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Dr. Joan Li is a Senior Lecturer and a Research Fellow with an established national and international reputation at The University of Queensland. She holds both an MD and a PhD, blending clinical and scientific expertise, which provides her with a unique perspective on research and education. While establishing an emerging profile in medical education, she maintains engagement in discipline-related biomedical research through collaboration and supervision.

With over seven years of teaching experience, Joan has actively engaged in face-to-face teaching in biomedical science and medicine courses, contributed to curriculum design, development, and course coordination for both undergraduate and postgraduate programs. She brings her strong analytical skills and critical thinking abilities, honed through her medical and biomedical research background, to her teaching practices. Driven by a genuine passion for teaching, Joan continuously strives for excellence, with specific interests in assessment, curriculum design, development and student learning experience. She has implemented innovative teaching methods, designed diverse and inclusive curricula, created new learning activities, and fostered student engagement as learning partners, with a consistent goal of improving curriculum quality and enhancing student learning outcomes.

Leveraging her medical knowledge, extensive experience in biomedical research, and growing understanding of medical education, Joan is committed to developing medical students into critical thinkers and lifelong learners with a genuine appreciation for medical practice and medical research, enabling them to better serve an ever-changing society. Drawing upon her extensive experience in developmental biology and physiology, particularly in cardiac and renal research, Joan actively supervises higher degree research students and continues to make significant contributions to discipline-related research through publications and collaborations.

Dr. Joan Li is a versatile academic professional with a rich background in biomedical research and an emerging presence in medical education research. Her dedication to teaching and learning, combined with her impressive track record in both disciplines, makes her a valuable asset to The University of Queensland and the broader academic community.

Dr. Guoquan Liu has more than ten years experience in sorghum tissue culture and genetic transformation. He developed a highly efficient sorghum particle transformation system in 2012. Since then, hundreds of transgenic plants have been regenerated from tens of constructs that are invoved in plant disease resistant genes (e.g. Lr34), report gene (gfp), specific-promoters (e.g. alpha- beta- kafirin, A2, LSG), G proteins etc.. He has trained many students how to transform sorghum including honor students, master students, and PhD students.

He has focused on improving sorghum grain yield and grain quality through biotechnologies including genetic transformation, genome-editing, synthetic biology, and plant apomixis.

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

Three PhD positions available in 2023-2025

Ongoing Projects

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; CLOSED)

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.

As an evolutionary quantitative geneticist, I conduct research that aims to extend our understanding of how genetic variation determines the capacity of populations to adapt. Over the 20+ years of my research career, I have designed experiments in species ranging from freshwater fish to Drosophila fruit flies. My research group uses a combination of statistics and machine learning to answer questions about the nature of genetic variation in complex traits, like swimming speed, wing shape and sex pheromones. This fundamental knowledge underpins predictions of the rate at which individual traits within the complex, multi-trait phenotype of organisms can evolve. We are particularly interested in understanding how historical adaptation might affect the ability of populations to adapt to changing conditions now and into the future. I’m interested in bringing evolutionary quantitative genetic tools to answer questions about natural and manipulated evolution in non-model species, in complex natural environments. I am passionate about training researchers in genetics and statistics, foundational skills for a range of careers addressing both applied and fundamental questions. I teach these skills to undergraduate and coursework Masters students, as well as research students ranging from undergraduate projects, through Honours and PhD.

I am a basic science researcher with training in cell biology, genetics and research translation. My research investigates the female reproductive system by focusing on the contribution of individual cells. I aim to understand the influence of genetic architecture, differentiation and maturation on these individual cells and how this contributes to changes in the microenvironment that can contribute to disease initiation and progression.

After the completion of my PhD in 2008 at the University of Queensland, I undertook post-doctoral studies at the University of Bern, Department of Biomedical Research (DBMR), focusing on endometriosis, ovarian and endometrial cancer. I curated patient samples from clinical research trials to investigate inflammatory and metabolic components of reproductive tissue and disease and began developing patient-derived models of the endometrium. I established a relationship between endometriosis lesions, nerves and pain and how this interaction was mediated by inflammation. I further developed patient-derived in vitro models to understand the interaction between inflammation and hormonal response of endometriotic lesions and how this could be utilized to target current and novel treatments. On returning to Australia in 2016 I joined the Genomics of Reproductive Disorders laboratory to integrate genetic background into patient-derived in vitro models. I established the Endometriosis Research Queensland Study (ERQS) in collaboration with the Royal Brisbane and Women’s Hospital (RBWH) and extended in vitro models into complex multi-cellular assembloids (combinations of organoids and surrounding stromal cells).

