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Scott Beatson is an Associate Professor and NHMRC Career Development Fellow at The University of Queensland (UQ). He specializes in bacterial pathogenomics: using whole-genome sequencing to investigate transmission, pathogenesis and antibiotic resistance in bacteria. Recent work from his group includes genomic analyses of pandrug resistant enterobacteriaceae and the multidrug resistant Escherichia coli ST131 pandemic clone. He was awarded a PhD from UQ for his work in bacterial pathogenesis in 2002 and developed his career in bacterial genomics in the United Kingdom with the support of fellowships from the Royal Commission for the Exhibition of 1851 (University of Oxford) and the UK Medical Research Council (University of Birmingham). Since returning to Australia he has held fellowships from both the NHMRC and ARC and has led a successful research group in the School of Chemistry and Molecular Biosciences at UQ since 2008. He is also a member of the Australian Infectious Diseases Research Centre and the Australian Centre for Ecogenomics. In 2016 he received the Frank Fenner Award from the Australian Society for Microbiology in recognition of his contribution to microbiology research in Australia.

As a teaching and research academic within the School of the Environment at the University of Queensland, I research the biology and genetics of mosquitoes in our region of the Indo-Pacific that delivers fundamental knowledge into the role mosquitoes play in mosquito-borne disease. This work moves across basic and applied research and has advanced our understanding of mosquitoes, their evolution, species’ distributions, permitting better focused mosquito control to be imagined. More recent research involves exploring new environmentally friendly biological control tools such as using the Wolbachia bacterium and genetic modification to combat mosquito-borne disease.

For more detail on my research please see below and at this link http://www.nigelbeebe.com

Dr Chan has a PhD in Genomics and Computational Biology from UQ. He underwent postdoctoral training at Rutgers University (USA) in algal genomics and evolution. He returmed to UQ in late 2011 as one of the inaugural Great Barrier Reef Foundation Bioinformatics Fellows.

Dr Chan joined the School of Chemistry and Molecular Biosciences in 2020 as a group leader at the Australian Centre for Ecogenomics (ACE). His group uses advanced computational approaches to study genome evolution and develop scalable approaches for comparative genomics.

Evolutionary and ecological genomics of marine invertebrate animals.

Animals evolve because their genomes need to respond to the constantly changing environment presented by both their external habitat and their internal microbial symbionts. Over evolutionary time, these different factors interact during development, when the animal body plan is being established, to generate the extraordinary animal diversity that graces our planet. In ecological time, early life history stages must detect and respond to the precise nature of their environment to generate a locally-adapted functional phenotype. Using coral reef invertebrates from phyla that span the animal kingdom, we study these gene-environment interactions using genomic, molecular and cellular approaches combined with behavioural ecology in natural populations. We work mostly with embryonic and larval life history stages of indirect developers, as these are crucial to the survival, connectivity, and evolution of marine populations. When not immersed in the molecular or computer lab, we are lucky enough to be immersed in the ocean, often in beautiful places!

Plant viruses and horticultural crop improvement

Dr Dietzgen is internationally recognised for his work on plant virus characterisation, detection and engineered resistance. Before joining UQ, Dr Dietzgen was a Science Leader in Agri-Science in the Queensland Department of Employment, Economic Development and Innovation. He previously held research positions at the University of Adelaide, University of California, Cornell University and University of Kentucky. Dr Dietzgen’s research interests are in molecular virus-plant-insect interactions, virus biodiversity and evolution, and disease resistance mechanisms. His focus is on the biology of RNA viruses in the family Rhabdoviridae and the molecular protein interactions of plant-adapted rhabdoviruses and tospoviruses. He has published extensively on plant virus characterisation and genetic variability, RNAi- mediated virus resistance and diagnostic technologies with 20 review articles and book chapters and over 65 peer-reviewed publications.

