BABS Annual Report 2010.indd

Transcription

School of Biotechnology and
Biomolecular Sciences
Annual Report 2010
Never Stand Still
Faculty of Science
School of Biotechnology and Biomolecular Sciences
Biological Sciences Building
The University of New South Wales
Kensington NSW 2033 Australia
www.babs.unsw.edu.au
Tel: 61 2 9385 2029 Fax: 61 2 9385 1483
Editor: Michele Potter
Design: Print Post Plus (P3) Design Studio
Printed: -XO\
Cover Images: 3
Disclaimer The information contained in this publication is correct at the time of printing but may be subject
to change without notice. Please check the School’s website for the latest information. The University of New
South Wales assumes no responsibility for the accuracy of information provided by third parties.
© 2011 The University of New South Wales
Published June 2011
CRICOS Provider Number 00098G
Biomolecular Sciences
Annual Report 2010
02 // BABS ANNUAL REPORT 2010
03
Contents
06 Foreword from Head of School
07 School Management
School Executive Committee
07
08 School at a Glance
10
12
18
Research
08
Learning and Teaching
09
Postgraduate Research
09
PhDs
09
Our People
Academic Staff
10
Professional & Technical Staff
10
Research Staff
10
Visiting Staff
11
Infectious Disease Group
Viruses and Breast Cancer
13
The Pathogenesis of the Emergent Pathogen
Campylobacter Concisus
14
The Role of Oral and Intestinal Bacteria in Chronic
Human Diseases
15
Frequent Multiple Hepatitis C Virus Infections Among Injection
Drug Users in a Prison Setting
17
Molecular Medicine Group
Immunoglobulin Genes, Repertoire Development and the
1000 Immunomes Project
19
Everything Old Can Be New Again
20
Human Telomeric DNA Sequences Major Target for Antitumour
Drug Bleomycin
21
22 Systems and Cellular Biology Group
Oxidative Stress
23
The Candidate Complex Approach for Linking Mutations with Disease
25
27 Environmental Microbiology Group
An Ocean of Microbes
28
Bacteria, Global Warming and Bleaching in a Marine Seaweed
30
Oxygenating the Earth: Resolving the Timing of the Origin of
Oxygen-Producing Photosynthesis in Cyanobacteria
32
34 Profile: Professor Bill Rawlinson AM
36 Profile: Professor David Sinclair
38 External Partners
40 Memberships in Societies and Associations
41
Research Centres
The Ramaciotti Centre for Gene Function Analysis
41
Centre for Marine Bio-Innovation
43
Evolution & Ecology Research Centre
45
Australian Centre for Astrobiology
46
47 Infrastructure and Facilities
Seahorse Extracellular Flux (XF) Analyser
47
C1Si Confocal Microscope
47
Single-Cell Analysis Facility
47
UNSW Recombinant Products Facility
48
Canine Genetics Facility
48
Molecular and Image Analysis Facility (MIAF)
48
Other specialised amenities in BABS
48
49 Learning and Teaching
Innovations in Teaching
49
Recognition of BABS Teaching Staff
49
Modern Facilities
50
Outreach and Supporting Students
50
Undergraduate Degrees
51
Bachelor Programs
51
Majors
51
Combined Degrees
52
Honours
52
Postgraduate Degrees
52
MPhil (BABS)
52
53 2010 Student Awards and Prizes
54 BABSOC
Biotechnology and Biomolecular Science Students Society
55 2010 PhD Completions
56 2010 Honours Projects
58 Research Funding
63 2010 Publications
54
05
Vision
At the School of Biotechnology and
Biomolecular Sciences we believe that the
greatest challenges in biology are ahead.
Our vision and resources are directed
towards addressing these challenges and
communicating the results to the scientific
community and to the general public.
Mission
We aim to create a community dedicated to
achieving national and international levels
of scholarship in the fields of biotechnology
and biomolecular sciences.
Aims
The School of Biotechnology and
Biomolecular Sciences aims to:
be nationally and internationally
recognised as a source of scholarship
apply cutting-edge biotechnology to
capitalise on biomolecular discoveries
train and enthuse students
further interdisciplinary research
positively interact with researchers and
students across the university, the state,
the nation and the globe
Foreword from Head of School
I am pleased to present the 2010 Annual Report
and to have the opportunity to showcase the
School’s collective successes and achievements in
what was an exciting, challenging and stimulating
year for BABS.
This past year the School augmented its traditional
strengths through provision of further high quality
laboratory space and cutting-edge technologies.
Considerable refurbishments to the Biosciences
Building were completed, including updated PC1
and PC2 tissue culture laboratories and a state-ofthe-art PC2 teaching laboratory. We also welcomed
upgrades to some meeting spaces and to the staff
breakout area, the Samuels Tearoom.
During 2010, the School was recognised by the
Australian Academy of Science, with Scientia
Professor Staffan Kjelleberg elected a member of
the Academy and Dr Mark Tanaka awarded the
prestigious Moran Medal. The School now hosts
three members of the Academy, highlighting
distinct pinnacles of research excellence.
The School has 33 academic staff, with the
number of ARC and NHMRC research fellows
growing substantially over the past 3 years. At the
time of writing, the School is now home to 1 ARC
Federation Fellow, 1 ARC Professorial Fellow, 2
ARC QEII Fellows, 2 ARC Future Fellows, 2 ARC
Postdoctoral Fellows, and 1 NHMRC Training
(Postdoctoral) Fellow. Our researchers continue
to achieve competitive success rates, with a
strong trend in increased Category 1 funding. In
2010, researchers in the School were awarded 7
Category 1 grants totalling $3.338M, and School
staff authored or co-authored 181 refereed
publications, of which 164 were in ERA ranked
journals.
to the excellent shared facilities available to our
researchers. This includes a Seahorse Extracellular
Flux (XF) Analyser, a recent technology that
dramatically improves cellular bioenergetic studies,
one of only two such analysers in Australia. We
also purchased a revolutionary true spectral
imaging confocal laser microscope system with the
capability to acquire 32 channels of fluorescence
spectra over a 320 nm wide wavelength range in a
single pass.
The School is committed to high quality research
training, and currently employs 25 Postdoctoral
Research Fellows on a wide variety of grants
and research projects. Another important group
for BABS is our postgraduate students, the next
generation of researchers. Postgraduate research
student numbers have grown substantially over the
past 3 years, with 152 in 2010.
The School’s teachers continue to perform
above the general high standard of the Faculty
of Science, with Dr Louise Lutze-Mann being
recognised with the Vice-Chancellor’s 2010 Award
for Teaching Excellence as well as an Australian
Learning and Teaching Council Teaching Citation.
Undergraduate student enrolments in BABS1201
peaked at 996 in 2010, and we expect that student
numbers in second and third year subjects should
increase accordingly in coming years.
Other significant events during the year included
the School becoming a member of AusBiotech,
introduction of the BABS Head of School Paper
of the Month award, another successful offsite
research day for all our researchers, and
continuation of the School’s strong seminar
program, including a summer series on
Bioinformatics.
As the number of talented researchers joining the
School has increased, greater depth and breadth
in research capacity and expertise has been
achieved. This expertise was recognised in the
2010 ERA scores, where in the high level Category
06 for Biological Sciences, the University of NSW
was awarded the top rating of 5 overall.
I would like to thank all those who contributed to
the School’s success during 2010, particularly the
Executive Committee for their valuable support and
assistance.
Our commitment to support and enhance research
was demonstrated by success in obtaining funding
for major equipment, enabling the School to add
PROFESSOR
BALLARD
PR
P
OFESSOR BILL BA
Head of School
07
School Management
School Executive Committee
The School is managed by the Head of School, assisted by the Deputy Head of School and Executive
Committee and by various other committees responsible for key areas of operations.
Head of School
Professor Bill Ballard
Deputy Head of School
Associate Professor Andrew Collins
Executive Committee
Associate Professor Andrew Brown
Dr Louise Lutze-Mann
Associate Professor Vincent Murray
Professor Brett Neilan
Associate Professor Peter White
Professor Marc Wilkins
Brett Neilan, Vincent Murray, Louise Lutze-Mann, Andrew Brown, Marc Wilkins, Bill Ballard,
Peter White and Andrew Collins
School at a Glance
BABS Offsite Research Day 2010
Environmental Microbiology
Infectious Disease
Molecular Medicine
Systems and Cellular Biology
Biomolecular science encompasses the disciplines
of chemistry, biochemistry, molecular biology and
cell biology, and includes the specialist areas of
genetics, genomics, bioinformatics, proteomics
and chemical biology. Biotechnology underpins
much of the research.
Research
The School of BABS occupies a total of 7,524
square metres across two buildings, and provides its
researchers with a world-class research environment.
Excellence in scientific research is an essential
component of the School of BABS, which has a
strong international reputation for quality research in
fundamental and applied science. Researchers in the
School are aligned into four discipline areas.
The School’s research ranges from human bacterial
pathogens, hepatitis viruses, tissue engineering,
cancer, cell biology, genetics, bioinformatics
and functional genomics to astrobiology and
extremophiles. Our staff have an international
reputation for research and have established
collaborative links with industry and other research
institutions in Australia and overseas. During 2010,
School researchers were awarded 7 Category 1
grants totalling $3.338M and authored or coauthored 164 publications in ERA ranked journals.
BABS hosts a number of important research
centres that conduct pioneering research and
provide the highest level of technological expertise
and services in their respective fields. This
expertise was recognised in the 2010 ERA scores,
with the University of NSW awarded the top rating
of 5 in Category 06 for Biological Sciences.
09
The School offers a comprehensive range of
undergraduate and postgraduate Degrees and
caters for a variety of career paths. The exceptional
standard of education within our Degree programs
is provided by dedicated and experienced staff
and access to the latest scientific equipment and
technologies. During 2010 a state-of-the-art PC2
teaching lab was completed, with a re-fit of a PC1
teaching lab to cater for 70 students scheduled for
completion during 2011. Our teaching staff were
once again recognised with University and external
teaching awards during 2010.
Postgraduate Research
UNSW is a leader in Australian and International
research, having around 3,500 postgraduate
research candidates in 2010. The School of BABS
offers Doctor of Philosophy (PhD) and Master
of Science (MSc) research-based Degrees
to qualified students who have completed a
four-year undergraduate Science degree with
Honours or equivalent. In addition, the Master of
Philosophy in Biotechnology and Biomolecular
Sciences (MPhil BABS) provides students with an
emphasis on research training supplemented by a
substantial coursework component.
PhDs
The School of BABS is one of the highest recruiters
of PhD students at The University of New South
Wales, and has the highest number of postgraduate
students in the Faculty of Science. Of the 138 HDR
students in 2010, 107 were progressing towards
a PhD, about twenty five per cent higher than the
mean for other GO8 Schools of similar core research
area and relative size. A large number of our PhD
students are supervised by eminent Visiting Staff
who are located at institutions where the School has
long-established research links, including the Garvan
Institute of Medical Research, the Victor Chang
Cardiac Research Institute and the Prince of Wales
Hospital Clinical School.
Our People
Academic Staff
Lecturers
Anne Galea
Scientia Professors
John Wilson
Ian Dawes FAA
Staffan Kjelleberg FAA
Bill Ballard
Head of School
Rick Cavicchioli
Merlin Crossley
Dean, Faculty of Science
Brett Neilan
ARC Federation Fellow
Hazel Mitchell
Marc Wilkins
Malcolm Walter FAA
ARC Professorial Fellow
Associate Professors
Rebecca LeBard
Professional &
Technical Staff
Ms Michele Potter BA (USyd)
School Manager
Mr Adam Abdool
Administrative Officer
Ms Kylie Jones
Mr Wolf Nittel
Andrew Brown
Ms Penny Hamilton BA (UNE)
Administrative Assistant
Andrew Collins
Deputy Head of School
Mr Geoff Kornfeld
Professional Officer
John Foster
Dr Jani O'Rourke BSc (USyd), PhD (UNSW)
Professional Officer Lab Manager
Ruiting Lan
Mark Tanaka
ARC QEII Fellow
Vincent Murray
Noel Whitaker
Peter White
Rob Yang
ARC Future Fellow
Senior Lecturers
Wallace Bridge
Dr Rohan Singh-Panwar BSc Hons
(UNSW), PhD (UTS)
Professional Officer OHS & Safety
Dr Jeff Welch BSc Hons, PhD (UNSW)
Professional Officer Infrastructure
Mr Matt Clemson BSc Hons, PhD (UNSW)
Technical Officer
Mr Ned Elkaid
Technical Officer
Dr Daud Khaled BSc Hons, MSc
(Dhaka), PhD (UNSW)
Technical Officer
Brendan Burns
Belinda Ferrari
Michal Janitz
Louise Lutze-Mann
Chris Marquis
Vldimir Sytnyk
Torsten Thomas
Alan Wilton
Li Zhang
Research Staff
Associate Lecturers
Sven Delaney
Professors
Ms Lily Zhang BEng (Tianjin)
Technical Officer
Dr Elessa Marendy BSc Hons, PhD (JCU)
Technical Officer
Ms Sharon Murarotto BAppSc (UTS)
Technical Officer
Ms Kim Nguyen BSc (UNSW)
Technical Officer
Ms Shamima Shirin
Technical Officer
Ms Doris Suen
Technical Officer
Ms Giti Agahi
Research Assistant
Dr Michelle Allen
Postdoctoral Fellow
Dr Mark Brown
ARC QEII Fellow
Dr Timothy Charlton
Research Fellow
Ms Angela Chilton
Research Assistant
Mr Matthew DeMaere
Research Associate
Dr Nandan Deshpande
Postdoctoral Fellow
Dr Robin Du
Research Fellow
Dr Suhelen Egan
Senior Research Associate
Ms Melissa Erce
Postdoctoral Fellow
Dr Stephen Fei
Dr David Fung
Postdoctoral Fellow
Dr Alister Funnell
Research Associate
Dr Michelle Gehringer
Ms Hannah Ginn
Research Assistant
Dr Kate Jackson
Postdoctoral Fellow
Mr Young Jae Jeon
Research Manager
Dr Nadeem Kaakoush
Research Associate
Dr John Kalaitzis
Research Associate
Ms Ika Kristiana
Research Assistant
Dr Yuen Lam
Postdoctoral Fellow
11
Dr Federico Lauro
Research Fellow
Dr Tim Williams
Dr Graham Vesey
Senior Visiting Fellow
Ms Helene Lebhar
Research Officer
Dr Jonci Wolff
Research Fellow, APD
Dr Volga Bulmus
Visiting Fellow
Dr Iryna Leshchynska
Research Fellow
Ms Simone Li
Research Assistant
Dr Ruby Lin
Research Fellow
Mr Helder Marcal
Research Associate
Dr Diane McDougald
Senior Research Fellow
Mr Toby Mills
Research Assistant
Mr Scott Minns
Research Assistant
Dr Shauna Murray
Research Fellow
Dr Leanne Pearson
Research Associate
Dr Richard Pearson
Dr Gabriel Perrone
Research Fellow
Dr Louise Puslednik
Postdoctoral Fellow
Dr Bettina Rosche
Dr Gillian Scott
VC Postdoctoral Research Fellow
Dr Khawar Siddiqui
Dr Ping Su
Research Fellow
Ms Natalie Twine
Research Assistant
Dr Mike Manefield
ARC Future Fellow
Biosciences Building
Visiting Staff
A/Prof Kevin Barrow
Professorial Visiting Fellow
Prof Haluk Ertan
Prof David James FAA
Em/Prof James Lawson
Em/Prof Peter Rogers
Honorary Visiting Professor
Dr Laurent Rivory
Visiting Associate Professor
Dr Gregory Arndt
A/Prof Michael Edwards
A/Prof Annette Gero
Dr Alison Murray
A/Prof Thomas Preiss
Dr Alison Todd
Ms Vibeke Catts
Visiting Fellow
Dr Antony Cooper
Visiting Fellow
Dr Frances Foong
Visiting Fellow
Dr Wendy Glenn
Visiting Fellow
Dr Andrew Netting
Visiting Fellow
Dr Francesco Pomati
Visiting Fellow
Prof Bill Rawlinson AM
Visiting Fellow
Dr Charles Svenson
Visiting Fellow
Dr Kathy Takayama
Visiting Fellow
Dr Sheila Van Holst
Pellekaan
Visiting Fellow
Prof Philipp Wiedemann
Visiting Fellow
Dr Jeremy Webb
Adjunct Senior Lecturer
INFECTIOUS
DISEASE GROUP
INFECTIOUS DISEASES cause some of the world’s most critical health problems and are
responsible for around one-third of annual deaths worldwide. Emerging pathogens such
as SARS and swine influenza are a constant and rapidly evolving threat.
Infectious Disease
Academic Staff
Professor Hazel Mitchell
Associate Professor Ruiting Lan
Associate Professor Noel Whitaker
Dr Mark Tanaka, Senior Lecturer
Dr Li Zhang, Senior Lecturer
Members of the Infectious Disease research group are
committed to a broad range of research and teaching activities
in Sydney and around the world. Research focuses on molecular
epidemiology, with an aim to combat the invisible microbes that
remain a huge biological challenge affecting both human and
animal health.
The group brings together a wide array of internationally
recognised research expertise to investigate the microbiological
factors affecting a range of vital health issues.
The burden of infectious disease continues to be significant in
Australia. The potential for serous outbreaks presents a major
public health challenge and requires planning and vigilance.
Research is conducted in collaboration with other research
institutions, public health organisations, quarantine, and
agricultural and animal production sectors.
13
VIRUSES AND BREAST CANCER
Associate Professor Noel Whitaker, Dr Louise Lutze-Mann,
Emeritus Professor James Lawson, Dr Wendy Glenn
For over 100 years, eminent
scientists have been trying to
find the causes of breast cancer.
While many of the risk factors
have been identified and most
are associated with female
sex hormones, the underlying
causes remain elusive.
In 2003, the Whitaker group
initiated a study to explore the
role of viruses in breast cancer.
The direction of the research
was greatly influenced by the
increased risk of breast cancer
following migration of individuals
from Eastern to Western
countries. The most obvious
explanation for this heightened
risk would appear to be the
change in food consumption.
This has a direct influence
on the levels of circulating
hormones, which in turn alter the
risk of breast cancer. However,
this seemingly simple causeand-effect hypothesis is not
supported by the evidence. As
repeated studies (almost all
conducted in Western countries)
have shown no relationship
between diet and breast cancer,
the Whitaker group searched
for alternative hypotheses. One
feasible hypothesis is that some
breast cancers may be caused
by hormone-dependent viruses.