Bryan is a graduate in medicine from the University of Queensland and holds a BA (Hons) degree in philosophy from the University of Western Australia. A medical specialist in psychiatry, he is a clinician researcher, who is Conjoint Professor at the Queensland Brain Institute, University of Queensland, and Director of Genetics at the Queensland Centre for Mental Health Research. His primary research interest is the molecular genetics of schizophrenia, and holds a MD degree (University of Queensland) in this field. Since 1990, he has conducted studies, with national and international collaborators, to identify susceptibility genes for this disorder. He is the recipient of grants from the Australian NHMRC and the US NIMH.

The primary research goal is to identify and functionally characterise susceptibility genes for schizophrenia and related disorders. A special focus is on the study of large collaborative samples and ethnically homogeneous populations. Key methodologies used in the lab include genome-wide association studies, next-generation sequencing, transcriptome profiling of post-mortem brain samples, neurocognitive and neuroimaging phenotyping and induced pluripotent stem cells.

Current areas of interest include pharmacogenomics of clozapine treatment response, whole exome sequencing focused on de novo mutations, and the neuroimmunology of schizophrenia

Dr Moyle’s laboratory (www.moylelab.com) uses cutting edge technologies for the synthesis of peptides, protein expression, and protein semi-synthesis to gain insights into the functional roles played by various biochemical pathways, to engineer better protein and peptide therapeutics, and to improve the delivery characteristics of various therapeutic molecules. Specific current areas of interest are detailed below:

1. Subunit Vaccine Development: methods to develop improved vaccines through the combination of recombinant and synthetic approaches to improve immunopotency and tailor immune responses (links to reseach articles on semisynthetic vaccines and peptide vaccines; reviews on vaccine development).
2. Delivery Systems for Nucleic Acid-Based Molecules: multi-component synthetic and recombinant approaches to improve the cellular uptake, and targeted delivery of various oligonucleotide molecules (e.g. siRNA, mRNA, pDNA and CRISPR-Cas9) as an exciting approach to treat or prevent various diseases (links to research articles and reviews).
3. Deciphering the Roles of Post-Translational Modifications: The combination of peptide synthesis and protein semisynthesis to enable the production of large amounts of site-specifically modified species, that can be used to deconvolute the roles played by various post-translational modifications (links to research articles).
4. Peptide/Protein Drugs and Delivery: The study of methods to improve the delivery characteristics of peptide/protein drugs (e.g. poor oral absorption, instability to chemical/enzymatic degradation, and the inability to reach their site/s of action) through chemical engineering approaches.
5. New Approaches for Superbugs: the development of antivirulence approaches, and formulations (e.g. various types of nanoparticles - silver, protein, mesoporous silica), which reduce the ability for microbes to cause disease, and make them more readily treated with antimicrobials, by providing access to synergistic combinations, and reducing the risk of antimicrobial resistance.

Information for Potential Students:

The Moyle lab considers applications from potential students and postdoctoral fellows with an interest in: i) infection control (including subunit vaccine and antimicrobial development); ii) delivery systems for peptide therapeutics; iii) targeted delivery systems; iv) studying the function of posttranslational modifications; and v) delivery systems for nucleic acid-based therapeutics (e.g. siRNA, shRNA, miRNA, mRNA, pDNA and CRISPR-Cas9). If you are interested in working in any of these areas please feel free to contact Dr Moyle (p.moyle@uq.edu.au). Please ensure that you supply an up to date CV; describe why you would like to work in the Moyle lab; provide a listing of publications (preferably with impact factors and citation counts); and indicate what skills you would bring to the lab. Detailed information on our laboratory is available at www.moylelab.com. Preference will be given to students and postdoctoral fellows who have their own funding.