Genetics of mental health (new research)

We are using the genetic model organism, C. elegans, do investigate the genetic basis of both normal and disordered behaviour. Our current interests are identifying the genes responsible for anxiety and depression as well as the genes for eating disoders and addiction. Using C. elegans as a model organism will also allow us to study gene function as it relates to behaviour.

Molecular mechanisms of phosphine resistance (other research)

Genetic mapping of oxidative stress resistance genes. The fumigant phosphine disrupts oxidative metabolism, resulting in the production of reactive oxygen intermediates. This causes the premature ageing and death of targeted pests. Insect pests of stored grain in Australia now exhibit resistance to phosphine at levels more than 200 times the normal lethal dose.

We have genetically mappedf and identified the genes responsible for phosphine resistance in tall major insect pests of stored grain. We are using a systems biology approach in the model organism C. elegans to understand the molecular basis of phosphine action. Our genetic studies have recently shown that resistance to phosphine is associated with an extension of lifespan

The molecular evolution of cytochrome P450 Enzymes: biological catalysts of unprecedented versatility.

Cytochrome P450 enzymes (CYPs, P450s) especially those responsible for drug metabolism in humans, are the unifying theme of the research in our lab. These fascinating enzymes are catalysts of exceptional versatility, and functional diversity. In humans they are principally responsible for the clearance of a practically unlimited variety of chemicals from the body, but are also critical in many important physiological processes. In other organisms (plants, animals, bacteria, fungi, almost everything!) they carry out an unprecedented range of functions, such as defense, chemical communication, neural development and even pigmentation. P450s are involved in the biosynthesis of an unequalled range of potent, biologically active natural products in microbes, plants and animals, including many antibiotics, plant and animal hormones, signalling molecules, toxins, flavours and fragrances. We are studying how P450s have evolved to deal with novel substrates by reconstructing ancestral precursors and evolutionary pathways, to answer such questions as how did the koala evolve to live on eucalyptus leaves, a toxic diet for most mammals.

The capabilities of P450s are only just coming to be fully recognized and structural studies on P450s should yield critical insights into how enzyme structure determines function. For example, recently we discovered that P450s are present within cells in the Fe(II) form, a finding that has led to a radical revision of the dogma concerning the P450 catalytic cycle, and has implications for the control of uncoupling of P450 activity in cells. Importantly, the biotechnological potential of P450s remains yet to be exploited. All of the specific research themes detailed below take advantage of our recognized expertise in the expression of recombinant human cytochrome P450 enzymes in bacteria. Our group is interested in finding out how P450s work and how they can be made to work better.

Artificial evolution of P450s for drug development and bioremediation: a way of exploring the sequence space and catalytic potential of P450s. The demonstrated catalytic diversity of P450 enzymes makes them the ideal starting material for engineering sophisticated chemical reagents to catalyse difficult chemical transformations. We are using artificial (or directed) evolution to engineer enzymes that are more efficient, robust and specialized than naturally occurring enzymes with the aim of selecting for properties that are commercially useful in the areas of drug discovery and development and bioremediation of pollutants in the environment. The approach we are using also allows us to explore the essential sequence and structural features that underpin all ~12000 known P450s so as to determine how they work.

Synthetic biology of enzymes for clean, green, solar-powered chemistry in drug development, bioremediation and biosensors. We have identified ancestral enzymes that are extremely thermostable compared to their modern counterparts, making them potentially very useful in industry, since they can withstand long incubations at elevated temperatures. They can be used as ‘off the shelf’ reagents to catalyse useful chemistry, such as in in drug discovery and development, fine chemicals synthesis, and cleaning up the environment. Working with drug companies, we are exploring how they can be best deployed in chemical processes and what structural features make them efficient, robust and specialized. We are also immobilizing P450s in virus-like-particles as ‘designer’ reagents that can be recovered from reactions and reused. To make such processes cheaper and more sustainable, we are using photosynthesis to power P450 reactions for clean, green biocatalysis in microalgae.

