The Ramaciotti Centre for Gene Function Analysis provides:
•
a major focus for research in Functional Genomics in Australia
•
a central facility to enable researchers determine how organisms respond to
change
•
expert personnel and state-of-the-art equipment to integrate DNA technology with
protein analysis
•
training in these technologies to develop research expertise
1
The Ramaciotti Centre for Gene Function Analysis
Core Facility
School of Biotechnology and Biomolecular Sciences, University of New South Wales
Nodes
School of Pathology, University of Sydney
Department of Genetics, University of Newcastle
College of Science and Technology, Macquarie University
Victor Chang Cardiac Research Institute
Westmead Millennium Institute
Additional Partners
Faculty of Informatics, Science and Technology, University of Western Sydney
Garvan Institute of Medical Research
Kolling Institute
New Children's Hospital
Expertise
Functional genomics
DNA microarraying including Affymetrix system
Robotics
Gene knockout technology
DNA sequencing
High capacity PCR
Bioinformatics
2
Management Committee
Professor Peter Bergquist
Professor Ian Dawes (Director)
Professor Tony Cunningham
Professor Richard Harvey
Professor Nick Hunt
Professor Peter Little
Professor Nicolle (Nicki) Packer
A/Professor Roger Read
Professor Rodney Scott
Professor John Turtle
Dr Alan Wilton
Independent Chair
University of New South Wales
Westmead Millennium Research Institute
Victor Chang Cardiac Research Institute
University of Sydney
University of New South Wales
Macquarie University
University of New South Wales
University of Newcastle
Clive and Vera Ramaciotti Scientific Committee
University of New South Wales
Alternates
Dr Barry Slobedman for Professor Tony Cunningham
Professor Ron Trent for Professor Nick Hunt
Professor Kaisu (Helena) Nevalainen for Professor Nicki Packer
Dr Cliff Meldrum for Professor Rodney Scott
Management Committee meetings were held on 18th April, 22nd August and 14th
December, 2007.
Scientific Advisory Committee
Professor David Bowtell
Dr Annabelle Duncan
Professor Chris Goodnow
Professor John Mattick
Scientific Director,
Peter MacCallum Cancer Research Institute
Deputy Director and Chief Operating Officer,
Bio21 Molecular Science and Biotechnology
Institute,
University of Melbourne
Chief Scientific Officer,
Australian Phenomics Facility,
John Curtin School of Medical Research,
Australian National University
Professor of Molecular Biology,
Institute for Molecular Bioscience,
University of Queensland
3
Chief Investigators
Professor Rob Baxter
Professor Peter Bergquist
Professor Judy Black
Dr Michael Buckley
Dr Ricardo Cavicchioli
Professor Colin Chesterman
Professor David Cook
Professor Tony Cunningham
Professor Ian Dawes
Dr Michael Gillings
Professor Bob Graham
Professor Peter Gunning
Professor Richard Harvey
Professor Nick Hunt
Professor Staffan Kjelleberg
Professor Peter Little
Professor Geoff McCaughan
Professor Brian Morris
Dr David Mowat
Dr Greg Peters
Professor Rodney Scott
Professor John Shine
Dr Barry Slobedman
Professor Rob Sutherland
Kolling Institute of Medical Research
Director, Biotechnology Research Institute,
Macquarie University
Department of Pharmacology, University of
Sydney
School of Pathology, University of New South
Wales
School of Biotechnology and Biomolecular
Sciences, University of New South Wales
School of Pathology, University of New South
Wales
Department of Physiology, University of Sydney
Westmead Millennium Institute
School of Biotechnology and Biomolecular
Sciences, University of New South Wales
School of Biological Science, Macquarie
University
Victor Chang Cardiac Research Institute
Oncology Research Unit, New Children's
Hospital, Westmead
Victor Chang Cardiac Research Institute
Department of Pathology, University of Sydney
Centre for Marine Biofouling and Bioinnovation
University of New South Wales
School of Biotechnology and Biomolecular
Sciences, University of New South Wales
AW Morrow Gastroenterology and Liver Centre,
University of Sydney
Department of Physiology, University of Sydney
School of Women’s and Children’s Health,
University of New South Wales
The Children’s Hospital, Westmead
School of Biomedical Sciences, University of
Newcastle
Garvan Institute of Medical Research
Westmead Millennium Institute
Garvan Institute of Medical Research
4
CONTENTS
Director's Report
6
Staff
9
Services
11
The Facility
12
Research and Development
15
Printed Arrays
15
Affymetrix Service
16
DNA Sequencing
17
Collaborations
18
Grant Awards
19
Activity Profiles
23
Canine genetics
23
Peter Wills Bioinformatics Centre
25
Education and Training
28
Students
28
Workshops and Seminars
30
Publications and Presentations
32
Financial Statement
43
5
DIRECTOR'S REPORT
The technologies on which the
Ramaciotti Centre is based are expanding
rapidly. Transcriptomics is now merging
with other aspects of genomics with the
recent appearance of new microarray
platforms and chips. In addition to the
availability of gene expression arrays
with up to 44,000 transcripts and exon
arrays, there are a number of important
other systems that have been developed.
Tiling arrays provide very novel ways to
study gene transcription, replication,
recombination and micro RNA transcription across the entire genome. Micro RNAs
are now subjects of considerable research and array technology is very appropriate to
the study of their distribution, regulation and function. Microarray technology can
also be used to identify changes in the epigenetic status of the genome. Gene mapping
is being revolutionised by the recent availability of very high density (>500,000) single
nucleotide polymorphism arrays (SNP) arrays and other techniques for detecting
genetic polymorphisms and this has major implications in medicine and agriculture.
Hence there is now a spectrum of genomic technologies that fall in to the
transcriptomics/genomics area. Array technologies can also be used to study
molecules other than the nucleic acids, including proteins and carbohydrates. Even
microbial cells have been arrayed.
These technologies are very important for current and future medical research,
addressing pathogenesis and drug development for many diseases including cancer,
heart disease, arthritis and inflammatory disease. They are also increasingly being
recognised for their potential in agricultural research.
With the advent of
metagenomics (sequencing of many organisms’ genomes from an environmental
sample) and the sequencing of consortia of organisms in particular environmental
niches, microarray technologies will provide a platform to study changes in
environmental flora in response to seasonal variation, environmental change or toxic
pollutants. This will require either capacity to spot oligonucleotides or the ability to
produce oligonucleotide arrays synthesised following the design of the researcher.
2007 was a very significant year for the Ramaciotti Centre for Gene Function
Analysis, when we expanded our core role as a direct open access service facility with
a strong record in provision of services in the transcriptomics and functional genomics
areas and merged with the UNSW DNA Sequencing Facility. The Facility was
founded in 1995 with the objective of establishing a modern facility to supply
molecular and cellular biological researchers with an automated service for efficient,
high capacity DNA sequencing. It has been extremely successful in reaching this
objective, and provides a cost-effective service for researchers at UNSW, across the
Sydney region and beyond for the generation of sequence data and DNA fingerprinting
by microsatellites. Over its 12 years of operation the Facility has provided low cost,
high quality data for hundreds of research groups with thousands of students, and
provides basic data that contribute to hundreds of scientific publications each year. It
also supplies low cost consumables through the joint buying power of many users.
6
The DNA Sequencing Facility has an annual turnover of $800,000, and the strength of
its position is reflected in this year’s financial report. It currently has about 150 active
customers and serves local researchers in BABS, BEES, CEIC and SOMS at UNSW
as well as Prince of Wales Hospital. External clients include the University of Sydney,
Macquarie University, Royal North Shore Hospital, Garvan Institute of Medical
Research, Victor Chang Cardiac Research Institute, NSW Department of Agriculture,
Royal Botanical Gardens and the Australian Museum. To keep pace with demand the
Facility has had several upgrades with the addition of robotics in 1999 and a high
throughput capillary sequencer in 2003 through Capital Grants Funding.
Another very important development has been the implementation of active
collaboration with the Peter Wills Bioinformatics Centre (PWBC) at the Garvan
Institute, in order to provide high level bioinformatics resources for our customers and
colleagues. A computer server and software for the secure archiving and analysis of
microarray data is located in the PWBC and known as the Garvan's GeneSpring
WorkGroup. This now houses the Ramaciotti Centre’s Affymetrix array data and
provides a secure work space for individual users. The work of the PWBC is profiled
in this report.
Yet again the Ramaciotti Centre was successful in applying for LIEF funding for
major items of equipment, and the 4-year support from NCRIS, which leveraged
funding from the NSW Government and UNSW, will enable us to increase our
expenditure on service provision in transcriptomics and bioinformatics. As new
technologies have become available the demand for printed arrays has declined to the
stage where we no longer need to dedicate a member of staff to their production, and
towards the end of the year Dr Shining Yuan left the Centre to continue her career at
the Red Cross Blood Bank.
This year we have also restructured the Centre’s Management Committee. Professor
Peter Bergquist is the independent Chair and Professor Nicki Packer has replaced him
as Macquarie University’s representative; Professor Helena Nevalainen is her
alternate. Dr Alan Wilton, Manager of the DNA Sequencing Facility, was invited to
serve on the Management Committee on the merger of the two organisations, and
Professor Richard Harvey has replaced Professor Bob Graham to represent the Victor
Chang Cardiac Research Institute. At end of 2007 Professor Peter Little resigned from
UNSW and therefore also from the Committee. I would like to thank all the members
of the Management Committee for their valued input in the face of so many competing
commitments.
The Centre continues to support the highest quality research, as exemplified by the
output of publications and presentations listed in this Annual Report. Work by
Thomas Preiss and colleagues at the Victor Chang Cardiac Research Institute on how a
network of multiple regulatory layers shapes gene expression was the subject of a
Research Highlight report in the Nature Reviews Genetics (Flintoft L. Gene
regulation: A multilayered take on gene expression. Nat Rev Genet 2007; 8:407). The
Centre’s students are also contributing to its high profile. Dr Ben Tang, whose PhD is
co-supervised by Professor Anthony McLean at Nepean Hospital and Dr Ruby Lin and
myself at the Ramaciotti Centre, was awarded the Nepean Hospital Medal for his
research on the detection of sepsis in intensive care patients. Ben’s publication of his
7
findings in the American Journal of Respiratory Critical Care Medicine earned an
editorial in the same issue.
