School of Biotechnology and Biomolecular Sciences
Biological Sciences Building
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
EDITOR: Michele Potter
DESIGN/PRINTING: UNSW P3 Design Studio
COVER IMAGES: Marc Wilkins // Ross V. Hyne // Howard Lam // Michele Potter
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.
© 2010 The University of New South Wales
Published May 2010
CRICOS Provider Number 00098G
SCHOOL OF
BIOTECHNOLOGY AND
BIOMOLECULAR
SCIENCES
annual
09 report
02 // BABS ANNUAL REPORT 2009
03
CONTENTS
06 FOREWORD FROM HEAD OF SCHOOL
07 SCHOOL MANAGEMENT
2009 School Executive Committee
07
08 SCHOOL AT A GLANCE
Research
08
Teaching
08
PhDs
08
Postgraduate research
08
09 SYSTEMS AND CELLULAR BIOLOGY
The NSW Systems Biology Initiative
11
Why did we evolve cholesterol?
12
Bioenergetics and the role of mitochondria in ageing
14
15 ENVIRONMENTAL MICROBIOLOGY
The fight against potent toxins formed in
cyanobacteria (blue-green algae)
17
Traditional medicine relevant in the 21st century
19
Microbiology of early earth ecosystems
20
Gaining insight into the microbial ecology of
Sub-Antarctic soils
21
Microbial Ecology, Evolution and Genomics
22
23 MOLECULAR MEDICINE
The evolution of bacterial genomes
25
Genomics and evolution of human bacterial pathogens
26
Polymers overcoming delivery problems of
biotherapeutics
27
Cell adhesion molecules in healthy and diseased
brains
28
Investigating transcriptomics of neurodegenerative
diseases
29
Bioprocess engineering of proteins
30
Second Generation Biofuels - NCRIS-Funded Biofuels
Laboratory
31
04 // BABS ANNUAL REPORT 2009
32 2009 RESEARCH FUNDING
35 EXTERNAL PARTNERS
36 MEMBERSHIPS IN SOCIETIES AND ASSOCIATIONS
37 RESEARCH CENTRES
The Ramaciotti Centre for Gene Function Analysis
37
Centre For Marine Bio-Innovation
38
Australian Centre for Astrobiology
39
Evolution & Ecology Research Centre
40
41 SPECIALISED EQUIPMENT AND FACILITIES
UNSW Recombinant Products Facility
41
Single-Cell Analysis Facility
41
Microbiology Culture Collection
41
Canine Genetics Facility
41
42 LEARNING AND TEACHING
Undergraduate degrees
43
Majors
43
Combined Degrees
44
Postgraduate research
44
Graduate diploma
44
Teaching innovation in BABS
44
46 2009 RESEARCH, VISITING AND PROFESSIONAL
& TECHNICAL STAFF
Research Staff
46
Visiting Staff
46
Professional and Technical Staff
47
48 2009 STUDENT AWARDS AND PRIZES
49 BABSOC
Biotechnology and Biomolecular Students Society
50 2009 PHD COMPLETIONS
51 2009 HONOURS PROJECTS
54 PUBLICATIONS
49
5
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
06 // BABS ANNUAL REPORT 2009
FOREWORD FROM HEAD OF SCHOOL
The School of
Biotechnology
and Biomolecular
Sciences at The
University of New
South Wales is
among the largest
and most prestigious
such Schools in
Australia. The
research conducted
by the distinguished
academic
staff covers a diverse range of disciplines in
the biological sciences. With key strengths in
environmental microbiology, systems and cellular
biology and molecular medicine, our researchers
continue to produce scientific discoveries of
international renown, with an impressive amount of
media coverage during 2009.
The School had a productive research year
in 2009 with several notable highlights. These
included a third Eureka Prize awarded to
Professor Brett Neilan, an ARC Professorial
Fellowship to Malcolm Water, appointment of
Associate Professor Rob Yang as an inaugural
ARC Future Fellow, and the award of a Fulbright
Fellowship to Associate Professor John Foster. In
total, research grant income increased to $4.86M
with 126 peer-reviewed publications.
The School also excels in teaching, with an
innovative teaching program and state-of-theart facilities playing a key role in producing
Australia’s next generation of scientists. In 2009,
we saw a 15% increase in Higher Degree by
Research enrolments, and our overall student
satisfaction index increased in 2009 as a result
of the high level of commitment shown by staff.
Notable among these quality educators is
Senior Lecturer Dr Louise Lutze-Mann. In 2009,
Louise was awarded a Faculty of Science Award
for Excellence in recognition and celebration of
excellence in teaching. In 2010, I look forward to
the discussions resonating around the restructure
of our 3rd year courses.
The School has also been active in developing
international and national networks. Internationally,
Professor Staffan Kjelleberg established a formal
collaboration between UNSW and the Nanyang
Technological University in Singapore through
the creation of the Advanced Environmental
Biotechnology Centre at NTU. While on sabbatical,
Associate Professor Andrew Collins travelled to
Stanford University in California to engage Nobel
Prize-winning geneticist Andrew Fire in a project to
unravel the mysteries of repertoire development in
health and disease. Nationally, Associate Professor
Peter White collaborates with the New South
Wales Department of Health to coordinate the New
Zealand and Australian Norovirus Surveillance
Network, which reports to the global network
Noronet.
The School faced financial hurdles in 2009, but it is
with a sense of optimism that I approach my third
year as Head of School. The School Executive has
been proactive and decision-minded while working
within tight budgetary guidelines. I wish to thank
these individuals and all members of the staff for
working with me to help increase the productivity
of the School, while fostering a landscape of
collegiality and purpose.
PROFESSOR BILL BALLARD
Head of School
07
2009 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
Associate Professor John Foster
Dr Louise Lutze-Mann
Associate Professor Vincent Murray
Professor Brett Neilan
Associate Professor Peter White
Brett Neilan, Vincent Murray, Louise Lutze-Mann, Andrew Brown, John Foster, Bill Ballard, Peter White and Andrew Collins
SCHOOL MANAGEMENT
SCHOOL MANAGEMENT
08 // BABS ANNUAL REPORT 2009
SCHOOL AT A GLANCE
TEACHING
The School offers a comprehensive range of
undergraduate and postgraduate Degrees in
the modern life sciences to cater for a variety
of career paths. The exceptional standard of
education within our Degree programs is provided
by dedicated and experienced staff and onsite access to the latest scientific equipment
and technologies. Our academic staff have
been recognised for their teaching expertise at
university and state level, while our research output
especially in the area of biotechnology and applied
microbiology ranks very strongly among the G08
universities.
Biological Sciences Building reflected in windows of Lowy Cancer Research Centre
RESEARCH
The research structure of the School consists
of three main groups, which also interact and
collaborate on a number of projects.
Environmental Microbiology
Systems and Cellular Biology
Molecular Medicine
The School’s research spans the fundamental
to applied sciences, and ranges from human
bacterial pathogens, hepatitis viruses, tissue
engineering, cancer, cell biology, genetics,
bioinformatics, functional genomics, stem cells
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. BABS hosts a number of research
centres that also conduct cutting-edge research
and services in their respective fields.
PhDS
BABS is one of the highest recruiters of PhD
students at The University of New South Wales
and performs consistently well in measures of
satisfaction for higher degrees. The number of
PhDs for the size of the School is around twenty
five per cent higher than the mean for GO8
Schools of similar size and core research area.
The School has long-established research links
with the Garvan Institute of Medical Research,
Victor Chang Cardiac Research Institute and the
Prince of Wales Hospital, with academic staff in
the School supervising a large number of PhD
students based at these off-campus locations.
POSTGRADUATE RESEARCH
Doctor of Philosophy (PhD) and Master of Science
(MSc) research-based Degrees are offered to
qualified students who have completed a fouryear undergraduate science degree with honours
or equivalent. Graduates from the School have
successful careers in a wide range of industries
and research-based roles.
09
9
SYSTEMS AND CELLULAR BIOLOGY
10 // BABS ANNUAL REPORT 2009
SYSTEMS AND CELLULAR
BIOLOGY ACADEMIC STAFF
Professor Bill Ballard
Scientia Professor Ian Dawes
Professor Marc Wilkins
Associate Professor Andrew Brown
Associate Professor H Rob Yang
Dr Alan Wilton, Senior Lecturer
Dr Dallia Catzel, Associate Lecturer
Dr Rebecca LeBard,
Associate Lecturer
THE SYSTEMS AND CELLULAR BIOLOGY GROUP
UNDERTAKES RESEARCH IN THE BIOLOGY OF
EUKARYOTES. 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.
A number of our research groups use baker’s yeast as a
model organism, which provides strong opportunities for
scientific collaboration and the sharing of skills.
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. Professor Ian Dawes is the
Director of the Ramaciotti Centre and Professor Marc Wilkins
and Dr Alan Wilton are members of its board and/or have
roles in its management. Professor Wilkins is the founder and
Director of the NSW Systems Biology initiative and Professor
Dawes is a member of the board. 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.
11
SYSTEMS AND CELLULAR BIOLOGY
THE NSW SYSTEMS BIOLOGY INITIATIVE
Professor Marc Wilkins
The NSW Systems Biology
Initiative was established in mid2008 with foundation funding
from the NSW State Government
and the University of New South
Wales. Our mission is to build
capabilities and expertise in
bioinformatics for genomics and
proteomics and to disseminate
this expertise through
collaboration. We work closely
with users of the NCRIS-funded
‘omics’ facilities, specifically
the Ramaciotti Centre for
Gene Function Analysis, the
Bioanalytical Mass Spectrometry
Facility (BMSF), the Australian
Proteome Analysis Facility and
Southern Cross University Centre
for Plant Conservation Genetics.
We also provide collaborative
bioinformatics support to groups
at UNSW and elsewhere.
Who we are, what we do
Network biology
Since inception, we have
focused our activities on network
biology and the analysis of
next-generation sequence data.
In network biology, we have
worked on the construction and
analysis of biological networks
(including protein-protein
interaction networks and those
integrated with gene regulation,
signal transduction and metabolic
pathways) and how these can be
used to interpret gene and protein
expression data. A particular
interest is how these networks
can assist us in understanding
the interrelationships of different
elements of the cell or the function
of specific genes or proteins. For
next-generation sequencing, we
have focused on the development
and deployment of infrastructure
to underpin this data-intensive
science.
We have developed new
technology for the visualisation and
analysis of biological networks.
The GEOMI platform can now build
network ‘movies’, which show how
a network changes over time. This
has been useful for the analysis
of time series protein and gene
expression data in the context
of protein-protein interactions. In
collaboration with Yose Widjaja
and Dr Tim Lambert (CSE, UNSW)
The interactorium (top and above). Visualisation of protein
interaction networks, protein complexes and protein 3-D
structures in the context of a virtual cell
12 // BABS ANNUAL REPORT 2009
we have built the Interactorium,
a virtual 3-D cell, which allows
networks to be viewed at the
level of the cell, the organelle
or protein complex, and allows
seamless navigation to the
level of protein 3-D structure.
We are using both of the above
technologies in a number of
projects, including a large
systems biology project with
the Australian Wine Research
Institute.
Next-generation
Sequencing
The Ramaciotti Centre for Gene
Function Analysis installed two
next-generation sequencers in
mid-2009. The Systems Biology
Initiative has raised funding
to support two infrastructure
projects. The first, Genomic
Data Storage, has been cofunded by the Australian
National Data Service. This
has built a web-based system
for the storage of the massive
quantities of sequence data that
are inherent to next-generation
sequencing. The second,
Genomic Data Analysis, is an
Intersect Innovation project. It
has built pipelines on NSW and
National supercomputers for
the assembly and annotation of
genome sequences.
proteomics data (Dr. Graham
Robertson, Concord Hospital
and University of Sydney), the
assembly and annotation of two
bacterial genomes (Professor
Hazel Mitchell, BABS), peptidebased analysis of the human
proteome (Dr. Valerie Wasinger,
UNSW), construction of a nonredundant database for HLA
typing of tissues in transplant
(Dr. Wallace Bridge, BABS)
and the RNA-seq analysis of
differential gene splicing in
Alzheimer’s disease (Dr. Michal
Janitz, BABS).
