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!
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
· Senior Staff Specialist (Public Health Medicine), Queensland Health
· Principal Research Fellow, Centre for Clinical Research - University of Queensland
· Adjunct Professor, Griffith University Medical School
RECENT POSITIONS
· General Practitioner, Indooroopilly General Practice
· Senior Staff Specialist (Public Health Medicine), Metro South, Metro North, Central Queensland, and West Moreton Public Health Units (January 2021 to July 2022)
· Director, Queensland Centre for Intellectual and Developmental Disability (to January 2021)
· Senior Medical Officer, Mater Intellectual Disability and Autism Service (to November 2020)
· General Practitioner, Cornwall Street Medical Centre (to November 2020)
Introduction
I am a public health physician, zoologist, epidemiologist, and general practitioner. I commenced my clinical career in Far North Queensland in the early 1990s. I gained experience in Indigenous health, remote health, obstetrics and other areas of medicine. I also completed my specialist training in Public Health Medicine in Cairns in the early 2000s. From 2002 to 2008 I combined clinical work in adult developmental disability medicine at Queensland Centre for Intellectual and Developmental Disability Medicine (QCIDD) with general practice and travel medicine. While working as Senior Fellow at The National Centre for Epidemiology and Population Health (NCEPH), Australian National University (ANU) I managed patients at Interchange General Practice, a clinic specialising in the health of people who use drugs, refugee health, and blood-borne viruses, among other areas. Until the end of 2020 I consulted clinically at the Mater Intellectual Disability and Autism Service and in general practice. I practiced at Indooroopilly General Practice until October 2022.
I've maintained a strong interest in the biological world since my first degree in zoology and via study of vector associations of Ross River virus during my PhD. The biological factors involved in the transmission of arboviruses has remained a particular interest, especially for Ross River virus and dengue. In the case of the former I have published a highly cited review detailing vector associations and reservoir hosts (Harley, Sleigh and Ritchie, Clinical Microbiology Reviews, 2001) and original research on vector associations in Far North Queensland (Harley et al., American Journal of Tropical Medicine and Hygiene, 2001). More recently I have published on rainfall cut-points for outbreak prediction in the Northern Territory (Jacups et al., Journal of Medical Entomology, 2011), and modelling incorporating vegetation and macropod populations (Ng et al., Vector-borne and zoonotic diseases, 2014). I have published modelled projections for populations of Aedes aegypti, the vector of dengue, with climate change (Williams et al., Parasites and Vectors, 2014).
My research scope is broad. My four most highly cited publications (one with over 400 and one over 300 citations, Google Scholar) span arbovirology (Harley, Sleigh and Ritchie, Clinical Microbiology Reviews, 2001), psychiatry (Tyrer et al, Lancet, 2008), disability (Palmer and Harley, Health Policy and Planning, 2011) and climate change and health (Butler and Harley, Postgraduate Medical Journal, 2010).
Qualifications
I hold general and specialist registration as a medical practitioner. I am a Fellow of the Australasian Faculty of Public Health Medicine (Royal Australasian College of Physicians) and the Australian College of Tropical Medicine.
I have a PhD in Tropical Health from the University of Queensland and a Master of Medical Science in Clinical Epidemiology from The University of Newcastle. I have a first class honours degree in zoology from the University of Queensland.
Advocacy, lobbying and consultancies
I've contributed actively to my college, The Royal Australasian College of Physicians (RACP), and faculty, The Australasian Faculty of Public Health Medicine. I have joined working parties on Indigenous health, the health of disabled people (deputy chair), and most recently climate change and health. The work on the second and third working parties resulted in production of RACP position papers. In 2016 I represented the college in meetings with parliamentarians in Canberra on climate change and health. I'm currently a member of college reference groups on the NDIS and on global heating and health.
I represented the Royal Australasian College of Physicians at roundtable meetings on the health of people with intellectual disability, the first on 2 August 2019 (see Microsoft Word - D19-1158817 Roundtable on the Health of People with Intellectual Disability - Summary and Recommendations(2)). The roundtable was convened by the former Commonwealth Minister for Health, Mr Greg Hunt. Subsequent to the roundtable Minister Hunt released a National Roadmap for Improving Health Services for People with Intellectual Disability (see https://www.health.gov.au/initiatives-and-programs/national-roadmap-for-improving-the-health-of-people-with-intellectual-disability).
The Roadmap includes a wide range of measures including short-term measures focused on:
· Programs in Primary Health Networks (PHNs) to improve the capacity and skills of GPs and other primary health services to meet the needs of people with intellectual disability. This will initially be in four PHN lead sites with a view to national rollout after four years.
· Better use of existing Medicare items, including those for annual health assessments of people with intellectual disability.
· Better coordination between the health sector and other sectors such as disability and education.
