronics – analogues of electronic systems that are based on the transport of cold atoms.

The successful applicant will be a member of an international collaboration that includes two institutes in Brazil. The applicant will enrol through the School of Mathematics and Physics.

This PhD project is suitable for a highly motivated and enthusiastic student who has completed Honours or Masters in Mathematics or Physics. A sound background in quantum physics is essential, and a good understanding of Lie algebras and representation theory is desirable. Some knowledge of integrable systems (classical or quantum), general quantum many-body theory, or Bose-Einstein condensates will be advantageous.

*The successful candidate must commence by Research Quarter 1, 2021. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

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.

The successful applicant 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

Please contact the Chief Investigator to check on this project's availability.

*The successful candidate must commence by Research Quarter 3, 2020. You should apply at least 3 months prior to the research quarter commencement date. Due to time constraints, only Domestic and on-shore International applicants will be considered.

Professor Matthew Sweet

m.sweet@imb.uq.edu.au

Characterizing mechanisms by which histone deacetylases control macrophage-mediated inflammation

The innate immune system has key roles in both protecting against infectious diseases and driving pathology in many inflammation-mediated diseases. This project will explore the role of a family of enzymes known as the histone deacetylases (HDACs) in regulating innate immunity and inflammation. HDACs remove acetyl groups from lysine residues on target proteins, and have been widely studied as epigenetic regulators by virtue of their roles in histone deacetylation. However, we now know that these enzymes post-translationally modify thousands of cellular proteins and control numerous biological processes, including cell signalling. HDAC inhibitors have been used in the clinic to treat certain cancers for many years, and there is great interest in the anti-inflammatory effects of these agents. This project will explore the role of specific HDAC enzymes in driving inflammatory and metabolic processes in macrophages and in vivo. It will also investigate approaches to suppress HDAC-driven inflammation. Methods to be employed include molecular and cellular biology (cloning, gene over-expression/silencing/knock-out, microscopy, immunoblotting, qPCR, RNAseq analyses, ELISA and other cellular read-outs), as well as in vivo models of inflammation.

Bachelor's degree with honours in the fields of immunology, cell biology or biochemistry

Previous research experience in molecular, biochemical, cell-based and/or immunological techniques is highly desirable (e.g. cloning, gene over-expression/silencing/knock-out in cells, microscopy, immunoblotting, ELISAs, animal studies etc).

*The successful candidate must commence by Research Quarter 4, 2021. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Dr Jie Tang

j.tang3@uq.edu.au

Green nanotechnology-based antibiotic-free poultry feed development

Current poultry feeds rely on antibiotics to keep animals healthy, creating antibiotic resistant superbugs that can infect people and are often difficult to treat. This project will use state-of-the-art nanotechnology to load Lysozyme, a natural antimicrobial/anticoccidial and immune-boosting protein, into designed nanoparticles as an anti-infective feed additive. The nano-formulation supplemented poultry feed will provide long-term anticoccidial and broad-spectrum disease-resistance, boosting productivity and reducing reliance on antibiotics.

Materials science or chemistry, a knowledge/ background in biochemistry or biomedical engineering, experience in animal test (poultry) and bacteria culturing would also be advantageous.

*The successful candidate must commence by Research Quarter 1, 2021. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Dr Tyler Neely

t.neely@uq.edu.au

Superfluid Turbulence Cascades in a Dilute Atomic Film

Uniformly trapped Bose-Einstein condensate (BEC) superfluids have recently emerged as the premier system for the experimental study of two-dimensional quantum turbulence and point vortices. This PhD project aims to answer open questions in turbulence by stirring many vortices into a superfluid Bose-Einstein condensate. This will be accomplished through technical innovations on the UQ BEC apparatus enabling the trapping and manipulation of larger superfluids. The project seeks to determine how an effective viscosity can be experimentally realised in a superfluid through vortex shedding, how vortex dynamics redistribute energy across broad length scales in superfluids, and how superfluid turbulence can arise from classical fluid instabilities. The outcomes of this project will elucidate the links between quantum and classical fluids, and provide unambiguous tests of theoretical models in real-world systems. These results will be beneficial to the understanding of the physics of quantum superfluids, and will inform the engineering of quantum-enhanced devices that utilise trapped superfluid media for precision sensing.

This experimental project will allow for the development of diverse and transferable skills, including electronic and optical design, experimental system design and implementation, software design, and data analysis. This project will also allow for attendance of related international workshops and conferences.  There will also be the opportunity to interact with other projects within the ARC Centre of Excellence for Engineered Quantum Systems (EQUS), as well as the theoretical quantum atom optics group at the University of Queensland.

Students will enrol through the School of Mathematics and Physics.

The candidate should have a masters or honours-equivalent degree in Physics/Optics or closely related fields, including a significant research component. In particular, coursework in quantum optics and condensed matter is highly valued. Previous laboratory experience in a ultracold atoms lab and/or publications are highly desired. The ideal candidate will be able to communicate effectively and actively participate in weekly group meetings and journal club presentations as well as physics seminars and colloquia.

*The successful candidate must commence by Research Quarter 4, 2021. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Dr Roger Marek

r.marek@uq.edu.au

Neural Circuitry that underlies fear and its extinction

We are seeking a full-time, highly motivated PhD candidate to perform cutting-edge research in the field of neuroscience. The successful candidate will be working under the supervision of Dr Roger Marek and Prof. Pankaj Sah, to undertake their PhD at the Queensland Brain Institute. The candidate will join a multidisciplinary team of scientists in the fields of synaptic plasticity and neural circuitry linked to emotional learning.

The PhD project aims to investigate neural function and circuits that drive fear and its extinction. Specific brain regions have been identified to control fear-related learning, yet the detailed neural circuitry and function that underpins this behaviour is not completely understood. The project will require either the use sophisticated electrophysiological tools using patch-clamp recordings in brain slices, or behavioural testings combined with various expression systems and optogenetics techniques, or a combination of both. The project will allow the candidate to pursue experiments at the forefront of modern neuroscience.

The research Institute is located at our picturesque St Lucia campus, renowned as one of Australia’s most attractive university campuses, and located just 7km from Brisbane’s city centre. Bounded by the Brisbane River on three sides, and with outstanding public transport connections, our 114-hectare site provides a perfect work environment – you can enjoy the best of both worlds: a vibrant campus with the tradition of an established university.

Masters, first class honours or equivalent with intensive research focus in either electrophysiology or animal physiology and/or animal behaviour. Knowledge about patch clamp recording or complex animal behaviour will be considered favourable. The candidate should have either a background in behavioural neuroscience, neurophysiology, or electrophysiology.