Suspicions that viruses may
play a role in breast cancer
were first raised by John Bittner
of the US as long ago as 1936.
Bittner discovered a ‘milk factor’
transmitted from mouse mothers
to pups that developed breast
cancer (mouse mammary
tumours) as adult mice after
a prolonged latent period.
A
C
After the WWII years, this milk
factor was shown to be a virus,
and given the name mouse
mammary tumour virus (MMTV).
Despite intense research, no
definitive findings of a similar
virus involved in human breast
cancer emerged until 1995,
when MMTV-like sequences
were identified in human breast
cancer by Beatriz Pogo in New
York.
In 2002, Professor James Lawson
initiated studies of MMTV and
breast cancer in collaboration with
BABS Visiting Fellow Professor
Bill Rawlinson at Sydney’s Prince
of Wales Hospital, resulting in
the first identification of MMTV
in Australian breast tumours.
During this same period, other
known cancer-causing viruses
were identified in breast tumours,
including high-risk human
papillomavirus (HPV) and Epstein
Barr virus (EBV). The Whitaker
group was the first to report the
presence of HPV in Australian
breast cancer and, importantly,
that while the HPV is present in the
B
D
HPV in cancer cells
of ductal carcinoma
in situ breast cancer
demonstrated by
in situ PCR; same
specimen in all panels
Modified from Heng B,
Glenn WK, Ye Y, Tran
B, Delprado W, LutzeMann L, Whitaker NJ
& Lawson JS, 2009,
‘Human papilloma
virus is associated with
breast cancer’, British
Journal of Cancer, 101:
pp. 1345-1350.
cancerous cells, it is not found in
the normal surrounding tissue (see
Figure).
The group has since
demonstrated the presence of
MMTV, HPV and EBV in breast
cancer, indicating a potential role
for each of these viruses in some
breast cancers.
In an effort to arrive at conclusive
evidence of causation of breast
cancer by these viruses, a
patient follow-up study is
currently being conducted to
identify any viruses that may
have been present in non-breast
cancer breast tissue collected by
biopsy several years prior to the
breast cancer developing.
This work is being conducted
in collaboration with Professor
Warick Delprado, Director of
the major Australian pathology
service Douglass Hanly Moir.
Similar work is also progressing
on the role of viruses in prostate
cancer, which at this early stage
appears to have many parallels
to the breast cancer findings.
THE PATHOGENESIS OF THE EMERGENT PATHOGEN
CAMPYLOBACTER CONCISUS
Professor Hazel Mitchell
Mitchell lab staff
(L-R) Si Ming Man,
Hazel Mitchell,
Natalia CastanoRodriguez, Nadeem
Kaakoush
Professor Hazel Mitchell, Dr
Nadeem Kaakoush and their
team are investigating the role
and pathogenic mechanism of
the bacterium Campylobacter
concisus in gastrointestinal
disease. C. concisus is a motile
Gram-negative, spiral/curved,
mucosa-associated bacterium
that requires a microaerobic
hydrogen-enriched environment
for growth. Historically, it has
been associated with gingivitis
and, more recently, with
gastroenteritis. In addition, in
recent studies they reported
an increased prevalence of C.
concisus in children with newly
diagnosed Crohn’s disease
(CD) compared with controls,
and have cultured C. concisus
from biopsy samples of children
with CD. Due to its association
with acute gastroenteritis and
CD, which is a chronic intestinal
infection, C. concisus has been
described as an emergent
pathogen of the human intestinal
tract. Currently, however, there is
limited knowledge regarding its
pathogenic mechanism.
In recent studies, the Mitchell
lab investigated the ability of
C. concisus strains isolated
from children with CD to attach
to and invade Caco-2, HT-29
and LS147T human intestinal
epithelial cell-lines, using
attachment and gentamicin
protection assays and Scanning
Electron Microscopy (SEM).
They then compared this with
from patients with acute
gastroenteritis, and a healthy
control. The results showed that
C. concisus strains isolated from
CD children were able to attach
to and invade Caco-2, HT-29 and
LS147T and to cause damage
to epithelial barrier function
by preferential attachment to
cell-cell junctions. In contrast,
from acute gastroenteritis
patients provided strong
evidence that differences exist
in the pathogenic potential of C.
concisus strains.
To gain a deeper understanding
of these differences, the genome
of a C. concisus strain isolated
from a child with CD (UNSWCD)
was sequenced and compared
with the genome of the only other
fully sequenced C. concisus
strain BAA-1457, which had been
isolated from a patient with acute
gastroenteritis. The genomic
and proteomic similarities and
differences between C. concisus
UNSWCD and BAA-1457 were
then analysed in order to identify
putative factors responsible for
the increased pathogenesis of C.
concisus UNSWCD. The research
has revealed that significant
differences do exist between the
two sequenced strains, which
have the potential to explain the
increased pathogenic potential of
the C. concisus strains associated
with CD.
In associated work and
in collaboration with
gastroenterologist Associate
Professor Andrew Day from
the UNSW Faculty of Medicine,
and Drs Torsten Thomas and
Michal Janitz from BABS, the
Mitchell and Kaakoush group is
investigating differences in the
intestinal microbiome of children
with CD and controls using high
throughput sequencing. They
are also studying changes in the
intestinal microbiome in these
CD children during and following
treatment with exclusive enteral
nutrition and at relapse. To
date, pilot studies in this area
have shown that the intestinal
microbiome of children with CD
differs from that in controls.
15
THE ROLE OF ORAL AND INTESTINAL BACTERIA IN CHRONIC
HUMAN DISEASES
Dr Li Zhang
in its development, however,
the exact microorganism(s)
causing human IBD is still under
investigation.
Dr Li Zhang investigates the role
of oral and intestinal bacteria
in chronic human diseases,
including chronic inflammatory
and neurological diseases,
and autoimmune diseases.
She is particularly interested in
studying the immunopathogenic
mechanisms of specific oral
and intestinal bacterial species
in initiating or facilitating
development of such chronic
disorders. Her current research
focus is investigating the role
of Campylobacter species in
inflammatory bowel disease
(IBD) and chronic neurological
diseases.
In 2009, researchers from
UNSW, with Dr Zhang as
first author, were the first to
report an association between
Campylobacter concisus and
CD in children. More recently,
in collaboration with Professors
Stephen Riordan and Michael
Grimm from the UNSW Faculty
of Medicine, the group has
detected a significantly higher
prevalence of C. concisus in
the large intestine of adult CD
patients compared with the
controls. These results have
provided evidence to support the
hypothesis that different bacterial
species may be associated with
CD occurring at different sites of
the gastrointestinal tract.
The group has also shown that
C. concisus is ubiquitous in the
human oral cavity, forming part
of the human oral microbiota
from early stages of human life.
Comparison of oral and intestinal
C. concisus isolated from
paediatric and adult patients
with IBD showed intestinal C.
concisus originating from the
patient’s own oral C. concisus.
These results suggest that the
human oral cavity serves as a
source for intestinal C. concisus
infection, and emphasise the
need to further investigate the
role of specific oral C. concisus
strains involved in human IBD.
Currently, investigations are
focused on the interaction
between C. concisus and the
gut mucosal immune system,
to further elucidate the possible
immunopathogenic role of C.
concisus in human IBD.
C. concisus ?
Intestinal epithelial cells and production of IL-8 thro
activation of Nuclear Factor kappa
kappa-B
B (NF-B)
(NF B) pathw
IL-1R
PRRs
TNFR
Plasma membrane
IKK activation
IKK
IBD
IB
NFkB
IBD is a chronic inflammatory
disorder of the gastrointestinal
tract, the two major forms being
Crohn’s disease (CD) and
Ulcerative Colitis. The aetiology
of IBD is unknown. Studies
have shown that intestinal
microflora plays a key role
Activation of NF-kB
Phosphorylation of IkB
q
of pp-IkB
Ubiquitination
P P
P P
Proteosome
Degradation
Nuclear membrane
IL-8 and IB
DNA
Transcription at NFkB bindng DNA motif
Diagram of activation
of nuclear factor
kappa B pathway by
C. concisus
IB- IB
Tubulin
The role of oral and
intestinal bacteria in chronic
inflammatory demyelinating
polyneuropathy (CIDP) and
Parkinson’s disease
Some bacterial species have
been indicated to trigger
the development of chronic
neurological disorders. This
part of Dr Zhang’s research, in
collaboration with researchers
at the University of Sydney and
clinical professionals from the
UNSW Faculty of Medicine, aims
to investigate the possible role
of specific oral and intestinal
bacterial species in triggering
CIDP and Parkinson’s disease.
0
10
15
30
120%
100%
IkB
B- level (%)
CIDP is a chronic progressive
neurological disorder, caused by
the immune system attacking the
myelin sheath of the peripheral
nerve. Parkinson’s disease
is a chronic degenerative
neurological disease, resulting
from the progressive loss of
dopamine-producing neuronal
cells in the central nervous
system.
Time
(minute)
80%
60%
40%
20%
0%
0
10
15
Time (minutes)
Degradation of IkB-D in HT-29 cells induced by
C. concisus
30
17
FREQUENT MULTIPLE HEPATITIS C VIRUS INFECTIONS AMONG
INJECTION DRUG USERS IN A PRISON SETTING
White lab staff (L-R) Kun Lee Lim,
Rouba Ballouk, Sean Pham, Peter
White, Rowena Bull, John-Sebastian
Eden, Melanie Walker, Camelia Quek
The inmates were followed
prospectively until they became
HCV positive.
As part of the Hepatitis C
Incidence and Transmission
Study (HITS), and in
collaboration with Professor
Andrew Lloyd and his team
in the UNSW Faculty of
Medicine, the White lab has
comprehensively investigated
multiple HCV infection and reinfection in a cohort of 500 highrisk seronegative injecting-druguser inmates in a NSW prison.
Strikingly, the research
performed between 2008 and
2010 showed that the prevalence
(25%) and incidence (40/100
person-years) of multiple HCV
infection among NSW prisoners
was far more common than
previously reported. A number
of these cases were re-infected
with new HCV strains after
more than a year of clearance
since the primary infection – a
finding that sits uneasily with
The research addressed the
prevalence and incidence of
multiple HCV infection as well
as the natural history of infection
with two or more viruses,
including HCV displacement,
and identification of viral factors
that predict the outcomes of viral
competition. Two novel nested
reverse transcription-polymerase
chain reaction (nRT-PCR) assays
for the detection of multiple
viruses were developed and
used to screen 87 inmates who
had been identified with a new
HCV infection.
HCV vaccine researchers. Other
cases were persistently infected
with a dominant HCV, but were
transiently superinfected with
up to three further viruses, each
of which was cleared, leaving
the dominant virus as a chronic
infection.
The study also suggests
that HCV RNA levels play
an important role in viral
competition, where those viruses
with high RNA levels outcompete other viruses. Further
investigations are therefore
warranted to provide further
insights into infection dynamics
and immunity after exposure
to several viral strains. This will
form an important body of work
for vaccine developers.
Photo by Sean Pham
Hepatitis C virus (HCV)
infects 2-3% of the world’s
population. The majority of
infected individuals develop
persistent infection, with the
associated risk of progressive
fibrosis, cirrhosis, liver failure
and hepatocellular carcinoma.
In Australia, with approximately
210,000 chronically infected
people and 10,00 new infections
every year, the virus remains a
serious public health burden.
Injecting drug use is the most
common route of transmission,
with the possibility of multiple
HCV strains in one infection
leading to reduced chances of
viral clearance and potentially
faster disease progression.
MOLECULAR
MEDICINE
GROUP
MOLECULAR MEDICINE within BABS combines fundamental biological and
biomolecular sciences with a strong applied biotechnology and medical focus.
Collaborative research efforts across discipline boundaries have resulted in fundamental
discoveries, generation of commercial opportunities and clinical research.
Molecular Medicine
Academic Staff
Professor Merlin Crossley
Associate Professor John Foster
Associate Professor Vincent Murray
Dr Wallace Bridge, Senior Lecturer
Dr Michal Janitz, Senior Lecturer
Dr Louise Lutze-Mann,
Senior Lecturer
Dr Chris Marquis, Senior Lecturer
Major research strengths of the group currently exist in
biomaterials, immunology, bioinformatics, cancer and genetics.
The group uses a wide range of cutting-edge molecular
and bioinformatic tools to understand and combat genetic
disease and cancer. Expertise from members of the Molecular
Medicine group naturally integrates into projects within the
School’s research areas of ageing and proteomics.
Members of the Molecular Medicine group have been active
in securing infrastructure funding in proteomics and protein
expression. This facility naturally fits into the strong proteomics
theme present in the School’s Systems and Cellular Biology
group and underpins large projects involving other groups in
BABS.
Dr Vladimir Sytnyk, Senior Lecturer
Dr Anne Galea, Lecturer
Further growth designed to complement current strengths
is envisaged in the areas of ageing and personalised
medicine. These growth areas will enhance existing research
areas and provide opportunities for new collaborations.
19
IMMUNOGLOBULIN GENES, REPERTOIRE DEVELOPMENT AND THE
1000 IMMUNOMES PROJECT
At a time when whole-genome
sequencing is becoming almost
routine, significant gaps still
remain in our knowledge of
regions of the human genome
that are critical to human
health. The immunoglobulin
gene loci are clear examples of
this. Although they have been
a focus of intensive genetic
research since the 1970s
and 1980s, there is still little
knowledge of immunogenotypes,
the different sets of germline
genes that may be found in
different individuals, and of how
different immunogenotypes
affect immunocompetency.
And despite the fact that
immunoglobulin genes arise by
chromosomal recombination, we
have absolutely no phased data
providing knowledge of human
immunohaplotypes, the sets of
germline genes that are found
together on a chromosome in an
individual.
Working with Professor
Andrew Fire and Dr Scott
Boyd of Stanford University,
and Dr Bruno Gaeta of the
UNSW School of Computer
Science and Engineering, we
have pioneered an approach
to immunogenotyping that
allows us to efficiently infer
immunogenotypes.
More recently, with Dr. Katherine
Jackson, who completed
her PhD in BABS and is now
working at Stanford University,
we have been developing an
analytical approach to allow
us to deduce phased data
(immunohaplotypes) for the
entire heavy chain gene locus.
Collins lab staff
(L-R) Sven Warris,
Daniel Ford,
Zhiliang Chen,
Katherine Jackson,
Andrew Collins,
Bruno Gaeta, Marie
Kidd, Yan Wang
Working with BABS Honours
student Marie Kidd, we have
achieved a major breakthrough
in this project. Our published
studies have shown that
real differences exist in the
expressed antibody repertoires
of different individuals.
Haplotyping has now shown
that these differences include
many immunoglobulin gene
duplications that until now have
been impossible to detect.
Haplotyping has also confirmed
that deletion polymorphisms are
common, and these seem to be
associated with what can best
be described as distortions of
the antibody repertoire. It is likely
that this results from alterations
in the regulatory elements that
control gene recombination.
Allelic differences between
individuals are also associated
with dramatic differences in
the proportions of the primary
repertoire that utilise particular
genes. Together, this evidence
leads us to hypothesise that
variation between individuals
in their ability to generate a
protective humoral immune
response, and variation in their
propensity to antibody-mediated
pathology, could be the result
of such immunogenotypic
differences.
Our knowledge of
immunogenotypes and
immunohaplotypes has not been
advanced by either the human
genome project or the HapMap
project, and will not be advanced
by the 1000 Genomes Project.
We are working to plug
this gap by investigating
immunogenotypes and
immunohaplotypes in
populations of various
ethnicities, and in both healthy
and diseased individuals. We
are also investigating how
different allelic variants and
deletion polymorphisms shape
the expressed immunoglobulin
V(D)J repertoire, by looking
at the relationships between
haplotypes and gene
rearrangement frequencies.
As a result of studying
repertoire development in the
context of immunoglobulin
gene haplotypes, we hope to
better understand individual
susceptibility to disease.
EVERYTHING OLD CAN BE NEW AGAIN
Dr Louise Lutze-Mann, Dr Vibeke Catts, Associate Professor Noel Whitaker
With the ageing of the baby
boomers, the incidence of
age-related diseases such
as cardiovascular disease
and cancer will increase, with
the corresponding need for
better targeted therapies.
The Lutze-Mann group is
interested in identifying novel
chemotherapeutics for the
treatment of cancer. This can be
extremely costly, both in terms of
time and money, from the initial
identification of a drug through
to laboratory testing and the
animal and human trials. It would
therefore be preferable to find
drugs that are already approved
for use in humans and repurpose
them for cancer treatment.
The research has focused on
two quite distinct sets of drugs
that fall into the ‘old for new’
category. The first is the class
of drugs called antipsychotics,
which are used to treat patients
with schizophrenia. Large-scale
analysis of patient cohorts
from around the world has
revealed that those suffering
schizophrenia have a lower
incidence of some cancers
compared with the general
population. When investigated
further, it was found that this may
be due, in part, to the long-term
use of antipsychotic drugs by
such patients.
Lutze-Mann lab staff (L-R) Benjamin Heng, Vanessa Tan, Harvey Fernandez,
Louise Lutze-Mann, Rebekka Williams, Nirmani Wijenayake, Joyce Lee
These drugs are very effective
in killing some cancer types,
including those that are highly
recalcitrant to treatment, such as
the brain tumour glioblastoma
multiforme (less than 5%
patient survival one year after
diagnosis). The Lutze-Mann
group has now discovered the
mode of action for these drugs,
with animal trials commencing as
a prelude to human treatment.
The second type of ‘old for new’
drugs are those that are classed
as nucleoside analogues.
Nucleosides are the building
blocks of genetic material and
as such are essential for cell
survival. Their analogues are
nucleosides with slightly altered
chemical structures, which
the cell will attempt to use, but
which will then interfere with the
correct functioning of the genetic
material, often leading to cell
death.
Some of these drugs were first
tested in BABS as promising
anti-malarial treatments. The
current work has now found
that they are very effective in
killing cancer cells, including
those that have mutations in
the most commonly mutated
tumour suppressor gene, p53.
Investigations are now centred
on how these drugs may
selectively target cancer cells
with mutations in p53.
21
HUMAN TELOMERIC DNA SEQUENCES MAJOR TARGET FOR
ANTITUMOUR DRUG BLEOMYCIN
Associate Professor Vincent Murray and PhD candidate Trung Nguyen
Bleomycin is widely used as
an anti-tumour agent to treat
various cancers, including
germ cell tumours, certain
types of lymphoma and
squamous cell carcinomas.