Some of our collaborations
in 2009
We are funded to collaborate with
you. For more information, please
see www.systemsbiology.org.au
In 2009, our collaborations have
been in the areas of network
analysis of colon cancer
Comparative view of a C. concisus reference (13826) genome, mapped using the Mauve aligner, against a C. concisus CD genome
(Crohn’s Disease), assembled using Velvet (0.7.57) assembly tool
WHY DID WE EVOLVE CHOLESTEROL?
Associate Professor Andrew Brown and Dr Anne Galea
At times, trying to second guess nature can yield
fresh insights into major biological questions –
pondering why cholesterol evolved is a case in
point. Understanding how cholesterol evolved is
important for a number of scientific disciplines,
including biochemistry, evolutionary biology and
the earth sciences. This is because cholesterol
and related sterols are the hallmark of eukaryotes,
which encompass everything from humble yeast
to humans.
Cholesterol is often seen as something we should
avoid, and yet this notorious component of our makeup is an essential molecule with unusually diverse
functions. Since its manufacture by organisms is
an extremely oxygen-intensive process, cholesterol
could only evolve as oxygen levels increased. Indeed,
the relationship between cholesterol and oxygen is
intricately intertwined.
13
Associate Professor Andrew
Brown and Dr Anne Galea
have provided a new twist on
why nature may have crafted
cholesterol. They gathered several
lines of evidence to support the
novel idea that cholesterol was in
fact a countermeasure to protect
our eukaryotic ancestors against
rising oxygen levels on Earth.
The evidence pertains to
cholesterol and related sterols,
and includes: (i) coincidence of
atmospheric oxygen and sterol
evolution; (ii) sterols regulate
oxygen entry into eukaryotic cells
and organelles; (iii) sterols act as
oxygen sensors across eukaryotic
life; and (iv) sterols serve as a
primitive cellular defence against
oxygen (including reactive oxygen
species).
The idea that nature crafted
cholesterol partially as an adaptive
response to the rise of oxygen
levels, rather than merely as
a consequence of it, has an
attractive symmetry to it. Moreover,
this evolutionary perspective can
usefully inform medical research
on cholesterol to address healthrelated issues. For example,
the cholesterol content of red
blood cell membranes affects
the oxygen-carrying capacity of
haemoglobin – patients with high
blood cholesterol levels have
SYSTEMS AND CELLULAR BIOLOGY
The pulmonary surfactant of the
earliest air breathers, lungfish,
is particularly rich in cholesterol,
in keeping with the possible
protection cholesterol afforded
against aerobic living
less oxygenation, which can be
reversed with cholesterol-lowering
drugs. Therefore, another benefit
of cholesterol-lowering therapies
may be to improve tissue
oxygenation and hence reduce
the damage caused by a blocked
artery, as experienced during
chest pain.
Sterol
A schematic representation of
our hypothesis: sterols negatively
feedback on one of its key inputs,
oxygen, by limiting its entry into
the cell. This hypothesis is built on
several lines of evidence, in addition
to the known requirement of oxygen
in sterol synthesis and the recognised
feedback mechanisms whereby
sterols inhibit their own synthesis
O2
A t lC
Acetyl
CoA
A
14 // BABS ANNUAL REPORT 2009
BIOENERGETICS AND THE ROLE OF MITOCHONDRIA IN AGEING
Professor Bill Ballard and Postdoctoral Fellow Dr Jonci Wolff
Biogerontology is the biological
study of longevity, ageing
(phenotypic changes that occur
after reproductive maturity)
and senescence (deteriorative
ageing). It is based on our
understanding of the evolutionary
forces shaping lifespan and
ageing, and the mechanistic
understanding of how the genes,
hormones, tissues and cells
involved mediate ageing.
courtesy of Felix Zajitschek
Mitochondria are crucial to the
links between life-histories, diet
and nutrition, and the cellular
mechanisms that result in ageing.
Oxidative phosphorylation
(OXPHOS) and energy production
in mitochondria result in
byproducts of reactive oxygen
species (ROS). The damage done
by ROS to DNA, cell membranes
and lipids is thought to be a
major cause of senescence.
Further, damage to mitochondria
DNA (mtDNA) can result in the
Linking organismal phenotype to mitochondrial genotype
production of more damaging
mutant proteins leading to a selfamplifying cycle of damage.
mitochondrial genotype; or (2) an
interaction between mitochondrial
genotype and nuclear loci.
In addition, because ROS are
produced in close proximity to
mtDNA, somatic mtDNA mutations
occur that appear to cause loss
of bioenergetic function during
ageing. Naturally occurring
mtDNA variation has been shown
to alter organism performance
and fitness, and such variation
can cause various bioenergetic
diseases.
In a cross-disciplinary ARC
Discovery Project, Professors
Bill Ballard and Robert Brooks
(School of Biological, Earth and
Environmental Sciences) target
the role of naturally occurring
mtDNA variation, mtDNA
damage and the level of ROS
production and resulting oxidative
stress in the links between
sex-dependent reproductive
effort, diet and longevity in
crickets. This collaboration
is a prime example of how
strengths of distinct research
areas can be combined to target
complex questions, allowing
for insights into mechanisms
and pathways otherwise limited
by unidisciplinary research
approaches.
Longevity in humans is
associated with specific
mitochondrial haplogroups, but
the mechanism(s) by which
this occurs have not been
satisfactorily explained due to
lack of mitochondrial variation in
current models. Under constant
environmental conditions,
extended longevity may be
conferred directly by (1) inherited
As an expert in genome evolution
with particular interest in
mitochondrial DNA, Bill Ballard
seeks to reveal how mutations
in mitochondrial DNA translate
into phenotypic changes on the
organismal level. Simultaneously,
Robert Brooks aims to identify
phenotypic changes in relation to
genetic variation and the influence
of such variation on an array of
life-history traits.
Combining genetic, behavioral
and evolutionary perspectives
into experimental design and
analysis will help to resolve
how the complex relationships
between reproductive effort, diet,
nutrient storage and allocation,
and bioenergetics all interact to
shape sex differences in longevity
and ageing, and also whether
these differences are reflected in
genetic variation in the nuclear
and mitochondrial genome.
Credit Colin Hood, Photo courtesy NSW State Water Corporation
15
Colligen Creek Off-take to the Edward River, Deniliquin NSW
ENVIRONMENTAL MICROBIOLOGY
16 // BABS ANNUAL REPORT 2009
ENVIRONMENTAL
MICROBIOLOGY ACADEMIC
STAFF
Professor Rick Cavicchioli
Scientia Professor Staffan Kjelleberg
Professor Brett Neilan
Professor Malcolm Walter
Dr Brendan Burns, Senior Lecturer
Dr Belinda Ferrari, Senior Lecturer
Dr Torsten Thomas, Senior Lecturer
John Wilson, Lecturer
ONE OF AUSTRALIA’S STRONGEST GROUPS OF WORLDCLASS MICROBIOLOGISTS AND BIOTECHNOLOGISTS IS
LOCATED IN BABS, WHICH HAS LONG BEEN RECOGNISED
FOR ITS EXPERTISE. THE MEMBERS OF THIS RESEARCH
GROUP FORM A STRONG CRITICAL MASS UNDERPINNED
BY RESEARCH EXCELLENCE THAT COLLECTIVELY
ADDRESSES GLOBALLY RELEVANT RESEARCH THEMES.
The group’s areas of research excellence include
environmental health and sustainability, microbial processes,
biomaterials and nanotechnology, environmental genomics,
biodiversity and conservation, and bioprospecting for enzyme
and drug discovery.
Fundamental discovery science uses cutting-edge
biosciences technologies to achieve practical societal
and economic benefits in areas of novel biocatalysts and
bioactives, biofilm and biofouling control, water quality and
water re-use, bioremediation and biofuels and monitoring and
maintaining the health of Australian ecosystems.
Current research includes national and international networks
with Asian, European and US-based research institutes and
universities.
A measure of the significance and impact of water research
carried out by Environmental Microbiology researchers
during 2009 included the adoption by a range of international
groups, including the World Health Organisation, of
techniques developed for the rapid and accurate detection
of toxic cyanobacteria in drinking water supplies. These
patented tests are now the standard means of assessing
environmental health, with the research also leading to the
design of antidotes to cyanobacterial poisoning.
Algal bloom in NSW
THE FIGHT AGAINST POTENT TOXINS FORMED
IN CYANOBACTERIA (BLUE-GREEN ALGAE)
Professor Brett Neilan
The cyanobacteria research
group at UNSW is considered
to be one of the world’s
leaders in the genetics of toxic
cyanobacteria (blue-green
algae). Members of the group
have undertaken research
that has led to the discovery
of four biochemical pathways
responsible for the production
of potent bacterial and algal
toxins that contaminate our
water supplies and accumulate
in seafood. The results of this
basic research and other work
on the evolution of cyanobacteria
have revolutionised an entire
field of environmental biology
and engineering. Water is the
ultimate example of an essential
global nutrient, and hence this
research has brought much
international acclaim.
In 2009 the research was
acknowledged with the
Australian Museum’s Eureka
Prize for Water Research and
Innovation being awarded to
Professor Brett Neilan, his third
Eureka prize. Brett was also
named NSW Scientist of the Year
in the category of Environment,
Water and Climate Change
Sciences.
Having characterised the genetic
basis for production of these
toxins, work in the Neilan lab
has moved on to the analysis of
ecological factors that regulate
their production in algal blooms.
Apart from microcystin, the lab
has discovered biosynthetic
pathways for the production
of the potent toxins nodularin,
cylindrospermopsin and
saxitoxin. The latter compound is
the first example of an alkaloidencoding gene cluster to be
characterised in a bacterium,
and is the only example of the
transfer of genes between two
domains of life.
This research has also
introduced UNSW and the
Australian Government to
aspects of scientific research
related to biosecurity. Transfer of
laboratory data into information
that improves water quality
and land management has
been achieved by liaison
and communication with the
numerous environmental
agencies. Recently, the science
has been applied to assessing
the drinking water supply of
Sydney as well as the Murray
River. In 2005, Brett chaired the
US-EPA genomics committee
ENVIRONMENTAL MICROBIOLOGY
Credit Colin Hood, Photo courtesy NSW State Water Corporation
17
Credit Steve Lunam, Photo courtesy Australian Museum
18 // BABS ANNUAL REPORT 2009
2009 UNSW Eureka Prize Awards Recipients (l-r) Justin Gooding, Brett Neilan, Greg Leslie and Stuart Wenham
Microfossil evidence reveals
that cyanobacteria are some
of the oldest forms of life on
Earth, with extant analogues
found in stromatolites in Western
Australia. Work in this area
was initiated when Brett was
a NASA fellow at Stanford
University, and continues with
studies on the adaptation and
evolution of microorganisms
in harsh environments. In the
past few years, the Neilan team
has identified and classified
cyanobacteria from coastal
waters in Queensland, drinking
and recreational lake sediments
and hypersaline pools in Western
Australia, granite in Antarctica, church walls in Brazil, aquaculture
lakes, thermal springs and volcanoes in the Philippines, and unwell
Yaks in Bhutan. This work is performed under the auspices of the
Australian Centre for Astrobiology (ACA) at UNSW.
Regional biodiversity has also enabled the stockpiling of a library
of genes encoding enzymes that produce toxin-like molecules. By
recombining these genes, new toxins may be produced that can
be used, for example, as antibiotics. These gene libraries represent
the conserved stocks of Australian molecular diversity. In the future,
this program will be central to continuing the study of the molecular
biology and genetics of secondary metabolite and bioactive natural
product biosynthesis. A major source of these genes will be from
plants that are used in traditional medicines.
Credit Miro Peterman,
Photo courtesy NSW Office of Water
for introducing new cyanotoxin
guidelines and co-authored
their report on harmful algae in
drinking water. The research has
formed the basis for New South
Innovations and Diagnostic
Technology Pty Ltd to initiate
a business plan for offering
water quality assessment using
genetic methods.