Finally, I would like to pay tribute to all the staff of the Centre’s core facility at
UNSW, who continue to work beyond the call of duty to promote its success and
satisfy its customers.
Ian W. Dawes
Director
8
STAFF
Microarray Manager
Dr Bronwyn Robertson was appointed to the
position of Manager of the Microarray
Facility from October, 2000 and continued to
manage the research of the facility until
August 2005, when she took maternity leave.
She returned on a part time basis at the end of
August 2006.
Bronwyn has a PhD in
Microbiology from the University of New
South Wales and was a Research Fellow at
the Japan Science and Technology Agency
from 1998 to 2000.
Microarray Manager
Dr Helen Speirs took up the position of
Manager of the Microarray Facility in
September 2005 and led the Centre’s
development of its expertise in Affymetrix
arrays until she took maternity leave in
September 2006. She returned to the Centre
on a part-time basis in May this year. Helen
has a PhD from Edinburgh University and
her early postdoctoral work focused on blood
coagulation, hypertension and thrombosis.
In Sydney she joined Acyte Biotech as a
senior research scientist, and before joining the Centre she managed the central
molecular biology facility at the Institute for Biomedical Research at Sydney
University.
9
DNA Sequencing Manager
Angela Higgins is the Service Manager of the
DNA Sequencing Facility. Her background
is in population and plant genetics and
microbiology. Angela is responsible for the
day-to-day management of the Facility,
including sample preparation (sequencing and
genotyping), results analysis, customer liaison
and supervision of research assistants and
students. She also provides a troubleshooting
service for customers. Angela was first
employed by the UNSW Sequencing Facility
in April 1997 and over the 10 ensuing years has been instrumental in its ongoing
success.
Technical Manager
Geoff Kornfeld is the Technical Manager of
the Facility. He is responsible for the Centre's
IT, and is invaluable in the selection, ordering
and installation of the Facility's equipment.
Geoff's time is an in-kind contribution from
the University of New South Wales.
Postdoctoral Research Fellow
Dr Ruby Lin joined the Centre in
September 2003 as the Ramaciotti
Research Fellow. Ruby completed her
PhD at Sydney University under the
supervision of Dr Brian Morris in 2002.
She was awarded the prestigious Peter
Doherty Fellowship from the National
Health and Medical Research Council in
2005 and has successfully applied for a
range of grants supporting research
collaborations and contributing to Centre
infrastructure. She is actively collaborating with several external research groups,
applying the Centre’s technological approach to a range of medical fields.
10
SERVICES
The Centre provides a central facility to assist researchers to determine how the genes
in an organism respond to change. The facility offers a wide range of resources to
genomics researchers, including:
•
Manufactures and analyses cDNA and oligonucleotide microarrays
•
Provides high throughput robotics for analysis of gene function
•
Generates specific genome arrays
•
Facilitates the making of expressed sequence tag libraries from cells undergoing
normal or pathological development
•
Provides full services for users of the Affymetrix GeneChip® System
•
Provides a DNA sequencing service
•
Provides access to the Saccharomyces cerevisiae genome-wide deletion strains
•
Provides robotics for protein analysis and identification
•
Reduces costs to users by accessing consumables and licences (such as the
GeneSpring licence, Affymetrix chips and sequencing reagents) at bulk rates.
11
THE FACILITY
The focus of the Centre occupies 240 square metres in the first floor of the Life
Sciences Building at the University of New South Wales. It includes a state-of-the-art
microarraying and DNA sequencing facility, a wet laboratory and offices. The Centre
incorporates an impressive range of major equipment underpinning its services and
located at the UNSW facility and the Centre nodes.
Ramaciotti Equipment Register
Location
Contact
UNSW
Helen Speirs
Microarray
Tel: +61 2 9385 1241
Facility
Fax: +61 2 385 1277
Email: ramaciotti@unsw.edu.au
Item
GCAS Affymetrix Robotics
for Expression Arrays
Affymetrix GC3000 System
Piezoelectric Microarraying
printer (Biochip Arrayer –
Perkin Elmer)
Agilent Bioanalyzer
Apple Raid Discserver
Axon Microarray Scanner
4000B
Phosphoimaging equipment
MJ Research Tetrad PCR
machine
Beckman Biomek 2000 with
stacker and Spectromax 190
plate reader
Speed Vac 2-25 rotational
vacuum concentrator
-80°C freezer (Revco
ULT2186)
20 Telechem SMP
Microarraying pins
ABI PRISM 7700 sequence
detection system
Genetix ESI DNA
microarrayer
Robbins Hydra liquid
handling system
ArrayWorX scanner
Corbett q-RT-PCR machine
BioRad Chipwriter Mini
Mac G5 Rack Mount
computer
Genetix QArrayII (property of
Macquarie Uni)
12
Location
UNSW
DNA
Sequencing
Facility
Contact
Angela Higgins
Tel: +61 2 9385 1237
Fax: +61 2 9385 1483
Email: sequencing@unsw.edu.au
Item
ABI 3730 48 capillary DNA
sequencer
ABI 9600 PCR machine
Sydney
University
Nick Hunt
Tel: +61 2 9036 3242
Fax: +61 2 9036 3286
Email:
nhunt@pathology.usyd.edu.au
AllTech HPLC
Controller
Autosampler
Pump
Degassing
Robotics – liquid handling
system (Corbett Research)
CAS1201
Microplate System (BioRad
Ultramark)
Microarray Scanner (Axon
AX AGP 4000B)
Real Time DNA
Amplification system (Corbett
Rotor Gene 3000)
ABI PRISM 7700 sequence
detection system
Microarray Scanner (Axon
4000B)
(SUPAMAC) Ron Trent
Tel: +61 2 95157514
Fax: +61 2 9550 5412
Email: rtrent@med.usyd.edu.au
(Westmead
Millennium
Institute)
AB 3730xl DNA Fragment
Analyzer upgrade
3100-01 ABI Prism 3100
Genetic Analyzer, Applied
Biosystems
SNP analyzer: ABI PRISM
7900HT sequence detection
system with automation
accessory
ABI 3700 Genetic Analyser
Microarray Scanner (Axon
Tony Cunningham
4000B)
Tel: +61 2 9845 9005
Fax: +61 2 9845 9100
Email:
tony_cunningham@wmi.usyd.edu.au
13
Location
Macquarie
University
Contact
Belinda Ferrari
Tel: +61 2 9850 9252
Email: bferrari@cmbs.mq.edu.au
Moreland Gibbs
Tel: +61 2 9850 6955
Email: mgibbs@els.mq.edu.au
Nicki Packer
Tel: +61 2 9850 8176
Fax: +61 2 9850 8313
Email: npacker@cbms.mq.edu.au
Anwar Sunna:
Tel: +61 2 9850 4220
Email: asunna@els.mq.edu.au
Item
FACSAria Flow Cytometer
Robotics (BioRobots)
Eppendorf epMotion robot
DNA Scanner
Bio-Plex Suspension Array
Systems
Robotic Colony Picker
(located UNSW)
ABI PRISM 7700 sequence
detection system
Newcastle
University
Rodney Scott
3730 DNA Fragment
Tel: +61 2 4921 4974
Analyzer
Email: Rodney.Scott@newcastle.edu.au Illumina Bead station
PCR Machines (4)
Qiagen Robotics
Microarray Scanner (Axon
4000B)
Laser dissection microscope
Pyrosequencer
Qiagen BioRobotics M48
SNP detector (Varian Helix
System): 2
TECAN upgrade
ABI PRISM 7900HT
sequence detection system
Victor
Chang
Cardiac RI
Daniela Stock
Tel: +61 2 9295 8560
Email: d.stock@victorchang.edu.au
Dr Owen Prall
Tel: +61 2 9295 8522
Email:
o.prall@victorchang.unsw.edu.au
Crystallisation Robot (TTP
Labtech Mosquito)
Microarray Scanner (Axon
4000A)
14
RESEARCH AND DEVELOPMENT
Printed arrays
Demand for printed arrays in 2007 was exactly the same as that in 2006. However,
this largely reflects interest in the Exiqon LNA microRNA set that was printed and
offered to researchers in March of this year (see below). There were no requests for
the majority of printed arrays offered by the Centre in 2007, including mouse and
human arrays. During the year overall demand dropped to a very low level, and from
September to November no printed arrays were sold. As a result the Centre is no
longer employing a staff member to manage this part of its service.
1. Yeast (Saccharomyces cerevisiae)
Microarrays printed from the MWG Yeast 6K genomic set, supplemented with
oligonucleotides designed in-house to cover genes not included in the original MWG
set, continued to be requested in 2007 and slightly more were sold than in 2006. The
Centre is the only facility in Australia that offers printed microarrays for yeast
researchers. The complete Euroscarf set of yeast knockout mutants is also available.
2. Rat
There was still significant demand during the first half of the year for the 10K rat
arrays, which were the Centre’s most successful product in 2005. However, no orders
were received for the 27K set.
3. microRNAs
In March the Centre offered slides of the most comprehensive miRNA set available.
This is the Exiqon LNA microRNA set (V8.1), which contains 1500 unique target
oligos for all annotated miRNAs (vertebrates/invertebrates/plants/viruses) in the
Sanger miRBase as well as proprietary miRNAs from the Max Planck
Institute/Garching Innovation that are not in the Sanger miRBase. There was regular
demand for these slides from March to September, and they comprised 40% of the
Centre’s 2007 sales of printed arrays.
4. Custom array
Two orders for custom arraying were placed in 2007, resulting in sales of twice as
many custom arrays as in 2006.
Sales of printed arrays in 2006 and 2007
Organism
Yeast
Mouse
Rat
Human
Micro RNA
Custom array
TOTAL
Slide type
MWGSc6K
CGenMm22K
CombRat10K
OperRat27K
CGenHu30K
Chromarray
miRCURY
Slide number
2006
2007
120
132
81
0
18
44
85
0
12
0
39
0
not available
149
30
60
385
385
15
Affymetrix Service
In 2007 the Centre offered a full processing service for all the Affymetrix arrays
available at that time, including expression, exon, mapping, promoter, tiling and
targeted genotyping arrays. Moreover, the latest Affymetrix arrays were immediately
available from the Centre. For example, on May 21st Affymetrix announced the
launch of its Genome-Wide Human SNP Array 6.0, a single microarray that contains
more than 900,000 SNPs, and in July the Centre processed this chip for two customers.