*The successful candidate must commence by Research Quarter 4, 2020. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Professor Naomi Wray

naomi.wray@uq.edu.au

Prediction of complex traits in human populations

Complex traits in humans, including quantitative traits such as height and diseases such as diabetes, are determined by genetic and environmental factors. Accurate assessment of the genetic and environmental contributors to a trait is therefore key to realising the potential of genomic information and its application in personalised medicine.  For example, accurate assessment of genetic risk to heart disease could identify candidates for increased or early screening programs.  The aim of this project is to develop and evaluate novel methods for polygenic risk prediction, including the use of haplotypes and family information.  The project will use data from large publically available sources, such as the UKBiobank.

The candidate will conduct their research as part of the Program in Complex Trait Genomics (PCTG).  This research group is based at the Institute for Molecular Bioscience, at the St Lucia campus of the University of Queensland.  The group is lead by Profs Naomi Wray, Peter Visscher and Jian Yang who are leaders in field of quantitative genetics and authors of many highly cited papers.  The candidate will have the opportunity to join a vibrant group of over 50 researchers with expertise in quantitative genetics, statistics, computer programming and population genetics.

Candidates with a background in quantitative/population genetics, statistics, mathematics and other quantitative fields will be considered. Programming skills (R, C/C++) and prior experience in analysing genetic data (e.g. GWAS) are desirable.

*The successful candidate must commence by Research Quarter 4, 2022. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Dr Peter Moyle

p.moyle@uq.edu.au

Development of a multicomponent, targeted gene delivery platform

Gene delivery systems are important tools in biological research and offer many exciting future prospects. Delivering gene material is very difficult in practice: rapid deterioration, poor cell uptake, and reaching the right tissue and cell types are major obstacles. Ways to overcome each barrier individually have been suggested in existing research but these components have not yet been combined into a single solution, which this project will tackle. The project will create a gene delivery technology to stabilize and deliver active gene material (e.g. RNA interference, CRISPR and DNA) to target cells (e.g. tumours) based on successful preliminary data generated by our laboratories. The technology will be widely applicable and superior to current gene delivery tools; can be used for in vitro and/or in vivo applications; and will greatly advance biological research with many potential future applications (e.g. genome editing, basic research and drug development).

This project is multidisciplinary in nature, and will provide the student with an excellent grounding in peptide synthesis, purification and characterization, using advanced automated synthetic robots; as well as cutting-edge formulation approaches to improve the stability and capacity to translate these systems towards animal and/or human applications; and an advanced understanding of biological models for assessing and optimizing these systems for gene expression, knockdown and editing.

Applicants with a background in science, including health sciences (e.g. pharmacy) and other applied sciences are suitable to apply. Desirable (non-essential) candidate characteristics include: An understanding of cell biology, and the processes involved in gene expression, Experience with cell culture, Western blotting, flow cytometry and/or imaging, Formulation experience, in particular the development of liposomal formulations and means to stabilize these for in vivo applications, Candidates do not need to meet all of the above characteristics to apply.

*The successful candidate must commence by Research Quarter 1, 2021. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Dr Andrew Walker

a.walker@imb.uq.edu.au

Structural and functional characterisation of caterpillar venom toxins

Caterpillars such as nettle caterpillars (Limacodidae) and puss caterpillars (Megalopygidae) are covered in spines that protect them from vertebrate and invertebrate predators. However, almost nothing is known about the toxins that underlie the pain response induced by these venoms or their pharmacological effects. This project focusses on investigating the structure, function and evolution of caterpillar venom toxins with a particular emphasis on peptide and protein toxins. The research student will employ and receive training in techniques such as recombinant expression, nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry, RNA sequencing, electrophysiology, calcium imaging, and microinjection assays. We envisage this project will involve the discovery and characterisation of new venom peptides, their production in the laboratory, solution of three dimensional structures using NMR, and characterisation of toxin pharmacology using appropriate functional assays. The outcomes of the project will be increased knowledge of venom toxins and how they may be applied in medicine and biotechnology.

Applicants should hold a research-based Honours or Masters degree in a relevant field such as biochemistry, molecular biology, structural biology, pharmacology, toxinology, or neuroscience (or be able to demonstrate an equivalent level of research experience). The role would suit an individual with enthusiasm for discovery and dissemination of research. Authorship of publications or other evidence of independent research an advantage.

*The successful candidate must commence by Research Quarter 1, 2021. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Professor Gregory Monteith

gregm@uq.edu.au

Development of unique calcium channel pharmacological modulators

This PhD project aims to develop isoform-specific modulators of a family of calcium permeable ion channels.  Initially the project will focus on medicinal chemistry, involving the synthesis of small organic molecules and investigation of structure-activity relationships for modulation of calcium channels. This phase of the project will feature contemporary drug design techniques and compound screening in cell-based assays.  After promising compounds are identified, the project will progress to deeper pharmacological studies encompassing  assessing their effects on the activity on different calcium channel types. This phase will use high throughput assays of calcium influx in mammalian cells.

Essential: Honours degree or Masters degree in chemistry or a closely related discipline with strong practical experience in the synthesis of small organic molecules. Desirable: Experience in areas such as medicinal chemistry, pharmacology, cell biology, molecular modelling, and structural biology.

*The successful candidate must commence by Research Quarter 4, 2020. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Dr Christopher Baker

c.baker3@uq.edu.au

Superfluid Optomechanics

Cavity optomechanics focuses on the interaction between confined light and a mechanical oscillator. Techniques from this field enable a broad range of high-precision sensing capabilities, ranging from high-precision acceleration, force and magnetic sensing, to the recent observation of gravitational waves by the LIGO project.

This PhD project is articulated along two related research goals. The student will develop and fabricate precision optomechanical sensors based on chip-based photonic resonators. These will be employed to study the fundamental properties of superfluid helium, and in particular the dynamics of quantized vortices, microscopic ‘cyclones’ which determine the behaviour of this quantum fluid. The student will also have the opportunity to investigate the quantum technology applications of superfluid-based devices, such as ultra-high efficiency Brillouin lasers and inertial sensors.

Activities

The successful candidate will be part of a dynamic research team and have the opportunity to become proficient in the following techniques:

  • Design of photonic chips, using Finite element modelling/FDTD simulation techniques.
  • Cleanroom nanofabrication of on-chip photonic circuits using state-of-the-art instruments.
  • Cryogenics, carrying out experiments within a millikelvin temperature dilution fridge.
  • High-precision optical measurements, mostly on-chip and fiber-based.
  • Theory development and data analysis.

The candidate will be involved in all steps of the project, while having the possibility to place larger emphasis on some of the above listed activities, depending on his/her strengths and preferences. The PhD student will regularly attend and present results at domestic and international conferences and workshops.

We are looking for a driven and talented candidate with a background in physics or engineering. Excellent oral and written communication skills in English are desired. Some experience with photonics, cryogenics or cleanroom fabrication is a plus but not mandatory.