Stevens Weir, Colligen Creek
19
The Neilan Lab
Neilan Lab students enjoy an off-site gathering
Several students under the supervision of Professor
Brett Neilan are combining 21st century molecular
technology with 1000-year-old cultural knowledge
to understand the genetic basis for bioactivity in
traditional medicines.
In some Asian and African countries, up to 80 per
cent of the population depend on these ancient
medicinal practices for their primary healthcare
needs. Plants and their derived natural products
are frequently employed as traditional medicine,
and such plants are viewed as attractive targets for
the discovery of novel therapeutic agents in natural
product investigations. A variety of useful drugs,
such as morphine (analgesic), digitoxin (cariotonic)
and ephedrine (sympathomimetic), have been
discovered following investigations into traditional
herbs. These ethnopharmacology approaches
to drug discovery are based on the premise that
plants used as traditional medicines have shown
some form of bioactivity and therefore have the
increased likelihood of containing interesting drug
leads in comparison to plants selected at random.
The approach taken by the students is to isolate
bacteria and fungi that live in the medicinal plants,
and then investigate the genes responsible
for drug biosynthesis, something the group
has developed from previous work on the
genetics for toxin production by cyanobacteria.
Following these initial characterisation efforts,
sustainable production systems can be used
and the compounds assessed for targets, novel
chemistries and even redesign of the natural
structures.
Four systems of traditional medicine are being
drawn from by these young Australian drug
discovery researchers: Australian Aboriginal
(Shane Ingrey is an ARC Indigenous Grant
recipient); Papua New Guinean, (Jeffrey Noro holds
an Endeavour Scholarship for his anti-tuberculosis
work); Chinese (Kristin Miller and Ivan Wong have
been funded by the Australian-China Council); and
Indonesian (Alfonsus Alvin, who collaborates with
Atma Jaya University in Jakarta). To inform sample
collections, projects have been commenced using
traditional knowledge, often obtained from personal
family members, followed up by microbial, genetic
and chemical analyses in the laboratory.
ENVIRONMENTAL MICROBIOLOGY
TRADITIONAL MEDICINE RELEVANT IN THE 21ST CENTURY
20 // BABS ANNUAL REPORT 2009
MICROBIOLOGY OF EARLY EARTH ECOSYSTEMS
To understand the biology of an
ecosystem, a time separation of
billions of years seems to present an
insurmountable hurdle. In Australia, a
few modern analog ecosystems exist
that can act as a ‘worm-hole’ to the past,
allowing us to bring a contemporary
arsenal of tools to the field site. One of
the most famous and extensive sites
anywhere in the world is the collection
of stromatolites at Shark Bay in Western
Australia, a UNESCO World Heritage
Site. Stromatolites are biogeological
ecosystems resulting from the
metabolic activity of resident microbial
communities. The excitement stems from
the fact that there is a clear fossil record
of such structures dating back more
than 3 billion years.
Photo credit: Brendan Burns
Dr Brendan Burns
Stromatolite Cross-section
Photo credit: Brendan Burns
Dr Brendan Burns and his research
team have worked on various aspects of these
ecosystems in a bid to comprehensively characterise
their functional complexity. The goal is to thoroughly
understand the diversity, biogeochemistry and key
interactions of the microorganisms forming the Shark
Bay stromatolites. In addition to identifying potentially
novel microbial activities vital to the ecosystem’s
function, this understanding will provide a rational
focus when seeking biosignatures that will ultimately
help interpret the fossil record. By using a combination
of diverse and cutting-edge techniques, including
employing metagenomic analyses for the first time in
Brendan Burns and Professor Pieter Visscher from the University of
Connecticut at the Shark Bay World Heritage Site
these systems, the research will enable more
rational predictions on past environments and
build useful models to further our understanding
of early Earth communities.
In 2009, Dr Burns also teamed up with
Professor Pieter Visscher from the University
of Connecticut, who has conducted extensive
studies on the stromatolites located in the
Bahamas. Together, they conducted extensive
in-situ analyses of metabolic activities in
Shark Bay, measuring diel fluctuations in key
nutrients important in global cycling. Through
collaborations with NASA, Dr Burns is also
employing a state-of-the-art GigaPan Imager in
Shark Bay that utilises technology developed
for the Mars Rovers.
This research group’s findings have provided
crucial information vital to the conservation
of these unique resources (identified as
under threat to climate change in the recent
Garnaut Report), including careful monitoring
of changes in biological diversity that could
indicate possible threats to these evolutionally
significant systems.
21
Dr Belinda Ferrari, Senior Lecturer
In soil microbiology, estimates
suggest that over 99.9% of
microbes cannot be recovered
using traditional laboratory
methods, and novel cultivation
strategies that mimic natural
environments have been used to
address this problem. Currently,
of the 92 Divisions described,
approximately 39 contain no pure
culture representatives.
Photo credit: Josie van Dorst
Traditionally, microbiology has
focused on the analysis of largescale communities to gain an
understanding of an organism’s
overall function. We now know
that this approach is limited,
as it provides information on
the properties of a complex
population that may contain a
consortium of different individuals.
Today, the analysis of single cells
through fluorescence-based
technologies is enabling a greater
understanding of individual cells
within these mixed microbial
communities.
Sub-Antarctic Macquarie Island is the current focus of Dr Ferrari’s research
Past and present petroleum
hydrocarbon spills in polar soils are
extensive. Macquarie Island is a
sub-Antarctic island located in the
Southern Ocean, approximately
half way between Australia and
Antarctica. It has been affected by
petroleum contamination, however,
The soil slurry membrane system
due to a lack of site-specific data
is a technique that mimics the
the environmental impact on the
natural environment of soil
island’s soils is largely unknown.
bacteria and was developed
In January 2009, an expedition to
in the laboratory of Dr Belinda
Macquarie Island was undertaken
Ferrari. The approach results
by Dr Ferrari’s Honours student
in the recovery of slow-growing
Josie van Dorst. By combining
previously ‘uncultured’ bacteria
sophisticated single-cell
from a diverse range of Divisions,
technologies with novel cultivation
including those with no pure
efforts, insights were obtained
cultured representatives.
into downstream effects of diesel
contamination on the microbial
Through collaboration with the
community in this sensitive
Australian Antarctic Division,
environment. Results showed that
this ‘extreme culture’ approach
the aerobic fraction of soil microbes
to growing recalcitrant bacteria
was more susceptible to petroleum
is now the focus of Dr Ferrari’s
research, attempting to elucidate contamination than the anaerobic
fraction, and subsequent petroleum
the effects of petroleum
hydrocarbon additions significantly
contamination on the microbial
ecology within sub-Antarctic soils. altered the microbial community.
Sixteen isolates were recovered
from Macquarie Island soils,
including two potentially novel
genera and two potentially
novel families. Following further
characterisation, these isolates
may provide insights into future
bioremediation strategies for
cold regions. The alteration
of bacterial diversity and
abundance observed here
has relevance to future risk
assessment and remediation
strategies associated with
petroleum contamination in polar
soils.
In the future, further refinement
of the techniques by Dr Ferrari’s
group and continued collaboration
with the Australian Antarctic
Division will enable the impact of
petroleum contamination on polar
soils to be quantitatively assessed
and remediation end points to be
established.
ENVIRONMENTAL MICROBIOLOGY
GAINING INSIGHT INTO THE MICROBIAL ECOLOGY OF SUB-ANTARCTIC SOILS
22 // BABS ANNUAL REPORT 2009
MICROBIAL ECOLOGY, EVOLUTION AND GENOMICS
Senior Lecturer Dr Torsten Thomas
Prior to joining the School of
Biotechnology and Biomolecular
Sciences in 2009 I worked
in industry and academic
environments as a microbiologist.
Most recently I was a Senior
Research Fellow at the Centre
for Marine Bio-Innovation here
at UNSW, where I established
several research projects in
microbial and environmental
genomics. In my new role as
a Senior Lecturer, I have the
opportunity to work with a large
team of scientists with different
backgrounds and expertise, as
well as utilising state-of-the-art
equipment and infrastructure.
My research focuses on the
interaction of bacteria with
their environment and aims to
understand the function of the
enormous diversity of bacteria
in natural systems. Over the last
Figure Legend: The upper panel shows the physical
interaction of a novel G-proteobacterium (yellow)
with putative cyanobacterium (red) inside a sponge.
Images were produced by fluorescence in situ
hybridization (FISH). Lower part shows a section of the
G-proteobacterial genome and arrows indicate genes
involved in cell-cell interaction (blue and red). (Photo
courtesy of Michael Liu)
three decades, microbiologists
have used molecular techniques
to discover hundreds of thousands
of new bacterial lineages, yet
many (even most) of the dominant
and relevant bacteria in the
environment cannot be cultured
with traditional techniques. To
learn more about the ‘uncultured
majority’, my co-workers
and I apply high-throughput
techniques to sequence the
genetic code of bacteria directly
from the environment. We
then use various bioinformatic
approaches to reconstruct
the genome of the uncultured
bacteria and use this information
to make predictions about their
physiological, functional and
ecological properties. Ultimately,
we perform directed physiological
and biochemical experiments
to support our predictions and
establish a clear link between
function and diversity in the
environment.
One of the systems we study is
the symbiotic interaction between
bacteria and sponges. Marine
sponges are ancient, sessile
filter-feeding metazoans, which
represent a significant component
of the benthic community
throughout the world. Sponges
harbour a remarkable diversity
of bacteria, however, little is
known about their functional
properties as most are uncultured.
Recently we have generated the
genomic information of many
uncultured sponge bacteria and
have described, for example,
the functional characteristics
of a novel Gproteobacterium
associated with the sponge
Cymbastela concentrica.
Our predictions led us to the
hypothesis that this bacterium
lives in direct association with
other bacteria, and we have been
able to experimentally prove this
by identifying a cyanobacterium
as a likely host (see Figure 1).
This demonstrates some of the
complex interactions in natural
symbiotic systems. Other bacterial
systems we study include those
associated with marine seaweeds,
underground coal deposits,
marine seawater, freshwater and
sediment cores.
An associated research interest
of mine involves the investigation
of genetic heterogeneity of
bacterial populations. It has
been recently recognised that
bacterial strains in nature are
far from being clonal; rather,
they form populations of closely
related yet genetically distinct
individuals. This population
heterogeneity is predicted to
cause functional differences, as
individuals within the population
might carry different mutations in
functional genes. Up to now, these
difference could only be observed
in a handful of conserved genes,
but recent developments in highthroughput sequencing has made
it possible to measure variation
in every gene within the genome.
We have generated datasets that
contain hundreds of millions of
basepairs of bacterial populations
and apply bioinformatic
tools to define the population
heterogeneity both in terms of
distribution (e.g. hot spots) and
type (e.g. SNPs). Ultimately, we
want to determine if particular
gene variants are being selected
for, and why they are important for
the evolution of the population.
Photo credit: Howard Lam
23
Caption: Chromatography
MOLECULAR MEDICINE
24 // BABS ANNUAL REPORT 2009
MOLECULAR MEDICINE
ACADEMIC STAFF
Professor Hazel Mitchell
Associate Professor Andrew Collins
Associate Professor John Foster
Associate Professor Ruiting Lan
Associate Professor Vincent Murray
Associate Professor Peter White
Dr Volga Bulmus, Senior Lecturer
Dr Wallace Bridge, Senior Lecturer
THE MOLECULAR MEDICINE GROUP HAS A UNIQUE
STRENGTH IN COMBINING FUNDAMENTAL BIOLOGICAL
AND BIOMOLECULAR SCIENCES WITH AN APPLIED
BIOTECHNOLOGY AND MEDICAL FOCUS. THE GROUP
FACILITATES COLLABORATIVE RESEARCH EFFORTS ACROSS
DISCIPLINE BOUNDARIES FOR FUNDAMENTAL DISCOVERIES
AND CLINICAL RESEARCH, AND FOR GENERATING
COMMERCIAL OPPORTUNITIES.