Moreover, the Centre’s high quality performance is recognised by Affymetrix, which
has chosen the Centre as its worldwide testing site for the use of Affymetrix chips with
FFPE (formalin-fixed, paraffin-embedded) fixed tissue samples.
Demand for Affymetrix services continued to grow and remains the major source of
income for the Centre. In 2007 the Centre processed 699 Affymetrix arrays for
customers, an increase of 23% over 2006. The majority (77%) were expression arrays.
Human arrays were in greatest demand, but the range requested was wide and included
bovine, canine, rat, mouse, chicken, Saccharomyces cerevisiae and Pseudomonas
aeruginosa chips. Affymetrix service sales are detailed below.
Sales of Affymetrix Arrays 2007
Genechip type
Service level
Client
Sample
number
Expression arrays
full
Human HGU133 Plus 2.0
expression
hyb, wash & scan
full
Human gene array 1.0 ST
label, hyb, wash,
scan
Ramaciotti, UNSW
Garvan Institute
Pathology, USyd
Kolling Institute
Nepean Hospital
St Vincent’s Hospital
Cure Cancer
USyd
Children's Hosp Westmead
Neurology, USyd
SUBTOTAL
Med, USyd
CCIA
Biomed Eng, UNSW
Garvan Institute
SUBTOTAL
full
Human exon 1.0
hyb, wash & scan
full
Human exon array 1.0 ST
Human promoter 1.0R
Bovine expression
hyb, wash & scan
hyb, wash & scan
full
Griffith Uni
IMB, UQ
Physiology, USyd
SUBTOTAL
St George Hospital
Griffith Uni
MMB, USyd
SUBTOTAL
Garvan Institute
SUBTOTAL
Vet Science, USyd
CSIRO Livestock Industries
SUBTOTAL
9
31
2
26
35
14
2
16
25
40
200
30
4
12
6
52
8
4
9
21
6
6
11
23
76
76
13
68
81
16
Rat gene array
Mouse 430 2.0
expression
full
Garvan Institute
SUBTOTAL
6
6
22
6
6
4
38
12
12
8
8
10
10
2
9
3
14
2
2
TOTAL EXPRESSION ARRAYS
535
Children's Hosp Westmead
Griffith Uni
SUBTOTAL
Med Sci, UNSW
Med Sci, UNSW
SUBTOTAL
Garvan Institute
Peter Mac Institute
Sydney Children’s Hosp
SUBTOTAL
12
11
23
12
8
20
49
29
12
90
BABS, UNSW
30
SUBTOTAL
full
USyd
Med Sci, UNSW
Victor Chang
Baker Institute
full
Garvan Institute
full
IMB, UQ
full
Biol Sci, USyd
full
AWRI
UWS
Microbiogen
full
BABS, UNSW
SUBTOTAL
Mouse gene array ST1.0
Mouse exon 1.0
Chicken expression
S. cerevisiae genome
SUBTOTAL
SUBTOTAL
SUBTOTAL
SUBTOTAL
P.aeruginosa expression
Genotyping arrays
Human 250K Sty
mapping
100K HindIII/Xba
mapping
SNP 6.0
Canine 250K Sty
mapping
Other arrays
Test3
full
full
hyb, wash & scan
full
full
hyb, wash & scan
SUBTOTAL
30
TOTAL GENOTYPING ARRAYS
163
Neurology, USyd
1
TOTAL OTHER ARRAYS
1
TOTAL ALL ARRAYS
699
17
DNA Sequencing
By the end of the year the DNA sequencing service had a total customer list of
approximately 620, 150 of which were active. This service experiences high levels of
demand and almost every year since it began operating the sample numbers processed
have increased (see Table below). Business in 2007 increased by more than 50% over
that in 2006, with 93,337 samples sequenced.
Year
2002
2003
2004
2005
2006
2007
Sample numbers
23,896
26,473
61,863
85,236
63,137
93,337
Notes
AB 3730 Capillary DNA Analyser purchased July
Collaborations
The Centre collaborates actively with a wide range of research groups. Productive
collaborations include:
Cardiovascular disease
Dr Ruby Lin is collaborating with Dr Julie McMullen (Baker Institute, Melbourne) to
investigate gene expression of heart harvested from different mouse models of
pathological and physiological cardiac hypertrophy. She is also working with
Professor Judy Whitworth and Dr Yi Zhang (John Curtin School, ANU) on a model
for hypertension. This project investigates whether the ACTH-treated Sprague
Dawley rat is a suitable model for studying genes involved in the pathogenesis of
metabolic syndrome.
Human genetic defects
The Centre is working with Dr Greg Peters (Children’s Hospital, Westmead) on the
detection of small deletions, imbalances and dosage in the human chromosome.
Detection of sepsis
Dr Ruby Lin is working with Dr Ben Tang and Dr Anthony McLean (Nepean
Hospital) to develop a method for the accurate detection of sepsis in intensive care
patients. This year the research led to the detection of significant differences between
the responses of monocytes and neutrophils in sepsis. Ben was awarded the Nepean
Hospital Medal in September for his work.
Yeast deletion mutants
The collaboration with Professor Phil Hogg (Centre for Vascular Research, UNSW)
continues to be productive. This research applies the complete yeast genome deletion
set to screen drug candidates.
Data storage and analysis
The Centre continues to work with Dr Warren Kaplan (Garvan Institute Bioinformatics
Centre) to establish a valuable collaborative resource for data storage, linkage and
analytical options.
18
Grant Awards
The value of the Ramaciotti Centre to the research community is exemplified by the
number of grant applications featuring work with the Centre that are now being
funded. Australian researchers using the Facility commanded in excess of $9.5m of
competitive research grant funding in 2006. Currently, the Ramaciotti Centre Users
Group numbers 100 academic researchers, and more than 50 research staff currently
actively make use of the Facility. These researchers cover a diversity of research
interests across the spectrum of Life Sciences. While not the sole focus, it has a strong
interest in Health Science and Microbiology, reflecting the research interests of its
main users. The grants awarded for and during 2007 include:
Grants awarded for and during 2007
National Collaborative Research Infrastructure Strategy (NCRIS)
The Centre successfully applied for Federal Government NCRIS support under the
high priority capability area ‘Evolving biomolecular platforms and informatics’
(NCRIS 5.1). This funding established Bioplatforms Australia, which together with
the NSW State Government and UNSW will contribute a total of almost $1 m over 4
years in support of transcriptomics services and bioinformatics.
Australian Research Council
LIEF Grant
Dawes IW, Bergquist PL, Trent RJ, Scott RJ, Hogg PJ, Wilkins M, Reichardt JK, Hunt
NH, Baker MS and Dunkley PR. Advanced high throughput functional genomics and
gene mapping. 2008. $400,000
This application was to enhance the capacity of the Centre to link genomic analyses
(including those based on transcriptomics, proteomics and gene mapping) with cell
biology studies directed to analysing the function of genes (including phenomics).
This capacity is vital to maintain gene and protein functional analysis at the cutting
edge of current technology and complement the existing equipment. Once again the
application was successful, resulting in the unprecedented award of 8 sequential
Australian Research Council Linkage Infrastructure Equipment and Facilities grants to
the Centre. The ARC contributed $400,000 to the successful LIEF Grant for 2008,
which was led by UNSW.
Discovery Grants
Grau GE and Hunt NH. Microparticles as effectors of microvascular alterations in
brain inflammation. 2007-2009. $90,000 p.a.
Preiss T. Determining the sequence of events during eukaryotic translation initiation.
2007-2009. $235,000.
Preiss T and Beilharz TH. Role of mRNA polyadenylation control in gene expression.
2008-2012. $685,000.
19
Moscato, Scott RJ and Langston M. Application of novel exact combinatorial
optimisation techniques and metaheuristic methods for problems in cancer research.
2007-2009. $340,000.
Linkage Grants
Higgins VJ, Dawes IW and Rogers PJ. The role of redox balance and reactive oxygen
species in beer stability using an integrated transcriptomic and metabolomic analysis.
2007-2009. $315,000.
National Health and Medical Research Council
Project Grants
Grau GE, Cook DI, and Hunt NH. Relationship between cell-cell interactions and
disease severity in patients with cerebral malaria. 2007-2009. $135,000 p.a.
Preiss T. Probing the cellular functions of the translation factor p97. 2008-2010.
$355,500.
Australia-European Union Collaborative Grant.
Hunt NH. Pathogenic role of microparticles in cerebral malaria. 2007-2008. $161,000
p.a.
National Breast Cancer Foundation
Trau M, Forbes J, Clark S, Brown M, Francis G, Dobrovic A and Scott RJ. Novel
strategies for prediction and control of advanced breast cancer via nanoscaled
epigenetic-based biosensors. 2008-2012. $5,200,000.
Cure Cancer Australia Foundation
Suter C and Preiss T. (2007). Piwi RNAs as masters of gene silencing in cancer.
2008-2009. $72,000.
Dog breeders
Wilton AN. Contributions from various dog breeders and dingo researchers. 2007.
$100,000.
Hunter Children’s Research Foundation
Bowden NA and Scott R. Genome wide SNP association study of childhood acute
lymphoblastic leukaemia. 2008. $20,000.
20
Hunter Medical Research Institute
Research Grants
Bowden NA and Scott R. Gene expression profiling of xeroderma pigmentosum.
2007. $20,000.
Kim K and Scott R. Identification of novel markers in paediatric acute lymphoblastic
leukaemia; investigation of DNA methylations and non-coding small microRNAs.
2008. $20,000.
Levi C, Attia JR, Scott R and Thrift A. Genetic polymorphisms in the native
thrombolytic systems as risk factors for ischaemic stroke. 2007. $5,000.
Scott R and Bowden NA. Gene expression profiling of xeroderma pigmentosum.
2008. $100,000.
Scott R and Moscato PA. HMRI Emerging Research program - Information based
medicine. 2007-2009. $634,044.
Tooney PA, Michie PT, Schall UA, Scott R and Stain HJ. Brain science and young
people’s mental health: a gene expression study in young people at ultra high risk of
developing schizophrenia. 2008. $25,000.