Dr Moyle Biosketch:

Dr Moyle (H-index 30, >2600 citations; >95 publications; 13/8/2024; Google Scholar, ORCID, ResearcherID, and Publons profiles) received a PhD (Dec 2006) and a Bachelor of Pharmacy (Hons I) (Dec 2001) from The University of Queensland (UQ); graduated from the Pharmaceutical Society of Australia pre-registration pharmacist-training course (Nov 2002); and is registered with the Pharmacy Board of Australia. He currently works as an Associate Professor in the UQ School of Pharmacy, where he has been based since 2014.

Dr Moyle works in the fields of medicinal chemistry, chemical biology, and drug formulation, investigating subunit vaccine development, outcomes associated with histone post-translational modifications, and methods to improve the delivery characteristics of oligonucleotide (e.g. siRNA and pDNA), peptide, and protein therapeutics. During his PhD, Dr Moyle developed methods that enabled the synthesis of pure, lipid adjuvanted peptide vaccines, using advanced chemical ligation techniques. In addition, the conjugation of mannose to combined prophylactic/therapeutic human papillomavirus type-16 vaccines, to target dendritic cells, was demonstrated to significantly improve vaccine anti-tumour activity. This work, conducted with leading researchers at the QIMR Berghofer Medical Research Institute (Prof Michael Good & Dr Colleen Olive), established Dr Moyle’s national and international profile in the field of vaccine development, resulting in 11 peer reviewed papers, including top journals in the field (J Med Chem; J Org Chem), as well as 6 review articles and 2 invited book chapters.

Dr Moyle undertook his postdoctoral training in the laboratory of one of the world’s premier chemical biologists, Professor Tom Muir (the Rockefeller University, NY, USA; now at Princeton University, NJ, USA). During this time he developed an extensive knowledge of techniques for protein expression, bioconjugation, bioassays, and proteomics, which represent an essential skill set required for this proposal. As part of this work, Dr Moyle developed novel synthetic routes to generate site-specific ADP-ribose conjugated peptides and proteins. This research was hailed as a major breakthrough in the field, leading to several collaborations, and an exemplary publication in the prestigious chemistry journal JACS. This vast body of work identified the enzyme (PARP10) responsible for mono-ADP-ribosylation of histone H2B, and demonstrated interactions between this modification and several proteins, including BAL, which is associated with B cell lymphomas. In addition, a number of robust chemical methods were developed to enable the synthesis of a complete library of methyl-arginine containing histones, which were incorporated into synthetic chemically-defined chromatin to investigate the site-specific effects of arginine methylation on histone acetylation. This work led to a collaboration with colleagues at Rockefeller to investigate the effects of histone arginine methylation on transcription.

Teaching:

Dr Moyle teaches into the following subjects in the UQ School of Pharmacy.

• PHRM3011 (Quality Use of Medicines) - course coordinator
• PHRM4021 (Integrated Pharmaceutical Development)
• PHRM3021 (Dosage Form Design)
• PHRM2040 (Drug Discovery)

Awards:

2016 - Health and Behavioural Sciences (HABS) faculty commendation for Early Career Citations for Outstanding Contributions to Student Learning (ECCOSL)

2015 - ChemMedChem top 10 cited article of 2013 (link)

2014 - Highest ranked NHMRC development grant (2013; APP1074899)

2013 - Institute for Molecular Biology (IMB) Division of Chemistry and Structural Biology Prize

I completed a PhD in Neuroscience with Jack Pettigrew (FRS) at Vision, Touch & Hearing Research Centre followed by an NHMRC Clinical Research Fellowship at Alfred Health & Monash University.

Back in QLD I'm continuing a transdisciplinary research & innovation program to Bring Discoveries of the Brain to Life!

I'm currently focused on developing novel MedTech Biotech diagnostics & therapeutics for enhancing human performance, recovery & resilience with the following projects:

[1] Precision Pain Medicine — the largest genetic study of persistent (chronic) pain in Australia, in collaboration with QIMR Berghofer & Monash University, aims to identify pharmacogenomics causal pathways for the design of personalised therapeutics & effective early intervention approaches (e.g., screening, education, prevention).

[2] Brain Switcha — A digital transdiagnostic biomarker and cloud-based large-scale population phenotyping & analytics platform to improve early intervention strategies in sleep & mental health conditions (esp. at-risk youth cohorts) and recruitment screening for Defence forces.