The research strengths of this group are medical bacteriology,
biomaterials, medical virology, immunology, bioinformatics,
cancer and genetics. A wide range of cutting-edge molecular
and bioinformatic tools are employed to understand and combat
disease. The expertise developed in this group has natural
synergies with other projects within the School’s research in areas
including ageing, water research and proteomics. Of particular
focus are studies involving medically important bacteria and
antibiotic resistance, and medical virology.
Dr Michal Janitz, Senior Lecturer
Dr Louise Lutze-Mann, Senior
Lecturer
Dr Chris Marquis, Senior Lecturer
Dr Vladimir Sytnyk, Senior Lecturer
Dr Mark Tanaka, Senior Lecturer
Dr Noel Whitaker, Senior Lecturer
Dr Li Zhang, Senior Lecturer
Dr Frances Foong, Lecturer
Dr Sven Delaney, Associate Lecturer
Dr Anne Galea, Associate Lecturer
The biomaterials research in this group includes microbially
produced biopolymers and bioplastics for medical applications,
novel polymeric nanoparticles and biofuels. During 2009, UNSW’s
internationally recognised research in biofuels was given a $3
million infrastructure upgrade funded by the state and federal
governments. The Biofuels Research Laboratory is a leader in
new second-generation technology for converting non-food based
cellulosic biomass to ethanol. The Recombinant Products Facility
provides services in cell engineering, bioprocess development,
fermentation, cell culture and protein purification to the Australian
research community and industry. It represents one of four such
nodes to provide a coordinated national research infrastructure
capability.
25
Senior Lecturer Mark Tanaka, QEII Fellow 2009-2013
Bacteria have a remarkable
ability to survive and thrive in
changing conditions. For example,
pathogenic bacteria confronted
by antibiotics easily evolve
resistance to them. In my group,
we develop mathematical and
computational models to study
how bacterial genomes evolve,
and how the genetic structure of
bacteria confer flexibility in the
face of changing environments.
This work, funded by a Discovery
Project grant from the ARC, is
a collaboration with Associate
Professor Ruiting Lan here in
BABS and Associate Professor
Andrew Francis of the School of
Mathematics and Computing at
the University of Western Sydney.
One special feature of bacterial
genomes is that genes involved
in a common pathway are often
clustered on the chromosome.
An Honours project in this
group, taken up by Sara Ballouz,
involved the use of computer
simulation models to understand
the roles of natural selection
and horizontal gene transfer
in generating these structures
(Figure 1). Surprisingly, genes
fail to cluster under a wide range
of conditions. Direct and indirect
selection can both explain the
evolution of clusters as long as
certain conditions hold, including
high population sizes and high
rates of horizontal transfer. This
work has appeared in PLoS
Computational Biology.
Another aspect of bacterial
evolution we have been exploring
is the evolution of antibiotic
resistance. We have developed
a stochastic model of the
evolution of drug resistance in
Mycobacterium tuberculosis in
order to estimate key parameters
related to resistance at the
epidemiological level using
molecular fingerprinting data
(Figure 2). Specifically, we
estimated the cost of resistance
to disease transmission as well
as the overall reproductive fitness
of resistant strains compared
to sensitive strains within the
framework of approximate
Bayesian computation. This work
was done in collaboration with the
research group of Dr Scott Sisson
of the School of Mathematics and
Statistics at UNSW. We found
that while resistance appears to
come with a cost to transmission,
the overall fitnesses of resistant
and sensitive strains are
most likely equal. This is
because resistant strains
extend the duration of
infection, which leads to
new cases of tuberculosis
due to transmission of
resistant strains. This
work was published in
the Proceedings of the
National Academy of
Sciences USA.
Working with a former
postdoctoral researcher
from the group, Frank
Valckenborgh, who
is now a lecturer
in mathematics at
Macquarie University,
we are considering the
role of compensatory
mutations in the
dynamics of the
evolution of resistance.
In particular, under
stochastically fluctuating
environments in which the
concentration of antibiotics
changes over time, complex
dynamics can arise. I have a
general interest in evolutionary
genetics and population biology
beyond bacteria, and I collaborate
with researchers on a wide
range of problems. In addition to
researchers mentioned above,
recent collaborators include Kevin
Laland (St Andrews, UK), Jeremy
Kendal (University of Durham,
UK), Katia Koelle (Duke University,
USA), Roland Regoes (ETH,
Switzerland), and Carl Bergstrom
(University of Washington, USA).
Local collaborators include Miles
Davenport, Peter White, Garry King
and Des Cooper (UNSW).
MOLECULAR MEDICINE
THE EVOLUTION OF BACTERIAL GENOMES
Figure 1. Genes evolve into clusters through a series of sweeps in which the
chromosomal distance between genes decreases progressively
Figure 2. A schematic for the stochastic epidemiological model of drug
resistance evolving in the tuberculosis bacteria and spreading in a
population
26 // BABS ANNUAL REPORT 2009
GENOMICS AND EVOLUTION OF HUMAN BACTERIAL PATHOGENS
Associate Professor Ruiting Lan
Infectious diseases caused by pathogenic
bacteria are a major threat to global human
health. Our group takes a multidisciplinary
approach to the study of these bacteria, with our
research addressing how pathogens arise and
cause disease, and how such pathogens can
be identified and typed. We work on pathogenic
bacteria that cause cholera, bacillary dysentery,
salmonellosis and whooping cough. These
studies are significant in designing strategies
that will be effective in preventing the
emergence and spread of pathogens.
We employ a dual genomic and bioinformatic
approach to seek an understanding of evolution
and molecular epidemiology of bacterial
pathogens.
Australia
Japan
Finland
France
Netherlands
Canada
USA
Hong Kong
China
Minimum spanning tree of Bordetella
pertussis genotypes from Australia
and worldwide. Each circle represents
a genotype. The size of the circle is
proportional to the number of clinical
isolates studied. The coloured pie chart
within a circle represents proportions of
isolates from a particular country
Mexico
Italy
UK
Our research on pertussis,
commonly known as
whooping cough, is
highlighted due to the
increase in the number
of cases of Australians
contracting this highly
contagious respiratory
disease. Pertussis is
caused by Bordetella
pertussis and has
remained endemic in
Australia despite more
than half a century of
vaccination.
We used microarrays and
genome sequencing to
study B. pertussis. The B. pertussis genome
was explored for molecular markers that are
highly variable, and molecular methods based
on these markers have been developed. We
typed a large collection of clinical pertussis
isolates using these methods and identified
epidemic strains circulating in Australia as
well as two strains carrying variants of genes
encoding for antigens used in the acellular
vaccine. These genetic changes may have
been brought about by selection from vaccineinduced immunity. We aim to further understand
what genetic changes are altering the epidemic
nature of B. pertussis in Australia, and the
selection pressures from vaccination.
27
Senior Lecturer Dr Volga Bulmus
before
after
Human neuroblastoma cells before and after transfection with siRNA polymer conjugates developed by Dr. Bulmus and her
team to silence green fluorescence protein gene
Our team in the Bio/Polymers
Research Group at BABS
investigate the production and
application of novel nanoscale
polymeric systems to enable
the effective delivery of
biomolecular therapeutics. The
team`s recent research focuses
on development of systems
that improve serum stability,
biodistribution, membrane
transport and immunogenicity of
siRNAs for cancer treatment.
Outstanding progress in
cell biology, genomic and
proteomic research, and medical
biotechnology has led to the
emergence of biomoleculebased therapeutic strategies.
Short RNA duplexes silencing
disease-causing genes,
protein- and DNA-based
vaccines leading to desired
immune response are only a
few examples of biologics that
have enormous potential to treat
numerous diseases including
diabetes, hepatitis, AIDS and
cancer.
Despite their enormous potential,
the use of biomolecular agents as
clinically applicable therapeutics
has been severely challenged.
Delivering biotherapeutics to
the required site of the body at
a therapeutic concentration is
hindered by several inherent
features of biomolecular agents,
including low in vivo stability,
immunogenicity, and poor
biodistribution and membranetransport. Biomolecular
therapeutics such as proteins,
siRNA and DNA can be combined
with polymers to overcome such
delivery challenges. A number
of molecularly engineered
polymer therapeutics, so-called
nanomedicines, are in clinical
trials and some are marketed for
human use.
With collaborators at the
Children`s Cancer Institute
Australia (CCIA), the Centre
for Advanced Macromolecular
Design (UNSW) and the
Chemistry and Biochemistry
Department at the University
of California Los Angeles,
we used a recently emerged
polymerisation technique to
generate novel well-defined
siRNA-polymer conjugates and
nanoparticles. The research
performed in 2009 revealed that
the siRNA-polymer conjugates
have significantly improved
serum stability and gene
silencing efficiency in human
neuroblastoma cells. We also
investigated novel biomimetic
polymers and nanoparticles as
mediators enhancing the tissuespecific targeting and membrane
transport of siRNAs.
MOLECULAR MEDICINE
POLYMERS OVERCOMING DELIVERY PROBLEMS OF BIOTHERAPEUTICS
28 // BABS ANNUAL REPORT 2009
CELL ADHESION MOLECULES IN HEALTHY AND DISEASED BRAINS
Senior Lecturer Dr Vladimir Sytnyk
I joined the School of Biotechnology and
Biomolecular Sciences in September 2009. I was
previously located at the Centre for Molecular
Neurobiology at the Medical School Eppendorf
in Germany, where I led a research group in the
Institute for Biosynthesis of Neuronal Structures.
I was delighted to be given the opportunity to
join one of the most prestigious universities in
Australia and to work alongside world-class
scientists. I believe the excellent research
environment and state-of-the-art facilities
at UNSW and in the School offer enormous
potential for my future research.
The major focus of my group’s research is on
the mechanisms via which adhesion molecules
of the Immunoglobulin superfamily regulate the
development and functioning of the brain cells –
neurons.
abnormal expression of these molecules can
inflict or contribute to brain disorders, including
schizophrenia, Alzheimer’s disease, X-linked
disorders and Down syndrome.
An important direction of the work is the
investigation of how the posttranslational
modifications of cell adhesion molecules regulate
their functions. Acylation, glycosilation and
phosphorylation of the cell adhesion molecules
is currently being investigated. This research will
lead to better understanding of the aetiology of
brain disorders and will ultimately provide tools to
treat disorders associated with mutations in cell
adhesion molecules.
Cell adhesion molecules NCAM180 accumulates in synapses
of cultured neurons (confocal immunofluorescence image NCAM180 (green), synaptic marker synaptophysin (red))
Adhesion molecules are present at the cell
surface of neurons where they function as ‘shortrange detectors’ of the environment surrounding
neurons. In developing neurons, these
molecules either facilitate or block neuronal
growth and differentiation depending on whether
the environment is permissive or inhibitory.
In mature neurons, cell adhesion molecules
stabilise contacts between neurons and neurons,
and neurons and other cells. Cell adhesion
molecules also accumulate in synapses –
specialised contacts between neurons that
allow neurons to transmit information to each
other. Importantly, most models of learning and
memory invoke modification of synaptic strength
as the underlying mechanism for information
storage in the brain.
NCAM180
NCAM180
synapt.
y p
Previous work of the group members published
in the Journal of Cell Biology and Neuron
showed that the two adhesion molecules NCAM
and CHL1 accumulate in synapses and regulate
synapse assembly and functioning.
In recent research conducted in BABS, my group
has identified several new adhesion molecules
that accumulate at synapses. Using mice as
an animal model and cultured neurons as a
cellular model, the group is now investigating
the functions that these cell adhesion molecules
play in synapses, and how mutations or
axon
dendrite
Structure of a single hippocampal synapse at the electron
microscopical level
29
Senior Lecturer Dr Michal Janitz
Before joining the School of Biotechnology
and Biomolecular Sciences early in 2009,
I was a group leader in the Department of
Vertebrate Genomics at the Max Planck
Institute for Molecular Genetics (MPIMG) in
Berlin, where my research focused on the
application of genomic technologies in studying
mechanisms of transcription in the mammalian
cell in health and disease. In 2008, my interest
turned to the emerging next-generation
sequencing technologies and their application
in comprehensive transcriptome studies. Since
commencing at BABS, I have implemented the
RNA-Seq technology pipeline in collaboration with
Ramaciotti Centre for Gene Function Analysis and
the bioinformatics group led by Professor Marc
Wilkins. This initiative builds on the national and
international recognition of the School as a leader
in ground-breaking human genome research.