*The successful candidate must commence by Research Quarter 3, 2020. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Dr Jos Kistemaker

j.kistemaker@uq.edu.au

Explosives Detection using Nanotechnology

Vapour phase sensing of hazardous substances is the “Holy Grail” of detection methods as it enables standoff detection, reducing the threat to the operator. However, many hazardous substances have low saturated vapour pressures (e.g., explosives) with in field (open air) concentrations being significantly less. The ability to preconcentrate analytes and then release them in a concentrated burst for detection is an important pathway to enablement of vapour phase detection in real world applications. What is required for a portable detector device is a low power method for pre-concentrator materials to absorb and then release the analyte.

We offer an opportunity for an outstanding PhD candidate to work on an exciting project that aims to tackle this technological challenge of vapour detection making use of nanotechnology. The project will be undertaken at the Centre for Organic Photonics and Electronics (COPE) that has existing projects focused on the detection of explosives. The sensors team at COPE offers an ideal combination of experience and facilities for the synthesis, characterisation, testing and commercialisation of sensing solutions. The successful student will work on a challenging but rewarding research project under the direct supervision of DECRA recipient Dr Jos Kistemaker, and ARC Australian Laureate Fellow Professor Paul Burn.

Expressions of Interest are invited from outstanding and enthusiastic graduates with a First-Class Honours, or equivalent qualifications through a relevant Masters degree. Candidates will have a strong background in organic chemistry and outstanding hands-on laboratory skills with a preference for some experience in complex aromatic organic and/or polymer synthesis. A thorough understanding of the photophysical properties of organic chromophores is desirable.

Applicants must also fulfil the PhD admission criteria for the University of Queensland, including English language requirements, and demonstrate excellent capacity and potential for research. Demonstration of research ability through publication output in peer reviewed international journals is desirable.

*The successful candidate must commence by Research Quarter 1, 2021. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Associate Professor Josephine Bowles

jo.bowles@uq.edu.au

How do germ cells transition from mitosis to meiosis?

Germ cells are the precursors of the sperm and eggs and are, therefore, critical for fertility in both sexes. In order to generate the haploid gametes, diploid germ cells undergo a special type of cell division that is unique to the germline – meiosis. Although many steps of meiosis are highly conserved, the mechanisms underlying onset of meiosis are very different in mammals, compared with other species. We will acquire fundamental knowledge regarding how naïve germ cells are instructed to embark on and progress through meiosis. This information will be relevant to the management of fertility and infertility in livestock and humans as well as informing reproductive and stem cell biology more generally. 

BSc with Honours I or equivalent Preferably with a strong interest in Developmental and/or Cell Biology Preferably with demonstrated technical expertise relevant to Developmental and Cell Biology. Highly motivated.

*The successful candidate must commence by Research Quarter 4, 2020. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Dr James Wells

j.wells3@uq.edu.au

PhD Position in Immunology – CD4+/CD8+ Double-positive T cell regulation

We are seeking a highly motivated and enthusiastic PhD student to pursue a project into CD4+/CD8+ Double-positive T cells. The project goal is to understand the mechanisms through which this rare population of regulatory cells maintains skin integrity. Despite their importance, little is known about the regulatory pathways these cells utilise. Previous work from the team has described an innovative technique to enrich these cells for in-depth study and demonstrated their potent regulatory capacity in vivo. This project will enhance our understanding of these cells and uncover their mechanisms of action. The outcomes of this work will therefore provide fundamental new knowledge of skin and T cell physiology.

The candidate should have a background in immunology or a closely-related discipline. Excellent communication skills, strong drive and self-motivation, a passion for research and the ability to work in a team are required.

*The successful candidate must commence by Research Quarter 4, 2020. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Dr Rodrigo Suarez

r.suarez@uq.edu.au

Molecular and cellular evolution of the mammalian brain

While all mammals have a six-layered neocortex, only placentals (e.g rodents, humans) evolved a corpus callosum. What developmental processes differentially affect the early formation of this structure remains unknown, but transcriptomic, cellular and anatomical data of cortical development in mice and dunnarts (a marsupial experimental model) suggest that subtle differences in the timing of events might affect the development and evolution of new rules of neural wiring.
This project will combine high-throughput transcriptomic sequencing of brain areas during development in mice and dunnarts, studies on neurogenesis and cell-type differentiation, and in vivo experimental manipulations of genes/processes to selectively affect brain circuit formation.

Necessary requisites are either or both: (i) experience in RNAseq and bioinformatic analyses; (ii) advanced molecular biology skills (cloning, PCR, in situ RNA hibridisation). Please detail these in your application.

Additional desired experience, and/or a keen interest to develop at an advanced level, includes: developmental neurobiology, molecular neuroanatomy, advanced light microscopy, image processing and statistical analyses, and fundamentals of evolutionary theory (e.g. evo-devo).

Preferred educational backgrounds include, but are not limited to: - BSc with Honours (first class) or Masters thesis on: RNAseq and Bioinformatics, or Molecular Neurobiology. - BSc graduates (e.g., Biology, Chemistry, Bioinformatics, Biotechnology, Engineering) having passed at least four of the following courses at university level: Bioinformatics, Software Development, Statistics/Biostatistics, Biochemistry, Molecular Biology, Cell Biology, Developmental Neurobiology, Genetics, Developmental Biology/Embryology, Systems/Functional/Integrative/Introductory Neurosciences/Neuroanatomy/Neurophysiology, Evolutionary Biology. Publications, awards, teaching and service, are desired but not required.

*The successful candidate must commence by Research Quarter 4, 2020. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Professor Ian Henderson

i.henderson@imb.uq.edu.au

Phospholipid trafficking in Gram negative bacteria

The Gram-negative bacterial cell envelope consists of an outer membrane and an inner membrane separated by an aqueous periplasm containing a thin peptidoglycan layer. In E. coli the inner membrane is a symmetrical phospholipid bilayer composed primarily of phosphatidylethanolamine (PE; 75%), phosphatidylglycerol (PG; 20%) and cardiolipin (CL; 5%). The inner membrane contains a-helical integral membrane proteins and lipoproteins anchored into its periplasmic side. The outer membrane has a more complex organisation with lipopolysaccharide (LPS) and phospholipids, predominantly PE, PG and CL, forming an asymmetric bilayer containing integral b-barrel proteins and lipoproteins. These constituents work in concert to create a formidable barrier to antibiotics, detergents and other toxic chemicals.  Each component of the outer membrane is synthesised in the cytoplasm and trafficked across the inner membrane and the periplasm before incorporation into the outer membrane. Over the last twenty years pathways have been identified for trafficking of LPS, integral b-barrel proteins and peripheral lipoproteins from the membranes. However, the enduring major conundrum in the field is the mechanism of phospholipid trafficking to the outer membrane; this pathway remains unknown.  Using high through put genetic techniques we will determine if specific pathways are required for lipid trafficking.  Pathways identified through this approach will be studied further using biochemical and structural methods.  Identification of such key pathways offers potential to develop new medicines to combat antimicrobial resistant microorganisms.