PULSE Research Exchange
Lechner-Scott J and Scott R. 2008. $15,000.
Senior Research Fellowship
Attia JR, Gleeson M, Scott R, Carr VJ and Ackland S. 2008-2009. $160,000.
Pastoral Breeds Health Foundation
Wilton AN. Developing a DNA test for disease trapped neutrophil syndrome in border
collies. 2007-2008. £10,000.
Terry Snow, Canberra Airport
Wilton AN. Genetics of ataxia in kelpies. 2007. $50,000.
University of Newcastle
Milward EA and Scott R. Microarray analyses of genes important in iron regulation
and related disorders. 2007. $16,000.
Scott R and Moscato PA. PRC - Priority Research Centre for Bioinformatics,
Biomarker Discovery & Information-Based Medicine (CIBM). 2007-2008. $36,620.
21
University of New South Wales
Faculty Research Development Scheme
Lin R. 2007. $3,000
Faculty Research Grant
Lin R. 2007. $10,000
Goldstar Grants
Preiss T and Beilharz TH. Role of mRNA polyadenylation control in gene expression.
2007. $40,000.
Working Kelpie Council
Wilton AN. Genetics of ataxia in working kelpies. 2007. $8,000.
22
ACTIVITY PROFILES
The Ramaciotti Centre is a highly collaborative organisation and its success relies on a
diverse range of expertise. Each year the Annual Report focuses on and profiles
research by major collaborators and users of its resources, as well as different Centre
skills. This illustrates the broad applicability and increasing value of Functional
Genomics and microarray technology to research teams across the spectrum of
biological and medical research, never more so than the two profiles we present this
year. In 2007 the Centre merged with the DNA Sequencing Facility, and so this year
we are profiling the work of Dr Alan Wilton, the Sequencing Facility’s director. We
also initiated a very important collaboration with Dr Warren Kaplan at the Peter Wills
Bioinformatics Centre (Garvan Research Institute), with the aim of providing a better
bioinformatics service to our colleagues. This work is described in our second profile.
1.
Canine genetics (Dr Alan Wilton, Director, DNA Sequencing Facility, School
of Biotechnology and Biomolecular Sciences, UNSW).
Conservation of the Australian dingo
Dingoes are an enigmatic Australian
icon whose existence is under threat.
Their origins and relationship to other
canids was unknown till sequencing
work by Alan Wilton and Swedish
collaborators showed how closely
dingoes are related to domestic dogs.
Dingoes breed freely with domestic
dogs that have been released into the
wild and wild dingoes are being
replaced by these hybrids and domestic
dogs.
Wildlife
managers
need
information on the extent of the
problem to make management choices to help preserve the dingos.
Dr Wilton developed and
continues to refine DNA
testing
methods
to
differentiate
between
dingoes and domestic dogs
and their hybrids. In close
collaboration with dingo
conservation groups, his
group has been testing
breeding stock in captivity
to ensure the purity of these
last isolates of the pure
dingo. The research is also
being applied to wild dog populations through close collaboration with government
departments such as NPWS, NSW Dept Primary Industry, State Forests and Rural
Lands Protection Boards in various states. Thousands of wild animals have been
23
tested. Samples from Eastern States suggest that there are very few pure animals left
and that it will not be long before the dingo is extinct in the wild.
This research has enabled the scientific
evaluation of the plight of an Australian
icon, and provided the basis for legislation
and a conservation effort to preserve the
dingo based on a sound scientific footing.
The work is continuing to increase the
accuracy of detection of hybrids by using
high throughput genotyping techniques.
The sequencing of the dog genome has
provided many resources for dog research
and we are applying these to examine the
dingo and compare it to the dog. Dog SNP
arrays are being typed to test 50,000 sites in the dog genome simultaneously. High
throughput genomic sequencing is being undertaken through US collaborators to allow
SNP discovery to create tools for monitoring hybridisation that can be used on noninvasive samples such as scats.
Health and well-being of man’s best friend, the
dog.
The dog is without a doubt the most loved and
closest associated with man of all the domestic
animals. Dog breeds of various shapes and sizes
have been developed from small groups of
animals. This has lead to a high incidence of
genetic diseases in the breeds with each breed
having its own genetic problems. More medical
diagnoses and study of disease aetiology and
symptoms occur for dogs than any other animal,
which also makes them good models for human
inherited diseases. Dogs fill many functions in
today’s society from much loved, pampered pets
to working dogs for herding, guarding, police
Affected pup and unaffected sibling
work (detection and attack), and guide dogs. As
well as the suffering endured by animals with inherited disease, diseases in working
dogs cause financial loss from failure to perform.
Dr Wilton’s lab has worked closely with dog breed clubs to develop DNA tests for
some common devastating genetic diseases. The diseases studied had severe effects
on the health of the animals, and include nerve degeneration, immune problems and
instability. Such diseases also have an effect on the popularity of the breed, which has
financial consequences for breeders. Education campaigns for breeders about these
genetic problems have been developed in close association with breed clubs. A DNA
test was developed for an immune deficiency disease in Border collies in 2007 by PhD
student Jeremy Shearman and 2500 dogs from around the world were tested to
determine if they carry the disease. More than 10% did. Breeders can use test
information in selective breeding to eliminate the problem entirely from the breed. Dr
Wilton has been recognised for his work with the dog breeding community by being
made patron of three different Border Collie Clubs. His reputation in this field has
24
convinced other dog breeders to seek his assistance and he is now working on an
ataxia which is a common disorder in kelpies. This research is totally funded by the
breeders to the tune of $90,000.
This dog DNA research has
allowed for testing of genes
leading to lethal or severely
debilitating genetic diseases in
some dog breeds.
The tests
provide better health for dogs and
improve the reputation of the breed
as a good pet.
Dr Wilton’s
research with guide dogs, working
cattle and sheep dogs has also
improved these breeds so they can
be better relied on in their work.
The disease genes have their
equivalents in humans and make
good models for research into the treatment and aetiology of the human diseases.
2. The Peter Wills Bioinformatics Centre. (Dr Warren Kaplan, Mr Jim McBride and
Mark Cowley, Garvan Institute for Medical Research)
The Peter Wills Bioinformatics Centre (PWBC) at the Garvan Institute was established
in 2001, and named in recognition of the contribution made to the Garvan by its
previous board chairman, Peter Wills. It was the vision of Peter Wills who foresaw
that the sequencing of the human, and other, genomes together with new technologies
that use this sequence information would generate unprecedented amounts of data that
would need to be housed and analysed by a new generation of researcher, the
bioinformatics specialist. Drawing from the fields of computer science, statistics,
applied mathematics, physics, chemistry and biology, the PWBC’s teams work in the
areas of genomic and protein data-housing and analysis as well as clinical data
management.
Microarrays are one of the new technologies that use genome sequencing information
to enable biologists to simultaneously profile the expression of all the genes in a
genome instead of just a single gene, as used to be the case. Very early on the PWBC
looked to establish a system that could securely archive microarray data from the
Garvan's Affymetrix microarray system, and in collaboration with the Garvan's Cancer
Program and cancer researchers from across NSW was awarded a grant from the NSW
Cancer Institute to fund a computer server and software for the secure archiving and
analysis of microarray data. This archiving and analysis system is known as the
Garvan's GeneSpring WorkGroup.
The Ramaciotti Centre's acquisition of an Affymetrix Microarray System and its status
as an Affymetrix Core Facility contributed to the popularity of this service. Initially,
users' data at the Ramaciotti Centre were burned onto CDs and then as data sizes
increased onto DVDs. However, the continued increase in feature size on each
microarray made this approach no longer feasible and the PWBC was delighted to
reach an agreement with the Ramaciotti Centre for the housing of all its array data.
25
Now, data arising from the Affymetrix system at the Ramaciotti Centre are rapidly
moved across to the Garvan's GeneSpring WorkGroup where they are uploaded into
the user's private work-space. The users, who retain ownership of their data, are then
assigned a unique user-name and password for accessing their data via a web-browser.
To date we have uploaded more than 60 experiments from the Ramaciotti Centre with
the Garvan’s GeneSpring WorkGroup now containing more than 20,000 microarray
samples that were run on 65 microarray types. This arrangement with the Ramaciotti
Centre has also led to numerous collaborations between biologists using the Centre
and the PWBC. Typically, these collaborations involve the design and building of
customised bioinformatics solutions for each project where we perform full-scale
analyses, covering detailed quality control of the data, statistical analysis to identify
genes of interest, and then functional analyses to put these genes into a biological
context (Figure 1). These collaborative projects have spanned many organisms and
disease areas, including the identification of genes underlying organ transplantation
failure, the effects of obesity, thermodynamic regulation of poikilotherms, epigenetic
regulation of gene expression, and numerous cancer studies.
Figure 1: To assess the extent to which genetic variation influences the regulation of gene expression in different
tissues, we measured transcript abundance in three tissues from 31 recombinant inbred mouse lines, using
Compugen 22K Mouse OligoLibrary microarrays, printed by the Ramaciotti Centre. Network analysis of gene
expression reveals that a number of genes form highly co-regulated groups of genes in each individual tissue.
Combining these networks together identifies further groups of genes that are co-regulated in a at least one, two, or
all three tissues. Those groups of genes that are co-regulated in all three tissues are strong candidates for being
regulated by common mechanisms in all three tissues, of which some component has been perturbed by genetic
variation. (Figure taken from Mark Cowley’s PhD thesis).
26
Explaining how genes are regulated has become a grand biological challenge, and in
order to answer these sorts of questions biologists have looked to probe the genome for
factors such as epigenetic modifications of the DNA, alternate splicing of genes, the
identification of transcription factor binding sites via Chromatin Immuno Precipitation
(ChIP), and Single Nucleotide Polymorphism (SNPs). Microarray manufacturers like
Affymetrix have been quick to respond to these needs and have released exon, tiling
and SNP chips. All of these microarray types are housed and have been analysed by
the PWBC.
27
EDUCATION AND TRAINING
There are three main aspects to the Centre’s education and training activities.
Microarraying features in the work of a number of Honours and PhD students who are
using material from the Ramaciotti Centre. Throughout the year the Centre hosts
seminars presented by experts in its fields of research.