My team uses next-generation sequencing
technology to explore mechanisms of
transcriptome regulation in the human brain,
in both health and disease. In particular,
my research focuses on understanding the
causative linkage between altered alternative
splicing patterns and the process of neuronal
degeneration leading to Alzheimer’s disease.
Alternative splicing has played a major role in
the evolutionary expansion of the proteomic and
functional complexity underlying many cellular
processes in the vertebrate nervous system,
with emerging key roles in synaptogenesis,
neurite outgrowth, axon guidance, ion channel
activity and long-term potentiation. However,
the mechanisms that control neural-specific
alternative splicing and underlie the evolution of
increased nervous system complexity are poorly
understood. There is increasing recognition that
some neurological and neuromuscular diseases
are caused by errors in splicing – spinal muscular
atrophy and frontotemporal dementia being two
examples. The importance of individual splicing
choices and of splicing regulators in nervous
system development and function is becoming
clearer, but is far from complete.
Areas of the human brain affected
by Alzheimer’s disease. © 2010
Nucleus Medical Media
My laboratory has recently completed studies
on alternative splicing profiles in brain regions of
individuals with Alzheimer’s disease, using the
RNA-Seq technique (Fig. 1). Clear differences in
a number of detected spliced junctions between
normal and AD brain samples strongly indicate
that the splicing machinery is targeted and
that altered splicing could be causative in the
neurodegeneration process.
Quantitative analysis of the gene expression
on the genome-wide level in AD samples led to
identification of novel differential gene expression
patterns. Examples include up-regulation of the
Ribonuclease P RNA component H1 (RPPH1) and
Glutathione S-transferase M5 (GSTM5) genes
and down-regulation of the Ectodermal-neural
cortex (ENC1) and Secretogranin II (SCG2) genes.
Interestingly, our study revealed preferential
expression of the mRNA isoform of the amyloid E
(A4) precursor protein gene (APP) lacking exon 8
in the temporal lobe of the AD brain. In contrast,
this exon is present in the APP transcript mostly
expressed in the temporal lobe of the normal
human brain. This might indicate preferential
exon skipping in the brain tissue affected by the
neurodegeneration process.
Future studies will concentrate on the identification
of mRNA isoforms specifically expressed
in functionally distinct regions of the human
brain, such as the primary entorhinal cortex or
association cortex. Furthermore, the impact of
neuronal degeneration on splicing patterns of
these genes will be investigated, contributing
to a further understanding of the molecular
pathomechanism of Alzheimer’s disease.
MOLECULAR MEDICINE
INVESTIGATING TRANSCRIPTOMICS OF
NEURODEGENERATIVE DISEASES
30 // BABS ANNUAL REPORT 2009
BIOPROCESS ENGINEERING OF PROTEINS
Senior Lecturer Dr Chris Marquis
The Marquis Lab undertakes
collaborative research projects
in the area of bioprocess
engineering germane to proteins.
Collaborative projects include
those with Prof. Sam Breit (St
Vincent’s Centre of Applied
Medical Research), on peanut
allergen purification (with Dr.
Alice Lee of the School of
Chemical Sciences) and with
Prof. Rose Amal (School of
Chemical Sciences) on the
interface of nanomaterials
and biology, with a focus on
functional delivery of genes
to mammalian cells 1 and
nanotoxicity2.
Photo: Ming Lam
As part of this research I
manage the NCRIS-funded
UNSW Recombinant Products
Facility (www.proteins.unsw.
edu.au). The Facility is now fully
operational with 4 full time staff
(Edwin Huang, Scott Minns,
Helene Lebhar and Doris Suen:
all with industry experience)
and all major equipment in
place and commissioned. We
can run mammalian cell culture
expression to the 10L scale,
bioreactor fermentation of recombinant yeast and bacteria to 22.5L and
have all downstream components in place to recover protein products.
We have completed a number of projects for UNSW laboratories (BEES,
Optometry and Chemical Sciences), the University of Queensland,
external Institutes (Garvan, Heart Research, Victor Chang) and small
start-up companies. The capability forms part of a larger consortia of
national capabilities located at the University of Queensland, Monash
University, CSIRO, Hospira and Radpharm Scientific.
Recent References
1.
Arsianti M, Lim M, Marquis CP, Amal R. (2010) Assembly of Polyethylenimine-Based Magnetic Iron Oxide Vectors: Insights into Gene
Delivery. Langmuir. Jan 29. [Epub ahead of print]
2.
Gunawan C, Teoh WY, Marquis CP, Lifia J, Amal R. (2009) Reversible antimicrobial photoswitching in nanosilver. Small. Mar;5(3):341-4.
30L Bioreactor
31
Emeritus Professor Peter Rogers
Recent increases and volatility in the price of oil,
the security advantages of increased domestic
production, the environmental benefits of reduced
greenhouse gas (GHG) emissions and the potential
for regional development have all contributed
to greatly increased interest in the production of
biofuels such as ethanol.
Traditionally, ethanol has been produced from sugarand starch-based raw materials. However, in the
longer term, second generation processes based on
cellulosic materials from agricultural/forestry residues
and/or high-yield biomass energy crops offer
greater potential for increased ethanol production.
They largely avoid the food vs. fuel conflict, and it
is projected that by 2020 in the United States, twice
as much ethanol will be produced from cellulosic
biomass as from the traditional raw materials.
The environmental and regional economic drivers
behind the global expansion of biofuels are
relevant to Australia, with our rapidly increasing
oil imports (currently in the range of $A15-18Bn
per annum). In response to this, the New South
Wales Government has mandated the use of 2%
ethanol in petrol since 2008, rising to 10% by 2011.
This has already stimulated increased fuel ethanol
production in NSW and new agreements with oil
industry partners. The Queensland and Victorian
Governments are also planning fuel ethanol
mandates. R&D support for second generation
biofuels, which include cellulosic ethanol for
blending with petrol and biodiesel production
using oils from plants and lipids from algal sources,
is being provided by the Australian Government.
Key programs include the NCRIS Biofuels SubProgram ($14M from 2007-2011) and the Second
Generation Biofuels Research and Development
Program ($15M for 2009-2011).
Research at UNSW over the past decades has
focused on the development of high-productivity
continuous processes for fuel ethanol production
using both yeast and bacteria. Following an extensive
screening program, fast and efficient strains of the
bacterium Zymomonas mobilis (used for pulque
and tropical palm wines) were isolated and used in
these high-productivity fermentations. In more recent
research, recombinant strains of Z. mobilis have
been used to produce ethanol from C5/C6 sugars
(xylose/glucose), typical of those found in cellulosic
hydrolysates. High specific rates have been achieved,
together with 90-95% theoretical ethanol yields, and
stable flocculent strains of Z.mobilis have been isolated
that are capable of achieving continuous high-density,
high-productivity fermentations.
Commercial R&D projects using the Zymomonas
process have been carried out by our group with
CSR, Grain Processing Corporation (Iowa), Dupont
(Delaware) and the US Department of Energy through
the National Renewable Energy Laboratory (NREL),as
well as related R&D on higher value products involving
enzymatic biotransformations for pharmaceuticals with
Orica (formerly ICI Aust) and BASF (Germany).
MOLECULAR MEDICINE
SECOND GENERATION BIOFUELS - NCRIS-FUNDED BIOFUELS LABORATORY
Current ethanol R&D (with infrastructure support from
the NCRIS Program) is directed at the evaluation of a
range of cellulosic raw materials available in Australia,
which include bagasse from the sugar industry,
wheat and sorghum residues from crop production,
and biomass from cane and forest plantations. Pretreatment equipment (Parr reactor) and computercontrolled fermentors for
Computer Controlled 3L Fermentor for
use with recombinant
Bioethanol Production
micro-organisms are
available for commercial
evaluations and
collaborative research
projects.
More fundamental
studies are being carried
out on further genetic
manipulation and
metabolic engineering of
Z. mobilis, as well as on
production of higher-value
fermentation products
that could be associated
with ethanol production
when using renewable
cellulosic raw materials.
Current projects also
involve optimisation of the
enzymatic esterification of
plant-based oils that could
be used for the production
of biodiesel blends from
renewable resources.
Computer Controlled 3L and 20L Tower Fermentors
for High Productivity Bioethanol Production using
Flocculent Yeast or Bacteria
Figure: NCRIS fermentation facilities available in the School
32 // BABS ANNUAL REPORT 2009
2009 RESEARCH FUNDING
Grants commencing or in operation during 2009.
Australian Research Council –
Federation Fellowship
Neilan BA. The toxins of water-borne
cyanobacteria: Regulation and
exploitation of their biosynthesis. 20082012: $1,640,000.
Australian Research Council –QEII
Fellowships
Tanaka MM. Mathematical models and
bioinformatic analyses of bacterial
genome evolution. 2009-2013:
$614,870.
Brown MV. Towards a predictive
model for coastal marine microbial
assemblages. 2009-2013: $695,000.
Australian Research Council –
Inaugural Future Fellowship
Yang HR. The cellular dynamics of
lipid droplets: Implications for obesity
and biodiesel production. 2009-2013:
$788,800.
Australian Research Council –
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.
2007-2010: $500,000.
Burns BP (ARF), Walter MR. Functional
complexity of modern marine
stromatolites. 2006-2010: $542,000.
Coleman M (APD). Dispersal and gene
flow in habitat forming algae. 20062009: $335,000.
Dawes IW. Cellular gene regulation
networks. 2005-2009: $575,000.
Dawes IW, Yang HR, Breitenbach M.
Oxidative damage and cell ageing.
2008-2010: $564,000.
Foster LJR. Development of a
light-activated bioadhesive for lowtemperature tissue repair. 2007-2009:
$310,000.
Kjelleberg S, Yildiz HF, Rice SA,
McDougald SD, Matz C, Givskov M,
Bartlett DH. Roles for quorum sensing
and biofilm formation by Vibrio cholerae
in resistance to protozoan grazing.
2007-2009: $335,102.
Neilan BA (APF), Pomati F. Sodium
homeostasis and the molecular basis
for neurotoxin production by bacteria
and algae. 2005-2009: $960,000.
genomics and novel bioactives from
microbial communities on living
marine surfaces (APAI). 2006-2010:
$1,611,000.
Neilan BA, Moffitt MC, Bolch CJS.
Polyketides as the conserved basis
for diverse marine toxin biosyntheses.
2008-2011: $315,000.
Mahler SM, Naylor DJ, Marquis
C, Johnson BJ, Curmi PMG, Chin
DY (APDI). Determination of the
mechanisms of immune system
regulation of inflammation by the
human protein, chaperonin 10 (APAI).
2005-2009: $337,826.
Preiss, T. Determining the sequence
of events during eukaryotic translation
initiation. 2007-2009: $235,000.
Preiss T, Beilharz TH (ARF). Role of
mRNA polyadenylation control in gene
expression. 2008-2012: $685,000.
Yang HR. Genome-wide screening for
gene products that regulate the cellular
dynamics of lipid droplets. 2009-2011:
$170,000.
Australian Research Council – 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. 20082011: $1,129,607.
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. 20072010: $525,000.
Curmi PMG, Marquis C, Breit SN.
Structural and pharmaceutical studies
on a novel human protein, MIC-1. 20082011: $514,074.
Henderson RK, Stuetz RM, Bulmus V,
Peirson WL, Newcombe G, Jefferson
B. Optimising dissolved air flotation for
algae removal by bubble modification
in drinking water and advanced
wastewater systems. 2009-2011:
$621,000.
Higgins VJ, Dawes IW, Rogers PJ. The
role of redox balance and reactive
oxygen species in beer stability using
an integrated transcriptomic and
metabolomic analysis. 2007-2009:
$315,000.
Kjelleberg S, Venter JC, Thomas T
(APDI), Sutton G, Steinberg PD, Rusch
D, Holmstrom CG, Heidelbert KB,
Halpern A, Egan SG. Environmental
Manefield MJ, Schleheck DF, Kjelleberg
S, Guilhaus M. Microbial community
characterisation for bioprocessing of
chlorinated hydrocarbon contaminated
groundwater (APAI). 2006-2009:
$327,000.