BSc or equivalent in microbiology or biochemistry

*The successful candidate must commence by Research Quarter 4, 2020. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Dr Emma Gordon

e.gordon@imb.uq.edu.au

Defining mechanisms behind the formation of hierarchical vascular networks

Blood vessels form complex branched networks composed of arteries, capillaries and veins. The development and maintenance of different vessel systems (arteries and veins) is dependent on cell adherence properties within each vessel, yet how these are established and maintained remains unknown. This project aims to analyse the differences in junctional dynamics between sprouting arteries and veins, and to identify arterial and venous signalling networks that make and maintain vessel identity. This project aims to reveal how adhesiveness is regulated in order to make a hierarchical, functional vascular network. 

For this PhD project we will use novel mouse and zebrafish models and bioengineered human micro-vessels to analyse the effect of loss of c-Src kinase on cell-cell junctions in different vessel beds. This will provide fundamental knowledge on how adhesiveness contributes to forming a complex vascular network.

First class Honours or equivalent with a background in cell biology or developmental biology. Experience in either cell culture, mouse or zebrafish modelling and confocal imaging would be beneficial.

*The successful candidate must commence by Research Quarter 4, 2020. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Professor Kevin Thomas

kevin.thomas@uq.edu.au

Comprehensive characterisation of human PFAS exposure using nontarget analysis

Per- and polyfluoroalkyl substances (PFAS) are environmentally ubiquitous and frequently detected in humans worldwide. The OECD has to date identified >4,700 PFAS in use globally. Ninety percent of these have been identified as potential precursors to specific PFAS that bioaccumulate in humans. Despite the high number known to be in use, targeted biomonitoring typically looks for a limited number of ~30 analytes using tandem mass spectrometry (LC-MS/MS). Recognition of the PFAS exposome, i.e. the totality of human environmental exposures to the numerous PFAS compounds, is therefore likely to be limited amongst exposed individuals, the general population and public health regulators. This project aims to comprehensively characterise the PFAS exposome through a combination of nontargeted biomonitoring and in vitro precursor transformation experiments. Alongside this is an important task to communicate and contextualise what the PFAS exposome means for exposed individuals and the wider population.

Applicants must hold a 1st Class Honours or Masters degree (or equivalent) in analytical chemistry or related fields, with a background in mass spectrometry.

*The successful candidate must commence by Research Quarter 4, 2020. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Associate Professor Ben Schulz

b.schulz@uq.edu.au

The dynamic subcellular glycoproteome during influenza virus infection

How does influenza virus infection control the host cell?

What are the evolutionary trade-offs between antiviral resistance and viral fitness?

What can ground-breaking mass spectrometry analytics uncover about protein post-translational modifications?

An exciting new PhD position to study these questions is available at the School of Chemistry and Molecular Biosciences (SCMB) located on the St Lucia campus of The University of Queensland.

The project will use mass spectrometry glycoproteomics and proteomics, cell culture, and molecular biology to investigate at ultra-high spatial and temporal resolution how the cellular glycoproteome and proteome change during influenza infection. This project is part of a National Health and Medical Research Council-funded Ideas Grant. The candidate will ideally start the project in mid 2020.

The successful candidate will be working in the laboratory of Associate Professor Ben Schulz and will work closely with postdoctoral researcher Dr Cassandra Pegg to complete the project. The successful candidate’s research will benefit from access to high-end mass spectrometers located in the core proteomics facility and specialised bioinformatic software. In addition, SCMB provides generous student travel grants to attend international conferences.

Applicants should possess a BSc Hons, MSc, or equivalent, majoring in a relevant discipline (e.g. analytical biochemistry, bioinformatics, or virology). Ideal applicants should have a strong academic performance. Laboratory research experience with mass spectrometry, HPLC, and other proteomic techniques will be considered favourable. Excellent oral and written communication skills, motivation and the ability to work as part of a team is also required. Applicants must be eligible to enrol in a PhD with the University of Queensland. 

*The successful candidate must commence by Research Quarter 4, 2020. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Associate Professor Lee Hickey

l.hickey@uq.edu.au

Improving root system architecture of future crops

This PhD project will exploit recent advances and opportunities in root research at The University of Queensland to improve the productivity of durum wheat cultivars in water limited environments. This could be achieved by creating cultivars with 'designer' root systems that could target diverse environmental conditions with different levels of water availability. While the direction of root growth is important, insight of other root traits, like total root biomass is critical for effective manipulation of root system architecture with increased soil resource capture. Combining traits such as root biomass accumulation and root growth angle could result in development of elite cultivars with distinct root ideotypes that could be advantageous in different environment types. Development of such materials and field testing could help inform cultivar design and breeding, which could help expand the Australian durum production area, particularly throughout northern New South Wales, Queensland and Victoria. For example, a narrow and deep root system ideotype with increased root branching at depth could improve access to moisture particularly deep soils, and thereby minimize the impact of drought on yield.

This project aims to create elite introgression lines using rapid generation advance technology ‘speed breeding’ in combination with marker-assisted selection and new phenotyping approaches to fast-track the desired gene combinations into different backgrounds of Australian durum cultivars. Lastly, the elite durum introgression lines will be evaluated in diverse environmental conditions to determine the ideal root system ideotype for each environment type. The best performing genotypes under contrasting environments will be available for breeding programs to support the development of more productive durum wheat cultivars.

First Class Honours degree, Masters by research, Masters by coursework or equivalent. Basic expertise and experience is required in one or more of the following areas: plant genetics, plant breeding, plant physiology and quantitative genetics. Application are strongly encouraged when one of the previously mentioned disciplines is combined with basics in R programming skills. Strong academic performance demonstrated through publication output in peer reviewed international journals is highly desirable.

*The successful candidate must commence by Research Quarter 1, 2020. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons.

Associate Professor Peter Kopittke

p.kopittke@uq.edu.au

Examining root distribution in soils using X-ray tomography

Understanding root distribution in soil is critical in order to provide information on how soil properties and management practices impact upon plant performance and crop yield. However, roots are often referred to as the “hidden half” as they are difficult to examine. This project will help to develop synchrotron-based X-ray tomography as a technique for the routine analyses of roots directly (in situ) in soil. This technique will then be used to examine soil cores collected at trial sites from around Australia to understand how root distribution in soil is impacting on plant performance.

The successful candidate will collaborate closely with several postdoctoral positions using synchrotron-based approaches, including a postdoc that will be working on X-ray tomography. Other postdoc positions include one that is seeking to examine soil organic carbon as well as a position that is seeking to develop approaches for imaging nutrient distribution in soils.