[3] VCS — vestibulocortical stimulation: A simple, inexpensive, non-invasive & non-pharmacologic neurotherapeutic treatment technique for fibromyalgia (with US colleagues) and other centralised pain syndromes, sleep apnoea, dementia & mental health conditions (e.g., depression, PTSD, bipolar disorder).

I also have >5 years professional services experience providing specialist research performance evaluation, consultation, reporting & training workshops that successfully delivered several major strategic priorities to a large internal & external client base — such as organisational unit leaders/managers at multiple levels (e.g., Centre/Department) and senior executive business missions for national/international strategic partnerships. This work includes mapping, monitoring & benchmarking of research capacity, capabilities/strengths, gaps & collaboration networks (e.g., clinical, corporate & government) across diverse disciplines for Annual & Septennial Departmental Reviews (e.g., patent, policy & clinical guideline citations; external stakeholder engagement including media); ARC Engagement & Impact assessments; and workforce capability development (e.g., recruitment for senior leadership positions and ranking of NHMRC/ARC funding applicants).

In particular, I enjoy meeting & connecting people with a shared vision & commitment towards building innovative & sustainable public-private partnerships to deliver meaningful solutions for the wider community.

Dr Quan Nguyen is a Group Leader at the Institute for Molecular Bioscience (IMB), The University of Queensland. He is leading the Genomics and Machine Learning (GML) lab to study neuroinflammation and cancer-immune cells at single-cell resolution and within spatial morphological tissue context. His research interest is about revealing gene and cell regulators that determine the states of the complex cancer and neuronal ecosystems. Particularly, he is interested in quantifying cellular diversity and the dynamics of cell-cell interactions within the tissues to find ways to improve cancer diagnosis or cell-type specific treatments or the immunoinflammation responses that cause neuronal disease.

Using machine learning and genomic approaches, his group are integrating single-cell spatiotemporal sequencing data with tissue imaging data to find causal links between cellular genotypes, tissue microenvironment, and disease phenotypes. GML lab is also developing experimental technologies that enable large-scale profiling of spatial gene and protein expression (spatial omics) in a range of cancer tissues (focusing on brain and skin cancer) and in mouse brain and spinal cord.

Dr Quan Nguyen completed a PhD in Bioengineering at the University of Queensland in 2013, postdoctoral training in Bioinformatics at RIKEN institute in Japan in 2015, a CSIRO Office of Chief Executive (OCE) Research Fellowship in 2016, an IMB Fellow in 2018, an Australian Research Council DECRA fellowship (2019-2021), and is currently a National Health and Medical Research Council leadership fellow (EL2). He has published in top-tier journals, including Cell, Cell Stem Cell, Nature Methods, Nature Protocols, Nature Communications, Genome Research, Genome Biology and a prize-winning paper in GigaScience. In the past three years, he has contributed to the development of x8 open-source software, x2 web applications, and x4 databases for analysis of single-cell data and spatial transcriptomics. He is looking for enthusiastic research students and research staff to join his group.

Dr. Nguyen is an expert in applying long-read Oxford Nanopore Sequencing Technologies (ONT) in agriculture, particularly livestock and other sectors. Her groundbreaking contributions include being the pioneer in sequencing the genomes of Brahman and Wagyu cattle, developing an innovative epigenetic clock for age prediction in cattle, and successfully implementing ONT portable sequencers for Blockchain traceability systems in Australia.

As a leader in the field, Dr. Nguyen spearheads the use of ONT long-read technology to scaffold genome assemblies in livestock, plants, protists, and insects. Her multidisciplinary expertise in molecular biology, advanced genomics, and animal sciences also empowers her to explore causative markers for commercial SNP arrays and identify significant DNA variants from low-coverage sequencing data sets.

Dr. Nguyen's exceptional achievements and expertise have been acknowledged through the prestigious ARC Industry Fellowship, recognising her as a promising early career researcher. Her work has significantly contributed to advancing genomic research in agriculture and has opened new avenues for utilising ONT sequencing technologies across diverse domains.

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.