McMurtrie RE, Neilan BA, Eldridge DJ.
Is reintroduction of soil foraging animals
critical for the restoration of degraded
semi-arid woodlands? (APAI) 20082010: $196,462.
Neilan BA, Murray SA (APDI),
Hallegraeff GM. Uncovering the
genetic basis for saxitoxin production
in Australian marine and freshwater
systems: Novel molecular tools for
management (APDI). 2007-2010:
$244,608.
Parry DL, Gibbs KS, Neilan BA.
Management of acid mine drainage in
northern Australia using microbial mats.
2007-2010: $387,564.
Australian Research Council – Linkage
Infrastructure and Equipment Facilities
Dawes IW, Schuster SC, Trent RJ,
Henry RJ; Scott RJ, Paulsen IT,
Gibb KS, Thomas T, Kjelleberg SL,
Cavicchioli R, Neilan B, Reichardt JK,
Berquist PL, Stokes HW, Gillings MR,
Giffard PM, Dunkley PR, Foster PS.
Advanced high throughput genomics
facility for biological, medical,
agricultural, environmental and
evolutionary research. 2009: $950,000.
Collaborative Research Centres Environmental Biotechnology
Kjelleberg S. Core funding. 2004-2010:
$1,890,000.
Kjelleberg S, Rice SA, McDougald SD,
Manefield MJ. Biofilm fundamentals.
2007-2009: $234,248.
33
National Collaborative Research
Infrastructure Strategy (NCRIS)
Collins AM, Sewell WA, Rimmer J,
Gaeta BA. Identification of antigen
selection in the human IgE response
by analysis of somatic point mutations.
2007-2009: $246,750.
Dawes IW. Biomolecular Platforms.
2006-2011: $900,000.
Day AS, Mitchell HM, Zhang L, Leach
ST. Exclusive enteral nutrition in
children with Crohn’s disease. 20082010: $349,875.
Gilbert GL, Reeves P, Sintchenko
V, Lan R, Kong F, Huezenroeder M.
Optimisation of Salmonella genotyping
and epidemiological data analysis
for detection and investigation of
outbreaks. 2007-2009: $488,250.
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). 20082011: $1,000,000.
Other National and State Schemes
Australian Biological Resources Study.
Kritharides L, Scott JD, Brown AJ.
Regulation of apolipoprotein E secretion
by human macrophages. 2007-2009:
$496,500.
Ballard JWO, Russell R, Beebe N,
Yeates D. Taxonomy and phylogenetic
relationships of Australian Aedes
(Diptera: Culicidae). 2007-2009:
$100,000.
Kyd J, Cooley M, Pritchard D. Bacterial
QSSM effect on the host’s ability to
respond. 2006-2009: $245,250.
Australian Coal Association Research
Program (ACARP)
Lan R, Sintchenko V, Reeves P, Gilbert
GL. Molecular typing and epidemiology
of Bordetella pertussis in Australia.
2007-2009: $532,000.
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.
Simpson SJ, Le Couteur DG,
Raubenheimer D, Ballard JWO. The
nutritional geometry of ageing in a
rodent model. 2009-2011: $939,050
Sutton P, Ferrero R, Mitchell HM, Wee J.
Protease-activated receptor-1 (PAR-1)
and regulation of Helicobacter pylori
induced mucosal inflammation. 20082010: $458,750.
Yang HR, Brown AJ. Niemann Pick
disease type C and intracellular sterol
trafficking. 2008-2010: $305,500.
Yang HR, Brown AJ. The role of seipin
in lipid metabolism and adipogenesis.
2009-2011: $382,500.
National Health & Medical Research
Council Training Fellowships
Kummerfeld SK, Wilkins MR. The
molecular basis of aging: A highresolution 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.
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. 2008-2010: $400,000.
Cancer Council NSW
NSW Cancer Institute
Baker M, Robinson P, Packer
N, Clarke S, Daly R, Molloy M,
Verrills N, Kavallaris M, Reddel R,
Braithwaite A, Wilkins M. NSW cancer
glycoproteomics infrastructure initiative.
2007-2010: $1,040,000.
Raftery M, Guilhaus M, Khachigian L,
Hogg P, Wilkins M, Marshall G, Cheung
B, Haber M, Daly R, Corish M, Butt A,
Christopherson R. Orbitrap XL mass
spectrometer with electron transfer
dissociation and multidimensional LC.
2009: $1,052,000
Russell PJ, Yang JL, Thomas PS, Lin
RCY, Li Y, Lewis CR, Hawkins NJ, Crow,
PJ, Cozzi PJ. Tissue microarrayer to
enable pathological studies of cancer.
2005-2009: $118,000.
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. 20072011: $3,750,000.
NSW Office for Science and Medical
Research, China-NSW Collaborative
Research Program
Baker M, Hancock W, Molloy M, Clark
S, Wilkins M, He F, Jiang Y, Sun W, Xing
B. Proteomic discovery in the genesis,
spread and treatment of cancer. 20092011: $1,056,000.
Hogg PJ, Weerakoon L, Perrone G,
Lock RB, Dilda P, Dawes IW. New
arsenical-based cancer drugs. 20062010: $1,950,000.
Prostate Cancer Foundation of Australia
Carrick Project Grant
Rural Industries Research &
Development Corporation
Taylor C, Whitaker N, Lutze-Mann L,
Kofod M, Hughes C, Ross P. Using
threshold concepts to generate a new
understanding of teaching and learning
biology. 2008-2009: $391,000.
Conway PL. Investigate the value
added potential of the prebiotic
components of Australian honeys.
2007-2009: $52,168.
Department of Environment and Water
Resources - Australian Antarctic
Science Grants
Breadmore M, Powell S, Manefield
MJ. A new method for characterisation
of Antarctic microbial communities.
2008-2010: $73,000.
Grains Research & Development
Corporation
Neilan BA, Cuddy WS. Bioamelioration
of salinised soil for wheat cultivation.
2007-2009: $90,000.
Intersect Australia Ltd
Henry R, Wilkins M, Dawes I, Shannon
F. Genomic data analysis. 2009:
$180,000.
Brown AJ. Cholesterol, Statins and
prostate cancer. 2008-2009: $290,000.
Working Kelpie Council
Wilton AN. Genetics of ataxia in working
kelpies. 2007-2009: $17,000.
National Industry Schemes
DSM Food Specialties Australia Pty
Limited
Dunn NW, Foong F. Fundamental
research as well as practical studies
on dairy cultures and bacteriophage
that infect these cultures. 2005-2009:
$25,000.
Ecowise Environmental
White P. Detection of enteric viruses
in water and environmental samples.
2006-2009: $63,000.
RESEARCH FUNDING
National Health & Medical Research
Council Project Grants
34 // BABS ANNUAL REPORT 2009
International Schemes
Ara Parseghian Medical Research
Foundation (USA)
Yang H. Sterol-dependent interactions
between Ncr1p and Osh proteins in
the budding yeast. 2008-2010: USD
$265,000.
NASA Astrobiology Institute
Anbar A, Farmer J, Elser J, Knauth,
P, Christensen P, Oliver C, Walter M,
Greely R, Davies P, et al. Follow the
elements. 2008-2012: $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.
US Department of Airforce - Air Force
Office of Scientific Research Research
Cavicchioli R, Raftery M, Curmi PMG.
Uncovering mechanisms for repair and
protection in cold environments through
studies of cold-adapted Archaea. 20072009: $772,000.
BASF – Aktiengesellschaft
Rosche B. Biofilm Factories. 20052010: $720,000
Eli and Edythe L. Broad Foundation
USA
Zhang L, Mitchell H, Riordan S, Borody
T. Investigation of the possible role of
non-jejuni Campylobacter species in
inflammatory bowel disease in adult
population. 2009-2010. $153,939.
UNSW Internal Schemes:
UNSW Goldstar Awards
Cavicchioli R. Monitoring Environmental
Health and the Impacts of Climate
Change the Australian Southern-Ocean
Genome-Based Microbial Observatory
(ASOMO). 2009: $40,000.
Foster LJR. Application of novel
sutureless technology for eye surgery:
‘Patch and Pin’. 2009: $40,000.
Lan R. Genomic and metabolomic
analyses of virulence of Shigella
and enteroinvasive E coli: Potential
pathways for intervention. 2009:
$40,000.
Manefield MJ. The role of redox shuttles
in microbial consortia. 2009: $40,000.
White PA. Viral polymerases and
genetic variation in RNA viruses. 2009:
$40,000.
UNSW Strategic Priorities Fund
Cavicchioli R, Neilan BA, Kjelleberg S.
Environmental Microbiology Initiative.
2007-2009: $1,944,000.
Lloyd A, Dore G, Kaldor J, White P,
Rawlinson W, et al. The UNSW Hepatitis
C vaccine initiative. 2007-2009:
$2,790,000.
Lutze-Mann L, Crosky A, Hoffman M,
Allen B. Dissemination of best-practice
online learning technology within
the Faculty of Science. 2007-2009
$335,000.
UNSW Vice-Chancellor’s Postdoctoral
Fellowships
Lauro, F. 2009-2011
Lin, R. 2009-2011
Murray S. 2008-2010
Scott, G. 2009-2011
35
Advanced Environmental
Biotechnology Centre
Atma Jaya University, Indonesia
Laboratoire d’Océanologie
Biologique de Banyuls Université
Paris
Southern Cross University
Stanford University
Australian Coal Association
Research Program
La Trobe University
Sydney Institute of Marine
Science
Lowy Cancer Research Centre
Tasmanian Department of Health
Australian Drosophila Biomedical
Research Support Facility
Macquarie University
University of British Columbia
Marine Biotechnology Institute,
Kamaishi
University of California, Davis
Australian Institute of Marine
Science
Australian National University
Australian Nuclear Science &
Technology Organisation
Bar Ilan University
BASF The Chemical Company
Centenary Institute
University of California, Irvine
McGowan Institute for
Regenerative Medicine,
University of Pittsburgh
University of California (UCLA),
San Diego
Murdoch University
University of Cincinnati
Nanyang Environment and Water
Research Institute
University of Cologne
Nanyang Technological
University, Singapore
University of Copenhagen,
Denmark
University of Heidelberg
Centre for Vascular Research
Centre of Marine Biotechnology
Charles Sturt University
National Centre in HIV
Epidemiology & Clinical
Research
University of Konstanz
University of Manchester
University of Melbourne
Concord Hospital
University of Papua New Guinea
CSIRO Entomology
National Environmental Research
Institute of Denmark
Norwegian Veterinary College
University of Salzburg
Desert Research Institute
NSW Department of Primary
Industries (Fisheries)
University of Southern California
Diagnostic Technology Pty Ltd
NSW Food Authority
University of Technology Sydney
NSW National Parks and Wildlife
Service
University of Utah
Optigen
University of Wollongong
Helmholtz Centre for Infection
Research
Orica Limited
Victor Chang Institute
Penn State University
Westmead Hospital
International Society for Microbial
Ecology
Prince of Wales Hospital
J Craig Venter Institute
James Cook University
Royal Institute of Technology,
Stockholm
Japanese Border Collie Health
Network
SA Department of Primary
Industries
Karolisnka Institute: Department
of Microbiology
Scripps Institute of
Oceanography
University of Tasmania
DOE Joint Genome Institute
Hanze University of Applied
Sciences
University of Western Australia.
