REPORT 2007 - 2008
Bldg 21, James Cook University,
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
At the end of 2007, the members and affiliates voted
1) Convert all affiliate laboratories to full membership; and
2) Invite most of the remaining genetics laboratories at JCU to join
As a consequence of this decision, the Centre
underwent a major expansion and now consists of the following
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
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
• 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
• 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):
• 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
• 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.
Medical Genomics Research Group,
Autoimmunity Research Group, Comparative Genomics Centre, Key
Autoimmune diabetes, gene, genome, allele, locus, inherited, disease,
1 diabetes mellitus, childhood diabetes, lupus, systemic lupus
hemolytic anaemia, hemolytic anemia, Coombs' test, antinuclear
renal failure, glomerulonephritis, gastritis, type A gastritis,
anemia, immunology, popular science, biology.