ANNUAL REPORT 2008 - 2009

Comparative Genomics Centre,
Molecular Sciences Bldg 21, James Cook University,
Townsville, 4811, Queensland, Australia
Telephone: 61-7-4781 6265 Fax:  61-7-4781 6078

        The Comparative Genomics Centre (CGC) is a research centre at James Cook University, originally founded in 2003. It is run as a scientific cooperative with an elected Head, Prof Alan Baxter. At foundation, the overall aim of the CGC was to use a variety of genetic models, including staghorn coral, fruit fly and mice, to study human disease from an evolutionary perspective. As the Centre has grown, it has become a focus of resources and expertise in genetics for the University and the region. The member laboratories now cover a much broader range of applications of genetics and genomics, including the science of coral reef management and biotechnological applications.  Its member laboratories now span three Schools in two Faculties.

        The CGC now has an annual research income in excess of $8.2 M from peer-reviewed grants and research contracts. This represents a five-fold increase in research income over a five year period. The Centre is currently funded by the National Health and Medical Research Council (NHMRC), the Australian Research Council, Queensland Cancer Fund, MS Society, Department of Environment and Heritage, Seafood Cooperative Research Centre, ARC Centre of Excellence for Coral Reef Studies, AUSAID, Eurochem, Lions Club, Queensland Cancer Fund, Food Science Australia, Bundesministerium fuer Bildung und Forschung, Bill and Melinda Gates Foundation and JCU intramural funding schemes.

        In the next year at least three of the Centre’s groups will relocate to the new A$32m Australian Tropical Science and Innovation Precinct (ATSIP) at JCU in Townsville. There will be a large molecular laboratory in which these groups will operate.  The Precinct will also be occupied by the entire staff of the CSIRO Davies Lab: the existing Davies Lab buildings will be vacated.  Some members of CSIRO Livestock Industries will be relocating from Rockhampton to Townsville, and will make use of the new molecular lab for their work on cattle genetics.  Other occupants of the Precinct will include the Climate Change group (headed by Steve Williams) and the Australian Centre for Tropical Freshwater Research (headed by Damien Burrows).

        The Centre is also a significant beneficiary of the Queensland Tropical Health Alliance (QTHA) launched 30 October 2008 in Cairns by Queensland Premier Anna Bligh as part of the Government’s Q-Tropics strategy. New facilities for the Centre will include Biocore protein interaction analysis equipment, expansion of the existing microarray facilities to include high throughput genotyping, a Zeiss 720 confocal microscope, a high sensitivity 14-parameter fluorescence activated cell sorter and additional analytical flow cytometry capability. The University will also construct a new laboratory complex and facilities for studying air-borne vectors in Cairns and PC3 laboratories in Townsville.

        The Centre’s 13 laboratories accommodate 21 honours students, 57 postgraduate students, 17 postdoctoral fellows and 12 research assistants. Over the last fifteen months, the CGC has had 103 scientific manuscripts published in internationally recognised scientific journals.

The member laboratories of the CGC are:
1) The Medical Genomics Group (Group Head: Prof Alan Baxter)
The Medical Genomics Group is working to determine the genetic causes of autoimmune diseases using both cellular and genetic techniques. Current projects study: the genetics of autoimmune diabetes, multiple sclerosis gastritis and lupus in mice; the effects of mycobacteria on autoimmune diseases; and the role of immunoregulatory NKT cells in childhood diabetes. The lab is funded by the NHMRC, MSRA and the Lions Club.

2) The Coral Genomics Group (Group Head: Prof David Miller)
The Coral Genomics Group is studying a local Acropora (staghorn coral) as a model system, in order to investigate issues central to the evolution of animal genomes and developmental mechanisms. The laboratory is a member of the world leading ARC Centre of Excellence for Coral Reef Studies. 

3) The Biotechnology Group (Group Head: Prof James Burnell)
Biotechnology Group clones and expresses biological products of potential utility and is developing genetic recombinant plant crops with improved disease resistance and greater yields.

4) The Supramolecular Biology Group (Group Head: Dr Patrick Schaeffer)
The Supramolecular Biology Group (SSBG) focus is to study protein-ligand interactions and in particular Protein-DNA interactions. The discovery and characterization of novel protein interactions can lead to the production of new molecular tools with applications in the field of bio- and nanotechnology (e.g. molecular diagnostics, drug discovery, functional genomics and proteomics). The SSBG is currently developing innovative methods for the discovery, characterization and quantification of such interactions as well as novel ultrasensitive diagnostics. The research undertaken in the SSBG is multidisciplinary and spans across the disciplines of Biology, Biochemistry and Chemistry.

5) The Cellular Immunology Group (Group Head Ass/Prof Heinrich Korner)
The Cellular Immunology Group studies infections and inflammatory diseases in mice bearing targeted deletions of key immunological genes, in order to dissect the critical pathways involved in the initiation and resolution of immune responses.