Bleomycin is isolated from
Streptomyces verticillus and
consists of a closely related
family of glycopeptides. The
therapeutic efficacy of bleomycin
is believed to involve the direct
cleavage of DNA. However,
the precise mechanism of
action of bleomycin is not fully
understood.
In this project, we examined
the hypothesis that bleomycin
preferentially targets telomeric
repeat DNA sequences.
Telomeres are crucial
structures at the ends of human
chromosomes and consist of
a G-rich repeat, (GGGTTA)n.
Telomeres function to protect
the chromosomes from nonhomologous recombination and
end-to-end fusion. In normal
somatic cells, telomeres are
progressively shortened with
each round of cell division
due to the inability of the DNA
replication machinery to copy
the lagging telomeric DNA
strand. This is referred to as the
‘end replication problem’. Once
a significant loss of telomeric
sequence is reached, cells enter
replicative senescence and then
proceed to apoptotic cell death.
Telomere shortening is thought
to be a major contributor to
the ageing process. However,
cancer cells (and germ line cells)
generally activate telomerase to
avoid telomeric shortening and
cellular senescence.
It is known that bleomycin
preferentially targets GT DNA
sequences, and since human
telomeres consist of the repeat
sequence (GGGTTA)n it is likely
that telomeric DNA sequences
are a major target for bleomycin
damage. Utilising a newly
developed fluorescence
technique with an automated
DNA sequencer, we determined
the precise DNA targets that
are cleaved by bleomycin in
a DNA sequence containing
17 telomeric repeats. Our data
indicated that telomeric DNA
sequences are a major site for
bleomycin damage. Bleomycin
cleavage of telomeric DNA
sequences will lead to the
inhibition of DNA replication,
and ultimately, tumour cell death
by apoptosis. This implies that
telomeric DNA damage could be
an important component of the
anti-tumour activity of bleomycin.
Trung Nguyen and Vincent Murray
SYSTEMS AND
CELLULAR
BIOLOGY GROUP
THE SYSTEMS AND CELLULAR BIOLOGY GROUP undertakes research in the biology
of eukaryotes, and the molecular processes within and between cells. Members of the
group have overlapping research foci, many of which have been cemented by active
collaborations and joint research grants and projects. Research areas include cholesterol
and sterols, cell stress and ageing, genetic mapping of phenotype and disease, protein
interaction networks and systems biology.
Systems and Cellular Biology
Academic Staff
Scientia Professor Ian Dawes
Professor Marc Wilkins
Associate Professor Andrew Brown
Associate Professor H Rob Yang
Dr Alan Wilton, Senior Lecturer
Dr Rebecca LeBard,
Associate Lecturer
Researchers in this group study the selective forces that influence
the evolution of mitochondrial DNA and have used it as a model
to study the link between the genotype and the phenotype.
Mitochondrial DNA mutations can be important in determining
aspects of organism life history. One model organism common
to a number of research labs in this group is baker’s yeast,
providing opportunities for collaboration and sharing of skills.
Scientia Professor Ian Dawes leads research into the response of
eukaryotic organisms to oxidative stress and ageing, and was a
pioneer in the field of yeast responses to oxidative stress.
Staff in the Systems and Cellular Biology group are responsible
for two major research Centres in the School, the Ramaciotti
Centre for Gene Function Analysis and the NSW Systems Biology
Initiative. These two research initiatives are complementary, and
provide technology, capacity and collaborative expertise. The
co-location of two such centres of expertise serves as a focus for
many activities in the group as a whole.
23
OXIDATIVE STRESS
Scientia Professor Ian Dawes
Research in the Dawes laboratory
is aimed at identifying the
mechanisms whereby cells
respond to oxidative stress, how
oxidative stress contributes to
ageing, and how cells control their
intracellular redox environment.
Oxidative stress results when
cellular defence mechanisms
are unable to adequately adapt
to an oxidant challenge, leading
to oxidative damage to cellular
constituents, ageing and death of
cells.
Oxidative stress is caused by
reactive oxygen species (ROS),
which are formed from oxygen
in response to environmental
exposure to light, redox-active
compounds such as paraquat
ionizing, radiation or toxic metal
ions. The aerobic nature of many
organisms leads to their continual
exposure to ROS, since many of
the biologically relevant species
are generated as a result of
respiration-associated univalent
reduction of oxygen. These ROS
agents are capable of killing
cells rapidly and they have been
implicated in many diseases
including cancer, cardiovascular
disease, arthritis and ageing.
Oxidants can also have a more
positive role – those generated
by neutrophils and macrophages
also participate in the cytolysis of
invading microorganisms by these
cells. As a result of the continued
exposure to these oxidants,
organisms have evolved a complex
array of defences comprised of lowmolecular weight (non-enzymatic)
and enzymatic antioxidants.
Figure 1. roGFP2
structure (from
Hansen GT et al.,
2004, ‘Investigating
mitochondrial redox
potential with redoxsensitive green
fluorescent protein
indicators’, The
Journal of Biological
Chemistry, vol. 279,
no. 13, p. 13049.)
Brightfield
GFP
Cytosol
Mitochondrial
Matrix
Peroxisome
Figure 2. roGFP2
targeted to various
sub-cellular
compartments in
yeast cells
Work in the Dawes laboratory
has used the remarkable power
of yeast genomics to identify
the many genes involved in this
response and to characterise
the role of many of them in the
way cells counteract oxidative
damage. The group has had
a long interest in glutathione
as the major cell buffer acting
against oxidative damage,
and recent published work by
PhD student Anita Ayer has
shown that one of the essential
functions of glutathione is
to protect the mitochondrial
genome from damage. Anita and
other students and postdoctoral
fellows have extended the work
using genome-wide mutant
screens to identify the genes and
functions that affect the in vivo
redox potential (Eh) in several
cellular compartments, including
the cytoplasm, the mitochondrial
matrix and the peroxisome.
This has been made possible by
the development of a modified
green fluorescent protein that has
two cysteine residues that can
be oxidized to form a dithiol (see
Figure 1), and which has been
targeted to each of the organelles
(see Figure 2). This affects the
excitation spectrum of the protein,
and enables direct non-invasive
measurement of the redox
environment in a way that has not
been previously possible.
Postscript
During 2010, Scientia Professor Ian Dawes announced his
retirement, to take effect at the end of 2011. To mark his long and
distinguished academic and research career, a Festschrift in his
honour is being planned for September 2011.
As part of the Festschrift, the School is hosting a two-day scientific
symposium, with prominent national and international speakers
presenting talks in Ian’s areas of scientific research – oxidative
stress, ageing and genomics. This will be a fitting tribute to
honour and celebrate the contributions made by Ian to the School
of BABS, to UNSW and to the wider national and international
scientific community.
For further details, please contact the School.
25
THE CANDIDATE COMPLEX APPROACH FOR LINKING MUTATIONS
WITH DISEASE
When Charles Darwin proposed
that natural selection operated
on variation, he had no idea
what material produced the
observable differences. Ninetyone years later, Hershey and
Chase’s experiments with the
T2 phage identified the source
of inherited variation to be DNA.
Today, in the post-genomics
era, biologists are still struggling
to elucidate the details of the
interaction between genetic
variation and phenotypic
difference. One explanation for
the difficulty is that the organism
is more than a simple sum of
its nucleotides. Indeed, it may
now be argued that Darwin’s
entangled bank analogy applies
equally to genes within a
single organism and species
within a community. However,
for this analogy to be robust,
birds, insects and worms must
be replaced with differential
splicing/expression, posttranslational protein modification
and mobile elements.
complex approach to studying
mitochondria and mitochondrial
function. This approach maps
mutations in mtDNA and
nuclear-encoded subunits onto
a quaternary structure model
of the complex to predict their
functional significance, and
then tests the computational
predictions experimentally.
The broad goal of Bill’s work over
the past decade had been to
use mitochondria as a model to
link the genotype of an organism
with its phenotype. This goal has
been somewhat complicated by
the fact that mitochondrial DNA
(mtDNA) rarely recombines and,
as such, is inherited as a single
linked block. A consequence of
this linkage is that it is difficult
to determine which specific
mutation is causally responsible
for any observed bioenergetic
or biochemical response. Bill
embraced this challenge in 2004
and developed the candidate
The initial system to be studied
was complex IV (COX) in
Drosophila simulans flies.
COX was selected because
it is hypothesised to be the
rate-limiting step in oxidative
phosphorylation. Drosophila was
the model of choice because
of the genetic tractability of the
system. In 2008, the Ballard
group published the COX
quaternary structure model
for Drosophila based on the
bovine model and then mapped
mutations from apparently
‘normal’ wild-caught flies onto
the model. They predicted that
Quaternary 3-D
PyMOL model of
human mitochondrial
COX. Each protein
subunit is highlighted
by a different colour
six mtDNA and three nuclearencoded mutations were likely to
influence cytochrome c oxidase
activity. One of these nuclear
mutations has subsequently
been studied intensively and
provides proof-of-concept of the
idea.
The Ballard team has recently
extended this idea and
constructed a three-dimensional
model of human COX based on
the bovine model. Employing
this model, they identified
whether a specific amino acid
is interacting with amino acids
from the same or different protein
subunits. The model was first
used to make predictions on the
putative functional significance
of COX mutations found in
human disease, which identified
all disease-associated mutations
with reported reduction in
COX functional activity as
being functionally significant.
Second, COX variants that are
listed in databases but have
unknown biological function
were modelled. Surprisingly, it
is predicted that 75% of core
COX variants with unknown
biological activity are likely to
be functionally important. These
data suggest that mitochondria
are a highly dynamic molecule
that can respond to mild
dysfunction. The results also
strongly suggest that the
quaternary model will be a useful
bioinformatic tool for determining
functionality of known and novel
COX variants.
A next step is to test the
accuracy of these predictions in
individuals with a known medical
history or with an established
clinical phenotype. In particular,
it will be important to study
older people where long-term
implications of mitochondrial
dysfunction are more likely to
be clinically apparent (e.g.
age of onset and presence of
sarcopenia, neurodegenerative
disease and frailty).
The Seahorse
XF24 will be
used to test
the influence of
specific mutations
on mitochondrial
efficiency
27
ENVIRONMENTAL
MICROBIOLOGY
GROUP
ENVIRONMENTAL MICROBIOLOGY is the study of microorganisms and their
interactions, both within the environment and with each other. BABS is home to
some of Australia’s leading environmental microbiologists and biotechnologists who
are building excellence in environmental genomics applied to research themes in
environmental health and sustainability, water quality and water reuse, microbial
processes and climate change, biodiversity and bioprospecting.
Environmental Microbiology
Academic Staff
Scientia Professor Staffan Kjelleberg
Professor Rick Cavicchioli
Professor Brett Neilan
Professor Malcolm Walter
Dr Brendan Burns, Senior Lecturer
Dr Belinda Ferrari, Senior Lecturer
Dr Torsten Thomas, Senior Lecturer
Mr John Wilson, Lecturer
Areas of research excellence in the Environmental Microbiology
group include the origins, evolution, diversity and unique
physiologies of microbial life on Earth, expertise in the study of
stromatolite communities, and development of novel culturing
approaches and contributions to the development of fluorescencebased detection strategies for pathogens in soil bacteria.
Scientists in this group are considered world leaders in the
genetics of toxic cyanobacteria, with research that has led
to the discovery of the biochemical pathways responsible
for the production of potent bacterial and algal toxins that
contaminate our water supplies. BABS is also home to the world’s
leading laboratory on the molecular basis for cold adaptation
in archaea, Important contributions have been made to the
study of oligotrophic marine bacteria, focusing on proteomics,
comparative genomics and adaptation physiology, and genomebased studies of whole ecosystems.
AN OCEAN OF MICROBES
Dr Mark Brown, ARC QEII Fellow
Every millilitre of seawater
contains millions of microbes
that underpin the health of
our ocean ecosystems. They
represent 50-90% of total
ocean biomass, regulate
ocean chemistry, influence the
climate, and provide the energy
upon which all higher trophic
levels depend. Relatively little
is known about the microbes
inhabiting Australian waters,
how they change over seasons
or in relation to climatic and
oceanographic conditions, and
what, if any, may be the impacts
of ongoing changes in marine
systems due to regional climate
change.
The Brown lab couples cuttingedge molecular tools with
extensive sampling regimes to
provide temporal and spatial
information on the environmental
factors that impact microbial
(bacteria, archaea and microbial
eukaryotes) community
assembly, with a long-term
goal of incorporating microbial
community structure and
function into ocean circulation
models.
The major research questions are
Who are the dominant
microbes inhabiting
key Australian marine
environments?
What are the key chemical
cycling processes that these
organisms mediate and
how do phylogenetic and
physiological shifts influence
the state of key ecosystems?
Figure 1. Sea
surface temperature
plot highlighting the
interaction of the
EAC and the Tasman
Sea near the Port
Hacking NRS (Star).
Adapted from p.53
of the NSW-IMOS
Node Science and
Implementation Plan.
Main image by M.
Roughen (UNSW)
How do Australian marine
microbial communities and
their biogeochemical function
vary in space and time?
Will shifting ocean circulation
patterns alter microbial
community structure and
function in ways that will have
potential feed-back effects
on ecosystem stability?
In 2009, in conjunction with
the NSW Department of
Environment, Climate Change
and Water (DECCW) and the
Integrated Marine Observing
System (IMOS), the Brown lab
initiated a microbial observatory
at the Port Hacking National
Reference Station (NRS)
(34°05’S. 151°13’E). The Port
Hacking NRS is the site of
some of the longest ongoing
oceanographic monitoring in
the world, providing a near
continuous 50-year record
of chemical and physical
oceanographic data. The
microbial observatory is
dedicated to long-term temporal
characterisation of the coastal
pelagic microbial community
structure, and ensuing molecular
analyses will be incorporated
into this data.
29
The continental shelf in this
region is narrow, extending
~30-50 km offshore, and the
southward flow of the East
Australian Current (EAC)
dominates the hydrographic
regime for much of the year
(Figure 1). The EAC brings
warm, oligotrophic (low nutrient)
water from the Coral Sea down
the east coast of Australia,
ultimately extending as far
south as Tasmania, where an
increase in the duration of its
influence has led to these waters
being amongst the most rapidly
warming ocean region in the
world. Near Sydney, the EAC
breaks down and forms eddies
(circular spinning water-masses)
and mixes with the cold, nutrientrich waters of the Tasman Sea.
Using cutting-edge molecular
tools, Mark's team examines
planktonic microorganisms,
including bacteria and microbial
eukaryotes, to determine how
they change over seasons in
relation to water body chemistry
and physics. This long-term
strategy enables examination
Surface slick of
the cyanobacteria
Trichodesmium
sp., an important
nitrogen-fixing
organism that
inhabits lownutrient waters,
found in the EAC
of the effects of both local and
basin-scale events, such as the
Sydney dust storms in 2009 and
the strong La Niña Southern
Oscillation during the summer of
2010/11.
A particular focus in the next
twelve months is to correlate
the Port Hacking data with that
collected at the lab’s sister
station, the San Pedro Ocean
Time Series off the coast of Los
Angeles, California.
During 2010, Mark undertook a
research voyage into the EAC,
aiming to expand the spatial
representation of knowledge
being obtained from the
temporal monitoring at the Port
Hacking NRS site. The samples
collected during this voyage
will help test the following key
hypotheses:
1. Key Australian
oceanographic provinces
host discrete microbial
assemblages that:
a. are tuned to specific local
physicochemical features
of the environment
b. perform distinct
biogeochemical functions
that shape regionally
important marine
ecosystems
2. Climate change will alter
the distribution of microbial
populations and subsequently
shift the biogeochemical
status of some Australian
marine ecosystems.
Dr Mark Brown during his 2010 research voyage to study the flow of the EAC
BACTERIA, GLOBAL WARMING AND BLEACHING IN A MARINE
SEAWEED
Scientia Professor Staffan Kjelleberg
Outbreaks of disease in natural
marine communities have
become increasingly apparent
over the past decade, with a
range of marine organisms from
seals to kelp suffering major
disease-related die-offs. In
the last several years, climate
change has been linked to
a change in ocean currents,
and this is evident right on our
doorstep with warmer water
being carried further south
with the shifting East Australian
Current. This shift is correlated
with increasing observations
of bleaching in marine coastal
benthic communities.
Temperature, disease and
algal chemical defence
Staffan Kjelleberg and his
colleagues at the Centre for
Marine Bio-Innovation (CMB),
Biomolecular Sciences and
School of Biological, Earth and
Environmental Sciences have
investigated the direct cause of
such bleaching effects. Using
the red alga Delisea pulchra as
a model, they explored the role
of bacteria in disease outbreaks,
which are increasingly observed
during summer when sea
surface temperatures are higher.
A complex interplay was found
between temperature, an algal
chemical defence mechanism
and bacterial virulence.
D. pulchra utilises a chemical
defence (furanones) to inhibit
colonisation and infection by
several bacterial pathogens.
With higher UV radiation during
summer, the alga’s furanone
concentrations are reduced,
while at the same time, bacterial
virulence appears to be induced
by elevated temperature. The
result is widespread bleaching
of the alga during summer,
when the alga is stressed and
has lowered defences, and
pathogen virulence is induced.
Prior to publication of this study
and our research on the specific
interaction between Nautella
sp R11, a member of the
ubiquitous marine Roseobacter
clade, and D. pulchra, the
complex interactions between
temperature, bacterial virulence
and a host’s chemical defence
had not been demonstrated in a
marine host-pathogen system.
Nautella sp. R11 genome (3499 protein coding genes) revealed putative virulence factors and
opportunistic lifestyle traits.
31
Virulence genes in marine
microbial pathogens
Delisea pulchra thallus showing
bleaching disease.
Succession ecology,
epiphytic bacteria and
bleaching disease
The complexity of interactions
between host benthic organisms
and bacterial pathogens also
reflects the involvement of
co-occurring species in the
epiphytic bacterial biofilm.
Researchers at the CMB have
applied ecological succession
models to D. pulchra’s epiphytic
bacterial community to explore
such interactions. The order of
arrival of bacterial colonisers in
post-disturbance succession
affects the outcome of the
established bacterial community,
such that early colonisers either
inhibit or tolerate subsequent
colonisers. For D. pulchra,
when the algal defence was
reduced, its co-occurring
bacterial community protected
the host by inhibiting pathogens,
for example, the Roseobacter
Phaeobacter spp. LSS9, and
thus, disease.