In addition, both the Microarray Users’ Group and the Centre’s core Facility organise
workshops and seminars, and provide technical support for scientists in the wider
research community.
Students
Honours and PhD students from the Centre nodes and other educational organisations
are benefiting from the centre’s resources. Ben Tang won the Nepean Hospital Medal
this year. Ben is a PhD student, and already has a Masters degree in clinical
epidemiology. He is working with the Ramaciotti Centre, where he is supervised by
Dr Ruby Lin, and Professor Anthony McLean at Nepean Hospital.
Honours/Diploma students
Student
Supervisor
University
Anita Ayer
UNSW
Simon Keam
Dr Gabriel Perrone
and Prof Ian Dawes
Prof Ian Dawes
Narada Kiriella
A/Prof Thomas Preiss
UNSW
/VCCRI
Zi Hui Lo
Dr Ruby Lin
UNSW
Shi-Xiong Tan
Dr Gabriel Perrone
and Prof Ian Dawes
UNSW
Callum Titmarsh
Michelle Wong
Prof Rodney Scott
Prof Rodney Scott
Newcastle
Newcastle
Internship students
Student
Julia Wegner
Supervisor
Stuart Cole
Pirooz Poursoltan
University
Dr Alan Wilton
MSc students (continuing)
Student
UNSW
UNSW/
Regensburg
Thesis title
Mitochondrial glutathione homeostasis in
Saccharomyces cerevisiae.
Methylglyoxal and ageing in
Saccharomyces cerevisiae.
Development of methodologies for the
identification of miRNA species bound to
human Argonautes and analysis of
miRNA localisation.
The roles of miRNA in transcriptional and
post-transcriptional regulation of FoxOrelated genes
Redox homeostasis in Saccharomyces
cerevisiae: cellular mechanisms involved
in reductive stress tolerance
Thesis title
Genetic basis of gestation in diabetes
mellitus
Supervisor
Prof Ron Trent
Prof Ron Trent
University
Sydney
Sydney
28
PhD students (awarded)
Student
Supervisor
University
Katie Baines
Julia Morahan
Prof Rodney Scott
Prof Ron Trent
Newcastle
Sydney
Chong-Han Ng
Prof Ian Dawes
UNSW
Martin
Ostrowski
A/Prof Rick
Cavicchioli
UNSW
Bente Talseth
Jason Withford
Cave
Xin {Maggie}
Wang.
Prof Rodney Scott
Prof Ron Trent
Newcastle
Sydney
A/Prof Mark Gorrell
Sydney
PhD students (continuing)
Student
Thesis title
Environmental toxicants in sporadic motor
neuron disease
The study of cellular physiology roles of
SUMO ligase in Saccharomyces cerevisiae
Adaptation to nutrient limitation in a marine
oligotrophic ultramicrobacterium
Sphingopyxis alaskensis.
Genetic analyses in elite endurance athletes
Fibroblast activation protein in cell biology
and liver fibrosis.
Supervisor
Katie Ashton
Selmir Avdic
Prof Rodney Scott
Dr Barry Slobedman
Sean Barclay
Britt-Louise Carlsson
Eva Chen
Allen Cheung
Dr Bill Sherwin
Dr Alan Wilton
Prof Ian Dawes
Dr Barry Slobedman
Sharon Chow
Prof William Rawlinson
Mathew Cox
Romi Das Gupta
Prof Rodney Scott
Dr Ruby Lin, Prof Ian Dawes and Prof
Phil Crowe
Dr Bill Sherwin
Prof Ian Dawes
Dr Bill Sherwin
Prof Nick Hunt
Prof Nick Hunt
Dr Bill Sherwin
Prof Rodney Scott
Prof Ian Dawes
Prof Ron Trent
Prof Ian Dawes
A/Prof Thomas Preiss
Prof Ian Dawes and Dr Vince Higgins
Prof Nick Hunt
Prof Ian Dawes
Prof Rodney Scott
Prof Rodney Scott
A/Prof Thomas Preiss
Dr Alan Wilton and Dr Robert Mulley
Prof Rodney Scott
Dr Bill Sherwin
A/Prof Thomas Preiss
Dr Alan Wilton
Celine Frere
Christy Gelling
Jouytsna Gupta
Leia Hee
Tareen Ho
Clare Holleley
Carla Kairupan
Monica Lam
Huong Le
Johnny Lee
Cheryl Li
Duncan Macinnis
James McQuillan
Nadia Minarovic
Sophia Moscovis
David Mossman
Marco Nousch
Brad Purcell
Stuart Reeves
Lee-Ann Rollins
Alex Shaw
Jeremy Shearman
University
Newcastle
Sydney/Westmead
Millennium Institute
UNSW
UNSW
UNSW
Sydney/Westmead
Millennium Institute
UNSW/Prince of Wales
Hospital
Newcastle
UNSW
UNSW
UNSW
UNSW
Sydney
Sydney
UNSW
Newcastle
UNSW
Sydney
UNSW
UNSW/VCCRI
UWS
Sydney
UNSW
Newcastle
Newcastle
UNSW/VCCRI
UWS
Newcastle
UNSW
UNSW/VCCRI
UNSW
29
Patsy Soon
Joanne Tan
Shixiong Tan
Ben Tang
Matthew Traini
Abraham Tsoi
Bonnie Tsoi
Riccardo Villain
Dr Kerrie McDonald, Dr Dindy Benn,
Prof Bruce Robinson and A/Prof. Stan
Sidhu
Dr Barry Slobedman
Prof Ian Dawes and Dr Gabriel Perrone
Prof Anthony McLean, Prof Ian Dawes
and Dr Ruby Lin
Prof Ian Dawes
Prof Ian Dawes
Prof Ian Dawes and Dr Vince Higgins
Prof Rodney Scott
Sydney
Sydney/Westmead
Millennium Institute
UNSW
Sydney
UNSW
UNSW
UWS
Newcastle
Workshops and Seminars
Once again the Centre’s 2007 workshop and seminar programme focused on education
in the technologies central to its core business. The 2007 Quantitative RT-PCR
workshop was held in April. It was led by Dr Ruby Lin and sponsored by the
Ramaciotti Centre and Invitrogen, and was specifically designed to contribute to
technological education within the Facility’s host School (BABS) at UNSW. The
theory session was attended by 65 people, and more than 10 attended each of three
practical laboratory sessions. The majority of attendees were, as intended, students
from BABS. Others included 4 students from the Faculty of Medicine at UNSW, 2
from the Garvan Institute and 2 from Sydney University. The programme is outlined
below:
Session 1. Theory and Experimental Design
Dr Ruby Lin
Dr Francesco Pomati
Mark Cowley
Quantification of transcriptomes using SYBRgreen:
Experimental design and data analysis
Quantification of transcriptomes using TaqMan:
Experimental design and data analysis
delta-delta-Ct method, why we use log2, and comparing
qPCR to microarray measurements.
Each presentation was followed by a Group Discussion
Session 2. Practical Labs
Experimental setup and troubleshooting (2.5 hours).
.-.-.-.-.-.-.
The Centre also arranged and hosted several seminars throughout the year.
May 2007: In May the Centre hosted Dr Jeremy Preston from Millennium Science,
who presented an update seminar on the Affymetrix technology entitled ‘Next
generation whole transcript based expression profiling using exon and the new Gene
1.0 ST arrays’. This presentation introduced the exon arrays that target >1 million
exons from human, rat or mouse and interrogate both gene-level expression and
alternative splice variation on a single array. The new Human Gene 1.0 ST Arrays
30
enables interrogation across the full length of transcripts and require smaller starting
amounts of RNA than the earlier chip. The exon-centric probes provide a fundamental
shift away from the limitations of 3’-based expression profiling. These arrays were
offered by the Centre in the second half of 2007.
August 2007: Interpretation of microarray data remains a complex issue, and this was
addressed in the August seminar which was held at The Faculty of Information
Technology, UTS. Associate Professor Michael Ochs, from the Sidney Kimmel
Cancer Center at Johns Hopkins University, Baltimore, MD, USA spoke on ‘Issues in
high-throughput biological data analysis.’ Analysis of the massive data sets generated
by whole genome measurements at the genetic, transcript, protein, and metabolite level
requires solving multiple problems not faced previously in biological and medical
studies. This talk focused on the need for data management, data analysis, and
visualisation systems that are integrated syntactically and semantically. Semantic
linking raises especially difficult issues, and the use of ontologies and controlled
vocabularies were discussed. In addition, since biological and medical data studies
often rely on model organisms, which require linking of orthologous genes and
pathways, the problem of ortholog prediction at gene and pathway levels was
addressed.
October 2007: In October the UNSW Facility hosted as seminar entitled ‘ABI Next
Generation Sequencing’. Dr Mike Payne discussed sequencing, mapping and
transcriptomics applications and the unique dinucleotide ligation chemistry of the ABI
SOLiD System.
31
PUBLICATIONS AND PRESENTATIONS
The quality and range of the Centre's research continues to be demonstrated by the
publications and presentations arising from it. Those for 2007 are listed here.
Publications 2007
Book chapters and Reviews
Mendes A, Scott RJ and Moscato P. (2007). Microarrays - identifying molecular
portraits for prostate tumors with different gleason patterns. In ‘Cancer Epidemiology’
Ed. Makresh Verma. Humana Press Inc.
Scott RJ and Lubinski J. (2007). Genetic epidemiology studies in hereditary non
polyposis colorectal cancer. In ‘Cancer Epidemiology’ Ed. Makresh Verma. Humana
Press Inc.
Journal papers and refereed conference proceedings
Attia J, Thakkinstian A, Wang Y, Lincz L, Parsons M, Sturm J, McGettigan P, Scott
R, Meldrum C, Levi C. (2007). The PAI-1 4G/5G gene polymorphism and ischemic
stroke: an association study and meta-analysis. J Stroke Cerebrovasc Dis 16, 173-9.
Beilharz TH and Preiss T. (2007). Widespread use of poly(A) tail length control to
accentuate expression of the transcriptome in S. cerevisiae. RNA 13, 982-97.
Beilharz TH and Preiss T. (2007). 'Cradle to grave' regulation of mRNA fate.
Microbiol Australia 28, 85-6.