Career Summary: 2009: PhD, University of Michigan, USA with training in cardiac physiology, modelling myocardial ischemia in vivo and in vitro, and development of therapeutic approaches for myocardial ischemia; 2009–2015: Postdoctoral Research Fellow, University of Washington, Institute for Stem Cell and Regenerative Medicine, USA with training in stem cell biology, genomics, genome editing, and cell therapeutics for ischemic heart disease; 2015–current: Group Leader, University of Queensland (UQ), Institute for Molecular Bioscience; 2022-current: Associate Professor, UQ; 2018–2021 and 2023-2026: National Heart Foundation Future Leader Fellow. Dr. Palpant’s research team has expertise in human stem cell biology, computational genomics, and cardiac physiology, which enables them to translate outcomes from cell biology and genomics to disease modelling, drug discovery, and preclinical modelling.

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 Cassandra Pattinson research centres around exploring the effects of sleep and circadian rhythms on health, wellbeing, and recovery across the lifespan. Dr Pattinson is a Senior Research Fellow at the Child Health Research Centre (CHRC) and the ARC centre of Excellence for the Digital Child. The Digital Child aims to support children growing up in the rapidly changing digital world, and provide strong evidence and guidance for children, families, educators, government and other concerned with children’s wellbeing. Her work has been supported by the ARC (including recently awarded an ARC Discovery Early Career Award, 2025), NHMRC, NIH and the DSTG, as well as the Australian Federal Government and Queensland Government.

Her research has involved a range of populations from children and adolescents, through to military personnel and athletes. Dr Pattinson's research spans a range of study designs and methodologies, including longitudinal studies tracking large child cohorts (>2000 children), standard observation techniques, survey and individualised standard child assessment, as well as studies employing physiological (actigraphy, spectrometry) and biological (hormones, proteomic, genomic) designs. Dr Pattinson also has a strong track record in research translation, these have included manuscripts in top scientific journals, reports for government and non-government organisations, development of professional development programs, as well as designing and presenting vodcasts and resources (e.g. fact sheets, workshops) to parent groups, young adults, government departments and the early childhood sector.

At CHRC Dr Pattinson is a part of the Community Sleep Health Group. This group collaborates with many other groups around broader issues of sleep and technology, sleep and the environment (including disasters), mental health and wellbeing, pain, disability, and new technologies and approaches.

My research interests have concentrated on the molecular genetic analysis of multigene phenotypes of bacteria encompassing pathogenicity, bacterial degradation of synthetic environmental pollutants, photosynthesis and the synthesis of antitumour antibiotics. My PhD research focussed on plasmids and mapping of the genome of the human pathogen P. aeruginosa (Pemberton,and Holloway, 1972a; Pemberton,and Holloway,1972b;Pemberton and Holloway,1973). I continued this research as a postdoc at UC Berkeley with John Clark in the Department of Molecular Biology in the Wendell Stanley Virus laboratory. I am grateful to Mark Guyer who taught me how to isolate large plasmid DNAs. In Robley Williams lab I learnt how to use the Kleinschmidt and Zahn technique for spreading the plasmid DNA on an electronmicroscope grid and metal shadow the sample to visualise it under an electron microscope; I am grateful to Robley Williams for showing me how to metal shadow my samples (Pemberton,1973; Pemberton and AJ Clark,1973; Miller, Pemberton and Richards,1974;Pemberton,1974;Miller,Pemberton and Clark,1977). After advice from John Clark and when I returned to Australia and took up an appointment with UQ I decided to diversify my research. During my postdoc I worked alongside Anne Emerick who was working with the CAM (camphor degradation) plasmid. John Clark put me on her advisory panel (alongside Mike Doudoroff and Norberto Palleroni) making her my first PhD student. The bacterial degradation of such complex naturally occurring molecules such as camphor required a large number of steps requiring a large number of genes hence a large plasmid. I decided to determine if soil bacteria had evolved plasmids which encoded the degradation of man-made molecules. I chose the synthetic herbicide 2,4-D. My research was the first to identify, isolate and clone genes responsible for the degradation of a man-made molecule –moreover the 2,4-D degradation was encoded by a broad host range plasmid, providing an explanation of how microorganisms rapidly evolve the ability to degrade and recycle a vast array of worldwide synthetic environmental pollutants which cause a range of diseases from cancer to birth defects (Pemberton & Fisher, Nature, 1977). One of the most widely studied microorganisms is the bacterium Ralstonia eutropha JMP134 pJP4 (Hgr) which has an extraordinary ability to degrade and recycle the most complex and most toxic synthetic molecules (Don and Pemberton, J.Bacteriol, 1981;Schmidt et.al.,2011. Catabolic Plasmids.Encyclopedia of Life Sciences). Famously more recent studies have shown that there are genes and gene clusters encoding the degradation of plastics, explosives and chemical weapons of war . Detailed studies of bacterial genes involved in the environmental degradation and recycling of a wide range naturally occurring and synthetic molecules show that degradation genes and degradation gene clusters play a major role in the worldwide carbon cycle.