A strong background in physics (or closely related field) with a clear understanding of X-ray tomography and tomography data segmentation

*The successful candidate must commence by Research Quarter 4, 2020. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons. 

Associate Professor Peter Kopittke

p.kopittke@uq.edu.au

Soil organic carbon: The key to improving soil fertility

This project aims to unravel changes in the forms and distribution of soil organic carbon in agricultural soils. Using innovative analytical methods (including synchrotron-based approaches) to examine soils used for agricultural production, the project is expected to provide an understanding of how organic carbon is stabilized and destabilized in soil. Furthermore, this research will assist in providing an understanding of how changes in soil organic carbon influence soil properties and productivity.

The successful candidate will collaborate closely with several postdoctoral positions. These other positions include one that is seeking to develop X-ray tomography for analyses of root distribution in large soil cores as well as a position that is seeking to develop synchrotron-based approaches for imaging nutrient distribution in soils.

Agriculture or environmental science, preferably with a strong background in soil science and a clear understanding of soil organic carbon.

*The successful candidate must commence by Research Quarter 4, 2020. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons. 

Dr Karen Cheney

k.cheney@uq.edu.au

Colour vision in animals with four - and more - spectral sensitivities

Colour vision is used by many animals to escape predation, communicate with other individuals, find food and mates, and navigate through complex habitats. Our understanding of animal vision has contributed to the development of digital cameras, image sensors, optical devices such as telescopes and microscopes, and computer vision algorithms. Furthermore, understanding the visual performance of animals has widespread implications in neuroscience, ecology, conservation, evolution and animal welfare.

Humans have the capacity to perceive millions of different colours with only three types of cone photoreceptors with different spectral sensitivities — red, green, and blue (RGB), or trichromacy. Other animals, including many species of birds and fish, have four or five spectrally distinct cones (tetra- and pentachromacy), often capable of detecting ultraviolet (UV) radiation and/or longer wavelengths. Theoretically, this should enable them to perceive and discriminate among billions of colours and utilise a colourful richness in visual scenes that we are unable to detect. Yet we do not know how tetrachromatic and potential pentachromatic animals combine information from these different photoreceptors, send it to the brain, and convert it into visual perception. This represents a significant gap in our basic understanding of animal vision.

As part of this PhD project, you will investigate the visual systems of marine fish, such as boxfish and seahorses. You will use avariety of techniques from behavioural experiments in the field and lab, to physiological and morphological analyses, to the molecular assessment of vision on genomic and transcriptomic levels. 

Masters, first class honours or equivalent with intensive research focus in animal behaviour, marine sciences and/or molecular focus.

*The successful candidate must commence by Research Quarter 4, 2020. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons. 

Dr Rebecca San Gil

r.sangil@uq.edu.au

and

Dr Adam Walker

adam.walker@uq.edu.au

Identifying regulators of the molecular pathologies associated with motor neuron disease and frontotemporal dementia

The associated PhD project aims to identify genes and proteins regulating cellular and molecular processes involved in motor neuron disease (MND) and frontotemporal dementia (FTD). Our laboratory specialises in understanding mechanisms of cellular stress, protein aggregation, and neuronal degeneration in the central nervous system of people living with MND and FTD. We are also focused on identifying and validating novel therapeutic strategies for these diseases by conducting preclinical testing in vivo. You will join an ambitious, inclusive, and collaborative group at the Queensland Brain Institute with access to world-class facilities and support to build your research career (https://walkerneurolab.org/).

There will be many opportunities to learn advanced techniques including, lentivirus production, CRISPR knockout and activation, in vivo preclinical testing of therapeutic strategies, high-end microscopy, and next generation sequencing. The PhD project is not prescriptive and will be developed in conjunction with the selected student depending on their research interests and their existing research skills.

First class Honours or Masters with an intensive research component in cell biology, biochemistry, and neuroscience is required.

*The successful candidate must commence by Research Quarter 4, 2020. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons. 

Dr Dietmar Oelz

d.oelz@uq.edu.au

Modelling and simulation of molecular motor driven cytoskeleton dynamics and its function in the secretory pathway

The project aims to elucidate the impact of cytoskeleton dynamics on morphology and function of neurosecretory cells and of neuron cells using computational simulation and continuum modelling. 

It is not well understood how the transport of secretory, respectively synaptic vesicles to their sites of exocytosis is guided and controlled. Since mechanical guidance through the cytoskeleton is believed to play a pivotal role it is our goal to identify the mechanism(s) by which cortical F-actin and microtubules as well as their associated motor proteins contribute to the processes leading to exocytosis, respectively neurotransmitter release. 

The applicant should have a background in (applied) mathematics or (computational) physics. Familiarity with partial differential equations and some programming language (e.g. Julia, MATLAB, Python, C, or other) is preferred.

*The successful candidate must commence by Research Quarter 4, 2022. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons. 

Dr Paul Dennis

p.dennis@uq.edu.au

Molecular analysis of soil microbes that form a living soil cover, so-called biocrusts, in Australia’s grazing lands to advance sustainable food production

Nitrogen (N) in pasture plants is eaten by cattle, assimilated into animal tissue, and exported to consumer markets. If this N is not replaced, rangelands become unproductive as fertiliser addition is impossible due to the scale of these areas. Biocrusts that form on soil surfaces, contain microorganisms that convert atmospheric N2 into plant-available N and replenish the N status of soil. These microbial communities are likely influenced by rangeland management and this has consequences for the sustainability of food production.

In this project, the successful candidate will determine the influence of grazing intensity and fire management on the diversity and function of N-fixing microbial communities in biocrusts. The project will involve bioinformatic and statistical analyses of shotgun metagenomic sequence data to identify which microbes are performing which functions, and how these relationships are affected by management of grazing lands.

This research forms part of a larger project, funded by Meat and Livestock Australia (MLA) in collaboration with university and government based scientists and practitioners. It is co-funded by the Australian Microbiome Initiative and has a focusses on fundamental and applied science of soil microbiomes.

Applications are sought from people with a Bachelor's degree in Computer Science, Bioinformatics, Microbiology, Environmental Science, or a related field.

Qualifications

  • You must hold a Bachelor's degree in Computer Science, Bioinformatics, Microbiology, Environmental Science, or a related field.

Knowledge, Experience and Skills

  • Knowledge, experience and skills in bioinformatics and statistics
  • Excellent written and verbal communication skills
  • Organisational and problem solving skills
  • Experience in assisting with the production of scientific reports, publications and standard operating procedures

Personal Qualities

  • Well-developed interpersonal skills, including the ability to work and communicate well in a multidisciplinary team.
  • Good time management skills with the ability to prioritise workload, work independently and meet deadlines.

*The successful candidate must commence by Research Quarter 4, 2020. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons. 