Queensland University
photo: Brendan Burns
Environmental Biotechnology
Cooperative Research Centre
RESEARCH FUNDING // EXTERNAL PARTNERS
EXTERNAL PARTNERS
36 // BABS ANNUAL REPORT 2009
MEMBERSHIPS IN SOCIETIES AND
ASSOCIATIONS
Alexander von Humboldt
Foundation
American Academy of
Microbiology
American Society for
Microbiology
American Society of Human
Genetics
Association of Vibrio Biologists
AusBiotech
Australasian Microarray &
Associated Technologies
Association
Australasian Proteomics Society
Australasian Society for
Immunology
Australasian Society for
Phycology and Aquatic Botany
Australian Academy of Science
Australian Atherosclerosis
Society
Buttressing Coalition of the
Papua New Guinea Institute of
Medical Research
Chronic Lymphocytic Leukemia
Australian Research Consortium
Council of the Human Proteome
Organisation
Forum for European-Australian
Science and Technology
Cooperation
Fulbright Alumni Association
Genetics Society of Australasia
Institute of Biology
International Society for
Microbiology
International Society for the
Study of Harmful Algae
International Society of Animal
Genetics
NASA Astrobiology Institute
Royal Society of Victoria
Australian Centre for Hepatitis
Virology
Society for General
Microbiology (UK)
Australian Institute of Policy &
Science
Tissue Engineering &
Regenerative Medicine
International Society
Australian Society for
Biochemistry & Molecular
Biology
Australian Society for Medical
Research
Australian Society for
Microbiology
BioEnvironmental Polymer
Society
Bioinformatics Australia
37
THE RAMACIOTTI CENTRE FOR
GENE FUNCTION ANALYSIS
The Ramaciotti Centre was initiated in 1999 with
the Millennium Award from the Clive and Vera
Ramaciotti Foundation and a Research Equipment
Infrastructure and Facilities Grant from the
Australian Research Council. The Centre is a not-for
profit facility, which provides service and expertise
in the use of microarrays, sequencing and other
high-throughput genomic technologies. It supports
genomics research throughout UNSW and its
associated research institutes by offering a range of
services and access to equipment.
The Ramaciotti Centre has a strong record in provision
of services in transcriptomics and functional genomics
with customers Australia-wide and overseas. Some of
the services offered include:
Microarray - Affymetrix and Agilent services
DNA sequencing and genotyping – Sanger
sequencing (Applied Biosystems)
Next-Generation sequencing – Roche 454 and
Illumina GAIIx services
Compound screening using yeast genome-wide
deletion strains
A major thrust in modern biology is the sequencing
of genomes of organisms and gene identification.
DNA sequencing has revolutionised the field of
genome research in the last decade. Starting with
the first genome sequence of a free-living organism
(the bacterium Haemophilus influenza in 1995)
and gaining worldwide attention in 2001 with the
publication of the human genome, the scientific
community now possesses access to thousands of
model genomes. Approximately 1,000 genomes have
been published, and close to 1800 bacterial/archaeal
and 940 eukaryotic genome projects are underway.
This exponential accumulation of genome sequences
has been made possible through the cost reduction
that a sequencing facility such as the Ramaciotti
Centre can provide, as well as through continuous
technological and operational improvements.
The availability of multiple genome sequences
from related organisms has truly enabled the
field of comparative genomics to relate genomic
differences (genotypes) with biological properties
(phenotypes) in a suite of model organisms, ranging
from microbes to plants and
mammals. However, what
has also become apparent
is that genomic variation
between individuals of a
species or within a population
is more pronounced than
previously anticipated, and
that comparative genomics
of individuals is required to
fully unravel the links between
genes and phenotypes. Hence,
we expect an increased need
for genome sequences for
the future, with the field of
genomics now on the verge of
a second revolution: the era
of “individual” or “personal”
genomics as evidenced by the
thousand genomes project.
UNSW students have contributed
to the exciting field of genomics
research by using the nextgeneration sequencers in the
Ramaciotti Centre to produce a
draft sequence of the Wollemi
pine (Wollemia nobilis). The
Wollemi pine (Wollemia nobilis)
was known to science from
fossil records, but was thought
to be extinct until 1994 when
David Noble discovered it in
a remote rainforest canyon in
Wollemi National Park, 150 kilometres north-west of
Sydney. These trees show an extremely low level of
genetic diversity and are threatened by introduced
fungal diseases and climate change. The students’
preliminary findings show that the Wollemi chloroplast
DNA is unique, but does share some features with
other pines such as the Kauri and Norfolk Island Pine.
Further analysis of the data will provide clues to the
evolution of the Wollemi and other pines. Exposure
to this technology is rare in degree-level science
programs, and was made possible by the outstanding
sequencing facilities at UNSW and an ongoing
collaboration between researchers at UNSW and the
Royal Botanic Gardens Sydney.
For further information on the Ramaciotti Centre
and the services offered, please visit:
www.ramaciotti.unsw.edu.au
MEMBERSHIPS IN SOCIETIES AND ASSOCIATIONS // RESEARCH CENTRES
RESEARCH CENTRES
38 // BABS ANNUAL REPORT 2009
CENTRE FOR MARINE
BIO-INNOVATION
The Centre for Marine
Bio-Innovation (CMB)
is an international focal
point for interdisciplinary
basic and applied
research into chemically
mediated interactions
Red algae that produces novel
between organisms. The
antifouling compounds
Centre’s primary aims are
to understand how the ecology and physiology of
organisms are mediated by chemical signals and
to apply this knowledge to the development of new
biotechnologies across environmental, industrial
and medical settings.
The linkage project will focus on finding
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.
The second discovery project will be run
The first of the discovery projects will
investigate the impact of marine pathogens
on kelps and other seaweeds when they are
stressed by temperature, elevated nutrients or
other anthropogenic stressors. Through this
project the CMB will participate in Australia’s
newly established Eastern Seaboard Climate
Change Initiative to drive further research into
the impact of climate change on disease in
seaweeds.
in collaboration with the Australian Institute
of Marine Science, and will test ecological
defence theories in bacterial systems to
determine whether the ecology of bacteria
operates by the same general rules as those of
plants and animals.
The third discovery project, administered by
the University of Technology, Sydney, will use a
novel approach to identify the mechanisms that
bacterial cells use to control their growth and
avoid attack by our immune system, hopefully
resulting in the identification of potential
targets for the development of new, effective
antibiotics.
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 that go on to work in academia and
industry both in Australia and overseas.
http://www.cmb.unsw.edu.au/
photo: Angela Moles
In 2009 the CMB moved forward in a number of
collaborative projects designed to enhance its
international profile as a leading-edge research
centre in the area of microbial biofilms and signalling.
The establishment of the Advanced Environmental
Biotechnology Centre at the Nanyang Technological
University (NTU) in Singapore is one example,
which will allow the CMB’s life-sciences expertise
and NTU’s engineering platforms to be combined
to deliver sustainable solutions to the Asia-Pacific
region. Another example is the partnership between
the CMB and the Sydney Institute of Marine Science
(SIMS). SIMS is a collaborative venture between four
Sydney universities, including The University of New
South Wales (UNSW), and a number of state and
federal government departments. From the CMB’s
perspective, the facilities at SIMS will enable us to
increasingly use molecular biological tools in ever
more realistic contexts in the marine environment.
novel ways to accelerate the conversion of
inaccessible coal to methane, providing energy
from a cleaner, greener fuel than coal.
In 2009, the CMB achieved great ARC funding
success, with the award of three ARC Discovery
Project grants together with the single largest
ARC Linkage Project awarded at UNSW, all
commencing in 2010.
Biofilm of fluorescent bacteria
39
RESEARCH CENTRES
AUSTRALIAN CENTRE FOR
ASTROBIOLOGY
The Australian Centre for Astrobiology is the
only major centre of astrobiological research in
Australia. Its key objectives are to make a unique
and highly significant contribution to understanding
the origin of life on Earth and to the search for life
on Mars and beyond.
Established in July 2001 at Macquarie University,
the Centre moved to UNSW in January 2008.
In 2002 it gained the formal status of Associate
Member of the NASA Astrobiology Institute, one
of only two such international members. The
Centre has close links with the European Space
Agency and other international space agencies
and institutions. Key goals include contributing to
the understanding of the origin of life on Earth and
playing a significant role in Mars missions.
“Living” stromatolites from Shark Bay, Western Australia
In 2009 Director Professor Malcolm Walter was
awarded an ARC Professorial Fellowship as part
of an ARC Discovery grant with Professor Brett
Neilan, Dr Simon George of Macquarie University
and colleagues at UCLA and MIT. The team
will study the timing of the origin of oxygenic
photosynthesis in cyanobacteria, a signal event
that led to the oxygenation of the atmosphere and
hydrosphere.
The Centre has a strong media, education
and outreach program related to its research.
Looking forward to 2010, the ACA’s Science
Communication Specialist Dr Carol Oliver will
oversee a large hands-on project for high school
students in Years 10-12 that has been awarded
almost $1M from the Australian Space Research
Program. Other partners in the program are the
Powerhouse Museum, the Australian Centre for
Field Robotics at the University of Sydney, and
Cisco Systems Australia.
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. One ACA student, Elizabeth
Blaber, recently won the Victorian Space Science
Education Centre-NASA Australian Space Prize
and will spend 10 weeks at NASA on a research
project. Three of the Centre’s PhD graduates now
work for NASA, one on the Mars Reconnaissance
Orbiter team.
Three billion year old fossilised stromatolites found in
the Pilbara region of Western Australia
Current research includes the geological
evidence for early life on Earth, the microbiology
of analogous modern systems (particularly those
including archaea and bacterial extremophiles),
biomarker geochemistry of modern and ancient
environments, infrared sensing of Venus and Mars
using ground-based telescopes, the search for
extrasolar planets, the chemistry of the interstellar
medium and science communication and
education within the framework of astrobiology.
Research in the Centre is funded by ARC
discovery grants, ARC Linkage grants, Space
Science Research Program grants, and contracts
from NASA.
Website: http://aca.unsw.edu.au/
40 // BABS ANNUAL REPORT 2009
EVOLUTION & ECOLOGY
RESEARCH CENTRE
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. The Evolution & Ecology
Research Centre (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 number of top-quality High Degree Research
students within the Centre continued to grow
via ongoing improvements to the Graduate
Program in Evolution & Ecology and aggressive
recruitment strategies, including promotion of
the Master of Philosophy as an alternative to the
traditional Honours year.
www.eerc.unsw.edu.au
Photo credit: Chris Hellyer
Photo credit: David Eldridge
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
external funding to Centre members, including
development of explicit strategies to diversify
funding, and to succeed in new schemes such as
Future Fellowships. It maintains a vibrant seminar
and visitor program.
Big Male Seahorse
Grazing
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.
In 2009 the E&ERC further built and supported
excellence in research in evolution and ecology.
The Centre continued to support the increase in
41
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
BD FACSAria three laser flow cytometer for cell sorting
mammalian cell culture to 10L
protein and antibody purification
protein characterisation and analysis including
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
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 FACSAria 1 flow cytometer
Olympus BX51 fixed stage fluorescence
microscope equipped with an Eppendorf
microdissector
MICROBIOLOGY CULTURE
COLLECTION
Dr Jani O’Rourke manages the UNSW culture
collection. It was established in 1969 and provides
cultures for education and industry, including a
catalogue of algae, bacteria, fungi and yeast. The
collection contains approximately 1,000 cultures,
mainly bacteria. It is a member of the World
Federation of Culture Collections
(http://wdcm.nig.ac.jp/hpcc.html).
The collection is registered in the World Data Centre
for Microorganisms, as collection number 248 with the
acronym UNSW (http://wdcm.nig.ac.jp/hpcc.html).
A collaboration with approximately 30 other microbial
collections in Australia is currently underway to
establish the Australian MIcrobial Resources
Information Network as part of the NCRIS-funded Atlas
of Living Australia project (www.ala.org.au).
(www.babs.unsw.edu.au/cultures.php)
FACSSort flow cytometer
www.babs.unsw.edu.au/singlecell_analysis_
facility.php
CANINE GENETICS FACILITY
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
RESEARCH CENTRES // SPECIALISED EQUIPMENT AND FACILITIES
SPECIALISED EQUIPMENT AND
FACILITIES
42 // BABS ANNUAL REPORT 2009
LEARNING AND TEACHING
Science students in BABS receive extensive training in experimental techniques
The quality of the teaching programs in the
School is widely recognised, with many individual
academics being acknowledged in recent
years for their outstanding contributions to
teaching and learning. In 2009, Dr Louise LutzeMann was the recipient of a Faculty of Science
award in recognition of Teaching Excellence
and the development of new resources for
our undergraduate courses. Si Ming Man, a
postgraduate student in the school, was also
recognised by the Faculty for his outstanding
contribution to Sessional Teaching, and for
his promotion of excellence in the teaching of
microbiology.