Photosynthesis is considered the most important biological process on earth. And one of the most intensively studied photosynthetic organisms is the bacterium Rhodobacter sphaeroides. To start the research a local strain of R.sphaeroides, designated RS601, was isolated by Bill Tucker (my first australian PhD student) from a water sample obtained from a roadside ditch in Brisbane (Pemberton and Tucker,1977;Tucker and Pemberton,1978;1979;1980). One of the first discoveries made with this strain was lysogenic conversion to antibiotic resistance by a naturally occurring virus .(JM Pemberton, WT Tucker - Nature, 1977).

Subsequently when this strain was infected withe the broad host plasmid RP1 carrying the mecuric ion transposon Tn501 chromosome transfer occurred. This allowed the construction of the first genetic map of a photosynthetic bacterium(Pemberton and Bowen, J.Bacteriol, 1981). Mapping revealed that the photosynthesis gene cluster was on the main chromosome. Remarkably chromosome transfer occurred from a site right next to the photosynthesis gene cluster with early transfer of the entire cluster into the recipent cell. This provides a potential mechanism for the evolution and spread of photosynthesis genes. A clone bank of RS601 was constructed using pHC79:: Tn5deltaBamH1. This vector allowed cosmid cloning into the BamH1 site of Tn5. These Tn5 cosmid clones were transposed onto the broad host range plasmid pR751. The ability to transfer the entire cosmid clone bank to a wide range of bacteria led to the first cloning and heterologous expression of a carotenoid gene cluster (Pemberton&Harding,Current Microbiology,1986 & 1987).This indicated that genes involved in photosynthesis could be transferred to and expressed in a range of unrelated non-photosynthetic bacteria. Subsequent heterologous expression of carotenoid genes in an increasing variety of plants led to the production of foods enriched in the precursors of vitamin A e.g. Golden Rice (Erik Stokstad, Science Nov 20, 2019) . Vitamin A deficiency is the major preventable cause of blindness in children under 5 years of age; it affects up to 500,000 children each year. Using the same clone bank in mapping experiments in Rhodobacter sphaeroides I observed a few pale colonies in which carotenoid biosynthesis was suppressed. Subsequent detailed analysis of one of these cosmids led to the discovery of the long sought master regulator (PpsR) of bacterial photosynthesis and provided the first detailed insight into the mechanism by which bacterial photosynthesis is regulated at the molecular level (A Gene from the Photosynthetic Gene Cluster of Rhodobacter sphaeroides Induces trans Suppression of Bacteriochlorophyll and Carotenoid Levels in R.sphaeroides and R.capsulatus (R.J.Penfold and JM Pemberton, Current Microbiology, 1991; Sequencing, Chromosomal Inactivation and Functional Expression in E.coli of ppsR a Gene which represses carotenoid and bacteriochlorophyll synthesis in Rhodobacter sphaeroides. RJ Penfold and JM Pemberton. J.Bacteriol May 1994).Early studies by Cohen-Bazire, Sistrom and Stanier (1957) revealed that oxygen and blue light had varying effects on photosynthesis in Rhodobacter. The effect of oxygen was profound. The effect of blue light was more muted. The initial sequencing of ppsR (Penfold and Pemberton, 1994) revealed the presence of only two cys residues suggesting a possible mechanism for the profound effect of oxygen on PpsR repressor activity. Studies of conformational changes/repressor activity of PpsR in the presence and absence of oxygen have produced mixed results(Gomelsky et al.,2000;Masuda and Bauer.,2002). In contrast the muted effect of blue light on photosynthesis appears to be due to the blue light sensitive, anti-repressor AppA. (Gomelsky and Kaplan,1995). It is not known if any other environmental signals modulate PpsR activity.The rhodobacter research led to the construction of pJP5603 which allowed the precise insertion of a defined segment of DNA into a bacterial genome (Penfold and Pemberton,1992 ; Zordan,Beliveau,Trow,Craig and Cormack, 2015). The technique was used to either add functional genes or groups of genes to a precise location in the genome or to precisely target and inactivate individual genes. The site of insertion/mutagenesis is tagged with an antibiotic resistance gene. This process is known as “recombineering” ( Zhang et al., 1988). As with all forms of mutagenesis there are “off target” mutations. The consequences of such ”off target” mutations can range from minimal to extensive.