· Support for people with intellectual disability and their families so that they can make informed decisions about health care and navigate the health care system.
The former LNP Government also committed $19.3 million in initial funding for the first actions in the Roadmap, including:
· $6.6 million to develop a Primary Care Enhancement Program for People with Intellectual Disability
· $6.7 million to improve implementation of annual health assessments for people with intellectual disability
· $4.7 million for curriculum development in intellectual disability health
· $1.4 million to scope and co-design a National Centre of Excellence in Intellectual Disability Health
A report from the Roundtable and the outline of the proposed national Roadmap at https://www1.health.gov.au/internet/main/publishing.nsf/Content/national-roadmap-for-improving-the-health-of-Australians-with-intellectual-disability and the Roadmap itself is abvailable at National Roadmap for Improving the Health of people with Intellectual Disability. The RACGP overview of the budget also lists a commitment for intellectual disability (RACGP | Overview of the Federal Budget 2021-22 (Health) | May 2021). I’ve been invited by the Commonwealth Department of Health to support the scoping and co‑design of models for a national centre of excellence in intellectual disability health (‘national centre’) and have been nominated by my college, the Royal Australasian College of Physicians (RACP), to represent the college through the process.
I've held various consultancies and panel memberships, including with AusAid and WHO.
Supervision
In my time working at The Australian National University (2008-2016) five honours students completed projects under my supervision. All obtained first class degrees. My first student, Melanie Bannister-Tyrrell was awarded a university medal, published her honours research (Bannister-Tyrrell et al., American Journal of Tropical Medicine and Hygiene, 2013), and is now a Senior Epidemiology Consultant to AusVet. Other students completed projects on tuberculosis management in the Torres Strait (Ellen Hart), tuberculosis diagnosis in Thailand (Eileen Baker), hypertension among Thai caregivers (Laura Saville), and mapping of renal disease risk in South Australia (Scott Pearce). I also supervised Ritwika Vinayagam's honours project at the University of Queensland, on diabetes and autism, in 2020.
Current PhD Supervision
· Semira Hailu - The burden of extra-pulmonary tuberculosis in Africa (UQ, associate advisor)
· Wei Qian - Ross River virus in Queensland (UQ, associate advisor)
· Tam Tranh - Road trauma in Vietnam (ANU, associate advisor)
· Cynthia Parayiwa - “Birth outcomes following maternal exposure to severe tropical cyclones in Queensland, Australia” (ANU, associate advisor)
Current Masters Supervision
· Suhasini Sumithra - Modelling Ross River virus in NSW (MPhil, ANU)
Completed PhDs
· Menghuan Song - Psychotropic prescribing to adults with intellectual and developmental disabilities (UQ, principal advisor)
· Sifat Sharmin - Dengue and climate in Bangladesh (ANU, Chair of Panel)
· Ray Lovett - Screening for drug and alcohol use in Indigenous community controlled health organisations (ANU, Chair of Panel)
· Philipa Dossetor - Children's health in Fitzroy Crossing, WA, with a focus on fetal alcohol spectrum disorder (ANU, Chair of Panel initially, then panel member)
· Kerri Viney - Tuberculosis in the South Pacific (ANU, Panel member)
· Lachlan McIver - Climate change and health in the South Pacific (ANU, Panel member, Chair of Panel for completion of PhD)
· Kazi Rahman - Visceral Leishmaniasis in Bangladesh (ANU, Panel member)
· Yani Sun - Tuberculosis in Henan Province, China (ANU, Panel member, awarded ANU "Top Supervisor" award)
· Vicky Ng - Modelling of Ross River virus in NSW (ANU, Panel member)
· Michael Palmer - Disability in rural Vietnam (ANU, Panel member)
Completed Masters
· Tran Tuan Anh Le - Health of Australian adolescents with intellectual disability (MPhil, UQ)
· Alexandra Marmor - MPhil (App Epi; ANU)
· Anna Gibbs - Gram negative sepsis in Queensland children (MPH, UNSW)
Research
I was chief investigator on two NHMRC project grants worth over $2 million while with the ANU. I was CIA for one of these grants, to research weather and dengue virus epidemiology in Far North Queensland. The second grant funded the Thai Health-Risk transition project, a longitudinal study of the health of Thai people living throughout the country. Both projects have produced important publications in my areas of interest including dengue and climate (e.g. Williams et al., Epidemiology and Infection, 2016; Viennet et al., Parasites and Vectors, 2014), disability and health (Yiengprugsawan et al., Asia Pacific Journal of Public Health, 2010), and the health of carers (Yiengprugsawan et al., BMC Public Health, 2012). Fruitful collaborations have arisen from both grants including co-supervision of my PhD student Sifat Sharmin with my NHMRC-funded post-doctoral researcher Elvina Viennet and honours student projects related to the Thai study (Eileen Baker and Laura Saville). Before commencing at ANU I gained research funding from The Royal Australian College of General Practitioners, Rotary, The University of Queensland, and James Cook University.