Ball HJ, Sanchez-Perez A, Weiser S, Austin CJD, Astelbauer F, Miu J, McQuillan J,
Stocker R, Jermiin LS and Hunt NH. (2007). Characterization of an indoleamine 2,3dioxygenase-like protein found in humans and mice. Gene 396, 203-13.
Bowden NA, Croft A and Scott RJ. (2007). Gene expression profiling in familial
adenomatous polyposis adenomas and desmoid disease. Hered. Cancer in Clin. Prac. 5,
79-96.
Bowden NA, Scott RJ and Tooney PA. (2007). Altered expression of regulator of Gprotein signalling 4 (RGS4) mRNA in the superior temporal gyrus in schizophrenia.
Schiz Res 89, 165-8.
Branka M, Cunningham A L and Diefenbach RJ. (2007) Residues F593 and E596 of
HSV-1 tegument protein pUL36 (VP1/2) mediate binding of tegument protein pUL37.
Virol 368, 26-31.
Catchpoole DR, Lail A, Guo D, Chen Q and Khan J. (2007). Identification of gene
expression profiles that segregate patients with childhood acute lymphoblastic
leukaemia: An independent validation study. Leukaemia Res 31, 1741-7.
32
Clancy JL, Nousch M, Humphreys DT, Westman BJ, Beilharz TH and Preiss T.
(2007). Methods to analyse microRNA-mediated control of mRNA translation.
Methods Enzymol 431, 83-111.
Cunningham AL, Harman AN and Donaghy H. (2007).
immune evasion and infection. Nat Immunol 8, 556-8.
DC-SIGN ‘AIDS’ HIV
Davies SC, Taylor JA, Sedyaningsih-Mamahit ER, Gunawan S, Cunningham AL and
Mindel A. (2007). Prevalence and risk factors for herpes simplex type 2 antibodies
among low- and high- risk populations in Indonesia. Sex Trans Dis 34, 132-8.
Dawes IW, Kornfeld GD and Perrone GG. (2007). Functional genomics in yeast.
Microbiology Australia 28, 51-4.
Debniak T, Scott RJ, Gorski B, Cybulski C, van der Wetering T, Serrano-Fernandez P,
Huzarski T, Byrski T, Nagay L, Debniak B, Kowalska E, Jakubowska A, Gronwald J,
Wokolorczyk D, Maleszka R, Kladny J and Lubinski J. (2007). Common variants of
DNA repair genes and malignant melanoma. Eur J Cancer Epub ahead of print Nov
20.
Dickson N, van Roode T, Herbison P, Taylor J, Cunningham AL and Paul C. (2007).
Risk of HSV-2 acquisition increases over early adulthood – evidence from a cohort
study. Sex Transm Infect. 83, 87-90.
Gao L, Kwan JC, Macdonald PS, Yang L, Preiss T and Hicks M. (2007). Improved
poststorage cardiac function by poly (ADP-ribose) polymerase inhibition: role of
phosphatidylinositol 3-kinase Akt pathway. Transplantation 84, 380-6.
Gorry PR, McPhee DA, Verity E, Dyer WB, Wesselingh SL, Learmont J, Sullivan JS,
Roche M, Zaunders JJ, Gabuzda D, Crowe SM, Mills J, Lewin SR, Brew BJ,
Cunningham AL and Churchill MJ. (2007). Pathogenicity and immunogenicity of
attenuated, nef-deleted HIV-1 strains in vivo. Retrovirology 4, 66.
Gowrishankar K, Slobedman B, Cunningham AL, Miranda-Saksena M, Boadle RA
and Abendroth A. (2007). Productive varicella-zoster virus infection of cultured
intact human ganglia. J Virol 81, 6752-6.
Gray L, Churchill MJ, Sterjovski J, Witlox K, Learmont JC, Sullivan JS, Wesselingh
SL, Gabuzda D, Cunningham AL, McPhee DA and Gorry PR. (2007). Phenotype and
envelope gene diversity of nef-deleted HIV-1 isolated from long-term survivors
infected from a single source. Virology 4, 75.
Hild E, Brumbley SM, O’Shea MG, Nevalainen KMH and Bergquist PL. (2007). A
Paenibacillus dextranase mutant pool with improved thermostability and activity.
Appl Microbiol Biotechnol 75, 1071-8.
Hunt NH and Stocker R. (2007). Heme moves to center stage in cerebral malaria.
Nature Medicine 13, 667-9.
33
Jakubowska A, Gronwald J, Menkiszak J, Gorski B, Huzarski T, Byrski T, Edler L,
Lubinski J, Scott RJ and Hamann U. (2007). The RAD51 135 G>C polymorphism
modifies breast cancer and ovarian cancer risk in Polish BRCA1 mutation carriers.
Cancer Epid Bio and Prev 16, 270-5.
Jakubowska A, Gronwald J, Menkiszak J, Gorski B, Huzarski T, Byrski T, Edler L,
Lubinski J, Scott RJ and Hamann U. (2007). Integrin {beta}3 Leu33Pro polymorphism
increases BRCA1-associated ovarian cancer risk. J Med Genet 44, 408-11.
Jakubowska A, Gronwald J, Menkiszak J, Górski B, Huzarski T, Byrski T, Edler L,
Lubiński J, Scott RJ and Hamann U. (2007). The VEGF_936_C>T 3'UTR
polymorphism reduces BRCA1-associated breast cancer risk in Polish women. Cancer
Lett. Dec 31 [Epub ahead of print].
Jaworowska E, Serrano-Fernandez P, Tarnowska C, Kram A, Masojic B, Scott R and
Lubinski J. (2007). Clinical and epidemiological features of familial laryngeal cancer
in Poland. Cancer Detect Prev Oct 10 [Epub ahead of print].
Kairupan C and Scott RJ. (2007). Base excision repair and the role of MUTYH. Hered
Cancer in Clin Prac 5, 199-209.
Lackner DH, Beilharz TH, Marguerat S, Mata J, Watt S, Preiss T and Bähler J. (2007).
A network of multiple regulatory layers shapes gene expression in fission yeast. Mol
Cell 26, 145-55.
Lin C.Y.R, Chong G, Zhang Y, Cowley M, Whitworth J and Dawes I W. (2007).
ACTH-treated rats: a model to study IGFR-PI3K regulon. Hypertension 49, 1471.
Lubinski J, Korzen M, Gorski B, Cybulski C, Debniak T, Jakubowska A, Medrek K,
Matyjasik J, Huzarski T, Byrski T, Gronwald J, Masojc B, Lener M, Szymanska A,
Szymanska-Pasternak J, Fernandez PS, Wokolorczyk D, Piegat A, Ucinski M,
Domagala P, Kladny J, Gorecka B, Scott R and Narod S. (2007). Breast cancer
susceptibility genes. J BUON Suppl 1, S23-9.
Matyjasik J, Cybulski C, Masojc B, Jakubowska A, Serrano-Fernandez P, Gorski B,
Debniak T, Huzarski T, Byrski T, Gronwald J, Zlowocka E, Narod SA, Scott R and
Lubinski J. (2007). CYP1B1 and predisposition to breast cancer in Poland. Breast
Cancer Res Treat April 26 [Epub ahead of print]
Mhaidat NM, Zhang ZD, Allen J, Kiejda-Avery K, Scott RJ, and Hersey P. (2007)
Temozolomide induces senescence but not apoptosis in human melanoma cells. Br J
Cancer 97, 1225-33.
Mommersteeg MTM, Brown NA, Prall OWJ, de Gier-de Vries C, Harvey RP,
Moorman AFM and Christoffels VM. (2007). Pitx2 and Nkx2-5 are required for the
formation and identity of the pulmonary myocardium. Circulation Res 101, 902-9.
Mommersteeg MTM, Hoogaars WMH, Prall OWJ, de Gier-de Vries C, Wiese C,
Papaioannou VE, Brown NA, Harvey RP, Moorman AFM and Christoffels VM.
34
(2007) Molecular pathway for the localized formation of the sinoatrial node.
Circulation Res 100, 354-62.
Morahan JM, Yu B, Trent RJ and Pamphlett R. (2007). Are metallothein genes
silenced in ALS? Toxicology Letters 168, 83-7.
Morahan JM, Yu B, Trent RJ and Pamphlett R. (2007). A gene-environment study of
the paraoxonase 1 gene and pesticides in amyotrophic lateral sclerosis.
Neurotoxicology 28, 532-40.
Myles S, Hradetsky E, Engelken J, Lao, O, Nurnberg P, Trent RJ, Wang, Z, Kayser M
and Stoneking M. (2007). Identification of a candidate genetic variant for the high
prevalence of type II diabetes in Polynesians. Eur J Human Genet 15, 584-9.
Nousch N, Reed V, Bryson-Richardson R, Currie P and Preiss T. (2007). The eIF4G
homologue p97/DAP5 can activate translation independent of caspase cleavage. RNA
13, 374-84.
Prall OWJ, Menon MK, Solloway MJ, Watanabe Y, Zaffran S, Bajolle F, Biben C,
McBride JJ, Robertson BR, Chaulet H, Stennard FA, Wise N, Schaft D, Wolstein O,
Furtado MB, Shiratori H, Hamada H, Black BL, Saga Y, Robertson EJ, Buckingham
ME and Harvey RP. (2007). A Nkx2-5/Bmp2/Smad1 negative feedback loop
orchestrates cardiac progenitor cell specification and proliferation in the second heart
field. Cell 128, 947-59.
Saunderson RB, Yu B, Trent RJA and Pamphlett R. (2007). An analysis of the
enteroviral binding domains of intercellular adhesion molecule-1 and coxsackie
adenovirus receptor in motor neuron disease. Amylotrophic Lateral Sclerosis 8, 26-30.
Saunderson RB, Yu B, Trent RJA and Pamphlett R. (2007). Low yield in screening
patients with sporadic motor neuron disease for Kennedy disease. Int Med J 37, 772-4.
Scandurra GM, Williams RBH, Triccas JA, Pinto R, Gicquel B, Slobedman B,
Cunningham AL and Britton WJ. (2007). Effect of phthiocerol dimycocerosate
deficiency on the transcriptional response of human macrophages to Mycobacterium
tuberculosis. Microbes and Infection 9, 87-95.