Associate Professor Eve McDonald-Madden

e.mcdonaldmadden@uq.edu.au

Tackling pests using game theory to support cooperative management

This project seeks to improve conservation management by designing cooperative planning tools for multiple conservation agencies. Using an interdisciplinary decision analytic approach combining game theory, spatial modelling, ecology, and cost-effectiveness analysis we aim to create a novel framework identifying how and when agencies might collaborate, and how collaboration might impact on costs and benefits of pest control strategies. This exciting PhD project aims to develop spatial approaches to modelling pest management for multiple agencies using Queensland as a case study.

This PhD project will specifically aim to develop novel spatial modelling and decision theoretic approaches to integrate data on pests, management effectiveness, and management actions available to different Queensland Government agencies. Then to use this to evaluate spatial priorities for the different agencies given their differing objectives.

The successful applicant will enrol through the School of Earth & Environmental Sciences. 

Hold a BSc or MSc degree in environmental sciences, agriculture, engineering, mathematics, economics or a related field • Have knowledge and experience with spatial analysis and modelling • Have knowledge of statistics and programming languages (Python, R or Matlab)

*The successful candidate must commence by Research Quarter 3, 2020. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons. 

Dr Gabriele Taraglino-Mazzucchelli

g.tartaglino-mazzucchelli@uq.edu.au

Supersymmetry and Supergravity: New Approaches and Applications

This project aims at improving our understanding of general supersymmetric theories and supergravity-matter couplings. The outcomes of this project will advance our knowledge of supersymmetry and its mathematical formulation towards the solution of challenging open questions in the study of quantum field theories and gravity. The project’s results will find potential applications to various research branches of high-energy theoretical physics such as quantum field and string theories, matter-coupled gravity, cosmology and holographic dualities.

The successful applicant will enrol through the School of Mathematics and Physics.

Theoretical and/or Mathematical Physics of fundamental interactions.

Compulsory: good knowledge of quantum field theory and General Relativity.

Preferred: knowledge of supersymmetry, supergravity and topics related to string theory.

*The successful candidate must commence by Research Quarter 4, 2020. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons. 

Professor Daniel Rodriguez

d.rodriguez@uq.edu.au

Optimising sorghum yield through agronomic management

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?

Across Australia’s Northern Grains Region, managing heat stress and dry spells around critical growth stages remain critical to increase farmers yields and reduce the likelihood of un-economical sorghum crops. For the case of heat stress at flowering, the main adaptation strategy farmers have to reduce yield losses, is to avoid the overlap between heat stress events and flowering, by targeting optimum flowering windows. Initial results show that to fit the flowering of sorghum around low risk windows for heat and water stresses, the crop would need to be sown into soil moisture, at soil temperatures lower than the recommended 16°C. Under these conditions, farmers need to achieve rapid and uniform crop establishments, and balance the decision on the likely benefits of reduced stresses around flowering, with the higher risk of early frost damage.

Topics that this PhD project could address include: crop establishment in cold soils; the crop sensitivity to early frost damage; how early sowing changes the frequency of stress environments around flowering, and how these changes impact yields; cropping systems benefits i.e. early crops offer the opportunity of sowing a winter crop after a short summer fallow; the existing genetic diversity and the role of different physiological traits in relation to early planting and stresses also require specific researching.

The successful student will enrol through Queensland Alliance for Agriculture & Food Innovation.

Agriculture, crop physiology, cropping systems, stress physiology

*The successful candidate must commence by Research Quarter 2, 2021. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons. 

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.  

The successful applicant 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.

*The successful candidate must commence by Research Quarter 2, 2020. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons. 

 

Professor Alan Rowan

alan.rowan@uq.edu.au

 

Dr Jan Lauko

j.lauko@uq.edu.au
Cellular mechanics in unusual systems

This project will use a multifaceted approach to investigate the effects of microgravity/force on cell differentiation in 3D biomimetic cell matrices and to quantify force-mediated changes in stem cell behaviour. This will be achieved through synthesis of novel synthetic extracellular matrix materials, their detailed mechanical characterisation and the study of their interactions with biological materials in altered gravity.

The successful applicant will enrol through the Australian Institute for Bioengineering and Nanotechnology.

Material chemistry or polymer chemistry or biophysics
background preferably with experience using/preparting synthetic ECM. Experience in mechanical characterisation of materials will be an advantage.

Please contact the Chief Investigator to check on this project's availability.

Professor Justin Marshall

justin.marshall@uq.edu.au
Unravelling reef fish vision through gene-editing and behavioural ecology

This project aims to enhance our understanding of visual neuroscience, genetic control of vision and
environmental ecology on The Great Barrier Reef (GBR). Using the anemonefish, as a model, together with new genetic, photographic and behavioural approaches, the project aims to reveal novel aspects of colour vision on the reef.

The successful applicant will enrol through the Queensland Brain Institute.

A Masters degree or equivalent in Evolutionary Biology, Neurosciences or Marine Sciences. Bioinformatic experience is preferred but not necessary.

Please contact the Chief Investigator to check on this project's availability.

Professor Bostjan Kobe

b.kobe@uq.edu.au
Molecular basis and inhibition of TIR-domain function in Toll-like receptor and neuronal cell-death pathways

TIR (Toll/interleukin-1 receptor) domains feature in TLRs (Toll-like receptors) and their adaptors involved in innate immunity, as well as the protein SARM1 (sterile-alpha and TIR motif containing 1) involved in axon degeneration. These pathways are associated with a number of pathological states ranging from infectious, autoimmune, inflammatory, cardiovascular and cancer-related disorders to neurodegenerative diseases. The proposed research will build on two key observations: (i) TIR domains signal through cooperative assembly formation (SCAF); and (ii) SARM1 TIR domain possesses SCAF-dependent enzymatic activity responsible for cleavage of NAD+, a key step in axon degeneration. The project will characterise the specificity of assembly formation in TLR pathways and the molecular and structural basis of NADase activity, test structure-based hypotheses for functional effects in cells, and design inhibitors of interactions by these proteins. The outcomes of the proposed research will include an improved understanding of signaling in TLR and SARM1 pathways, identify new target sites for therapeutic design, and provide inhibitory molecules as leads for therapeutic development against chronic inflammatory, neurodegenerative and related diseases.

The successful applicant will enrol through the School of Chemistry and Molecular Biosciences.

Biochemistry and molecular biology (preferably including adequate chemistry and physics background, and some lab experience, especially structural biology)

Please contact the Chief Investigator to check on this project's availability.

Professor Debra Bernhardt

d.bernhardt@uq.edu.au
Promoting new reaction pathways with nonequilibrium flow

This project aims to understand how to control reactions using external forces such as those due to shear.  Theoretical studies and molecular level computations will be used to gain insight into the mechanisms that promote reactions under shear, and how these are related to molecular structure and fluid composition. This is relevant for advancement of many technologies, from development of new synthetic pathways and products, to design of lubricants that can withstand extreme strain rates.

