COMPARATIVE GENOMICS CENTRE

ANNUAL REPORT 2007 - 2008

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 originally founded in 2003 by the School of Pharmacy and Molecular Sciences in association with the School of Medicine, at the James Cook University (JCU). It is run as a scientific cooperative with an elected Head. 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.
    At the end of 2007, the members and affiliates voted to:
1) Convert all affiliate laboratories to full membership; and
2) Invite most of the remaining genetics laboratories at JCU to join the CGC.
    As a consequence of this decision, the Centre underwent a major expansion and now consists of the following laboratories:

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, gastritis and lupus in mice; the effects of mycobacteria on autoimmune diseases; and the role of immunoregulatory NKT cells in childhood diabetes.

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 psychiatric problems, such as depression.

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: 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: 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: David Blair)
Study organisms are parasitic flatworms, mainly trematodes such as the Asian blood fluke and the lung flukes. Increasing emphasis is being put on invasive species arriving in Australia, and especially in the waters of the GBR. Most of the field work on parasites and some lab work is done in countries such as China, Vietnam and India.  Much of the analysis is done in Australia. 

12) The Conservation and Ecological Genetics Group (Group Head: 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: 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.

The Neurobiology Group, which has been a member of the Centre since 2004, will leave the Centre mid-2008, as Dr Gerald Münch, the laboratory head, will be relocating to the University of Western Sydney.

The CGC now accommodates 21 honours students, 66 postgraduate students (up from 41 in 2007), 12 postdoctoral fellows (up from 11) and six research assistants. Over the last fifteen months, the CGC has had 110 scientific manuscripts published in internationally recognised scientific journals (up from 68). It currently has an annual income in excess of $3.7 M from peer-reviewed grants (up from $2.0 M) awarded by the National Health and Medical Research Council (NHMRC), the Australian Research Council, Queensland Cancer Fund, Alzheimer’s Australia, MS Society, ANZ Trustees, Eurochem, Food Science Australia, Furfural Espanol, Transtech, Atlas South Sea Pearl, AstraZeneca Gronova Research Inc and JCU intramural funding schemes.

A significant advantage of the Centre operating across multiple Faculties is its ability to attract substantial funding for common items of infrastructure. LIEF applications for large items of equipment are generally supported by all members of the CGC, and as a result, the group is well resourced. New purchases include gel documentation system, to view and record information revealed using DNA and protein gels, and algal culture cabinets, to support the work of The Symbiosis Genomics Group. Other equipment available in the Centre includes a 96 capillary MegaBACE 1000 DNA Analysis System, a Dako CyAn 11-paramater flow cytometer and a Affymetrix GeneChip system comprising hybridisation oven, fluidics station and GeneChip Scanner 3000 7G.

Members of the Centre continue to be recognised nationally and internationally for their contributions to genetic research:
•    Prof James Burnell was appointed to a steering committee for an International consortium to develop C4 rice, which is seeking funding from the Bill and Melinda Gates Foundation.
•    Ms Fiona Millardin of the The Psychogenetics Group received an Alzheimer’s Australia Research Post Graduate Research Scholarship in Social Research and Dementia and well as an Eastern Australia Dementia Training Study Centre  (EADTSC) Scholarship
•    Prof David Blair is a visiting scientist involved with three different programs in China; one being a genome project to sequence the genomes of Schistosoma japonicum, the Asian blood fluke. 
•    Dr Patrick Schaeffer was sponsored by GE Healthcare to attend the 4th International Peptide Symposium.
•    A/Prof Heinrich Korner was awarded an Australian Academy of Sciences Travel Award.
•    Dr Bill Leggat was an invited faculty member of the 2007 Edwin W. Pauley Summer Program in Marine Biology entitled “The Biology of Corals: Developing a Fundamental Understanding of the Coral Stress Response” at the Hawaiian Institute of Marine Biology.

Recent publications in key international journals include:
•    Levy, O., Appelbaum, L., Leggat, W., Gothlif, Y., Hayward, D.C., Miller, D.J., Hoegh-Guldberg, O. (2007) Light-responsive cryptochromes from one of the simplest extant animal the coral Acropora millepora. Science 318(5849):467-470
•    Leggat, W., Ainsworth, T., Bythell, J., Dove, S., Gates, R., Hoegh-Guldberg, O., Iglesias-Prieto, R., Yellowlees, D. (2007) The hologenome theory disregards the coral holobiont. Nature Review Microbiology 5(10): doi:10.1038/nrmicro1635-c1
•    Moore, R.B., Obornik, M., Janouškovec, J., Chrudimsky, T., Vancova, M., Green, D.H., Wright, S.W., Davies, N.W., Bolch, C.J.S., Heimann, K., Slapeta, J., Hoegh-Guldberg, O., Logsdon, Jr. J.M., and Carter, D. 2008. A photosynthetic alveolate closely related to apicomplexan parasites. Nature 451:959-963
•    Tanner, N.A., Hamdan, S.M., Jergic, S., Schaeffer, P.M., Dixon, N.E., van Oijen, A.M. (2008) Single-Molecule Analysis of Escherichia coli DNA Replication: Helicase-Primase Interactions Compromise Fork Progression. Nature Structural Molecular Biology, 15, 170-6.
•    Hodgkin PD, Heath WR, Baxter AG. (2007) The Clonal Selection Theory: 50 Years Since the Revolution. Nature Immunol 8:1019-1026.
•    Baxter AG. (2007) Timeline: the origin and application of experimental autoimmune encephalomyelitis. Nature Reviews Immunol 7: 904-12.
•    Steiner FM, Schlick-Steiner BC, Moder K, et al. (2007) Abandoning aggression but maintaining self-nonself discrimination as a first stage in ant supercolony formation. Current Biology 17, 1903-1907.
•    Schlick-Steiner BC, Steiner FM, Konrad H, et al. (2008) Specificity and transmission mosaic of ant nest-wall fungi. Proceedings of the National Academy of Sciences of the United States of America 105, 941-944.




LINKS:



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.