Whole genome sequencing of
the two pathogens mentioned
above, and comparison of
their genomes with those of a
range of already sequenced
Roseobacter strains that can
colonise the algal surface but
not cause disease, led to the
identification of virulence factors
involved in disease initiation and
progression.
In addition to the metabolic
versatility characteristic of
the Roseobacter lineage, the
genomes were found to encode
several virulence factors and
their regulatory machinery. This
included adhesion mechanisms,
systems for the transport of algal
metabolites, enzymes that confer
resistance to oxidative stress,
cytolysins, chemotaxis receptors
and signal transducers.
Importantly, the two algal
pathogens were uniquely
different from the non-pathogenic
Roseobacter isolates in that
they contained a subset of five
genes, including one encoding a
quorum sensing (QS)-dependent
transcriptional regulator. Deletion
mutants in the QS system in
Nautella sp. R11 failed to cause
disease in D. pulchra.
This observation supports
the model that a combination
of virulence factors and
QS-dependent regulatory
mechanisms allows indigenous
members of the alga’s epiphytic
microbial community to switch
to an opportunistic pathogenic
lifestyle, especially under
the stressful environmental
conditions associated with
global warming.
OXYGENATING THE EARTH: RESOLVING THE TIMING OF THE ORIGIN
OF OXYGEN-PRODUCING PHOTOSYNTHESIS IN CYANOBACTERIA
Professor Malcolm Walter, ARC Professorial Fellow
The cell membranes of
Photo by Jessica Coffey.
Sedimentary rocks
2.7 billion years old
that contain putative
evidence of early
cyanobacteria,
Pilbara region, WA
It is almost universally
accepted that the oxygenation
of the previously anaerobic
Earth was driven by the
oxygenic photosynthesis of
cyanobacteria. However, there
are inconsistencies of hundreds
of millions of years in the
various lines of evidence for
the timing of the oxygenation
process. Professor Walter’s team
is combining evidence from
genomics and proteomics with
the fossil records to help resolve
this problem. In the Pilbara
region of Western Australia,
there is a remarkably wellpreserved succession of rocks
reliably dated as lying in the
disputed time range of the rise
to prominence of cyanobacteria,
2.6-2.7 billion years ago. Their
studies are focused there as well
as on extant cyanobacteria.
The main scientific problem
is reconciling evidence for an
early origin of cyanobacteria
with geochemical evidence for
the timing of the oxidation of the
Earth’s surface. That evidence, as
interpreted by some researchers,
seems to indicate that it was not
until the Great Oxidation Event
(GOE) at about 2.45-2.32 billion
years ago that the atmosphere
and shallow hydrosphere became
oxic. Others postulate early ‘whiffs’
of oxygen in the atmosphere some
50 million years prior to the GOE,
and still others have a radically
different view and see evidence of
oxic environments as far back as
3.5 billion years ago.
Some examples of the
significance of the oxygenation
event are its major effects on
biology:
Oxygen would have been
toxic to all life prior to the
event, so it probably led
to the extinction of many
species. It produced
the division of life into
anaerobic species, which
live in environments that
oxygen cannot get to, and
aerobic species that protect
themselves against oxygen
damage through use of
antioxidants and other
strategies.
eukaryotes are stiffened
by sterol molecules. The
biosynthesis of sterols has
several steps that require
oxygen. Had the Earth not
accumulated molecular
oxygen, it would still be a
procaryotic world.
It allowed the development
of aerobic respiration,
which is a far more efficient
energy conversion process
(36-38 ATPs per glucose
as against 2 ATPs for
anaerobic processes). This
efficiency made possible the
evolution of large and diverse
multicellular organisms.
It led to the formation of the
ozone layer, helping to allow
the subsequent emergence
of life on land.
The rocks that we are focusing
on are the best in the world
for such a study. They are
extraordinarily well preserved
and contain cellularly preserved
microfossils, abundant
stromatolites, which are reef-like
structures built by microbes, and
hydrocarbon biomarkers, which
are remnants of cellular material.
PhD student Jessica Coffey
has discovered that some of
the stromatolites contain a
wide range of biomarkers that
are indicative of the former
presence of complex microbial
communities. While there are
uncertainties in the interpretation
of this evidence, it seems
likely that the communities
included cyanobacteria and
eukaryotic algae, as some of
the stromatolites have shapes
33
that in the modern biosphere
are constructed only by
cyanobacteria.
During fieldwork in 2010,
PhD student David Flannery
discovered fossils of what are
called ‘tufted mats’, former
benthic communities of
filamentous microbes arranged
like the hairs of an artist’s brush.
All extant examples of such
communities are dominated by
cyanobacteria. Accordingly,
evidence for the presence of
cyanobacteria 2.7 billion years
ago is accumulating.
2a-methyl hopanepolyol.
Until recently, this compound
was considered diagnostic
of cyanobacteria, but recent
work has cast doubts on this.
Resolving this uncertainty
is important because the
geological derivative of this
compound, 2a-methyl hopane,
is found in the same rocks as the
2.7 billion year-old fossils.
This is a work in progress, but
it is expected that within a few
years the timing of the origin of
cyanobacteria and oxygenic
photosynthesis will be able to be
tightly constrained.
Photo by David Flannery
At the same time, PhD student
Tamsyn Garby is investigating
the phylogenetic distribution
of the gene responsible for
the synthesis of the putative
cyanobacterial biomarker
Tufted microbial
mat dominated
by filamentous
cyanobacteria,
intertidal zone,
Shark Bay, WA
PROFILE:
PROFESSOR BILL RAWLINSON AM
Director of Virology, Virology Division, SEALS Microbiology
BABS Visiting Fellow
Viruses are arguably
the most basic and
possibly the first
form of life – self
replicating RNA. They
range from extremely
common infections,
including the trivial
common cold, to
very uncommon but
appallingly severe infections such as haemorrhagic
fever due to Ebolavirus. So what are viruses and
how can they cause so much trouble?
Professor Bill Rawlinson has dedicated over 20
years to studying these smallest of organisms.
He started his career as a medical student at the
University of Sydney in 1979 with a keen interest
in infectious diseases. During these early years he
worked on leprosy, an infectious disease caused
by the bacteria Mycobaterium leprae, in Aboriginal
people in Darwin. He was fortunate in being
guided by Tony Basten of Sydney University, and
John Hargraves, the surgeon who trained the first
Aboriginal health workers in the Northern Territory.
Bill then undertook specialist clinical training in
infectious diseases, initially with Tania Sorrell,
Professor of Clinical Infectious Diseases at The
University of Sydney, leading to his real passion for
research into viruses. Shortly after returning from
Cambridge in the UK, where he completed his PhD
and postdoctoral training studying cytomegalovirus
(CMV) genomics, Bill commenced his roles as
medical virologist at South Eastern Area Laboratory
Services (SEALS) and Associate Professor at
UNSW. Today, Bill says he is fortunate to work
with a team of over 20 scientists and students in
virology research, studying the pathogenesis of
respiratory viruses and viruses in type-1 diabetes,
as well as the consequences of CMV infection.
CMV is the most common viral cause of congenital
infection, leading to severe foetal anomalies
or even death of the baby in the womb. “There
is a baby born every day in Australia who
has problems associated with CMV” said Bill.
Fortunately, most babies will not experience longterm problems, but some will develop blindness,
mental disabilities, heart problems, liver problems
and deafness. Bill is one of the key scientists
leading the research to understand this virus, with
the aim of reducing problems associated with
CMV infections. This work has led to long-term
collaborative studies with talented scientists in
the UNSW virology laboratories at the Prince of
Wales Hospital, funded by the NHMRC, ARC and
charitable organisations such as SIDSandKids and
the Stillbirth Foundation.
Bill was recently awarded the Member of the Order
of Australia (AM) for his services to the medical
sciences as a clinician, educator and researcher.
His work and collaborations have led to new testing
algorithms for common viral illnesses, analysis of
CMV genomes, unique studies of congenital CMV
and the placenta, and also some unique data on
endogenous viruses and cancer. “There’s no doubt
in my mind that we will find viruses in a number of
conditions that currently have unknown causes”
he said. “However, it is absolutely essential that we
apply rigorous science to these studies, to make
our findings a solid basis for understanding the
nature of the relationship between the presence of
viruses and the presence of disease.”
Bill directs the Virology Division at the SEALS
laboratories at Prince of Wales Hospital, where he
has been involved in developing tests, treatments
and vaccines for viruses, including the H1N1
influenza virus responsible for causing the swine
flu outbreak.
35
Bill is renowned for integrating new research
findings into clinical practices and management
of patients. As an admirer of Karl Popper, he
holds to the importance of hypothesis testing and
falsifiability in science. “It’s a great privilege to help
people solve problems, and to work with a group
of scientists who are passionate, highly intelligent
and driven to scientific discovery. I always have to
be aware of not only the joy of science, but also the
responsibility to do the work in a way that will stand
the test of time.”
Liver
Kidney
CMV infection in a
stillborn baby
Placenta
PROFILE:
PROFESSOR DAVID SINCLAIR
Harvard Medical School
BABS Alumnus
Why do we age? Is there
anything we can do
about it? These questions
have been around since
human consciousness,
but only in the past
decade have we had
sufficient technology and
scientific understanding
to seriously tackle them.
Fifteen years ago, the ageing field was a
backwater of biology, seen by many as a soft
science. That, however, didn’t stop David Sinclair,
a BABS PhD graduate in 1995, from heading to
Boston to apply his knowledge of genetics and
biochemistry to try to uncover the fundamental
mechanisms of ageing in budding yeast.
Today, David is a tenured professor and CoDirector of the Paul F Glenn Laboratories for
Aging Research at Harvard Medical School,
where he leads a team of 15 researchers in the
quest to understand how we might prevent and
treat the diseases of old age, including cancer,
cardiovascular disease, Alzheimer’s disease, and
type II diabetes. David is also a Conjoint Professor
in the UNSW Faculty of Medicine and is presently
building a research group in the new Lowy Cancer
Research Centre focused on training scientists
in ageing research, studying Australia’s unique
mammals, and promoting innovation.
Before starting his own lab at Harvard in 1999,
David spent four years in the lab of Lenny
Guarente, Director of the Glenn Laboratory for
the Science of Aging at MIT, during which time
the team discovered a cause of yeast ageing
(genomic instability) and a gene that slows ageing,
SIR2. This gene was the founding member of
the ‘sirtuin’ family of genes that encode protein
deacetylases and control the pace of ageing in
yeast and other simple organisms. “In humans,
there are seven sirtuins, SIRT1-7,” explains David,
“and our goal is to understand what each of these
is doing in mammals. So far, we know the most
about SIRT1, which regulates energy metabolism
and cell survival. Mice that have more SIRT1 are
resistant to diseases of ageing, such as cancer,
type II diabetes, and heart disease.”
In 2003, David’s lab published the finding that
resveratrol, a molecule found in red wine, is an
activator of SIRT1, and in 2005, he co-founded
Sirtris Pharmaceuticals to find more potent
synthetic molecules that activate SIRT1 to
treat diseases of ageing. The company, which
was purchased by GlaxoSmithKline in 2008,
is conducting Phase II efficacy trials in type II
diabetes and inflammatory diseases. The results
are promising so far, and will be released publicly
in June 2011.
“I feel extraordinarily fortunate to have been
educated at UNSW,” said David, “My BSc degree
at UNSW was very broad, covering ecology,
evolution, marine biology, and biochemistry, which
helped me see the big picture and ask the big
questions. A year of honours and a four-year PhD
in Professor Ian Dawes’s lab taught me rigorous
bench science and the fundamentals of yeast
genetics. When I arrived at MIT in Boston to do my
postdoc, I hit the ground running.”
Human SIRT1
37
Sinclair lab staff, Havard Medical School
David sees one of his roles as an advisor to other
scientists seeking to translate their research into
medicines. In 2006, with Harvard colleague Darren
Higgins, he co-founded the vaccine company
Genocea, which is working on vaccines against
Malaria, Streptococcus pneumoniae, and a variety
of common viral diseases. “Hopefully we can help
people in the developing world as well,” says
David. In April 2011 he also co-founded Ovastem
Inc, working to solve infertility problems in women
using newly discovered human egg stem cells.
Looking back on his time at UNSW, David says
he was also fortunate to have met his wife
Sandra Luikenhuis, who was a BABS visiting
student from Germany. Sandra completed her
Honours thesis with Professor Ian Dawes in 1997
before joining David in Boston. She obtained a
PhD at MIT, then helped build Magen, a small
biotechnology company whose goal was to
develop dermatological medicines (it was sold in
2009). “My days at UNSW were some of the best
of my life,” said Sandra. “Where else can you get
a world-class education so close to such beautiful
beaches. Coogee is a special place.”
Resveratrol-treated (left) and non-treated (right) mice
Today, David and Sandra live in the leafy suburbs
of Boston with their three children, but still call
Australia home and bring their kids back often.
“We never forget that we both owe our careers to
the world-class education we received at UNSW
in the BABS program,” says David. “Finding the
perfect partner was an added bonus”.
External Partners
ANZAC Research Institute
Arizona State University
Atma Jaya University Indonesia
Hamburg University Center for
Molecular Neurobiology
National University of Singapore
Hanze University of Applied
Sciences
Norwegian Veterinary College
Hebrew University of Jerusalem
NSW Department of Primary
Industries (Fisheries)
Helmholtz Centre for Infection
Research
NSW Food Authority
Australian Antarctic Division
Australian Coal Association
Research Program
Australian Coal Mining Industry
Australian Drosophila Biomedical
Research Support Facility
International Society for Microbial
Ecology
Northwestern University Chicago
NSW National Parks and Wildlife
Service
Optigen
J Craig Venter Institute
Australian Geographic Society
Orica Australia Pty Ltd
James Cook University
Australian Institute of Marine
Science
Japanese Border Collie Health
Network
Australian National University
Peking University Health Science
Center
Pennsylvania State University
Kamaishi Marine Biotechnology
Institute
Prince of Wales Hospital
Baker IDI Institute
Karolisnka Institute Department
of Microbiology
Queensland Parks and Wildlife
Service
Bar Ilan University
La Trobe University
Queensland University
BASF The Chemical Company
Rutgers University
Centre for Vascular Research
Laboratoire d’Oceanologie
Biologique de Banyuls Universite
Paris
Centre of Marine Biotechnology
Laurentian University Canada
Charles Sturt University
Lowy Cancer Research Centre
Scripps Institute of
Oceanography
Macquarie University
Seoul National University
Christchurch Hospital
Concord Hospital
Massachusetts Institute of
Technology
Singapore Advanced
Environmental Biotechnology
Centre
Australian Nuclear Science &
Technology Organisation
Centenary Institute
CSIRO Entomology
Denmark National Environmental
Research Institute
McGowan Institute for
Regenerative Medicine
SA Department of Primary
Industries
Murdoch University
Singapore Centre on
Environmental Life Sciences
Engineering
Nanyang Environment and Water
Research Institute
Singapore Institute of Molecular
and Cell Biology
Diagnostic Technology Pty Ltd
Nanyang Technological
University
Singapore Tropical Marine
Science Institute
DOE Joint Genome Institute
NASA Ames Research Centre
Southern Cross University
Dow Chemical Company
National Centre for Adult Stem
Cell Research Griffith University
Stanford University
Desert Research Institute
Nevada
DHI Singapore
Environmental Biotechnology
Cooperative Research Centre
Garvan Institute
National Centre in HIV
Epidemiology & Clinical
Research
Stockholm Royal Institute of
Technology
Sydney Children's Hospital
39
Sydney Institute of Marine
Science
University of Papua New Guinea
Sydney Royal Botanic Gardens
and Domain Trust
University of Salzburg
University of Queensland
University of Southampton
Tasmanian Department of Health
University of Southern California
Tsinghua University China
University of Sydney
University of Alberta
University of Tasmania
University of Auckland
University of Technology Sydney
University of British Columbia
University of Utah
University of California, Davis
University of Western Australia.
University of California, Irvine
University of Western Sydney
University of California, Los
Angeles
University of Wollongong
University of California, San
Diego
US National Institutes of Health
University of Cincinnati
Victoria University Wellington
University of Cologne
University of Copenhagen
Wake Forest Institute for
University of Heidelberg
Westmead Hospital
Victor Chang Institute
University of Konstanz
University of Melbourne
University of Minho Portugal
University of New Mexico
University of Otago
Photo by Michele Potter
University of Manchester
University of Ottawa Heart
Institute
Sydney Harbour
Bridge Southern
Pylon
Memberships in Societies and Associations
Alexander von Humboldt
Foundation
Australian Institute of Policy &
Science
Pacific Institutes of Marine
Science
American Academy of
Microbiology
Australian Neuroscience Society
Royal Society of Victoria
Australian Society for
Biochemistry & Molecular
Biology
Safety Institute of Australia
Australian Society for Medical
Research
Society for Neuroscience (USA)
Australian Society for
Microbiology
Tissue Engineering &
International Society
American Association for Cancer
Research
American Society for
Biochemistry and Molecular
Biology
Microbiology
Pharmacognosy
American Society of Human
Genetics
Association of Vibrio Biologists
AusBiotech
Australasian Microarray &
Associated Technologies
Association
BioEnvironmental Polymer
Society
Bioinformatics Australia
Buttressing Coalition of the
Papua New Guinea Institute of
Medical Research
Chronic Lymphocytic Leukemia
Australian Research Consortium
Council of the Human Proteome
Organisation
Australasian Proteomics Society
Endocrine Society of Australia
Australasian Society for
Immunology
Forum for European-Australian
Science and Technology
Cooperation
Australasian Society for
Phycology and Aquatic Botany
Australia and New Zealand
Society for Cell and
Developmental Biology
Australia and New Zealand
Society for Cell and
Developmental Biology
Australian Academy of Science
Australian Atherosclerosis
Society
Australian Centre for Hepatitis
Virology
Australian Institute of Dangerous
Goods Consultants
Fulbright Alumni Association
Genetics Society of Australasia
Geological Society of Australia
High Blood Pressure Research
Council of Australia
Institute of Biology
International Society for Microbial
Ecology
International Society for
Microbiology
International Society for the
Study of Harmful Algae
International Society of Animal
Genetics
NASA Astrobiology Institute
Society for General Microbiology
(UK)
41
Research Centres
The Ramaciotti Centre for Gene
Function Analysis
The Ramaciotti Centre is a leading highthroughput functional genomics service provider,
offering expertise in sequencing and microarray
technology. It supports genomics research
throughout UNSW and its associated research
institutes by offering a range of services and
access to equipment.