The successful applicant will enrol through the Australian Institute for Bioengineering and Nanotechnology.

Chemistry, Physics, Chemical Engineering, Mathematics

Please contact the Chief Investigator to check on this project's availability.

Dr Craig Hardner

c.hardner@uq.edu.au
National Tree Genomics Platform – Phenotype Prediction Toolbox

The PHD successful candidate will develop technology to support implementation of genome based prediction models in horticultural tree crops
Potential projects include:

  • genomic prediction models for priority traits (including vigour, phenology, precocity, fruit quality) in mango, macadamia, and citrus
  • genomic methods to fast track rootstock breeding in avocado for resistance to phytophthora and control of scion vigour and precocity,
  • genomic based global prediction of performance.

The successful candidate will develop skills in big data management, genomics, genetics, statistics, bioinformatics, and translation to applied genetic improvement and will work with international partners in mainland US and Hawaii, European Union, and China.

The successful applicant will enrol through the Queensland Alliance for Agriculture & Food Innovation (QAAFI).

Graduates with background in, or ability to learn, quantitative genetics and /or statistics, plant (preferably tree) biology, and bioinformatics. 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 Graduate School PhD program

Please contact the Chief Investigator to check on this project's availability.

Professor Tamara Davis

tamarad@physics.uq.edu.au
Understanding the Dark Universe

This PhD project will test models of dark energy, dark matter, and advanced theories of gravity.  We will use the latest observational data from supernovae, galaxies, and/or gravitational waves to test cosmological models and investigate the nature of the dark components of our universe.  The candidate will have the opportunity to be embedded in large international cosmology teams such as the Dark Energy Survey (DES) and the Dark Energy Spectroscopic Instrument (DESI).

The successful applicant will enrol through the School of Mathematics and Physics.

First Class Honours, or Masters, in astrophysics or related discipline

Please contact the Chief Investigator to check on this project's availability.

Associate Professor Mehdi Mobli

m.mobli@uq.edu.au
Accessing structurally elusive states of sodium channels as novel analgesic targets

The project involves identification and characterisation of structurally distinct and functionally important regions of sodium channels. These proteins are then used as targets for drug screening using biophysical assays.

The successful applicant will enrol through the Queensland Brain Institute.

Biochemistry, Chemistry, Biophysics, Molecular Biology

Please contact the Chief Investigator to check on this project's availability.

Associate Professor Mehdi Mobli

m.mobli@uq.edu.au
A new source of bivalent molecules from nature

The project aims to discover and characterise disulfide rich peptides with a tandem repeat architecture. The candidate will identify, produce and characterise novel tandem repeat peptides with the aim of discovering new protein structural arrangements and unique biological activities as a source for development of drugs and insecticides.

The successful applicant will enrol through the Queensland Brain Institute.

Biochemistry, Chemistry, Biophysics, Molecular Biology

Please contact the Chief Investigator to check on this project's availability.

Dr Patricio Opazo

p.opazo@uq.edu.au
The role of calcium/calmodulin-dependent protein kinase II in synaptotoxicity in Alzheimer's disease models

In this project, we aim to understand the molecular mechanism underlying synaptic loss in  Alzheimer’s disease models.

The successful applicant will enrol through the Queensland Brain Institute.

Biomedical Sciences and Neurosciences

Please contact the Chief Investigator to check on this project's availability.

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 successful applicant will enrol through the Australian Institute for Bioengineering and Nanotechnology (AIBN).
  • A bachelor’s degree with at least honours class IIA
  • A coursework master’s degree 

Please contact the Chief Investigator to check on this project's availability.

Associate Professor Cynthia Riginos

c.riginos@uq.edu.au
Tracking origins and spread of Crown-of-Thorns Seastars on the Great Barrier Reef

An Australian Research Council funded project will be examining key hypotheses regarding the spatio-temporal dynamics of Crown-of-Thorns Seastars (CoTS) outbreaking populations, drawing upon genomic and eDNA enabled tools and methodologies. We are seeking highly a motivated individual with experience or strong interests in some combination of population genomics, landscape genetics, invasive species/pathogen spread dynamics, and population modelling. Competitive applicants would have demonstrated relevant research experience in evolution and population genetics (Masters or Honours degree with associated publications) and some experience with bioinformatics and computer scripting (R, python, perl or other relevant language)

The successful applicant will enrol through the School of Biological Sciences.

Masters degree with experience in bioinformatics

Please contact the Chief Investigator to check on this project's availability.

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.

The successful applicant will enrol through the Queensland Alliance for Agriculture & Food Innovation (QAAFI).

Postgraduate studies in Agriculture, Biological Sciences

Please contact the Chief Investigator to check on this project's availability.

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.

The successful applicant will enrol through the Australian Institute for Bioengineering and Nanotechnology (AIBN).

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

Please contact the Chief Investigator to check on this project's availability.

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.

The successful applicant 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.

Please contact the Chief Investigator to check on this project's availability.

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.

The successful applicant 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.

Please contact the Chief Investigator to check on this project's availability.

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.

The successful applicant 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.

Please contact the Chief Investigator to check on this project's availability.

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.

The successful applicant 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.

Please contact the Chief Investigator to check on this project's availability.

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.

The successful applicant 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.

Please contact the Chief Investigator to check on this project's availability.

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).

The successful applicant 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).

Please contact the Chief Investigator to check on this project's availability.

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.

The successful applicant 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

Please contact the Chief Investigator to check on this project's availability.

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

The successful applicant will enrol through the School of Biomedical Sciences.

Bachelor with Honours or Masters

Please contact the Chief Investigator to check on this project's availability.

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

The successful applicant will enrol through the School of Biomedical Sciences.

Bachelor with Honours or Masters

Please contact the Chief Investigator to check on this project's availability.

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.

The successful applicant will enrol through the School of Biological Sciences.

Plant biology; molecular biology, physiology

Please contact the Chief Investigator to check on this project's availability.

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.  

The successful applicant will enrol through the Queensland Alliance for Agriculture & Food Innovation (QAAFI).

Masters in Agronomy 

Please contact the Chief Investigator to check on this project's availability.

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

The successful applicant will enrol through the Faculty of Medicine.

Bachelor with Honours or Masters

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

Associate Professor Eugeni Roura

e.roura@uq.edu.au

Peri-hatching strategies to endure enteric pathogens in broilers

The project aims to develop a perinatal program to improve embryonic development and post-hatching gut health in chickens. The embryonic interventions will be “in ovo” and will consist of using essential oils (EOs) selected based on antimicrobial, antioxidant and digestion stimulant activities to promote early feed intake, gut development and a stable healthy microbiome early in the life of the chicken.