6) The Psychogenetics Group (Group Head: Prof Bernard Baune)
The Psychogenetics Group studies the genetic control of inflammatory processes involved in the aetiology of neuropsychiatric problems, such as depression and cognitive decline. Current projects study: the effects of TNF on cognitive function; the role of TNF in neurodevelopment of the central nervous system; development of TNF targeted treatment strategies in the CNS.

7) The Drosophila Genetics Group (Group Head: Ass/Prof Bill Warren)
The Drosophila Genetics Group's main focus is to investigate human disease using the model organism Drosophila melanogaster (fruit fly). As Drosophila share many key genes regulating cell division in man, they can provide important insights into disorders of chromosome segregation and cell cycle regulation.

8) The Sociogenomics Group (Group Head: Prof Ross Crozier)
The Sociogenomics Group studies social insects, such as bees, ants and wasps, to model the genetics of social behaviours like altruism.  The chief current project examines the evolution of the immune system genes in social insects and birds in relation to factors such as social structure and habitat type. 

9) The Aquaculture Genetics Group (Group Head: Dr Dean Jerry)
The research focus of the Aquaculture Genetics Group at James Cook University is to acquire the statistical information and develop molecular tools that will allow the design and conduct of highly efficient selection programs for aquaculture species, primarily those farmed in tropical waters. Research conducted by the group falls within four major research strands – quantitative genetics, population genetics and development of molecular tools, gene expression analyses and chromosome manipulation. Aquaculture species currently worked with include the pearl oysters Pinctada maxima, P. margaritifera, P. fucata, barramundi Lates calcarifer, and redclaw Cherax quadricarinatus.

10) The Symbiosis Genomics Group (Group Head: Dr Bill Leggat)
Symbiosis Genomics group focuses on linking changes in the gene expression of the dinoflagellate Symbiodinium to physiological of the algae and the intact coral holobiont (its host), and subsequent ecological changes. Research of this type can broadly be called ecological genomics. In particular this group is interested in how these dinoflagellates respond to human induced stress, such as climate change, what effects these changes have on the coral host and how these responses of the alga effect the future of coral reefs as we know them. This laboratory is a member of the world leading ARC Centre of Excellence for Coral Reef Studies

11) Parasite and Pest Genetics (Group Head: Prof David Blair)
Study organisms are parasitic flatworms, mainly the trematodes that infect humans, such as the Asian blood fluke and the lung flukes. Most of the field-work on parasites and some lab work is done in countries such as China, Japan, Sri Lanka, Vietnam and India.  We are also getting more involved with work on blood flukes of marine turtles.  These are a major, and apparently increasing, cause of morbidity and mortality.   In conjunction with the Algal Biology Group (see below), we are undertaking molecular identification of endemic and invasive microalgae in waters of the Great Barrier Reef.

12) The Conservation and Ecological Genetics Group (Group Head: Dr Michelle Waycott)
This group has a focus on problem solving research utilising a broad range of molecular genetic approaches on a diverse group of organisms. Research include numerous collaborative projects with other CGC groups, other JCU researchers and external researchers. Studies include population genetic, phylogenetic, molecular ecological and plant breeding approaches and we incorporate molecular and whole organism approaches into our studies. Current and recent research includes studies on seagrasses, mangrove, dugong, turtle, flying foxes, sea snakes, tassel ferns, mistletoes, Melaleuca, sandalwood and invasive species such as Green Mussel. Recent research directions involve the assessment of thresholds of vulnerability to changing climates and species adaptability, DNA barcoding to assess species diversity, evolutionary diversification rates and marker assisted screening of population genetic health. Established the Global Initiative to Barcode Seagrasses (GIBS) as a pilot for adopting DNA barcoding to assist in ecological and evolutionary studies of taxonomically difficult groups.

13) Algal Biology Group (Group Head: Dr Kirsten Heimann)
The Algal Biology Group runs the North Queensland Algal Identification / Culturing Facility, which isolates and establishes microalgal cultures from the GBR to screen for: biotechnological applications (such as biofuel potential, antiviral etc. effects), industrial purposes (such as potential animal feeds and aquaculture), morphological and genetic identification of invasives and novel organisms and potential for genetic enhancement of desirable traits for industrial / biotechnological applications.

Recent key publications include:


Medical Genomics Research Group, Autoimmunity Research Group, Comparative Genomics Centre,  Key words: Autoimmune diabetes, gene, genome, allele, locus, inherited, disease, Type 1 diabetes mellitus, childhood diabetes, lupus, systemic lupus erythematosus, hemolytic anaemia, hemolytic anemia, Coombs' test, antinuclear antibodies, renal failure, glomerulonephritis, gastritis, type A gastritis, pernicious anemia, immunology, popular science, biology.