Services offered include:
DNA sequencing
DNA sequencing and genotyping
Sequencing consumable sales
Next-Generation Sequencing
Roche 454 GS-FLX service
Illumina GAIIx service (authorised service
provider)
Microarray
Affymetrix GeneChip service (authorised
service provider)
Agilent microarray service
Bioinformatics
Data resulting from these processes can be
analysed on a collaborative basis by staff
at the New South Wales Systems Biology
Initiative.
Ramaciotti Centre Staff (L-R) Marc Wilkins, Helen Speirs, Ruby Lin, Tonia
Russell, Natalie Twine, Bronwyn Robertson, Hannah Ginn, Jason Koval
Highlights from 2010
The Centre had a very productive year, with the
DNA sequencing service processing over 85,000
samples, and the microarray service processing
over 2,000 arrays. There was also a good uptake
of next-generation sequencing, which brought
many new customers to the Centre. In 2010 the
Centre facilitated more than 260 projects for
customers Australia-wide and overseas, with
their projects bridging a range of biomedical,
diagnostic, environmental and agricultural research
disciplines.
Some of the UNSW-based areas of research
that the Centre was involved in were genotyping
of Australians with deep aboriginal ancestry,
sequencing two bacterial genomes, RNA
sequencing of Alzheimer’s disease-affected brain
regions, study of paternal inherited obesity in rats,
and identifying biomarkers in myocardial infarction
in mice, which led to a US patent.
New laboratory space completed in 2010, custom
designed to house next-generation sequencers
Professor Ian Dawes announced his
retirement
The founding Director of the Centre, Professor
Ian Dawes, announced in July that he would be
retiring from his position at UNSW during 2011.
Ian and colleagues at UNSW and other NSW
universities established the Ramaciotti Centre in
1999. Over the last 11 years, this collaboration
has gone from strength to strength with the
award of 10 consecutive ARC LIEF grants,
which have been the main source of equipment
funding for the Centre.
Centre staff with Kevin King, CEO of Affymetrix Inc.
Professor Marc Wilkins, head of the New South
Wales Systems Biology Initiative, succeeded Ian
as Centre Director in January 2011.
GeneTitan service launched by Kevin King,
Affymetrix President & CEO
In August, the Ramaciotti Centre was honoured
to be visited by Kevin King, President and
CEO of Affymetrix, Inc. Kevin came to Australia
specifically to launch the Centre’s new
GeneTitan service. The GeneTitan automates
array processing from target hybridisation to
data generation, thereby increasing processing
efficiency.
The Centre is using the GeneTitan to perform
a 4,000-array genome-wide association study
aimed at discovering genetic factors that predict
complications in type 2 diabetes. Centre Manager
Dr Helen Speirs is an associate investigator on
the project, which is funded by a major NHMRC
research grant. This important study reinforces the
Centre’s position as the principal Affymetrix service
provider in Australia.
For further information on the Ramaciotti Centre
and the services offered, please visit our website:
www.ramaciotti.unsw.edu.au
43
Centre for Marine Bio-Innovation
The CMB is an international focal point for
interdisciplinary basic and applied research
into chemically mediated interactions between
organisms. Using a multidisciplinary approach,
the CMB aims to understand how chemical signals
mediate the ecology and physiology of organisms
and apply this knowledge to the development
of new biotechnologies across environmental,
industrial and medical settings.
The CMB integrates research across microbiology,
marine chemical ecology, ecological theory,
chemistry, and organism and community
genomics, to drive research excellence in studies
of microbial biofilms, bacteria-higher organism
interactions, colonisation biology of marine
sessile organisms, experimental marine ecology,
biofouling, biodiversity, bioremediation, interkingdom signalling and microbiology applied to
environmental engineering.
In 2010 the CMB’s international profile as a leadingedge research centre was further augmented, with
its co-director Professor Staffan Kjelleberg taking
on the role of founding director of the Singapore
Centre on Environmental Life Sciences Engineering
(SCELSE), a centre of excellence on biofilm
research established at Singapore’s Nanyang
Technical University (NTU). This development adds
to the present collaborative research conducted by
CMB at the joint UNSW-NTU operated Advanced
Environmental Biotechnology Centre, where
bioprocess expertise and microbiology are used to
deliver biotechnological solutions for sustainable
water and environmental practices.
The partnership between the CMB and the
Sydney Institute of Marine Science (SIMS), with
CMB co-director Peter Steinberg as director of
SIMS, is another example of an ongoing initiative
that enhances the Centre’s capabilities. SIMS
is a collaborative venture between four Sydney
universities, including UNSW, and a number of
state and federal government departments. The
facilities at SIMS enable CMB researchers to use
molecular biological tools in ever more realistic
Sydney Institute
of Marine
Science, Sydney
Harbour
contexts in the marine environment, delivering
ecologically relevant research and future marine
coastal management procedures.
Alongside these achievements, funding successes
in 2010 provide the financial platform for several
ongoing research initiatives, including:
CMB co-director Associate Professor Mike
Manefield was awarded an ARC Future
Fellowship with funding for a project harnessing
microbial respiration for pollutant degradation
and natural gas production. This research
seeks to exploit compounds that are naturally
produced by microorganisms to develop a
marketable green technology for environmental
restoration and clean energy generation
in Australia and abroad. Benefits of this
research include improved environmental and
human health for metropolitan and regional
communities, with economic benefits flowing
from global application.
ARC Linkage project grant ‘The multi-scale
strategy to manage chloramine decay and
nitrification in water distribution systems’.
Co-PIs Scott Rice and Nic Barraud will
collaborate with the Australian Water Quality
Centre and the Water Corporation of WA to
generate knowledge and technologies to
prevent chloramine decay, thereby greatly
benefiting the Australian water industry.
Outcomes of this project will provide the
highest possible water quality, economically
and reliably, providing the community with
safe drinking water and the assurance of
microbiological compliance.
CMB Researchers
Oliver Zemb and
Maria GutierrezZamora
ARC Discovery Project grant ‘Defining how
bacteriophage shape the biofilm lifecycle
of bacteria’ for Scott Rice and Diane
McDougald. Bacteriophages (viruses that
infect bacteria) represent a significant
selective pressure that drives the evolution of
bacteria. The project will focus on the genetic
mechanisms by which genes encoded by a
bacteriophage can contribute to increased
survival of bacteria in the environment.
Two further years of funding for the
Environmental Biotechnology Co-operative
Research Centre (EBCRC), of which the CMB
is a founding partner. The CMB will continue
to serve as a key research provider to
develop novel strategies to control the growth
of bacteria on surfaces. The program will
focus on collaborative projects with industrial
partners in the area of drinking water
purification, food processing systems and the
production of consumer products.
Across UNSW, the CMB provides life sciences
expertise and a skill base for key upcoming
initiatives in energy research, water and climate
change. The CMB is very active in the training
of research students, producing high calibre
graduates who achieve work in academia and
industry both in Australia and overseas.
For further information, please visit our website:
http://www.cmb.unsw.edu.au/
Bioremediation Trial
45
Evolution & Ecology Research
Centre
Photo: Angela Moles
The E&ERC was established in 2007 to provide
a cohesive and cooperative environment for
evolution and ecology research and research
training at The University of New South Wales. The
E&ERC draws together the diverse strengths from
the Schools of Biological, Earth and Environmental
Sciences, Biotechnology and Biomolecular
Sciences, Mathematics & Statistics, and Medical
Sciences. The Centre’s purpose is to build capacity
for and quality in research, including postgraduate
research and supervision. It provides seed funding
for innovative new research collaborations,
recognises excellence in research, learning and
supervision, runs an innovative Graduate Program
in Evolution & Ecology, and engages in public
outreach relating to evolution and ecology.
Daintree Rainforest Caterpillar
In 2010 the E&ERC further built and supported
excellence in research in evolution and ecology.
The Centre continues to support the increase
in external funding to its members, including
development of explicit strategies to diversify
funding, and to succeed in new schemes such as
Future Fellowships.
Photo: Angela Moles
Evolution is responsible for all of the biological
diversity in the natural world and the fossil record,
and occurs within the context of ecological
interactions between an organism and its
environment.
Camping in the Pleistocene
The Centre maintains a vibrant seminar and visitor
program. The number of top-quality High Degree
Research students within the Centre continued to
grow via ongoing improvements to the Graduate
Program in Evolution & Ecology, aggressive
recruitment strategies and support for graduate
students, including a Postgraduate Writing
and Skills Transfer Scholarship for graduating
exceptional PhD students.
www.eerc.unsw.edu.au
Photo: Dr Abigail Allwood
Photo: The Powerhouse Museum
Australian Centre for Astrobiology
3.42 billion yearold stromatolites in
the Pilbara dawn
Mars Yard and rovers located at Sydney's Powerhouse Museum for the
Pathways to Space project
The ACA has a strong media, education and
outreach program related to its research. The
outreach program itself is also the subject of
research into the long-term effectiveness of such
projects.
In 2010 the ACA’s science communication
researcher, Dr Carol Oliver, won a $1M grant
from the Federal Government’s Australian Space
Research Program for an education and research
project located at the Powerhouse Museum in
Sydney. The other partners in the Pathways to
Space project are the Powerhouse Museum,
the Australian Centre for Field Robotics at the
University of Sydney, and Cisco Systems Australia.
Dr Oliver also leads the Virtual Field Trip group
for the NASA Astrobiology teams at Arizona
State University and MIT, with VFTs undertaken
or planned to the Pilbara region and Shark Bay
in Western Australia, and the Flinders Ranges in
South Australia.
Science Education Centre-NASA Australian Space
Prize and during 2010 spent 10 weeks at NASA
on a research project. Elizabeth investigated
the influence of microgravity on human cellular
function, her research identifying many proteins
that can be correlated to systemic effects
experienced in space conditions. Three of the
Centre’s PhD graduates now work for NASA, one
on the Mars Reconnaissance Orbiter team.
www.aca.unsw.edu.au
The ACA provides a highly visible flagship
program that is able to attract quality science
and science communication PhD students to
pursue such research programs. In 2010, ACA
student Elizabeth Blaber won the Victorian Space
Elizabeth Blaber at NASA
47
Infrastructure and Facilities
Seahorse Extracellular Flux (XF)
Analyser
The Seahorse is a new technology that measures
the metabolic activity of cells in minutes, offering a
physiologic cell based assay for the determination
of basal oxygen consumption, glycolysis, ATP
turnover and respiratory capacity in a single
experiment. The two major energy producing
pathways of the cell, mitochondrial respiration and
glycolysis, are measured simultaneously and the
data generated provides the most physiologically
relevant bioenergetic assay available for the
determination of mitochondrial function.
Dr Vladimir
Sytnyk with the
new Confocal
Microscope
C1Si Confocal Microscope
The C1si is a revolutionary true spectral imaging
confocal laser microscope system with the
amazing capability to acquire 32 channels
of fluorescence spectra over a 320 nm wide
wavelength range in a single pass.
C1si useful for a wide range of applications. By
cleanly unmixing overlapping spectra of different
fluorescent labels, the C1si dramatically improves
dynamic observations of live cells and facilitates
the acquisition of detailed data.
The system can be used to study respiratory
malfunction in multiple diseases including cancer,
cardiovascular disease, aging-associated
disorders, mitochondrial diseases, immunological
disorders, neurodegenerative disease, obesity
and diabetes. The XF Flux analyser is useful to
anyone studying mitochondrial abnormality as a
consequence of environmental insult, mitochondrial
DNA or nuclear DNA mutation. Assays are
non-invasive allowing for further downstream
applications to be performed.
Single-Cell Analysis Facility
Dr Belinda Ferrari is the Director of this facility,
which contains the following equipment:
Beckman Coulter Quanta MPC fow cytometer
BD Biosciences three laser FACSAria llu flow
cytometer
Olympus BX51 fixed stage fluorescence
microscope equipped with an Eppendorf
microdissector
www.babs.unsw.edu.au/singlecell_analysis_
facility.php
UNSW Recombinant Products
Facility
This facility provides cell line development,
bioprocess development and protein production
services to the research community and to
industry, and the following range of services:
cell line and hybridoma development
cell line characterisation
bioprocess development and evaluation
microbial fermentation (e.coli and yeast) to 25L
imaging system, which uses a CCD camera with
very high sensitivity and is particularly useful for
chemiluminescence and densitometry. MIAF is a
multiuser facility that is accessed by researchers
from BABS, other Faculty of Science Schools and
other Faculties and UNSW-associated institutions.
Other specialised amenities in BABS
Biorad gel documentation system
FACSAria II for improved cell sorting and data
acquisition
mammalian cell culture to 10L
Inverted microscope
protein and antibody purification
Neon transfection system
protein characterisation and analysis including
Nikon TS100-F inverted microscope with an
protein gel electrophoresis, Western blotting,
Biacore SPF
LC-MS and other proteomic services via the
BMSF
cell line storage (-80oC and liquid nitrogen)
www.proteins.unsw.edu.au
LED source
Olympus FSX100 digital imaging system
PAM2500 Portable chlorophyll fluorometer
Polarstar omega microplate reader
Protean IEF system and criterion cell
QC1 and QC2 quarantine-approved premises
RT PCR system
Canine Genetics Facility
Semi-automatic microtome
SSBA (Security Sensitive Biological Organisms)
DNA testing is available for common diseases found
in Border Collies. These tests have been developed
from research primarily performed within BABS under
the supervision of Dr Alan Wilton.
www.babs.unsw.edu.au/canine_genetics_
facility.php
facility
TissueLyser LT cell lysis apparatus
TLC autospotter
Unichromat 1500-pro chromatography cabinet
for Akta systems
Whitley DG250 workstation for culturing
anaerobes
Molecular and Image Analysis
Facility (MIAF)
The MIAF was established through a UNSW Capital
Grant in 1997. After successful years of operation,
new equipment was purchased in 2003 through
funding obtained as part of an ARC Linkage,
Equipment and Facilities grant. MIAF contains
a Fujifilm FLA-5000 imaging system that allows
scanning of fluorescent and radioisotopic samples
as large as 40 x 46cm at pixel size as low as 10
microns. It can also be used for densitometry.
The MIAF also includes a Fujifilm LAS-3000
49
Undergraduate and Postgraduate Degree
programs in the School of BABS prepare students
for a variety of career paths within and outside
the sciences. Our graduates work in government
and privately sponsored industries, in areas
ranging from management, policy development,
production, quality control and research to
education. Our programs provide excellent
training in scientific methodology, creative thinking,
organisational skills, problem solving and analysis.
In addition, communication and information literacy
are also emphasised, providing our graduates
with a competitive edge for careers in journalism,
business and management.
Innovations in Teaching
Two new courses in rapidly evolving discipline
areas have been developed for 2011.
Dr Louise Lutze-Mann and Mr Geoff Kornfeld have
developed a new practical class in which students
will investigate changes in gene expression
following treatment of breast cancer cells with
a potential new chemotherapeutic drug. This
laboratory-based project will be coupled to a newly
developed virtual laboratory designed to support
the students’ analysis of the microarray data
generated by this project.
In addition to the introduction of new materials,
the School also regularly reviews its learning
and assessment practices in all courses and
programs. Starting in 2010, with the support of the
University and the Faculty of Science, the School
is working with Professor Jan Orrell (educational
consultant from Flinders University) on a review of
undergraduate assessment. The aim is to ensure
that our assessment supports learning, is kept real,
and is in line with our learning objectives.
Postgraduate: Astrobiology: Life in the
Universe (BABS6741) is the study of life in
the universe and the chemistry, physics, and
adaptations that influence its origin, evolution
and destiny. It is an interdisciplinary science
encompassing aspects of biology, chemistry,
geology and astronomy and attempts to define
life, and reveal how life is strongly coupled with
its environment.
Undergraduate: Current trends in
Biotechnology (BABS2011) covers emerging
technologies in the areas of medical,
environmental and molecular biotechnology
and their potential impact on the directions
of current products and services, product
development, research techniques and
manufacturing processes.
While BABS is home to internationally recognised
innovative researchers, it also has many members
of staff who are innovators in teaching and
learning. In a collaboration with and utilising
considerable support from the Ramaciotti Centre
for Gene Function Analysis, the School continues
to incorporate cutting-edge research into
undergraduate teaching.
Recognition of BABS Teaching Staff
The quality of the teaching programs in the
School is widely recognised within and outside
UNSW, with many individual academics being
acknowledged in recent years for their outstanding
contributions to learning and teaching.
In an exceptional year for recognition of her
educational excellence, Dr Louise Lutze-Mann was
awarded a 2010 Australian Learning and Teaching
Council Citation for Outstanding Contribution to
Student Learning for sustained development and
implementation of research-focused teaching
Senior Lecturer Dr
Louise Lutze-Mann
and PhD Candidate
James Krycer received
Vice-Chancellor’s
2010 Teaching Awards
New PC2 teaching lab
completed in 2010
resources for undergraduate Science students.
In addition, Dr Lutze-Mann was awarded the
UNSW Vice Chancellor’s Award for Teaching
Excellence in recognition of teaching excellence
and the development of new resources for our
undergraduate courses.
BABS postgraduate research student James
Krycer was also awarded a Vice Chancellor’s
Award for Teaching Excellence (sessional staff)
for his promotion of excellence in the teaching of
molecular biology and biochemistry.
Other members of academic staff continue to work
closely with the UNSW Learning and Teaching Unit
to promote the development and adoption of new
technologies to aid learning and teaching, as well
as to develop new courses and new approaches to
teaching and assessment.
Modern Facilities
A program of renovation of BABS teaching
laboratories has begun, providing state-of-theart laboratory teaching facilities for our students.
Our microbiology teaching laboratory has
been renovated to PC2 standard and contains
video display screens, tissue culture facilities,
demonstrator-led independent group areas
with video/computer/internet facilities, a new
preparation laboratory, and real-time microscope
projection. Renovation of the biochemistry/
molecular biology teaching laboratory to PC1
standard is due to commence in 2011.
Outreach and Supporting Students
The School recognises its responsibility for
outreach and raising public awareness of the
institution and the Science discipline. Academics
continue to contribute to activities designed for
secondary school students and science teachers.
Professor Malcolm Walter and Dr Carol Oliver
from the Australian Centre for Astrobiology have
developed a Mars surface simulation for high
school students and their teachers as part of the
Pathways to Space program. During 2010, BABS
Honours student Elizabeth Blaber, supervised by
Dr Brendan Burns, became the first Australian
student to join the NASA Academy, where she
spent 10 weeks developing her research into the
effects of space travel on the human body.