The successful applicant will enrol through the Queensland Alliance for Agriculture & Food Innovation (QAAFI).

Animal or Veterinary science. 
Biotechnology background would be of value.

*This project is available until September 2020 unless a suitable candidate is found prior.

Dr Matthew Holden

m.holden1@uq.edu.au

The value of model complexity for fisheries management

The project aims to quantify the benefits of using dynamic multi-species models (e.g. ODEs, difference equations, etc.) fitted to data for deciding how many fish can sustainably be removed from the ocean. Expected outcomes of the project include 1) guidance for fisheries scientists on when to use multi-species models for management, 2) improved decision making to reduce the risk of fishery collapse, 3) a new method for dynamic model validation in the face of limited data, and 4) enhanced collaboration between modellers and applied agencies.

The successful applicant will enrol through the School of Mathematics and Physics.

The applicant should have a background in applied mathematics, or statistics, or quantitative ecology. Familiarity with differential equations, calculus-based probability theory, and some programming language (e.g. R, MATLAB, Python, C, or other) is preferred.

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

Professor Anthony J. Richardson

a.richardson@maths.uq.edu.au

Future fisheries under climate change: the missing role of zooplankton

Tuna fisheries are some of the biggest, most valuable and iconic globally, but are found in the marine equivalent of deserts on land. How the marine food web supports these productive fisheries is an open question, as is how these fisheries will respond to climate change. This project will answer these questions by modelling the global marine ecosystem from bacteria to whales using size spectrum models, based on systems of partial differential equations. The successful student needs a background in applied mathematics and an interest in the natural world.

The successful applicant will enrol through the School of Mathematics and Physics.

BSc (Honours) in mathematics

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

Professor Kevin Thomas

kevin.thomas@uq.edu.au

and

Dr Phong Thai

p.thai@uq.edu.au

Estimating use of tobacco and nicotine products through wastewater analysis

This project aims to equip the Australian public health and security sector with a tool to accurately measure tobacco consumption in the general population. Specific human biomarkers in urine will be identified using nontarget approaches and their pharmacokinetics quantified.

The new data will address critical gaps in our knowledge on the population-level excretion of biomarkers for the consumption of tobacco and alternative nicotine products.

The outcomes of this project will provide reliable, cost-effective estimates of tobacco consumption for use with wastewater-based epidemiology assessments. This will enable changes in tobacco use to be accurately evaluated for the first time and improve the efficacy of tobacco control measures.

The successful applicant will enrol through the School of Pharmacy.

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

A background in pharmacology would be advantageous

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

Dr Chenming Zhang

chenming.zhang@uq.edu.au

Physical and geochemical coupling in a subterranean estuary

This four-year PhD project aims to determine and quantify key mechanisms governing chemical transport and transformation in a tidally dominated subterranean estuary.

Field campaigns will be carried out to monitor in long term the hydrodynamic and geochemical processes at the cross-shore transect near Moreton bay and Brisbane river estuary.

Laboratory work will be involved to analyse the samples from the field. Mathematical modelling will be carried out to describe the hydro-geo-chemical process identified from the field conditions.  

Students be enrolled through the School of Civil Engineering. and a larger team based in the Southern Cross University and Westlake University in China.

The successful applicant will enrol through the School of Civil Engineering.

Degree in Civil and/or environmental related disciplines;
Experience in programming;
Ability to work independently;
Excellent written and oral communications skills;
Formal research process including writing and presenting results/findings.

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

Dr Andrii Slonchak

a.slonchak@uq.edu.au

and

Professor Roy Hall

roy.hall@uq.edu.au

Noncoding RNAs of insect-specific flaviviruses: biogenesis and functions

This project aims to understand biogenesis and functions of viral noncoding RNA (sfRNA) produced by insect specific flaviviruses (ISFs). Flaviviruses is a large group of positive strand RNA viruses, which includes important human pathogens such as Dengue, Zika and West Nile virus. ISFs is a subgroup of flaviviruses that can only replicate in mosquito host and are not capable of propagation in vertebrates. They have recently attracted significant attention due to their potential use as a backbone for development of the vaccines against pathogenic flaviviruses. Flaviviruses have evolved to subvert host mRNA decay pathway to generate a functional noncoding RNA by incomplete degradation of their genomic RNA. Production of this RNA is highly conserved amongst all members of Flavivirus genus and has been identified as an important determinant of replication for pathogenic flaviviruses. However, the mechanism of action for sfRNA in insects is largely unknown.

In this project we will identify structural determinants of ISF sfRNA biogenesis, elucidate the role of sfRNA in their replication and identify host pathways targeted by sfRNA in mosquitoes. We will also asses if ISF-specific aspects of sfRNA production contribute to restriction of their replication in mammalian host. UQ researches involved in this project have always been at the forefront of flavivirus research with their achievements including discovery of sfRNA biogenesis and functions, characterization of novel insect-specific flaviviruses and testing their applications for vaccine development. By joining this project, the successful candidate will have an excellent opportunity to develop skills in RNA biology, molecular virology and bioinformatics.

The successful applicant will enrol through the School of Chemistry and Molecular Biosciences.

1st class Honours in virology, microbiology, molecular biology or related discipline. Experience required in isolation and handling of RNA, work with viruses and cell culture, recombinant DNA techniques, quantitative RT-PCR. Additional experience in computational biology/bioinformatics is preferred. Applicant should demonstrate good knowledge in virology, molecular biology and insect innate immunity.

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

Candidates cannot commence under this project prior to Research Quarter 1, 2020

Professor Hamish McGowan

h.mcgowan@uq.edu.au

Unlocking the archives of the Kimberley’s past

The project will focus on numerical modelling of the paleoclimates of the Kimberley region of northwest Australia. This will include downscaling of global climate model simulations with WRF.

A top-up scholarship of $5,000 is also available for this project.

The successful applicant will enrol through the School of Earth and Environmental Sciences.

First class Hons degree in geography, meteorology or maths/physics with experience in climate modelling including the use of WRF.

*The successful candidate must commence by Research Quarter 1, 2020. You should apply at least 3 months prior to the research quarter commencement date. International applicants may need to apply much earlier for visa reasons. ​

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.

The successful applicant 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 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.

The successful applicant 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 December 2019 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.

The successful applicant 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.

Dr Jacinda Ginges

j.ginges@uq.edu.au

Precision atomic theory and searches for new 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. 

The successful applicant 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 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.

The successful applicant will enrol through the School of Biological Sciences.

Plant biology; molecular biology, physiology

Please contact the Chief Investigator to check on this project's availability.

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.  

The successful applicant will enrol through the Queensland Alliance for Agriculture & Food Innovation (QAAFI).

Masters in Agronomy 

Please contact the Chief Investigator to check on this project's availability.