Shearman, JS and Wilton AN. (2007). Elimination of neutrophil elastase and adaptor
protein complex 3 subunit genes as the cause of trapped neutrophil syndrome (TNS) in
Border collies. Animal Genet 38, 188-9.
Siero F, Biben C, Martinez-Munoz L, Mellado M, Ransohoff RM, Li M, Woehl B,
Leung H, Groom J, Batten M, Harvey RP, Martinez-A, Mackay CR and Mackay F.
(2007). Disrupted cardiac development but normal hematopoiesis in mice deficient in
the second CXCL12/SDF-1 receptor, CXCR7. Proc Natl Acad Sci (USA) 104, 1475964.
Simpson JL, Powell H, Boyle MJ, Scott RJ and Gibson PG. (2007). Clarithromycin
targets neutrophilic airway inflammation in refractory asthma. Am J Respir Crit Care
Med Oct 18; Epub ahead of print
35
Stefani M, Markus M.A, Lin RCY, Pinese M, Dawes IW and Morris BJ. (2007). The
effect of resveratrol on a cell model of human aging. Ann NY Acad Sci 1114, 407-18.
Sterjovski J, Churchill MJ, Ellett A, Gray LR, Roche MJ, Dunfee RL, Purcell DFJ,
Saksena N, Wang B, Sonza S, Wesselingh SL, Karlsson I, Fenyo E-M, Gabuzda D,
Cunningham AL and Gorry PR. (2007). Asn 362 in gp120 contributes to enhanced
fusogenicity by CCR5-restricted HIV-1 envelope glycoprotein variants from patients
with AIDS. Retrovirology 4, 89.
Talseth BA, Ashton KA, Meldrum C, Suchy J, Kurzawski G, Lubinski J and Scott RJ.
(2007). Aurora-A and cyclin D1 polymorphisms and the age of onset of colorectal
cancer in hereditary nonpolyposis colorectal cancer. Int J Cancer Nov 20 [Epub ahead
of print].
Talseth BA, Meldrum CJ, Suchy J, Kurzawski G, Lubinksi J and Scott R.J. (2007).
MDM2 SNP309 alone or in combination with the TP53 R72P polymorphism does not
appear to influence disease expression and age of diagnosis of colorectal cancer in
HNPCC patients. Int J Cancer 120, 563-5.
Talseth B, Meldrum CJ, Suchy J, Kurzawski G, Lubinski J and Scott RJ. (2007). Lack
of association between genetic polymorphisms in cytokine genes and disease
expression in HNPCC patients. Scand. J. Gastroenterol 42, 628-32.
Tang BMP, McLean AS, Dawes IW, Huang SJ and Lin RCY. (2007). The use of
gene-expression profiling to identify candidate genes in human sepsis. Am J Resp Crit
Care Med 176, 676-84.
Verity E, Zotos D, Wilson K, Chatfield C, Lawson V, Dwyer D, Cunningham AL,
Learmont J, Sullivan J, Churchill M, Gorry P and McPhee D. (2007). Viral
phenotypes and antibody responses in long term survivors infected with attenuated
Human Immunodeficiency Virus Type 1 containing deletions in the nef and long
terminal repeat regions. J Virol 81, 9268-78.
Watson S, Mercier S, Bye C, Wilkinson J, Cunningham AL and Harman A. (2007).
Determination of suitable housekeeping genes for normalisation of quantitative real
time PCR analysis of cells infected with Human Immunodeficiency Virus and Herpes
Viruses. Virol J 4, 130.
Weiser S, Miu J, Ball HJ and Hunt NH. (2007). Interferon-γ synergises with tumour
necrosis factor and lymphotoxin-α to enhance the mRNA and protein expression of
adhesion molecules in mouse brain endothelial cells. Cytokine 37, 84-91.
Xu Y, Hunt NH and Bao S. (2007). The correlation between proinflammatory
cytokines, MAdCAM-1 and cellular infiltration in the inflamed colon from TNF-alpha
gene knockout mice. Immunol and Cell Biol 85, 633-9.
Zlowocka E, Cybulski C, Gorski B, Debniak T, Slowjewski M, Wokolorczyk D,
Serrano-Fernandez P, Matyjasik J, van de Wetering T, Sikorski A, Scott RJ and
36
Lubinski J. (2007). Germline mutations in the CHEK2 kinase gene are associated with
an increased risk of bladder cancer. Int J Cancer Oct 4 [Epub ahead of print].
Presentations 2007
Plenary and invited presentations
Cunningham AL. (2007). New control strategies for managing viral diseases.
Communicable Diseases Control Conference. 14-15 March (Canberra).
Cunningham AL. (2007). HIV uptake by and infection of DCs. Keystone Symposia
on HIV pathogenesis and vaccines. 25-30 March (Whistler, British Columbia,
Canada).
Cunningham AL. (2007). Towards a vaccine for genital herpes. Inaugural Symposium
Australian Centre for Vaccine Development, May (Brisbane).
Harvey RP. (2007). Coordination of the multiple roles of Bmps in cardiogenesis.
Gordon Conference: Myogenesis. Il Ciocco Resort, Italy (May).
Harvey RP. (2007). Identification and quantification of multipotent stem cells in the
mammalian heart. International Society of Stem Cell Research Meeting. Cairns (June).
Harvey RP. (2007). Cardiac development and congenital heart disease. Genetics
Society of Australia. June (Sydney).
Harvey RP. (2007). Cardiac development and congenital heart disease. Rosa
Beddington Lecture, 19th Annual Mouse Molecular Genetics Meeting. Sanger Centre,
Cambridge, UK (September).
Harvey RP. (2007). (2007). Multipotent progenitor cells in the developing and adult
murine heart. NHLBI Symposium on Cardiovascular Regenerative Medicine. National
Institutes of Health, Bethesda, MA, USA (October).
Hunt NH. (2007). Tryptophan metabolism and cerebral malaria. Australian Society
for Biochemistry and Molecular Biology. September (Sydney).
Abstracts
Carr VJ, Loughland CM, Draganic D, Lewin TJ, Schall U, Scott R, Jablensky A,
Mowry B, Michie P, Catts S, Hneskens F and Pantelis C. (2007). The Australian
Schizophrenia Research Band (ASRB). Int Cong Schizophrenia Res. March 28-April 1
(Colorado Springs, USA).
Catchpoole D. (2007) From inundated to understanding: tumours and microarray
analysis. Royal College of Pathologists Australia Pathology Update (Sydney).
37
Chiu J, Wouters MA and Dawes IW. (2007). Investigation of the role of a reactive
cysteine in Swi6p in the regulation of cell cycle progression. 28th Lorne Genome
Conference, 11-15 February (Lorne, Victoria). Abstract 026, p. 37.
Chiu J, Wouters M and Dawes IW. (2007). Investiugation of the oxidative stress
sensing mechanism of Swi6 for cell cycle regulation in Saccharomyces cerevisiae.
XXIII Int Conf Yeast Genet Mol Biol. 1-6 July (Melbourne). Yeast 24: S107.
Chiu J, Wouters MA, Rogers PJ and Dawes IW. (2007). Cell cycle regulation by
SWI6 in response to oxidative stress in Saccharomyces cerevisiae ComBio2007,
Combined Conf. Australian Soc. Biochem. Molec. Biol., Australia NZ Soc. Cell
Develop. Biol., Australian Soc. Plant Scientists. 22-26 September (Sydney) p. 132.
POS-TUE-23.
Choudhary PR, Gibbs MD, Reeves RA, Nevalainen KM and Bergquist PL. (2007).
Improvement on the alkaliphilic performance of a thermostable β-xylanase, XynB6,
isolated from Dictyoglomus thermophilum. Enzyme Engineering XXIX, 23-28
September (Harrison Hot Springs, BC, Canada).
Collinson EJ, Chan B and Dawes IW. (2007). Pkc1p interacts with PKA and Pde2p in
order to increase intracellular levels of glycogen, camp, programmed cell death and to
depolarise the actin cytoskeleton. XXIII Int Conf Yeast Genet Mol Biol. 1-6 July
(Melbourne). Yeast 24: S107.
Cowley MJ, Williams RBH, Cotsapas CJ, Chan EKF, Pulvers JN, Liu M, Nott DJ, Lin
RCY and Little PFR. (2007). Genetic variation affects mRNA levels in a tissue
specific manner. Cold Spring Harbor Laboratory meeting: The Biology of Genomes.
8-12 May (Cold Spring Harbor, NY, USA)
Cristescu R, Tanaka M, Herbert C, Carlyon K, Wilton A, Whisson D, Handasyde K,
Cahill V and Cooper D. (2007). Genetic variation in koalas on French Island and
Kangaroo Island and the likely effect of contraception protocols on its retention.
Genet Soc AustralAsia. 26 – 29 June (Sydney).
Dawes IW, Palmisano LJ and Kornfeld GD. (2007). An intronic sequence involved in
regulating expression of yeast genes encoding core spliceosomal proteins. 28th Lorne
Genome Conference, 11-15 February (Lorne, Victoria). Abstract 028, p. 38.
Gauci VJ, Rogers PJ, Dawes IW and Higgins VJ. (2007). The Saccharomyces
cerevisiae response to zinc deficiency involves an MSN2,4 transcriptional response
and G1 cell cycle arrest. XXIII Int Conf Yeast Genet Mol Biol. 1-6 July (Melbourne).
Yeast 24: S30.
Gelling C, Mühlenhoff U, Richhardt N, Kornfeld G, Lill R and Dawes IW. (2007). A
new iron-sulphur cluster metabolism protein. XXIII Int Conf Yeast Genet Mol Biol. 1-6
July (Melbourne). Yeast 24: S73
Gelling C, Mühlenhoff U, Richhardt N, Lill R and Dawes IW. (2007). Identification of
a new iron-sulphur cluster biogenesis factor in Saccharomyces cerevisiae.
ComBio2007, Combined Conf. Australian Soc. Biochem. Molec. Biol., Australia NZ
38
Soc. Cell Develop. Biol., Australian Soc. Plant Scientists. 22-26 September (Sydney)
p. 108. POS-MON-19.
Gibson PG, Baines KJ, Simpson JL and Scott RJ. (2007). Gene expression profiling
identifies neutrophilic and eosinophilic asthma as distinct subtypes. European
Respiratory Society Conference, 15-19 September (Stockholm).