The popularity of biotechnology and molecular
sciences continues to increase. This is in turn
increasing the demand for support and training
for secondary school science teachers. Dr
Jani O’Rourke and Dr Anne Galea continue the
School’s support of local high schools and high
school students. In addition, Associate Professor
Noel Whitaker and Dr Louise Lutze-Mann
have developed lecture material and practical
workshops for the NSW Teachers Professional
Development program.
51
Undergraduate Degrees
Our undergraduate programs in the biomolecular
sciences are designed to provide students with
rigorous training in the modern sciences and
are aimed at fostering an analytical approach
to problem solving. Students gain a strong
foundation in biology, chemistry and mathematics,
establishing a solid base of knowledge for
advanced coursework relevant to each specialised
program. The flexibility of our integrated
programs provides undergraduate students with
opportunities to interact with eminent researchers
in a variety of disciplines. Students develop
communication and information retrieval skills
necessary to stay up-to-date in rapidly evolving
areas of science, and so our programs are ideal for
those wishing to pursue research-oriented careers.
Bachelor Programs
We offer the following full-time professional
Bachelor programs:
Biotechnology (UNSW code 3052)
Bioinformatics (UNSW code 3674)
PC2
Teaching
Lab
extracting, organising, analysing, interpreting and
utilising biological information. Bioinformatics has
recently come to prominence with the analysis
of huge amounts of data generated by genome
projects and postgenomic biology.
For Science (3970), Advanced Science (3972)
and Medical Science (3991) programs, students
may choose to specialise in the disciplines of
biochemistry, biotechnology, genetics, medical
microbiology and immunology or microbiology and
molecular biology.
Science (UNSW code 3970)
Advanced Science (UNSW code 3972)
Medical Sciences (UNSW code 3991)
Biotechnology (3052) offers a comprehensive
education in all aspects of this multidisciplinary
field, leading to the award of a Bachelor of Science
Degree in Biotechnology with Honours. Starting
with an introduction to biotechnology, second-year
studies cover molecular biology and microbiology
with choices in chemistry or physiology. Third
year specialisations include biopharmaceuticals
and immunology, with optional environmental
biotechnology, environmental microbiology and
microbial genetics. The fourth year comprises
a research project and studies in commercial
biotechnology and professional issues.
Bioinformatics (3647) is jointly administered by
BABS and the School of Computer Science and
Engineering. Bioinformatics is a new and rapidly
expanding discipline at the convergence of
computing and the life sciences, and is focused
on the development of technologies for storing,
Majors
The School teaches within the Science discipline
areas of biotechnology, genetics, biochemistry,
molecular biology, microbiology, bioinformatics
and medical microbiology and immunology. In
conjunction with the Faculty of Medicine, we also
participate in the teaching of medical and science
students in the Bachelor of Medical Science
program. In this program students can study towards
a major and a minor in a particular specialisation,
with study plans provided for each discipline area.
Doctor of Philosophy (PhD) and Master of
Science (MSc) research-based degrees are
offered to qualified students who have completed
a four-year undergraduate Science degree with
Honours or the equivalent.
The BABS Graduate Diploma comprises a
specialised one-year period of full-time study
and research. It is designed for graduates from
overseas universities and those wanting to change
their career direction to encompass biotechnology
and molecular biological techniques.
BABS
Student
Computer
Lab
MPhil (BABS)
Combined Degrees
Science/Arts
(UNSW code 3930, 4 years full time)
Advanced Science/Arts
Bioinformatics/Science
Science/Education
Commerce/Science
Science/Law
The Master of Philosophy in Biotechnology and
Biomolecular Sciences is a research degree
that has been introduced as an alternative for
those considering Honours. The MPhil (BABS)
is designed to be taken over three semesters,
and comprises three coursework subjects and
a supervised research project. The program
provides students with a stronger qualification
through emphasis on research training, and
provides access to modern, sophisticated facilities
and techniques that apply to a wide range of
biotechnology and molecular biology fields. The
School’s first cohort of MPhil (BABS) graduated
during 2010.
Honours
An optional Honours year can be undertaken by
students with a credit average or above, involving
a full-time research project supervised by an
academic researcher. The Honours program
provides cutting-edge training in research
techniques, in modern laboratories.
Postgraduate Degrees
The School has a strong international reputation
for quality research in fundamental and applied
science. In 2010 the School had the highest
number of postgraduate students within the Faculty
of Science, with 138 Higher Degree by Research
students. Of these, 107 are progressing towards
PhDs. During 2010, 54 new Higher Degree by
Research students enrolled and 29 completed.
MPhil (BABS) Graduate, Karthikeyan
Gunasekaran
53
2010 Student Awards and Prizes
University Medal in Molecular Biology
University Medals in Genetics
Wee Siang Teo
Alison Kate McLean
Eliza KateCourtney
University Medal in Biotechnology
Ivy Kim NI Chiang
Jackson Prize for best overall performance in Honours year
Ivy Kim Ni Chiang
Jackson Prize for the best performance in Microbiology and Immunology
Nicole Hallahan
Shelston IP Prize for the best performance in BIOT3091 Professional Issues in Biotechnology
Natalie Wong
Life Technologies Prize for the best performance in BIOC3281 Recombinant DNA Techniques
and Eukaryotic Biology
Joseph Anthony Swift
School of Biotechnology and Biomolecular Sciences Prize for the best performance in
BIOC3111 Molecular Biology of Proteins
Amanda Jane Lawson
School of Biotechnology and Biomolecular Sciences Prize for the best performance in
Examinations in Level 2 Biochemistry courses
Shadi M El-Wahsh
School of Biotechnology and Biomolecular Sciences Prize for the best performance in Level
3 Biochemistry
Louise EllenCottle
Clinical Microbiology Update Program Prize for the best performance in MICR3081 Bacteria
and Disease
Melanie Rose Walker
Garry King Prize for the best Honours thesis in Molecular Biology or Genetics
Eliza Courtney
Meat and Livestock Australia Prize for the best performance in INOV4101-4301 Innovation in
Practice A-C
Kirsten Georgina Coupland
School of Biotechnology and Biomolecular Sciences Talented Student Scholarship for
Outstanding Achievement in Year 1
Christopher Brooks
Laura Ann Baker
Louise Ellen Cottle
Professor
Bill Ballard
presents
prize to Laura
Ann Baker
Prizegiving in the Rountree Room
BABSOC
Biotechnology and Biomolecular
Science Students Society
Dr Wallace Bridge, BABSOC mentor
Each Wednesday evening during the 2010
academic year, a team of 12 BABS undergrads
met to plan and manage the operation of the
School’s student society, BABSOC. These keen
students had seized the opportunity to join the
management executive, and were set to gain some
leadership experience and further develop their
sense of professional responsibility.
BABSOC’s
mission is to
build and sustain
a sense of
community and
pride within the
School. It does
this by hosting
numerous social
and professional
events
throughout the
year, including
BBQs for staff
and students
and themed
careers nights aimed at introducing students to
employment options available to them after they
leave UNSW.
Early in the year, a high priority task for the
management team was to source sponsors from
biotech-related industries to provide financial
support for events. In 2010, sponsorship was
generously provided by Cochlear, a leading
Australian biomedical device company. With this
support and subsidies from Arc, the UNSW student
association, BABSOC was able to deliver another
year of successful events.
Throughout 2010, BABSOC hosted several
lunchtime BBQs for staff and students on the
balcony of the newly renovated Samuels tearoom,
providing students with the opportunity to mingle
with each other and start putting out feelers for
potential Honours projects and supervisors. In
Semester 2, BABSOC
hosted two careers
evenings. First came the
BABSOC contribution to
the Meet the Entrepreneurs
series run by the Centre
for Innovation and
Entrepreneurship at the
Australian School of
Business. During the evening,
students heard from Dr Brad Walsh
(Minomic), Dr Phil Bell (Microbiogen) and Mr Robert
Birrell (Genetic Signatures), who told their stories
of involvement in the exciting yet tough world
of translating biological scientific discovery into
biotechnology-based products of commercial value.
The second event’s guest speakers were A/Prof
Jamie Vandenburg (Victor Chang Cardiac Research
Institute), Dr Darren Saunders (Garvan Institute) and
A/Prof Andrew Brown (BABS), who gave students
an insight into the realities of the eternal cycle of
publication, grants and fundraising that they should
expect if they choose to pursue a research career
path.
The pinnacle of the BABSOC social calendar is the
annual ball, now well established as an end-of-year
tradition within the School. This year’s theme was
‘Caesar’s Place: Vegas vs Rome’, with the ball being
held at the Italian Village in the Rocks. As we have
come to expect from previous years, the ball was
a great evening of celebration, complemented by
fine food, beverages, and dancing for all the suited
young gangsters and glamorous girls dressed in
their togas. Congratulations to those many brave
staff who dared to attend, in particular Alan Wilton,
Jeff Welch, and Brendan Burns, who over their many
years in BABS never seem to miss this opportunity to
support the students.
55
2010 PhD Completions
Last Name
First Name/S
Supervisor
Thesis Title
Aagaard
Vibeke
Staffan Kjelleberg
Utility of electron transfer mediators in the bioremediation of organochlorine
contaminated soil
Alexova
Ralitza D
Brett Neilan
The regulation of toxin synthesis in microcystis aeruginosa
Burg
Dominic W
Rick Cavicchioli
Cold adaptation in the Antarctic Archeaon Methanococcoides burtonii: The
Role of the Hydrophobic Proteome and Variations in Cellular Morphology
Burke
Catherine M
Staffan Kjelleberg
A metagenomic analysis of the epiphytic bacterial community from the green
macroalga Ulva australis
Chong
Grace HY
Mike Manefield
Intercellular bacterial signalling in activated sludge
De Francisci
Davide
Rick Cavicchioli
Characterisation of the RNA Polymerase Subunits E and F from the Antarctic
Archaeon Methanococcoides Burtonii
Eltahla
Auda A
Alan Wilton
Gestational Diabetes Mellitus: A Model for the Genetics of Type 2 Diabetes
Erce
Melissa A
Marc Wilkins
Analysis of the RNA degradosome complex from a Marine Vibrio species
Gunasekaran
Karthikeyan
Volga Bulmus
In-vitro investigation of reversible siRNA-poly(polyethylene glycol-acrylate)
conjugates
GutierrezZamora
Jimenez
Maria-Luisa
Jayawardena
Mike Manefield/
Staffan Kjelleberg
Development of a novel ribosomal RNA based method for fingerprinting
bacterial consortia
Menuk B
Staffan Kjelleberg
Stability and activity of self cleaning lipase based paints
Johal
Harpreet
William Rawlinson
The mouse mammary tumour virus - like virus in hormonally influenced human
tissues
Koorapati
Rakesh
Julian Cox
Comparison of vegetable and animal peptone-based culture media for
detection of Salmonella in poultry
Le
Lan HT
Mike Manefield
Community analysis and physiological characterisation of bacterial isolates
from a nitrifying membrane bioreactor
Man
Si Ming
Hazel Mitchell
The role of campylobacter species in inflammatory bowel diseases
Mohd Yatim
Abdul R
John Foster
Biotransformation of palm olein into sophorolipid biosurfactant
Moore
Zoe P
Diane McDougald
Molecular toolbox for the monitoring and control of water distribution biofilms
Moses
Joshua
Laurent Rivory
A critical evaluation of nucleic acid-based strategies for regulating the
transcription of genes
Ng
Shimin CM
Rick Cavicchioli
A metaproteomic analysis of microbial communities of Ace Lake, Antarctica
Pang
CN Ignatius
Marc Wilkins
The Dynamics of Protein Interaction Networks
Park
Ji H
Noel Dunn
Starvation and stress response in lactic acid bacteria
Penesyan
Anahit
Staffan Kjelleberg
Production of antimicrobial compounds by marine epibiotic bacteria
Reyes
Josephine F
Mark Tanaka
Theoretical studies on the evolution and genetic diversity of spoligotypes and
variable numbers of tandem repeat loci in Mycobacterium tuberculosis
Tay
Chin Y
Ruiting Lan
Population structure and genomic analysis of Helicobacter pylori
Ting
Lily LJ
Rick Cavicchioli
A quantitative proteomics investigation of cold adaptation in the marine
bacterium, Sphinopyxis alaskensis
Tsoi
Abraham MC
Ian Dawes
The role of amino acid metabolism in heat shock, one-carbon metabolism and
anaerobiosis in the yeast Saccharomyces cerevisiae
Whittall
Christine
Margaret Colley/
Andrew Collins
Interaction between N-(3-oxododecanoyl)-L-homoserine lactone and
peroxisome proliferator-activated receptor J
Yung
Pui YM
Staffan Kjelleberg
Metagenomics of the microbial communities associated with the marine
sponge Cymbastela concentrica
2010 Honours Projects
Surname
First Name
Supervisor
Title
Nik Mohd Zamri
Nik Mohd
Syazwan
Mike Manefield
Exploring the impact of electron shuttles on methanogenesis
Abd Rahman
Nadhiah
Mike Manefield
Improving the direct rRNA fingerprinting (DRF) technique to characterise
microbial communities in complex samples
Abdul Hamid
Noradilah
Chris Marquis
Developing and Characterising purified peanut allergens
Bahrame
Zahra
Ruiting Lan
Polymorphism in pertussis toxin promoter: A cause for pertussis resurgence?
Chiang
Kim (Ivy)
Robert Yang
Molecular characterisation of ORP5, a protein potentially involved in
cholesterol transport
Courtney
Eliza
Michal Janitz
Validation of alternative splicing patterns revealed by RNA-Seq in Alzheimer’s
disease and normal human brain RNA
Easton
Emma
Julian Cox
Production and application of serotype-specific ELISAs to measure
seroconversion in meat chickens after administration of a trivalent vaccine
Fife
Christopher
Gabriel Perrone
Redox Homeostasis in Saccharomyces cerevisiae
Ford
Daniel
Prof Andrew
Collins
An evaluation of the reported immunoglobulin lambda locus genes, and their
use in the generation of diversity
Hutton
Christopher
Wallace Bridge
Protection of human HepG2 cells against oxidative stress and apoptosis by
J-glutamylcysteine
Kornfeld
Shan
Michal Janitz
Defining the role of alternative splicing in the difference between normal and
Alzheimer’s diseased brains using transcriptomic approaches
Kwong
Tracy
Peter White
Viral Replication and Molecular Epidemiology of Norovirus Recombinant GII.b/
GII.3
Lang
Charmaine
Antony Cooper
Cellular stress and mitochondrial dysfunction in alpha-synuclein models of
Parkinson’s disease
Lim
Yu-Leng (Lester)
May Aung-Htut/
Ian Dawes
Changes in Saccharomyces cerevisiae during Cellular Ageing
Lim
Wooi Fang
(Catheryn)
Joyce Chiu/Ian
Dawes
The role of SWI6 and YAP1 in response to linoleic acid hydroperoxide
(LoaOOH)- induced oxidative stress in Saccharomyces cerevisiae
Lim
Boon Kiat
Brett Neilan
Investigating vector/promoter combinations for the heterologous expression of
secondary metabolite pathways in Synechocystis sp. PCC6803
Ly
Ken
Chris Marquis
The Production and Purification of Recombinant Biogeneric Human
Interleukin-2
Marks-Bluth
Jonathon
John Pimanda
Transcription factor binding predicts novel regulators of hematopoietic stem
cells
Minard
Annabel
Gabriel Perrone
Chewing the fat on redox: The role of lipid metabolism in oxidant tolerance and
compartmental redox homeostasis
Mohd Ismuil
Zul Aiman
Volga Bulmus/
Chris Marquis
Delivery of siRNA using a cholesterol-conjugated polymer
Mohd Kamal
Ahmad Ameen
Young-Jae Jeon/
Brett Neilan
Characterisation of Pyruvate Decarboxylase from Candida sp.
Murray
Daniel
Tony Kelleher
A systems biology approach to mapping miRNA changes in monocytes during
HIV-1 infection
Nawara
Diana
Richard Lock
The Role of the FoxO3a transcription factor in the induction of the Bim gene in
acute lymphoblastic leukemia cells upon glucocorticoid treatment
Norton
Laura
Merlin Crossley
The role of the transcription factor Krüppel-like Factor 3 (Klf3) in
Haematopoiesis
Sahrudin
Arisha
Noel Whitaker
A possible role of Human Papillomavirus in prostate cancer
Suffian
Muhammad Nur
Haizie
Bettina Rosche
Quorum Sensing Inhibition in Traditional Chinese Herbs
57
Tai
Yee Hong (Dyan)
Volga Bulmus/
Chris Marquis
Formulation and in vitro evaluation of siRNA polyplexes for potential non-viral
gene silencing therapies
Ton
Benson
Ruiting Lan
Single nucleotide polymorphism typing and nutritional requirements of Shigella
spp. and Enteroinvasive Escherichia coli
Vuong
Daniel
Peter White
Optimising cryopreservation of adipose derived stromal vascular fraction
containing mesenchymal stem cells
Wan Ahmad
Kamil
Wan Nur Ismah
Brett Neilan
Identification & Characterisation of a putative polyketide synthase (PKS) gene
cluster in Halomonas species strain PB24
Webster
John
Rick Cavicchioli
Analysing the genome of Methanogenium frigidum
Weragoda
Jake
Wallace Bridge
J-glutamylcysteine as an antidote for acetaminophen-induced cytotoxicity in
HepG2 cells
Wong
Siew Mun
Li Zhang
Investigation on the possible involvement of oral Campylobacter concisus in
development of Crohn’s disease
Yingchoncharoen
Phatsapong
Robert Yang
The role of non-essential gene in lipid droplet dynamics of Saccharomyces
cerevisiae
Research Funding
Grants awarded in 2010
commencing in 2011
Australian Research Council
Discovery Projects
Ballard JWO, Wolff JN (APD) &
Sutovsky P. Challenging current
dogma on the inheritance of
mitochondrial DNA. 2011-2013:
$370,000.
Cavicchioli R. Understanding
protein-nucleic-acid interaction
networks in cold-adapted
archaea. 2011-2013: $360,000.
Tanaka MM, White PA, Koelle KV
& Regoes RR. Understanding
mutation and genetic
reassortment in viruses: new
mathematical models of viral
dynamics and evolution. 20112013: $378,000.
Wilkins MR, Molloy MP & HartSmith GO (APD). The role and
regulation of protein methylation:
a study using the recently
developed methylation network
of yeast. 2011-2013: $300,000.