Major themes in my research are infectious diseases epidemiology, environment and health, and the health of disabled people.
In the first of these I have focussed on arboviruses, particularly Ross River and dengue viruses, but have also published on Chikungunya, Zika, Adenovirus, tuberculosis, and invasive meningococcal disease. Since the publication of my highly cited and wide ranging review on the first of these (Harley, Sleigh and Ritchie, Clinical Microbiology Reviews, 2001; 346 citations, Google Scholar, 16/1/2019) I have remained an authority on this virus. I am first author on the chapter on Ross River virus in the authoritative textbook Hunter's Tropical Medicine and Emerging Infectious Diseases (Harley and Suhrbier, Hunter's Tropical Medicine, 2019). I have also published on vector associations (Harley et al., American Journal of Tropical Medicine and Hygiene, 2001), clinical manifestations (Harley et al., Medical Journal of Australia, 2002), and behavioural risks (Harley et al., International Journal of Epidemiology, 2005). More recently I have published on environmental determinants of risk (Jacups et al., Journal of Medical Entomology, 2011; Ng et al., Vector-borne and zoonotic diseases, 2014). I also have a major interest in dengue and have published on the epidemiology of this important virus in Australia (e.g. Viennet et al., PLoS Neglected Tropical Diseases, 2016; Williams et al., Epidemiology and Infection, 2016) and Bangladesh (Sharmin et al., Transactions of the Royal Society of Tropical Medicine and Hygiene, 2015; PLoS Neglected Tropical Diseases, 2015; Statistical Methods in Medical Research, 2016). I have also published on the epidemiology of tuberculosis in China (e.g. Sun et al., PLoS One, 2017) and the Pacific (e.g. Viney et al., Tropical Medicine and International Health, 2015).
I have a particular focus on environment and infectious diseases (see dengue research in paragraph above; Harley et al., Asia Pacific Journal of Public Health, 2011; Harley et al., Infectious diseases: a geographic guide, 2010). I was an invited speaker on climate change and infectious diseases at the International Congress on Infectious Diseases in Hyderabad, India, during March 2016. I also co-authored, with Colin Butler, a conceptual paper on levels of impact from climate change on health (Butler and Harley, Postgraduate Medical Journal, 2010), and have written on the education of medical students on climate change and health (Green et al., Australian Family Physician, 2009) and impacts of climate change on immune function (Swaminathan et al., Children, 2014). I was invited to, and chaired the Infectious disease ecology and epidemiology stream, for the 2014 Theo Murphy High Flyers think tank, convened by the Australian Academy of Science, on Climate Change Challenges to Health.
When working at QCIDD ealier I led the Australian arm for an international multi-centre RCT on antipsychotic medication for aggressive behaviour in adults with developmental disabilities (Tyrer et al., Lancet, 2008; cited 365 times, Google Scholar, 19/8/2021). I have also researched the economic impact of disability in Vietnam (Palmer et al., International Journal of Health Planning and Management, 2011) and the asssociations of hearing impairment in Thailand (Yiengprugsawan et al., Asia Pacific Journal of Public Health, 2010) and co-authored an international review on models and measurement of disability (Palmer and Harley, Health Policy and Planning, 2011).
Editing and reviewing
I am a section editor for PLoS Neglected Tropical Diseases. I guest edited, with Shamshad Karatela, a special edition of The International Journal of Environmental Research and Public Health entitled "Environmental and Social Influences on Cognitive Development and Function" (https://www.mdpi.com/journal/ijerph/special_issues/cognitive_development). Journals I have reviewed for include Lancet Infectious Diseases, BMC Infectious Diseases, Science, The Medical Journal of Australia, PLoS Neglected Tropical Diseases, and Journal of Applied Research in Intellectual Disabilities.
Teaching
I taught epidemiology and evidence based medicine to medical students at The University of Queensland and ANU from 2002 to 2016. I was invited annually from 2012 to 2015 to teach epidemiology and outbreak control at Institut Pasteur and The Oxford University Clinical Research in Ho Chi Minh City, Vietnam. I was a foundation member of the teaching team for the ANU Master of Public Health (MPH) core subject, Fundamentals of Epidemiology, and have also instructed students on global health and climate change and health in the ANU MPH. In addition I've provided clinical teaching for ANU medical students in general practice and do so currently for third year UQ medicine students rotating to Cornwall Street Medical Centre in their general practice rotation.