In a study of a range of genes encoding secreted enzymes involved in the degradation of naturally-occurring biological polymers e.g xylanases, cellulases,amylases, chitinases etc I attempted to obtain secretion genes from Chromobacterium violaceum. Again using the pHC79:: Tn5deltaBamH1 vector used in the study of the photosynthesis genes (Pemberton&Harding,Current Microbiology,1986 & 1987) I constructed a cosmid clone bank of C.violaceum. The clone bank I constructed did not produce secretion genes but instead 2-3 of the clones expressed the intense purple pigmented violacein in E.coli(Pemberton,1986). Subsequent subcloning revealed the gene cluster occupied 8kb and transposon mutagenesis revealed intense blue and intense green intermediates. (Pemberton et.al.,Current Microbiology,1991). I am grateful to Trudy Grossman for the detailed study of this cluster which included sequence analysis and functional characterisation of the violacein biosynthetic pathway (August et al., 2000). The functional analysis of the violacein gene cluster revealed that VioA VioC and VioD belong to the PheA(phenol) /TfdB (2,4-D) group of FAD dependant mono-oxygenases. TfdB is encoded by the 2,4-D degradation gene cluster of the broad host range IncP plasmid pJP4 carried by Ralstonia eutropha JMP134. This provides a link between the degradation of a man-made molecule-2,4-D and the synthesis of an anti-tumour antibiotic-violacein. Remarkably, under certain circumstances this 2,4-D degradation pathway can convert 2,4-D into the well known plant antibiotic-protoanemonin (Blasco,R et al., 1995).In 1983 Burt Ensley , Barry Ratzkin and co-workers (Ensley et al.,Science,1983) discovered that the naphthalene dioxygenase gene from Pseudomonas putida enabled E.coli K12 to synthesise the famous blue dye indigo from tryptophan; a second gene, VioD, from the violacein gene cluster also enabled E.coli K12 to produce indigo (Cheah et al.,Acta Crystallographica,1998). Further studies using the violacein gene cluster led to the development of techniques and vectors that should allow cloning and stable, high level expression of more antibiotic biosynthesis pathways in E.coli K12, particularly pathways from the prolific antibiotic producers the Streptomycetes providing novel antibiotics in the fight against antibiotic resistant pathogens (Sarovich and Pemberton,2007; Philip,Sarovich and Pemberton,2008 & 2009;Ahmetagic & Pemberton, 2010 & 2011;Ahmetagic, Philip ,Sarovich,Kluver and Pemberton,2011).An article published in June 2013 by Stevens and co-workers PLoS ONE 8(5) showed that a native gene cluster from Streptomyces rimosus encoding tetracycline can be directly expressed in E.coli K12.

For the first time researchers have showed the expression of the violacein gene cluster in a eukaryote-the yeast Saccharomyces cerevisiae (Lee et al., 2013). Such a discovery may indicate that the violacein gene cluster can be expressed in organisms which range from microbes to man. It may also indicate that major pathways from microorganisms can be engineered and expressed in a range of eukaryotes. Since violacein is a potent anticancer agent it is of interest to determine if the violacein cluster engineered into bacteria of the microbiome of an animal reduces cancer rates. Alternatively it may be possible to engineer the violacein pathway directly into an animal and observe if cancer rates are reduced. In view of the purported prokaryotic ancestry of eukaryoyic organelles such as mitochondria and chloroplasts ,one possible way of boosting violacein synthesis in eukaryotic cells could be to integrate the violacein gene cluster into organelle DNA.