Linkage Projects
Murray SA, O’Connor WA
& Seebacher F. Differential
accumulation of algal biotoxins
within diploid and triploid Pacific
Oysters and Sydney Rock
Oysters. 2011-2013: $115,000.
Linkage Infrastructure and
Equipment Facilities
National Health & Medical
Research Council Training
(Postdoctoral) Fellowship
Ballard JWO, Brooks RC,
McArthur C, Herberstein ME,
Simpson SJ, Moles AT, Leishman
MR, Poore AG, Oldroyd BP,
Taylor PW, Banks P, Kemp
DJ, Beekman M & Sword GA.
Sydney basin multi-purpose
spectral analysis facility for
evolutionary and ecological
studies. 2011: $160,240.
Kaakoush N. Australian Based
Biomedical Category. 20112014: $290,032.
Future Fellowship
Manefield MJ. Harnessing
microbial respiration for pollutant
degradation and natural
gas production. 2011-2015:
$808,000.
National Health & Medical
Research Council Project
Grants
Brown, A. Novel control points in
cholesterol synthesis. $354,208
Lan R, Sintchenko V, Gilbert
G, McIntyre P, Marshall H &
Wood N. Evolution of pertussis
epidemics and effect of
genotypes on infection outcomes
and immunisation. $638,100.
Sytnyk, V. The impact of the
changes in levels of adhesion
molecules NCAM2 and DsCAM
on synapse formation and
function: implications for Down
syndrome. $322,524.
Other National Schemes
National Breast Cancer
Foundation Novel Concept
Awards 2011
Lawson J, Whitaker NJ & Glenn
WK. Viruses and breast cancer:
Normal patient follow up project.
2011-2012: $200,000.
UNSW Internal Schemes
UNSW Major Research
Equipment Infrastructure Initiative
Ballard JWO, Neilan BA, LutzeMann L, Whitaker NJ, Sytnyk V,
Brown AJ, Dawes IW, Marquis
CP & Brooks R. Seahorse F
Analyzer; Fisher Scientific*
Isotemp* Plus Chromatography
Refrigerator. 2011: $150,000.
Brown AJ, Yang H, Sytnyk
V, Zhang L, Manefield MJ,
Kjelleberg S, Cavicchioli
R, Wilkins MR, Marquis CP
& Janitz M. Nikon C1 Plus
Routine Confocal System. 2011:
$226,283.
UNSW Goldstar Awards
Janitz M & Kril J. Defining the
human brain transcriptome:
Determination of alternative
splicing and gene expression
patterns using high-throughput
sequencing. 2011: $40,000.
Mitchell HM, Day A, Janitz
M, Kaakoush NO, Lemberg
DA, Thomas T & Zhang L.
Investigation of the causative
agent/s of Crohn’s Disease in
children, using high throughput
sequencing. 2011: $40,000
Yang H. The role of phosphatidic
acid in adipogenesis and lipid
droplet formation. 2011: $40,000
Faculty of Science Silverstar
Award
Foster LJR. A unique
multifunctional biomaterial for
wound sealing and regional
delivery of antibiotics. 2011:
$35,000
Grants commencing or
operating in 2010
Discovery Projects
Brooks RC & Ballard JWO.
Linking the evolutionary and
bioenergetic causes of sex
differences in lifespan and
ageing. 2009-2011: $560,000.
Bulmus V, Davis TP, Kavallaris
M & Maynard HD. Development
and evaluation of well-defined
polymer-RNA conjugates as
improved therapeutics. 20072010: $500,000.
Burns BP (ARF) & Walter MR
(APF). Functional complexity of
modern marine stromatolites.
2006-2010: $542,000.
Cavicchioli R, Lauro F, Guilhaus
M, Raftery MJ, Rintoul SR &
Riddle MJ. Microbial genomics
of the southern ocean:
monitoring environmental health.
2010-2014: $950,000.
Dawes IW, Yang HR &
Breitenbach M. Oxidative
damage and cell ageing. 20082010: $564,000.
Dawes IW. How do cells regulate
redox environment at the
subcellular level? 2010-2010:
$420,000.
Cavicchioli R, Thomas T, Sava
A, Richardson PM, Raftery
M, Kyrpides N, Guilhaus M
& Baker MS. Environmental
metagenomics, metaproteomics
and novel bioactives from
microbial communities in
Antarctic lakes. 2007-2010:
$525,000.
Neilan BA (ARCFF), Moffitt MC
& Bolch CJS. Polyketides as
the conserved basis for diverse
marine toxin biosyntheses. 20082011: $315,000.
Curmi PMG, Marquis C &
Breit SN. Structural and
pharmaceutical studies on a
novel human protein MIC-1.
2008-2011: $514,074.
Preiss T & Beilharz TH (ARF).
Role of mRNA polyadenylation
control in gene expression.
2008-2012: $685,000.
Kjelleberg S, Venter JC, Thomas
T (APD), Sutton G, Steinberg
PD, Rusch D, Holmstrom
CG, Heidelbert KB, Halpern
A & Egan SG. Environmental
genomics and novel bioactives
from microbial communities on
living marine surfaces. 20062010: $1,611,000.
Waite TD, Collins RN, Neilan
BA, Sinclair G & Ring RJ.
Biogeochemical controls on
efficacy and sustainability of
uranium heap leaching. 20102013: $300,000.
Walter MR, Neilan BA, George
SC, Summons RE & Schopf
JW. Oxygenating the Earth:
Using innovative techniques
to resolve the timing of the
origin of oxygen-producing
photosynthesis in cyanobacteria.
2010-2014: $715,000.
Wilkins MR. Protein methylation:
A fundamental regulator of
the interactome. 2010-2012:
$285,000.
Linkage Projects
Cavicchioli R, Thomas T, Munroe
PR, Guilhaus M & Chen V.
Improving the sustainability of
Australia’s water resources:
An effective approach for
diagnosing and treating foulants
on water recycling membrane
filters. 2008-2011: $1,129,607.
Manefield MJ, Thomas T,
Kjelleberg SL & Steinberg PD.
In situ microbial conversion of
coal to methane: Biotechnology
development for clean use of
Australian coal. 2010-2013:
$1,237,600.
McMurtrie RE, Neilan BA &
Eldridge DJ. Is reintroduction
of soil foraging animals critical
for the restoration of degraded
semi-arid woodlands? 20082010: $196,462.
Neilan BA, Murray SA (APD)
& Hallegraeff GM. Uncovering
the genetic basis for saxitoxin
production in Australian marine
and freshwater systems: Novel
molecular tools for management.
2007-2010: $244,608.
Parry DL, Gibbs KS & Neilan
BA (ARC FF). Management of
acid mine drainage in northern
Australia using microbial mats,
2007-2010: $387,564.
RESEARCH FUNDING
59
Linkage Infrastructure And
Equipment Facilities
Braet FC, Soon L, Overall RL,
Day DA, Waterhouse PM, Marc
J, Conigrave AD, Weiss AS,
Newsome TP, Meikle SR, Götz
J, Goldsbury CS, Hambley TW,
Ramzan IM, Young PM, Traini D,
Grewal T, Fleming SC, Murphy
CR, Grau GE, Weninger W,
Dos Remedios CG, WimmerKleikamp S, Munroe PR,
Stevens-Kalceff MA, Foster LJ
& Mitchell H. A 5-D Correlative
Imaging Platform: Combining the
strengths of light and electron
microscopy. 2010: $720,000.
George SC, Nelson PF, Gore DB,
Jamie JF, Brocks JJ, Neilan BA,
Kannangara GS, Snape I, Volk H
& Wilson MA. Time-of-flight mass
spectrometer for analysis of
complex mixtures in oils, ancient
rocks, recent sediments, natural
products and atmospheric
aerosols. 2010: $160,000.
Stocker R, Hunt NH, Mason
RS, Witting PK, Roufogalis BD,
Lay PA, Davies MJ, Dawes
IW, Drummond GR, Geczy
CL, Khachigian LM, Hogg PJ,
Lackmann M, Tiganis T, Thomas
SR, Croft KD, King NJ, Tilley L
& James DE. Oxidative stress
bioanalytical facility. 2010:
$330,000.
Thordarson P, Neto C, Gooding
JJ, Warr GG, Poole-Warren LA,
Coster HG, Davis TP, Weiss AS,
Ladouceur F, Perrier S, Chen
V, Hawkett BS, Stenzel M, Bilek
MM, Martens PJ, Gaus K, Sunde
M, Harris AT, Bulmus V & Neilan
BA. A unique soft matter highperformance scanning probe
microscopy (HP-SPM) facility.
2010: $450,000.
Trent RJ, Waterhouse PM,
Dawes IW, Paulsen IT, Henry
RJ, Crossley M, Bergquist PL,
Janitz M, Arthur JW, Reichardt
JK, Packer NH, Yu B, Scott RJ &
Wade CM. Systems biology: New
generation DNA sequencing
to functional analysis. 2010:
$850,000
Sutton P, Ferrero R, Mitchell
HM, Wee J. Protease-activated
receptor-1 (PAR-1) and
regulation of Helicobacter pylori
induced mucosal inflammation,
2008-2010: $458,750.
Yang H, Brown AJ. Niemann Pick
disease type C and intracellular
sterol trafficking, 2008-2010:
$305,500.
Federation Fellowship
NHMRC Development Grant
Neilan BA. The toxins of
water-borne cyanobacteria:
regulation and exploitation of
their biosynthesis, 2008-2012,
$1,640,000.
Foster LJR, Sutureless
Technology for Cranial Surgery.
2010: $213,125
NHMRC Training Fellowships
Qeii Fellowships
Brown MV. Towards a predictive
model for coastal marine
microbial assemblages. 20092013: $695,000.
Tanaka MM. Mathematical
models and bioinformatic
analyses of bacterial genome
evolution. 2009-2013: $614,870.
Future Fellowship
Yang HR. The cellular dynamics
of lipid droplets: implications for
obesity and biodiesel production,
2009-2013, $788,800.
NHMRC Project Grants
Day AS, Mitchell HM, Zhang
L, Leach ST. Exclusive Enteral
Nutrition in children with Crohn’s
disease, 2008-2010: $349,875.
Mitchell HM, Zhang L, Otley A,
Day AS. Investigation of the role
of specific mucous associated
bacteria in children and young
adults with Crohn’s disease,
2008-2010: $414,375.
Kummerfeld SK, Wilkins MR.
The molecular basis of aging: A
high-resolution systems biology
approach, 2007-2010: $310,466.
Luciani F, Tanaka M. Modelling
the evolution of Hepatitis C virus
by integrating large sequence
and immunological databases.
2008-2011: $279,000.
National Collaborative
Research Infrastructure
Strategy (NCRIS)
Dawes IW. Biomolecular
Platforms, 2006-2011: $900,000.
Marquis C. Biotechnology
Products – Recombinant
Proteins, 2006-2010: $1,750,000
Rogers PL. Biotechnology
Products – Biofuels, 2006-2011:
$1,350,000.
Wilkins MR. Biomolecular
Platforms – Systems Biology
Centre (SBS), 2008-2011:
$1,000,000 (2008 funding:
$292,500).
Other National Schemes
Cancer Institute NSW
National Industry Schemes
Australian National Data Service/
EIF Super Science Program
Baker M, Robinson P, Packer
N, Clarke S, Daly R, Molloy M,
Verrills N, Kavallaris M, Reddel
R, Braithwaite A & Wilkins MR.
NSW Cancer Glycoproteomics
Infrastructure Initiative. 20072010: $1,040,000.
CRC for Environmental
Biotechnology
Hogg PJ, Williams KM,
Weerakoon L, Ward RL, Perrone
G, Lock RB, Liauw WS, French
J, Dilda P, Decollogne SM, De
Souza PL, Dawes IW & Bardell
J. Anti-Mitochondrial Cancer
Drugs, 2007-2011: $3,750,000.
Ara Parseghian Medical
Research Foundation (USA)
Department of the Environment
and Water Resources Australian Antarctic Science
Grants
NASA Astrobiology Institute
ARDC Linked International
Glycomics Repository &
Instrument Data Capture. 20102011: $25,000.
ANZAC Health and Medical
Research Foundation
Fung DCY, Lo AWC, Wilkins
MR. Analysis and classification
of colorectal cancer. 2010:
$11,000.
Australian Centre for HIV and
Hepatitis Virology
White PA, Bull RA & Arndt
G. Identification of chemical
compounds for hepatitis C virus
polymerase inhibition. 20102011: $105,000
Australian Coal Association
Research Program (ACARP)
Scott JA & Rosche B. Removal
of methane from mine ventilation
air by biofiltration, 2008-2011:
$140,754.
Australia India Strategic Fund
Ball A & Manefield MJ.
Bioremediation of oil
contaminated marine and
freshwater environments. 20082010: $400,000.
EIF Super Science Project/
Bioplatforms Australia
Wilkins MR. Build foundation
datasets and technology in
association with the major -omics
facilities in NSW. 2010-2014:
$2.0M.
Cancer Council NSW
Hogg PJ, Weerakoon L, Perrone
G, Lock RB, Dilda P & Dawes
IW. New arsenical-based cancer
drugs, 2006-2010: $1,950,000.
Breadmore M, Powell S,
Manefield MJ. A new method
for characterisation of antarctic
microbial communities. 20082010: $73,000.
Department of the Environment,
Water, Heritage and the Arts/
Australian Biological Resources
Study National Taxonomy
Research Grant Program
Brown MV & Murray SA.
Identifying and describing new
lineages of benthic marine
alveolates (Alveolata) from the
Indian Ocean, Western Australia.
2010-2013: $30,000.
Department of Health and
Ageing)/Australian Centre for
Hepatitis and HIV Virology
Research
White PA. Identification of
Chemical Compounds for
Hepatitis C Virus Polymerase
Inhibition. 2010-2011: $105,000.
Prostate Cancer Foundation of
Australia/Project Grants
Krycer JR & Brown AJ. Exploiting
cholesterol metabolism to fight
prostate cancer.
Kjelleberg S. Core funding.
2004-2010: $1,890,000.
International Schemes
Yang H. Sterol-dependent
interactions between Ncr1p
and Osh proteins in the
budding yeast, 2008-2010: USD
$265,000.
Anbar A, Farmer J, Elser J,
Knauth, P, Christensen P, Oliver
C, Walter M, Greely R, Davies P,
et al. Follow the elements, 20082012: $11,565,000.
Susan G Komen Breast Cancer
Foundation (USA)
Lawson JS, Whitaker NJ. Human
papilloma viruses and human
breast cancer, 2008-2010:
$405,000.
International Industry
Schemes
BASF – Aktiengesellschaft
Rosche B. Biofilm Factories.
2005-2010: $720,000
UNSW Internal Schemes
UNSW Strategic Priorities Fund
Murray S. Lateral gene transfer
from prokaryotes to eukaryotes:
the evolution of saxitoxin
synthesis in dinoflagellates 20082010: $264,000.
RESEARCH FUNDING
61
UNSW Goldstars
Brown AJ. Novel control points in
cellular cholesterol homeostasis.
2010: $40,000.
Bulmus EV. Biomimetic
polymer hybrids: Targeting
the intracellular drug delivery
challenge. 2010: $40,000.
Ferrari BC. Can microbial
nitrogen cycling in terrestrial
Antarctic soils provide a future
guide to climate change impacts
on worldwide microbial diversity?
2010: $40,000.
Sytnyk V. The impact of the
adhesion molecules NCAM2 and
DsCAM on synapse formation
and function: Implications for
Down syndrome. 2010: $40,000.
2010 Publications
Abraham G, Mccaroll J, Byrne F,
Saricilar S Kavallaris M & Bulmus
V. (2010) ‘Block co-polymer
nanoparticles with degradable
cross-linked core and lowmolecular-weight peg corona
for anti-tumour drug delivery’,
Journal of Biomaterials SciencePolymer Edition, 22, pp. 10011022.
Ahmed T, Marcal H, Lawless M,
Wanandy NS, Chiu A & Foster
LJ. (2010) ‘Polyhydroxybutyrate
and its copolymer with
polyhydroxyvalerate as
biomaterials: Influence on
progression of stem cell cycle’,
Biomacromolecules, 11, pp.
2707-2715.
Al Tebrineh J, Mihali TK,
Pomati F & Neilan BA. (2010)
‘Detection of saxitoxin-producing
cyanobacteria and Anabaena
circinalis in environmental water
blooms by quantitative PCR’,
Applied and Environmental
Microbiology, 76, pp. 7836-7842.
Allen B, Crosky AG, Yench E,
Lutze-Mann L, Blennerhassett
P, Lebard R, Thordarson P
& Wilk K. (2010) ‘A model
for transformation: A
transdisciplinary approach to
disseminating good practice in
blended learning in a science
faculty’, Ascilite. Sydney,
December 5-8.
Allen MA, Neilan BA, Burns
BP, Jahnke LL, & Summons
R. (2010) ‘Lipid biomarkers in
Hamelin Pool microbial mats
and stromatolites’, Organic
Geochemistry, 41, pp. 12071218.
Allwood AC, Kamber BS,
Walter MR, Burch IW & Kanik I.
(2010) ‘Trace elements record
depositional history of an Early
Archean stromatolitic carbonate
platform’, Chemical Geology,
270, pp. 148-163.
Andres S, Schmidt HA,
Mitchell HM, Rhen M, Maeurer
M & Engstrand L. (2010)
‘Helicobacter pylori defines
local immune response through
interaction with dendritic cells’,
FEMS Immunology and Medical
Andreyeva A, Leshchyns’ka I,
Knepper M, Betzel C, Redecke
L, Sytnyk V & Schachner M.
(2010) ‘CHL1 is a selective
organizer of the presynaptic
machinery chaperoning the
SNARE complex’, PLOS One, 5,
pp. e12018-819.
Arsianti M, Lim M, Marquis C
& Amal R. (2010) ‘Assembly
of polyethylenimine-based
magnetic iron oxide vectors:
Insights into gene delivery’,
Langmuir, 26, pp. 7314-7326.
Arsianti M, Lim M, Marquis C &
Amal R. (2010) ‘Polyethylenimine
based magnetic iron-oxide
vector: the effect of vector
component assembly on cellular
entry mechanism, intracellular
localization, and cellular viability’,
2521-2531.
Ayer A, Tan SX, Grant CM,
Meyer AJ, Dawes IW & Perrone
GG. (2010) ‘The critical role of
glutathione in maintenance of
the mitochondrial genome’, Free
Radical Biology and Medicine,
49, pp. 1956-1968.