Biosketch:

After graduating from UQ with first class Honours in Biochemistry, Elizabeth took up a Royal Commission for the Exhibition of 1851 Overseas Scholarship to pursue doctoral work at Oxford University then undertook postdoctoral work at the Center in Molecular Toxicology and Department of Biochemistry at Vanderbilt University School of Medicine with Prof. F.P. Guengerich. She returned to UQ in 1993 to take up a position in Pharmacology and joined the School of Chemistry and Molecular Biosciences in 2009 as a Professor of Biochemistry.

I am a developmental neuroscientist and bioinformatician interested in the molecular evolution of the mammalian brain. I completed a PhD on the molecular development of vasculature in the primate retina at the Australian National University, followed by a postdoctoral position at the Institut de la Vision in France that was supported by a NHMRC CJ Martin fellowship, where I investigated the role of guidance factors in the formation of commissural neurons within the mammalian hindbrain. My current research focuses on the development and evolution of the mammalian forebrain, in particular understanding the regulatory mechanisms and molecular evolutionary processes that control specification of cortical neuron subtypes.

Bio

Dr. Yang Liu is an evolutionary geneticist, currently working at the University of Queensland (UQ) as a Research Fellow. Prior to UQ, he obtained a PhD from the University of British Columbia (UBC) and did a postdoc research at UBC and University of Cambridge. He is broadly interested in the eco-evolutionary dynamics of plant populations that have undergone environmental heterogeneity over spatiotemporal scales. The goal of his research is to increase our understanding of the impacts of major episodes in plant demography and life histories on trait evolution and to foster sustainability. He tackles research questions at the interface between ecology and evolutionary biology with the integration of population genetics and quantitative genomics to elucidate the ecological and genetic basis of phenotypic traits and biological adaptation.

Currently, he leverages available Arabidopsis natural accessions across its geographic distribution range, coupled with their genomic data, to perform common-garden and divergent selection experiments. From these he aims to dissect features of the genetic architecture of traits and to reveal their relationships to environmental conditions. He is focusing on the shoot branching phenotype and its associated traits including flowering timing.

ECO-EVO-GENOMICS TEAM

Ongoing Projects

Three PhD positions available in 2023-2025

Project 1: Unification of selection and inheritance informs adaptive potential for generations to come (Applications open in 2023; CLOSED)

Natural selection acts on phenotypes and produces immediate phenotypic effects within a generation. In this short-term process, some phenotypes are more successful than others. Use of single traits for selection analysis could generate opposing outcomes and cannot predict how selection operates on an organism. In contrast, multivariate selection in trait combinations utilizes the attribute of functional integrations to reveal how selection works in a multi-dimensional trait space. Selection is an important force driving evolution but not equal to evolution; the latter leads to changes in genetic variation. Only through assessment of the evolutionary responses of phenotypes can we understand the transmission of such selection from one generation to the next. How does selection occurring within a generation affect evolution across generations? In the project, we aim to address the question by unifying the two processes to forecast evolutionary potential in relation to selection. To that end, we partition genetic variance into components based on an experimental design, employ experimental evolution to estimate additive genetic variance-covariances (G) on quantitative scales and evaluate G-matrix evolution. We eventually hope to elucidate how populations subjected to artificial selection move along evolutionary trajectories and whether there are genetic constraints making the fitness optimum evolutionarily inaccessible.

Project 2: Genetic and ecological bases of shoot branching divergence across Arabidopsis species-wide accessions (Applications open in 2024)