Finally, violacein is chemically related to the well known anti-cancer drug staurosporine and possesses anticancer, antifungal, anti-parasite, antibacterial and antiviral activities;it might be possible to synthesise structural variants of violacein with more potent activity against various cancers and drug/antibiotic resistant pathogens. Interestingly is now known that violacein producing bacteria associated with the skin microbiome of certain frogs provides some protection against extinction by the worldwide spread of ‘chytrid’ fungus(Harris et.al., 2009). In addition, frogs have been used in cancer studies and may provide a simple model to test the anticancer properties of violacein. Since the violacein gene cluster is expressed in a wide range of bacteria ( Dr D S Philip, personal communication;D.S/Philip.PhD Thesis 2010) and has potent activity against the malarial parasite Plasmodium falciparum and other mosquito borne parasites, there is the possibility that mosquitoes engineered to carry the violacein gene cluster might be resistant to parasite infection. The cluster could be stably incorporated in the genomes of bacteria normally inhabiting the surface or the gut of the mosquito.A recent patent application (United States Patent Application 20170280730) indicates that Chromobacterium introduced into the microbiome of mosquitoes is useful for the prevention of transmission of malaria and dengue virus.In addition, chemical modification of violacein may produce drugs with even higher levels of activity against parasites including the malarial parasite ( Wilkinson et al., 2020). Violacein has activity against the pandemic virus Covid19 and there is some knowledge of its mode of action (Duran et al., 2021). Testing may reveal if it has activity against both Kappa and Delta Covid19 variants.Violacein can inhibit infection by HIV and COVID (Doganci et al., 2022)

• Fellow, American Society for Microbiology
• Fellow, Australian Society for Microbiology

Selected Publications:

• Ahmetagic, Adnan, Philip, Daniel S., Sarovich, Derek S., Kluver, Daniel W. and Pemberton, John M. (2011) Plasmid encoded antibiotics inhibit protozoan predation of Escherichia coli K12. Plasmid, 66 3: 152-158. doi:10.1016/j.plasmid.2011.07.006
• Ahmetagic, Adnan and Pemberton, John M. (2011) Antibiotic resistant mutants of Escherichia coli K12 show increases in heterologous gene expression. Plasmid, 65 1: 51-57. doi:10.1016/j.plasmid.2010.11.004
• Ahmetagic, Adnan and Pemberton, John M. (2010) Stable high level expression of the violacein indolocarbazole anti-tumour gene cluster and the Streptomyces lividans amyA gene in E. coli K12. Plasmid, 63 2: 79-85. doi:10.1016/j.plasmid.2009.11.004
• Philip, Daniel S., Sarovich, Derek S. and Pemberton, John M. (2009) Complete sequence and analysis of the stability functions of pPSX, a vector that allows stable cloning and expression of Streptomycete genes in Escherichia coli K12. Plasmid, 62 1: 39-43. doi:10.1016/j.plasmid.2009.03.002

I graduated from The University of Tasmania, and received my PhD in Developmental Biology from The University of Queensland in 2003. My PhD, performed at the Institute for Molecular Bioscience with Prof. Melissa Little, centred on understanding the cellular and molecular mechanisms underlying embryonic kidney development. My first postdoc was performed with Prof. Christine Holt at The University of Cambridge, UK, where I studied the mechanisms by which axonal growth cones navigate to their targets in the brain, using the frog Xenopus laevis as a model system. In my second postdoctoral position, with Prof. Linda Richards at the Queensland Brain Institute at The University of Queensland, my work focussed on understanding the molecular mechanisms of neural progenitor cell specification in the developing cerebral cortex. In late 2010, I took up a joint position with the Queensland Brain Institute and The School of Biomedical Sciences (SBMS) to continue my research into the mechanisms underlying neural stem cell differentiation. I have held numerous fellowships during my career, including an NHMRC Howard Florey Fellowship, an NHMRC CDF and an ARC Future Fellowship. I currently hold a continuing Teaching and Research position within SBMS, and am currently the Director for Higher Degree Research Training at SBMS.