I have contributed to building capacity internationally through strong engagement in supervision and teaching. I have supervised students from China, Vietnam, and Bangladesh. I have also taught epidemiology and outbreak control to many students from low income countries in South East Asia as an invited instructor with Institut Pasteur and Oxford University in Ho Chi Minh City annually from 2012 to 2015.
Research Interests
· Infectious disease epidemiology
· Adult developmental disability medicine
· Indigenous health
· Public Health Medicine
Qualifications
· Bachelor of Science, The University of Queensland
· BSc (Hons I Zoology), The University of Queensland
· Bachelor of Medicine and Bachlor of Surgery, The University of Queensland
Insects are commonly infected with viruses. We study the interactions between viruses and their insect or arthropod hosts.
Viruses are obligate parasites, that is, they are completely dependent on the host cell machinery to complete their replication cycle. During infection, viruses commonly cause pathology in the host. For these reasons, viruses and hosts are in a constant evolutionary arms race. The host evolves antiviral mechanisms to prevent virus infection, while the virus adapts to overcome these host responses. Insects are ideal hosts to understand both the host response and the virus mechanisms for controlling the host.
My research group investigates the interactions between viruses and insects, primarily using Drosophila as a model. In this model we can control the genetics of both the host and the virus to tease apart the contribution of each partner to the interaction.
We discovered that a bacterium, Wolbachia, mediated antiviral protection in insects. We have several projects investigating both the mechanisms that protect the insects from virus infection and the impact of this protection on virus transmission.
Research interest: Monitoring ecosystem health of coral reefs and seagrass habitats, integrating field and remote sensing image datasets, and the developing applied cost-effective mapping and monitoring approaches. Developed approaches have been adopted as standard practice globally, making a difference in conservation of these valuable habitats. The long term monitoring studies at Heron and Moreton Bay formed the basis for the development of mapping and monitoring over time and space at local to global scale.
Current projects:
1) Long term monitoring of benthic composition at Heron Reef (2002-ongoing). Annual photoquadrate surveys are being collected at Heron Reef, Southern Great Barrier Reef. Initiated to develop remote sensing mapping approaches and assess coral composition over time. The resulting Maps, photo quadrate and benthic data, spectral reflectance are accessible online.
2) Long term monitoring of seagrass composition and abundance in Moreton bay Marine Park (2000-ongoing). For Eastern Banks it included monitoring seagrass species, cover and biomass 15x times since 2004 using photoquadrate survey and satelite imagery and for Moreton Bay it included seagrass extent and cover (2004, 2009, 2015, 2021, 2022), all data accessible via Moreton Bay Research Station.
3) Smart Sat CRC Hyperspectral Remote Sensing of Seagrass and Coral Reefs 2023-2027. Collaborative effort with CSIRO, Adelaide University, DES Adelaide Coastal Waters.
4) 3D GBR Habitat Mapping Project 2015 - ongoing: Mapping and monitoring geomorphic zonation, bottom type and predicted coral type habitat for every Great Barrier Reef within the Marine Park.
5) Global habitat mapping project 2019-2023 Developed and implemention of global habitat mapping as part of the Allen Coral Atlas resulting in extent, geomorphic and benthic maps for reefs globally, funded through with Vulcan Philanthropies in partnership with; Planet; the Arizona State University and the National Geographic Society.
Other projects: Advisor for Reef Cloud Australian Institute of Marine Science and Coordinated Global Research Assessment of Seagrass System (C-GRASS).
Current position: Associate Professior in Marine Remote Sensing. Academic Director Heron Island Research Station and affiliated researchers with Centre for Marine Science and Centre for Biodiversity and Conservation Science
Citizen science: Strong supporter of citizen science based projects, as trainer, organiser and advisor for Reef Check Australia, CoralWatch, Great Reef Census and UniDive.
Faculty of Engineering, Architecture and Information Technology
Availability:
Available for supervision
Dr T. Thang Vo-Doan is a Lecturer of the School of Mechanical and Mining Engineering at the University of Queensland. He was a postdoctoral researcher at the Institute of Biology I, University of Freiburg, Germany (2019-2023). He was also a Research Fellow at Nanyang Technological University (NTU), Singapore (2016-2018). He was awarded his PhD in Mechanical Engineering from the School of Mechanical & Aerospace Engineering, NTU in 2016. He received his M.Eng. degree in Manufacturing Engineering and B.Eng. degree in Mechanical Engineering from Ho Chi Minh City University of Technology, Vietnam in 2010 and 2008 respectively. He was awarded the prestigious Human Frontier Science Program Cross-disciplinary Fellowship (2019-2022).
He directs the UQ Biorobotics lab after joining in the University of Queensland. Current research activities of the lab focus on insect-machine hybrid robots, bio-inspired robotics, insect structures and functions, biomechanics, fast lock-on tracking, and brain imaging in untethered insects.
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.