Spatial patterns of genetic variation are shaped by environmental factors, topological features, and dispersal barriers. As a result, we often can identify population genetic structure stratified by geographic locations or ecological niches, the drivers of population isolation by distance or the environment, clinal genetic variation over space in alignment with gradually varying environment gradients, and adaptive genetic variation in relation to environmental variables. At the ecological level, assembly rules uncover the coordination of phenotypic traits along environmental clines. Tradeoffs between traits represent the consequence of environmental filters and reflect adaptation to environmental heterogeneity. For example, three fundamental adaptive strategies are delineated by a CSR theory, that is, Competitors, Stress-tolerators, and Ruderals. As such, ways of genetic and phenotypic assemblage over space and throughout time point to a role for natural selection driven by spatially varying environmental conditions to maintain genetic variation that confers natural variation in phenotypes. In this project, we focus on an important agronomic trait – shoot branching – due to its important contribution to the overall shoot architecture of a plant and being a potential target for yield optimization. We aim to dissect features of the genetic architecture of the trait and to reveal its relationships to environmental conditions. We integrate geographic, environmental, and genomic data from the 1001 Arabidopsis Genomes Project, coupled with the branching phenotype measured in selected accessions and then forecasted for the rest of the 1001 accessions using machine-learning models, to investigate the ecological relevance and genetic underpinnings of branching divergence across the Arabidopsis species-wide accessions. Our study has implications for enhancing our understanding of the genetic and ecological basis of shoot branching divergence and the potential for generating novel knowledge for improving phenotypic predictability.

Project 3: Dimensionality, modularity, and integration: Insights from the architecture features of pan-genomes, pan-transcriptome, pan-epigenomes, and pan-chromatin (applications open in 2025) Application Portal ALSO ACCEPTING EXPRESSION OF INTEREST FROM INTERNATIONAL APPLICANTS

Organisms are functionally integrated systems, where interactions among phenotypic traits make the whole more than the sum of its parts. How is a suite of traits assembled into an adaptive module? How is an intramodule rewired to form a regulatory network? What is the persistence and stability of a module under exposures to perturbations triggered by altered interactions between the response to disparate environmental conditions or between the responses of multiple traits to the same environment? What constrains modules to vary independently, reflecting the integration and canalization of evolutionary trajectories? In this project, we utilize a compilation of pan-genomes, pan-transcriptome, pan-epigenomes, and pan-chromatin resources of Arabidopsis thaliana to uncover how dimensionality, modularity, and integration are organized at different omics levels including genetic polymorphisms, structural variants, RNA isoforms, expression abundance, epigenetic imprinting, and chromatin accessibility. Ultimately, we apply such functional elements to multivariate genomic selection, in the hope of enhancing multilayered omics-enabled prediction.

In The Ortiz-Barrientos Lab we seek to understand how natural selection drives the origin of traits and new species. We combine empirical and theoretical approaches from across multiple disciplines.

We are located in beautiful Brisbane, Australia, in the School of The Environment at The University of Queensland.

Please explore our pages to learn about research, culture, and the team of scientists that bring their passion and creativity to discovering how nature works.

I am a molecular virologist and postdoctoral research fellow in Prof. Alexander Khromykh's laboratory, specialising in virus evolution, virus bioinformatics, and reverse genetics.

My research journey began with a Bachelor of Science, First Class Honours in Molecular Biology from The University of Queensland (2015). I then pursued my PhD (2016-2021) at UQ's School of Biology under Prof. Sassan Asgari, where I analysed the virome and microbiome of Aedes aegypti and Aedes albopictus mosquitoes, focusing on their interactions with Wolbachia pipientis infections.

Since 2021, I have been a postdoctoral researcher in Prof. Alexander Khromykh's RNA Virology lab. Here, I contributed to developing the SARS-CoV-2 circular polymerase extension reaction (CPER) reverse-genetics methodology. As a physical containment 3 (PC3) researcher, I examine the virological properties of Flaviviruses and SARS-CoV-2 viruses under stringent PC3 conditions. Recently, with support from Therapeutic Innovation Australia and the Australian Infectious Diseases Research Centre, I have been utilising the Kunjin virus replicon system as a versatile and durable self-replicating RNA platform for vaccine and protein replacement therapy.

Beyond my virology work, I actively provide bioinformatics and phylogenetics support within UQ and internationally. Let's connect if you’re interested in collaborating on differential gene and ncRNA expression analysis, ATAC-sequencing, ancestral state prediction, virus discovery, or microbiome analyses.