Hardiman E, Gibbs M, Reeves R and Bergquist P. (2007). Directed evolution of a
beta-glucosidase using random drift mutagenesis. Enzyme Engineering XXIX, 23-28
September (Harrison Hot Springs, BC, Canada).
Lam YT, Dawes IW and Stocker R. (2007). Effects of antioxidants on yeast S.
cerevisiae replicative ageing.
ComBio2007, Combined Conf. Australian Soc.
Biochem. Molec. Biol., Australia NZ Soc. Cell Develop. Biol., Australian Soc. Plant
Scientists. 22-26 September (Sydney) p. 75. Symp 46-04.
Lam YT, Suarna C, Stocker R and Dawes IW. (2007). Effects of antioxidants on yeast
cell replicative ageing. XXIII Int Conf Yeast Genet Mol Biol. 1-6 July (Melbourne).
Yeast 24: S121.
Lin RCY, Williams RBH, Du XJ, Gao XM, Kiriazis H and McMullen JR. (2007).
Gene expression profiling in a mouse model of myocardial infarction with enhanced or
depressed PI3K activity. High Blood Pressure Research Council of Australia, 5-7
December (Adelaide).
Lyons V, Rogers PJ, Dawes IW and Higgins VJ. (2007). Functional genomic analysis
of H2S production in an industrial strain of yeast. XXIII Int Conf Yeast Genet Mol Biol.
1-6 July (Melbourne). Yeast 24: S33.
Macinnes D, Rogers PJ, Smillie R, Dawes IW and Higgins VJ. (2007). A
metabolomics type investigation into the effect of the deletion of the isoamyl acetate
hydrolase gene, IAH1. XXIII Int Conf Yeast Genet Mol Biol. 1-6 July (Melbourne).
Yeast 24: S33.
Minarovic N and Dawes I. (2007). A novel regulatory site in the GCV2 promoter.
XXIII Int Conf Yeast Genet Mol Biol. 1-6 July (Melbourne). Yeast 24: S85.
Mirto LV, Thorpe GW, Beh EJ, Dawes IW and Higgins VJ. (2007). The age old
mystery of aging - a genome-wide functional analysis in Saccharomyces cerevisiae.
XXIII Int Conf Yeast Genet Mol Biol. 1-6 July (Melbourne). Yeast 24: S123.
Mossman D and Scott RJ. (2007). Global DNA methylation levels and response to
treatment with a methyltransferase inhibitor. HMRI Cancer Research Program
Meeting, 15-16 March (Newcastle, Australia).
Mossman D and Scott RJ. (2007). Global methylation analysis by high performance
liquid chromatography. 11th Int Congress of Human Genet. 6-10 August (Brisbane).
39
Mossman D and Scott RJ. (2007). Cancer cells differ in their ability to perform DNA
methylation which may be responsible for tumour development. Epigenet Conf. 4-7
November (Perth).
Ng C-H, Schmidt B, Dawes I and Hogg P. (2207). The role of disulphide bond on
copper loading of Sod1p. XXIII Int Conf Yeast Genet Mol Biol. 1-6 July (Melbourne).
Yeast 24: S74.
Park DR, Dilda PJ, Perrone GG, Dawes IW and Hogg PJ. (2007). Defining the
molecular target of the new cancer drug, GSAO. ComBio2007, Combined Conf.
Australian Soc. Biochem. Molec. Biol., Australia NZ Soc. Cell Develop. Biol.,
Australian Soc. Plant Scientists. 22-26 September (Sydney) p. 100, POS-SUN-77.
Rollins. LA. (2007). Range expansions, rare mutations and novel environments:
evolution in progress? Australasian Evolution Society 5th Annual Conference, 12-15
June (Sydney).
Rollins. LA. (2007). Range expansions, rare mutations and novel environments:
evolution in progress? Genet Soc AustralAsia 54th Annual Conference, 27-29 June
(Sydney).
Rollins. LA. (2007). The importance of winning the battle - even if you can't
win the war. Soc for Conservation Biol, Australasian Section: Biodiversity Extinction
Crisis Conference - A Pacific Response, 10-12 July (Sydney).
Rollins. LA. (2007). Genetic changes in invasive populations on the edge of a range
expansion. ConGen3: The 3rd International Conservation Genetics Symposium, 27-29
September (American Museum of Natural History, New York, USA).
Rollins. LA. (2007). Genetic changes in invasive populations on the edge of a range
expansion. The 6th International Zoo and Wildlife Research Conference on
Behaviour, Physiology and Genetics, 7-10 October (Berlin, Germany).
Rudolph HK, Moser S, Ehehalt D, Soehnlen S, Philipp R, Riedmaier S, Kraus S,
Zappe A, Fiebig, Bandzuchova E, Hauser K, Handaja C, Breitling J, Perrone G, Dawes
IW and Madeo F. (2007). Distinct Ca2+ or Mn2+ fluxes via the Hailey-Hailey disease
ortholog Pmr1 are vital during ageing and heat. XXIII Int Conf Yeast Genet Mol Biol.
1-6 July (Melbourne). Yeast 24: S124.
Tan S, Mariati, Traini M, Perrone G and Dawes I. (2007). Cellular mechanisms
involved in defense against conditions that generate endoplasmic reticulum stress.
XXIII Int Conf Yeast Genet Mol Biol. 1-6 July (Melbourne). Yeast 24: S153.
Temple MD and Dawes IW. (2007). WWW.Yeastinformatics.org. 28th Lorne
Genome Conference, 11-15 February (Lorne, Victoria). Abstract 105, p. 52.
Tan S, Teo M, Traini MD, Perrone GG and Dawes IW. (2007). Genome-wide screen
of Saccharomyces cerevisiae deletion collection using different conditions that
generate endoplasmic reticulum stress reveal cellular mechanisms required for ER
stress tolerance. ComBio2007, Combined Conf. Australian Soc. Biochem. Molec. Biol.,
40
Australia NZ Soc. Cell Develop. Biol., Australian Soc. Plant Scientists 22-26.
September (Sydney) p. 124. POS-MON-83.
Tsoi A, Lee JC, Gelling CL, Kornfeld GD and Dawes IW. (2007). The role of Lthreonine metabolism in the yeast Saccharomyces cerevisiae. XXIII Int Conf Yeast
Genet Mol Biol. 1-6 July (Melbourne). Yeast 24: S154.
Tsoi AM, Lee JC, Gelling CL, Kornfeld GD and Dawes IW. (2007). Modelling amino
acid catabolic pathways. ComBio2007, Combined Conf. Australian Soc. Biochem.
Molec. Biol., Australia NZ Soc. Cell Develop. Biol., Australian Soc. Plant Scientists.
22-26 September (Sydney) p. 125. POS-MON-88.
Tsoi B, Beckhouse A, Chui J, Rogers PJ, Higgins VJ and Dawes IW. (2007). The role
of Gcn4p in adaptation to anaerobic growth of Saccharomyces cerevisiae. XXIII Int
Conf Yeast Genet Mol Biol. 1-6 July (Melbourne). Yeast 24: S41.
Tsoi BM, Beckhouse AG, Chiu J, Rogers PJ, Higgins VJ and Dawes IW. (2007). The
role of Gcn4p and Bas1p in adaptation to anaerobic growth of Saccharomyces
cerevisiae. ComBio2007, Combined Conf. Australian Soc. Biochem. Molec. Biol.,
Australia NZ Soc. Cell Develop. Biol., Australian Soc. Plant Scientists. 22-26
September (Sydney) p. 104. POS-MON-03.
Wang XM, Cordoba S, Evans K, Marguet D, Rettig W, Schnapp A, McCaughan GW
and Gorrell MD. (2007). Improved hepatic fibrosis in a model of chronic liver injury is
associated with fewer intrahepatic B cells in fibroblast activation protein and
dipeptidyl peptidase IV gene knockout mice. Combio2007. Combined Conf. Australian
Soc. Biochem. Molec. Biol., Australia NZ Soc. Cell Develop. Biol., Australian Soc.
Plant Scientists. 22-26 September. Sydney. Proc Australian Soc Biochem and Mol
Biol 39, 122.
Wang XM, Cordoba S, Marguet D, Retting W, Schnapp A, McCaughan GW and
Gorrell MD. (2007). Reduced hepatic fibrosis is associated with fewer intrahepatic B
cells in fibroblast activation protein and dipeptidyl peptidase IV gene knockout mice.
58th Annual Meeting of the American Association of the Study of Liver Diseases.
November (Boston, USA). Hepatol, 46 (Suppl) 299A.
Wilton AN. (2007). DNA Methods of Diagnosing Disease In Animals. 32nd World
Small Animal Veterinary Association Congress. 20-23 August (Sydney). In:
http://www.ivis.org/proceedings/wsava/2007/pdf/54_20070331221535_abs.pdf
Wilton AN and Shearman JS. (2007). Use of comparative genomics in Identifying
disease genes in dogs. Genet Soc AustralAsia. 26 – 29 June (Sydney).
Wilton AN and Shearman JS. (2007). Use of homozygosity to detect disease genes in
dogs breeds. 6th Australasian Human Gene Mapping Conference – GeneMappers.
29-31 August (Brisbane).
Wong NC, Heath J, Algar E, Mossman D, Scott RJ, Craig J, Saffery R and Ashley D.
(2007). Uncovering epigenetic changes in paediatric acute lymphoblastic leukaemia.
Cancer Genet & Epigenet. 20-25 May (Il Ciocco, Lucca, Italy).
41
Wright E, Aldrich-Wright JR, Wheate NJ, Dawes IW and Higgins VJ. (2007). The use
of Saccharomyces cerevisiae deletion mutant library to elucidate the molecular
mechanisms involved in the eukaryote response to the novel platinum anticancer
compound 56MESS. XXIII Int Conf Yeast Genet Mol Biol. 1-6 July (Melbourne).
Yeast 24: S139.
Wright E, Aldrich-Wright JR, Wheate NJ, Dawes IW and Higgins VJ. (2007).
Molecular mechanisms involved in the Saccharomyces cerevisiae response to the
novel anticancer platinum compound 56MESS. J. Biol. Inorg. Chem. 12:S139.
42