Baalawi F, Robertson P &
Rawlinson WD. (2010) ‘Detection
of human cytomegalovirus
IgG antibody using automated
immunoassay with recombinant
antigens gives uniform results to
established assays using whole
virus antigens’, Pathology, 42,
pp. 578-580.
Ballard JWO & Melvin RG. (2010)
‘Early life benefits and later
life costs of a two-amino acid
deletion in Drosophila Simulans’,
Evolution, doi: 10.1111/j.15584646.2010.01209.x.
Ballard JWO & Melvin RG.
(2010) ‘Linking the mitochondrial
genotype to the organismal
phenotype’, Molecular Ecology,
19, pp. 1523-1539.
Ballard JWO, Melvin RG,
Lazarou, M, F.J. Clissold & et
al,. (2010) ‘Cost of a naturally
occurring two-amino acid
deletion in cytochrome c
oxidase subunit 7A in Drosophila
simulans.’, American Naturalist,
176 (4), pp. e98-e108 .
Ballestriero F, Thomas T, Burke
CM, Egan SG & Kjelleberg
S. (2010) ‘Identification of
compounds with bioactivity
against the nematode
Caenorhabditis elegans by a
screen based on the functional
genomics of the marine
bacterium Pseudoalteromonas
tunicata D2’, Applied and
Environmental Microbiology, 17,
pp. 5710-5717.
Ballouz S, Lan R, Francis AR &
Tanaka M. (2010) ‘Conditions for
the evolution of gene clusters
in bacterial genomes’, PLoS
Computational Biology, 6, p.
e1000672.
2010 PUBLICATIONS
63
Beilharz TH, Humphreys D
& Preiss T. (2010) ‘miRNA
effects on mRNA closed-loop
formation during translation
initiation, miRNA Regulation of
the Translational Machinery, pp.
99-112, Springer-Verlag, Berlin
Heidelberg .
Blaber E, Marcal H & Burns BP.
(2010) ‘Bioastronautics: The
influence of microgravity on
astronaut health’, Astrobiology,
10, pp. 463-473.
Blaber E, Marcal H, Foster LJ
& Burns BP. (2010) ‘In space
no one can hear you sneeze’,
Australasian Science Magazine,
June 10, pp. 29-31.
Bose U, Bala V, Rahman AA &
Shahid IZ. (2010) ‘Evaluation
of phytochemical and
pharmacological properties of
Aegiceras corniculatum blanco
(Myrsinaceae) bark’, Latin
American Journal of Pharmacy,
29, pp. 1126-1131.
Boyd S, Gaeta BA, Jackson KJ,
Fire AZ, Marshall EL, Merker
JD, Maniar JM, Zhang LN,
Sahaf B, Jones CD, Simen BB,
Hanczaruk B, Nguyen KD,
Nadeau KC, Egholm M, Miklos
DB, Zehnder JL & Collins AM.
(2010) ‘Individual variation in the
germline immunoglobulin gene
repertoire inferred from variable
region gene rearrangements’,
Journal of Immunology, 184, pp.
6986-6992.
Boyer CA, Priyanto P, Davis TP,
Pissuwan D, Bulmus V, Kavallaris
M, Teoh WY, Amal R, Carroll
M, Woodward R & St Pierre T.
(2010) ‘Anti-fouling magnetic
nanoparticles for siRNA delivery’,
Journal of Materials Chemistry,
20, pp. 255-265.
Boyer CA, Whittaker M, Bulmus
V, Liu J & Davis TP. (2010)
‘The design and utility of
polymer-stabilized iron-oxide
nanoparticles for nanomedicine
applications’, Nature NPG Asia
Material, 2, pp. 23-30.
Brew BJ, Davies NW, Cinque
P, Clifford D & Nath A. (2010)
‘Progressive multifocal
leukoencephalopathy and other
forms of JC virus disease’,
Nature Reviews Neuroscience, 6,
pp. 667-679.
Brown AJ & Galea AM. (2010)
‘Cholesterol as an evolutionary
response to living with oxygen’,
Evolution, 64, pp. 2179-2183.
Brown AJ. (2010) ‘Does upsizing
statins have a downside?’, Drug
Safety, 33, pp. 435-436.
Bull RA & White PA. (2010)
‘Genome organization and
recombination’, Caliciviruses:
Molecular and Cellular Virology,
pp. 45-63. Caister Academic
Press, Portland, USA.
Bull RA, Eden J-S, Rawlinson
WD & White PA. (2010)
‘Rapid evolution of pandemic
noroviruses of the GII.4
lineage’, PLoS Pathogens, 6, p.
e1000831.
Burg DW, Lauro FM, Williams
TJ, Raftery MJ, Guilhaus M &
Cavicchioli R. (2010) ‘Analyzing
the hydrophobic proteome
of the Antarctic archaeon
Methanococcoides burtonii
using differential solubility
fractionation’, Journal of
Proteome Research, 9, pp. 664676.
Burns BP. (2010) ‘Life: Not as we
know it’, Journal of Cosmology,
13, pp. 3621-3624.
Cairns K, Wolff J, Brooks RC &
Ballard JWO. (2010) ‘Evidence
of recent population expansion
in the field cricket Teleogryllus
commodus’, Australian Journal
of Zoology, 58, pp. 33-38.
Carland M, Grannas MJ,
Cairns MJ, Roknic VJ,
Denny WA, McFadyen WD &
Murray V. (2010) ‘Substituted
9-aminoacridine-4-carboxamides
tethered to platinum(II)
diamine complexes: Chemistry,
cytotoxicity and DNA sequence
selectivity’, Journal of Inorganic
Biochemistry, 104, pp. 815-819.
Chatelain EH, Pichaud N,
Ballard JWO, Tanguay RM,
Morrow G & Blier PU. (2010)
‘Functional conservatism among
Drosophila simulans flies
experiencing different thermal
regimes and mitochondrial
DNA introgression’, Journal
of Experimental Zoology Part
B-Molecular and Developmental
Evolution, doi: 10.1002/
jez.b.21389.
Chen M, Schliep M, Willows RD,
Cai ZL, Neilan BA & Scheer H.
(2010) ‘A red-shifted chlorophyll’,
Science, 10, pp. 1318-1319.
Chen V, Mansouri J & Charlton
TS. (2010) ‘Biofouling in
membrane systems’, Membrane
for Water treatment, vol. 4, pp.
25-51, Wiley-VCH, Great Britain.
Chen Z, Collins AM, Wang Y &
Gaeta BA. (2010) ‘Clusteringbased identification of clonally
related immunoglobulin
gene sequence sets’, Ninth
International Conference on
Bioinformatics, Tokyo, Japan, 2628 September.
Cheng X, Guerasimova A, Manke
T, Rosenstiel P, Haas S, Warnatz
HJ, Querfurth R, Nietfeld W,
Vanhecke D, Lehrach H, Yaspo
ML & Janitz M. (2010) ‘Screening
of human gene promoter
activities using transfected-cell
arrays.’, Gene, 450, pp. 48-54.
Coolen MW, Stirzaker C, Song
JZ, Statham AL, Kassir Z,
Moreno CS, Young AN, Varma V,
Speed TP, Cowley M, Lacaze P,
Kaplan W, Robinson MD & Clark
SJ. (2010) ‘Consolidation of the
cancer genome into domains
of repressive chromatin by
long-range epigenetic silencing
(LRES) reduces transcriptional
plasticity’, Nature Cell Biology,
12, pp. 235-246.
Cooley MA, Whittall C & Rolph
MS. (2010) ‘Pseudomonas signal
molecule 3-oxo-C12-homoserine
lactone interferes with binding
of rosiglitazone to human
PPARgamma’, Microbes and
Infection, 12, pp. 231-7-54.
Courtney E, Kornfeld S,
Janitz K & Janitz M. (2010)
‘Transcriptome profiling in
neurodegenerative disease’,
Journal of Neuroscience
Methods, 193, pp. 189-202.
Croucher DR, Rickwood D,
Tactacan CM, Musgrove EA
& Daly RJ. (2010) ‘Cortactin
modulates RhoA activation and
expression of Cip/Kip cyclindependent kinase inhibitors to
promote cell cycle progression in
11q13-amplified head and neck
squamous cell carcinoma cells’,
Molecular and Cellular Biology,
30, pp. 5057-5070.
Davis RA, Carroll AR, Andrews
KT, Boyle GM, Tran TL, Healy
PC, Kalaitzis JA & Shivas RG.
(2010) ‘Pestalactams A-C:
Novel caprolactams from the
endophytic fungus Pestalotiopsis
sp’, Organic and Biomolecular
Chemistry, 8(8), pp. 1785-1790.
Devanathan V, Jakovcevski
I, Santuccione A, Li S, Lee
HJ, Peles E, Leshchyns’ka
I, Sytnyk V & Schachner
M. (2010) ‘Cellular form of
prion protein inhibits Reelinmediated shedding of Caspr
from the neuronal cell surface
to potentiate Caspr-mediated
inhibition of neurite outgrowth.’,
Journal of Neuroscience, 30, pp.
9292-9305.
Dong Q, Liu Y, Scott KF, Levin L,
Gaitonde K, Bracken RB, Burke
B, Zhai QJ, Wang J, Oleksowicz
L & Lu S. (2010) ‘Secretory
phospholipase A2-IIa is involved
in prostate cancer progression
and may potentially serve as a
biomarker for prostate cancer’,
Carcinogenesis, 31, pp. 19481955.
Eden J-S, Bull RA, Tu ET, McIver
CJ, Lyon MJ, Marshall JA, Smith
DW, Musto J, Rawlinson WD &
White PA. (2010) ‘Norovirus GII.4
variant 2006b caused epidemics
of acute gastroenteritis in
Australia during 2007 and 2008’,
Journal of Clinical Virology, 49,
pp. 265-271.
El-Hajj ZW, Allcock DJ, Tryfona
T, Lauro FM, Sawyer L, Bartlett
DH & Ferguson GP. (2010)
‘Insights into piezophily from
genetic studies on the deepsea bacterium, Photobacterium
profundum SS9’, Annals of the
New York Academy of Sciences,
February, pp. 143-148.
Erce MA, Low, J & Wilkins MR.
(2010) ‘Analysis of the RNA
degradosome complex in Vibrio
angustum S14’, FEBS Journal,
277, pp. 5161-5173.
Flynn J, Dore GJ, Hellard M,
Yeung B, Rawlinson WD, White
PA, Kaldor JM, Lloyd AR &
Ffrench RA. (2010) ‘Early IL-10
predominant responses are
associated with progression
from acute to chronic hepatitis
C virus infection in injecting
drug users’, Journal of Viral
Hepatitis, doi:10.1111/j.13652893.2010.01335.x.
Ford JL, Kaakoush NO
& Mendz GL. (2010)
‘Phosphonate Metabolism in
Helicobacter pylori’, Antonie
van Leeuwenhoek International
Journal of General and
Molecular Microbiology, 97, pp.
51-60.
Foster LJ, Thomson KA, Marcal
H, Butt J, Watson SL & Wakefield
D. (2010) ‘Chitosan-vancomysin
composite biomaterial as a laser
activated surgical adhesive with
regional antimicrobial activity’,
3563-3570.
Foster LJ. (2010) ‘PEGylation
and bioPEGylation of
polyhydroxyalkanoates:
Synthesis, characterisation and
applications’, Biopolymers, pp.
243-256, Sciyo.
Galea AM & Murray V. (2010)
‘The influence of chromatin
structure on DNA damage
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Westphal D, Sytnyk V, Schachner
M & Leshchyns`ka I. (2010)
‘Clustering of the neural cell
adhesion molecule (NCAM) at
the neuronal cell surface induces
caspase-8 and -3 dependent
changes of the spectrin
meshwork required for NCAMmediated neurite outgrowth’, The
Journal of Biological Chemistry,
285, pp. 42046-42057.
Wiklund ED, Catts VS, Catts
SV, Ng TF, Whitaker NJ,
Brown AJ & Lutze-Mann LH.
(2010) ‘Cytotoxic effects of
antipsychotic drugs implicate
cholesterol homeostasis as a
novel chemotherapeutic target’,
International Journal of Cancer,
126, pp. 28-40.
Wiklund FE, Bennet AM,
Magnusson PK, Eriksson UK,
Lindmark F, Wu L, Yaghoutyfam
N, Marquis CP, Stattin P,
Pedersen NL, Adami HO,
Gronberg H, Breit SN & Brown
DA. (2010) ‘Macrophage
inhibitory cytokine-1 (MIC-1/
GDF15): A new marker of allcause mortality’, Aging Cell, 9,
pp. 1057-1064.
Wilkins MR. (2010) ‘GlycoViewer:
A tool for visual summary
and comparative analysis of
the glycome’, Nucleic Acids
Research, 38, pp. W667-670.
Wilkins MR. (2010) ‘Identification
of arginine- and lysinemethylation in the proteome of
Saccharomyces cerevisiae and
its functional implications’, BMC
Genomics, 11, pp. 92-8.
Wilkins MR. (2010) ‘Proteins
deleterious on overexpression
are associated with high intrinsic
disorder, specific interaction
domains, and low abundance’,
Journal of Proteome Research,
9, pp. 1218-1225.
Wilkins MR. (2010) ‘Using
the clustered circular layout
as an informative method for
visualizing protein-protein
interaction networks.’,
Proteomics, 10, pp. 2723-2327.
Williams TJ, Burg DW, Ertan H,
Raftery MJ, Poljak A, Guilhaus
M & Cavicchioli R. (2010)
‘Global proteomic analysis
of the insoluble, soluble,
and supernatant fractions of
the psychrophilic archaeon
Methanococcoides burtonii.
Part II: The effect of different
methylated growth substrates’,
Journal of Proteome Research,
9, pp. 653-663.
Williams TJ, Burg DW, Raftery
MJ, Poljak A, Guilhaus M,
Pilak O & Cavicchioli R. (2010)
‘Global proteomic analysis
of the insoluble, soluble,
and supernatant fractions of
the psychrophilic archaeon
Methanococcoides burtonii. Part I:
The effect of growth temperature’,
Journal of Proteome Research, 9,
pp. 640-652.
Williams TJ, Zhang CL, Scott
JH & Bazylinski DA. (2010)
‘Evidence for autotrophy via the
reverse tricarboxylic acid cycle
in the marine magnetotactic
coccus Strain MC-1’, Applied
and Environmental Microbiology,
72, pp. 1322-1329.
Wilson JP, Fischer WW, Johnston
DT, Knoll AH, Grotzinger JP,
Walter MR, McNaughton NJ,
Simon M. Abelson J, Schrag DP,
Summons R, Allwood A, Andres
M, Gammon C, Garvin J, Rashby
S, Schweizer M & Watters WA
. (2010) ‘Geobiology of the late
Paleoproterozoic Duck Creek
formation, Western Australia’,
Precambrian Research, 179, pp.
135-149.
Wiogo HT, Lim M, Bulmus V, Yun
J & Amal R. (2010) ‘Stabilisation
study of carboxyl coated iron
oxide nanoparticles in biological
media’, Chemeca. (2010):
The 40th Annual Australasian
Chemical and Process
Engineering Conference, Hilton
Adelaide, 26-29 September.
Wong LJ, Sevimli S, Zareie
MH, Davis TP & Bulmus V.
(2010) ‘PEGylated functional
nanoparticles from a reactive
homopolymer scaffold modified
by thiol addition chemistry’,
Macromolecules, 43, pp. 53655375.
Woolnough CA, Yee LH,
Charlton TS & Foster LJ. (2010)
‘Environmental degradation
and biofouling of ‘green’
plastics including short
and medium chain length
polyhydroxyalkanoates’, Polymer
International, 59, pp. 658-667.
Yang H. (2010) ‘Toward one step
analysis of cellular lipidomes
using liquid’, Molecular
Biosystems, 6, pp. 1008 1017.
2010 PUBLICATIONS
71
Ye C, Lan R, Xia S, Zhang J, Sun
Q, Zhang S, Jing H, Wang L, Li
Z, Zhou Z, Zhao A, Cui Z, Cao
J, Jin D, Huang L, Wang Y, Luo
X, Bai X, Wang Y, Wang P, Xu Q
& Xu J. (2010) ‘Emergence of a
new multidrug-resistant serotype
X variant in an epidemic clone
of Shigella flexneri’, Journal of
Clinical Microbiology, 48, pp.
419-426.
Yee LH, Aagaard V, Johnstone A,
Lee M, Kjelleberg SJ & Manefield
M. (2010) ‘Development of a
treatment solution for reductive
dechlorination of hexachloro-1,3butadiene in vadose zone soil’,
Biodegradation, 21, pp. 947-956.
Yung PY, Burke CM, Lewis M,
Kjelleberg S & Thomas T. (2010)
‘Novel antibacterial proteins
from the microbial communities
associated with the sponge
Cymbastela concentrica and
the green alga Ulva australis.’,
Microbiology, 77 (4), pp. 15121515.
Zemb ON, Lee M, Low AB &
Manefield MJ. (2010) ‘Reactive
iron barriers: A niche enabling
microbial dehalorespiration of
1,2-dichloroethane’, Applied
Microbiology and Biotechnology,
88, pp. 319-325.
Zhang L, BudMan V, Day AS,
Mitchell HM, Lemberg DA,
Riordan SM, Grimm M, Leach
ST & Ismail Y. (2010) ‘Isolation
and detection of Campylobacter
concisus from saliva of healthy
individuals and patients with
inflammatory bowel disease’,
Journal of Clinical Microbiology,
48, pp. 2965-2967.
Zhou Y, Ganda L, Lim M, Yuan
Z, Kjelleberg S & Ng WJ. (2010)
‘Free nitrous acid (FNA) inhibition
on denitrifying poly-phosphate
accumulating organisms
(DPAOs)’, Applied Microbiology
and Biotechnology, 88, pp. 359369.
Zhou Z, Li X, Liu B, Beutin L, Xu
J, Ren Y, Feng L, Lan R, Reeves
PR & Wang L. (2010) ‘Derivation
of Escherichia coli O157:H7
from its O55:H7 precursor’, PLoS
ONE, 5, e8700, pp. 1-14.
Sydney Harbour from 2010 BABS Staff Christmas Cruise
Photo by Michele Potter
Faculty of Science
The University of New South Wales
SYDNEY NSW 2052 AUSTRALIA
www.babs.unsw.edu.au
Tel: 61 2 9385 2029 Fax: 61 2 9385 1483

BABS Annual Report 2010.indd

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