I am also on the organising committee of MicroSeq (2023-2024), an Australasian Microbiology conference focused on microbial sequencing promoting PhD students and early career researchers. Additionally, I am an incoming Ex Officio member of the Australian Society for Microbiology (ASM) Queensland branch.

Dr Shapter's background was originally in Agricultural Science and higher education which evolved to the completion of her PhD in molecular genetics in 2008. Prior to her current appointments she was the senior researcher on ARC linkage, Australian Flora Foundation and RIRDC research grants looking at the genetic foundations of domestication and adaptation in Australian native grasses. She supervised two HDR students and has a strong publication record in this field. Her research interests centre on identifying and developing practical applications for gene sequencing. Fran is passionate about teaching and has worked as a facilitator commercially and trained early career researchers and PhD candidates in Project Management, IP and commercialisation and Leadership. She was a participant in the 2020 summit and was appointed to the federal advisory Rural R&D Council in 2009. Dr Shapter was also a sitting member of the Office of the Gene Technology Regulator's Ethics and Community Consultative Committee, 2016-2020.

Fran began tutoring at the UQ School of Veterinary Science in 2011, in large animal production, parasitology and microbiology. Since then she has held a variety of teaching, research and professional roles based around project management, curriculum design and blended learning design. She was the project manager for a Scholarship of Teaching and Learning (SoTL) grant which developed 40 vertically and horizontally integrated, online, adaptive tutorials for veterinary science students and was co-author on the manual developed by this project. She assisted with the development of a new flexible delivery laboratory animal science course in 2015 and delivers 5 weeks of online learning units into this course currently. She has been part of the SoTL research and evaluation associated with both these projects and has reported outcomes at University showcases annually since 2016.

In 2017 Fran became the new Student Clinical Skills Hub Coordinator, a purpose-built, state-of-the-art self-directed learning facility for students of veterinary science. Whilst undertaking this role student usage, resource availability and online support for the Hub has increased more than tenfold. Fran's aim is to provide a safe, authentic, self-directed learning environment where students can practice their clinical skills in accordance with individual competences, beyond the scheduled contact hours of their programs and further enhance their capacity for self-directed, lifelong learning whilst acknowledging the vast array of qualifications, previous training, life experience and cultural backgrounds each student brings with them to the Hub.In 2020 Fran recieved a UQ Teaching Excellence Award due to the demonstarted impact of the SVS Student Clinical Skills Hub.

In 2019 Fran was appointed as a Lecturer in Veterinary Science, while continuing her role as the Hub's coordinator. She continues to maintain her teaching roles into the veterinary program in animal handling, animal production, reproduction, microbiology, parasitology and plant identification. Fran has an additional role in the School with regard to asissting with the design, development and integration of blended learning resources, after working with the Science faculties blended learning design team in 2018. However her SoTL portfolio is best showcased by the development of the online learning community and training resources she has developed for the Student Clinical Skills Hub. As of June 2021, Fran has also taken on the role of the School of Veterinary Science Honours Program Coordinator.

My research interests are centred around the structure and function of venom and silk polypeptides produced by arthropods, and their use in biotechnology and medicine. I am a Postdoctoral Fellow in the King laboratory in the Institute for Molecular Bioscience, the University of Queensland, Australia. Currently, I am investigating the composition, function and evolution of neglected insect venoms produced by assassin bugs (Hemiptera: Reduviidae), robber flies (Diptera: Asilidae) and nettle caterpillars (Lepidoptera: Limacodidae).

I have a keen interest in the evolutionary relationships that underpin symbioses, particularly those involved in plant disease. There are countless examples of how diseases have impacted on different crops throughout history, and this is an ongoing issue that deleteriously impacts food security. My research involves developing a better understanding of the epidemiology of plant diseases and pests, and delivering improved diagnostics and field management. Working with collaborators and international experts, my work involves research on a broad range of plants that are affected by bacteria, fungi, oomycetes and viruses. I have a strong interest in the biotic factors that govern soil health and the methods by which we can promote the development of beneficial microbial communities.