Other members of the academic staff have worked
closely with the Learning and Teaching staff of
UNSW to promote the adoption and development
of new technology to aid teaching and learning.
Dr. Rebecca LeBard was one of a handful of
UNSW academics to be chosen to test the new
Blackboard Learning Management System in
2009, and her use of Blackboard to enhance
student online collaboration has been brought to
the attention of the wider university community
through UNSW TV. Student evaluations of their
learning experiences are closely monitored. The
School continues to receive excellent feedback
from students, and courses delivered by the
School have some of the highest satisfaction rates
at UNSW.
Degree programs in the School 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.
43
UNDERGRADUATE DEGREES
Our undergraduate programs are designed
to provide students 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. 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.
We offer the following full-time professional
Bachelor programs:
Biotechnology (UNSW code 3052)
Bioinformatics (UNSW code 3674)
Science (UNSW code 3970)
discipline at the convergence of computing and
the life sciences, focused on the development of
technologies for storing, extracting, organising,
analysing, interpreting and utilising biological
information. Bioinformatics has come to
prominence with the analysis of the huge amounts
of data generated by genome projects and postgenomic biology.
For 3970 Science, 3972 Advanced Science
and 3991 Medical Science programs, students
may choose to specialise in the disciplines of
biochemistry, biotechnology, genetics, medical
microbiology and immunology or microbiology and
molecular biology.
LEARNING AND TEACHING
The Honours program provides cutting-edge
training in research techniques, in modern
laboratories. Our flexible, integrated programs in
the biomolecular sciences provide 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 researchoriented careers.
MAJORS
The School teaches within the Science discipline
areas of Biotechnology, Genetics, Biochemistry,
Molecular Biology, Microbiology, Bioinformatics
and Medical Microbiology and Immunology. It
also participates in conjunction with the Faculty of
Medicine in the teaching of medical and science
students in the BMedSci program. Students can
study towards a major and a minor in a particular
specialisation, and study plans are provided
for each discipline area. For example, under
BSc (3970) there are study plans for Majors in
Biochemistry, Biotechnology, Genetics, Molecular
Biology, Microbiology, and Medical Microbiology
and Immunology.
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. Thirdyear 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 the
School of Computer Science and Engineering.
Bioinformatics is a new and rapidly expanding
Medical students are provided with training in microbiology, biochemistry and genetics by
BABS, including experience in laboratory techniques that underpin these disciplines
44 // BABS ANNUAL REPORT 2009
COMBINED DEGREES
GRADUATE DIPLOMA
Science/Arts – UNSW code 3930 (4 years full
This comprises a specialised one-year period
of full-time study and research designed for
graduates from overseas universities and
those wanting to change their career directions
to encompass biotechnology and molecular
biological techniques.
time)
Advanced Science/Arts – UNSW code 3931 (5
years full time)
Bioinformatics/Science – UNSW code 3755 (5
years full time)
Science/Education – UNSW code 4075 (4 years
full time)
Commerce/Science – UNSW code 3529 (4
years full time)
Science/Law – UNSW code 4770 (5 years full
time)
POSTGRADUATE RESEARCH
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
equivalent.
The Master of Philosophy in Biotechnology and
Biomolecular Sciences, MPhil (BABS), includes
advanced treatment of all areas of biotechnology.
This program provides students with a stronger
qualification through emphasis on research training
supplemented with a substantial coursework
component. This program provides access to
modern, sophisticated techniques that apply to a
wide range of biotechnology and molecular biology
fields. The MPhil is a research degree designed for
3 semesters, or 1.5 years, during which 3 subjects
of coursework are undertaken and the rest of the
time is spent doing a research project.
TEACHING INNOVATION IN BABS
While BABS is home to internationally recognised
innovative researchers, it also has many members
of staff who are innovators in teaching and
learning. This is exemplified by projects funded
by the Australian Learning and Teaching Council
that explore novel approaches to student learning.
An important project that was completed in 2009
helped students learn how to structure scientific
communication. John Wilson from BABS was a
key UNSW contributor to this collaborative project
between a number of Sydney universities.
One ongoing project is investigating threshold
concepts that act as barriers to student
understanding. This work is a collaboration
between UNSW, University of Sydney and UWS
and has been used as the basis of workshops
held in all six states of Australia. The project
will influence the way we teach and present
challenging material, and is led by Dr. Noel
Whitaker and Dr. Louise Lutze-Mann in BABS.
In addition to these funded, scholarly projects,
many innovative tools are being developed and
implemented within BABS. For example, a number
of our courses now use Wiki student learning
environments. This innovation was introduced to
Second year BABS students working with a computer-generated simulation (a virtual laboratory) on the function of the electron transport chain
45
Here in the School we have also pioneered
a project to simulate a complex laboratory
experiment by developing virtual experiments
to explore the use of oxygen electrodes. These
experiments illuminate conceptually challenging
material for the students while also teaching
a variety of experimental approaches. The
Virtual Laboratory was set up using an Adaptive
eLearning Platform (AeLP). By monitoring the
student’s interaction in real time, the AeLP’s
adaptive engine is able to: offer students
remediation based on their specific individual
interaction; provide the instructor with information
about individual student’s progress; and identify
areas of common misconception.
A screen shot of the virtual laboratory apparatus developed in BABS
The School of Biotechnology and Biomolecular
Sciences is earning a reputation as one of the
most active UNSW schools in video production.
Although we also use a range of online resources,
including popular and informative YouTube clips,
such resources don’t meet all our audio-visual
needs. Consequently, many short instructional
videos were produced in 2008 and 2009 to
aid the delivery of learning material to large
student groups. For example, First Year Biology
students receive training in microscopy and other
technically demanding laboratory techniques
through short in-house videos. Additional videos
are now being planned for second and third year
courses.
The academic staff of BABS will do whatever is
necessary to engage students in biology. Dr Anne
Galea has used champagne flutes, marbles,
jelly and fruit juice to demonstrate the action of
proteolytic enzymes in digestion. And if you see Dr
Louise Lutze-Mann carrying a beach ball, she is
more likely to be heading to the lecture theatre than
the beach – she uses beach balls to demonstrate
the movement of organelles along microtubule
tracts in the cell.
LEARNING AND TEACHING
the School in 2007, when Associate Professor
Andrew Collins developed the Wikimmune site
to promote student learning in immunology.
This project aimed to correct and extend the
immunological material in Wikipedia. Through the
detection of errors and oversights in the Wikipedia
material, students came to see that their university
studies had truly given them expertise, and that
they could speak with confidence to the general
community on immunological issues. Wikis of this
kind have more recently been adopted in the cell
biology teaching program, with great effectiveness.
46 // BABS ANNUAL REPORT 2009
2009 RESEARCH, VISITING AND
PROFESSIONAL & TECHNICAL STAFF
RESEARCH STAFF
Dr Ika Kristiana
Research Assistant
Dr Bronwyn Robertson
Senior Research Associate
Dr Michelle Allen
Postdoctoral Fellow
Dr Sarah Kummerfeld
NH&MRC CJ Martin Fellow
Dr May Thandar Aung-Htut
Postdoctoral Fellow
Dr Gillian Scott
Vice-Chancellor’s Postdoctoral
Research Fellow
Dr Federico Lauro
Vice-Chancellor’s Postdoctoral
Research Fellow
Dr Bettina Rosche
Senior Research Fellow
Ms Qiong Li
Research Assistant
Dr Sohail Siddiqui
Senior Research Fellow
Ms Simone Li
Research Assistant
Dr Helen Speirs
Senior Research Associate
Dr Ruby C Y Lin
Research Fellow UNSW
Dr Ping Su
Research Fellow
Dr Diane McDougald
Senior Research Fellow
Dr Tim Williams
Postdoctoral Fellow
Dr Mike Manefield
Senior Research Associate
Dr Jonci Wolff
Postdoctoral Fellow
Mr Christopher Bielby
Research Assistant
Dr Mark Brown
ARC QEII Fellow
Dr Joyce Chiu
Postdoctoral Fellow
Dr Rowena Bull
Research Fellow
Dr Matthew DeMaere
Research Associate
Dr X. Robin Du
Postdoctoral Fellow
Dr Weihua Fei
Postdoctoral Fellow
Dr Michelle Gehringer
Postdoctoral Fellow
Dr Cristy Gelling
ARC Postdoctoral Research
Fellow
Dr Troco Mihali
Postdoctoral Fellow
Mr Scott Minns
Research Assistant
Dr Sophie Octavia
Postdoctoral Fellow
Dr Leanne Pearson
Research Associate
Ms Hannah Ginn
Research Assistant
Dr Shauna Murray
Postdoctoral Fellow
Dr Nadeem Kaakoush
Research Associate
Mr Gabriel Perrone
Research Fellow
Dr John Kalaitzis
Research Associate
Dr Oliver Pilak
Postdoctoral Research Fellow
Mr Jason Koval
Research Assistant
Dr Louise Puslednik
Postdoctoral Fellow
VISITING STAFF
Ms Anitha Alagappan
Visiting Fellow
Dr Gregory Arndt
Senior Visiting Fellow
Assoc. Prof. Kevin Barrow
Professorial Visiting Fellow
Ms Vibeke Catts
Visiting Fellow
Dr Margaret Cooley
Visiting Fellow
Prof. Pauline Doran
Professorial Visiting Fellow
A/Prof. Michael Edwards
Senior Visiting Fellow
47
Ms Yamila Gurovich
Visiting Fellow
Prof. Haluk Ertan
Professorial Visiting Fellow
Mr Vincent Higgins
Visiting Fellow
A/Prof. Peter Holden
Visiting Associate Professor
Prof. David James
Professorial Visiting Fellow
Dr Iryna Leshchynska
Visiting Fellow
Dr Andrew Netting
Visiting Fellow
Dr Francesco Pomati
Visiting Fellow
A/Prof. Thomas Preiss
Senior Visiting Fellow
Prof. William Rawlinson
Visiting Fellow
Em. Prof. Peter Rogers
Honorary Visiting Professor
Charles Svenson
Visiting Fellow
Dr Kathy Takayama
Visiting Fellow
A/Prof Alison Todd
Professorial Visiting Fellow
Dr Sheila Van Holst Pellekaan
Senior Visiting Fellow
PROFESSIONAL AND
TECHNICAL STAFF
Mr Adam Abdool
Administrative Officer
Mr Greg Aldis
Technical Officer
Dr Russell Cail
Professional Officer
Mr Bryan Croll
Senior Technical Officer
Ms Christine Dimova
Administrative Officer
Mr Nedhal Elkaid
Senior Technical Officer
Dr Wendy Glenn
Professional Officer
Mr Steve Gouras
Finance Clerk
Ms Penny Hamilton
Administrative Assistant
Mrs Ghada Hanna
Technical Officer
Dr Edwin Huang
Project Officer
Ms Suzanne Jackson
Administrative Assistant
Dr Young-Jae Jeon
Laboratory Manager
Ms Kylie Jones
Administrative Assistant
Dr Daud Khaled
Technical Officer
Mr Geoff Kornfeld
Professional Officer
Dr Elessa Marendy
Technical Officer
Mrs Sharon Murarotto
Technical Officer
Mrs Kim Nguyen
Senior Technical Officer
Mr Wolfgang Nittel
Finance Officer
Mr Malcolm Noble
Professional Officer
Dr Jani O’Rourke
Professional Officer
Ms Michele Potter
School Manager
Ms Shamima Shirin
Technical Officer
Dr Rohan Singh Panwar
Technical Officer
Ms Doris Suen
Technical Officer
Dr Jiewei Wei
Technical Officer
Dr Jeff Welch
Professional Officer
Ms Lily Zhang
Technical Officer
2009 RESEARCH, VISITING AND PROFESSIONAL & TECHNICAL STAFF
Assoc. Prof. Annette Gero
Senior Visiting Fellow
48 // BABS ANNUAL REPORT 2009
2009 STUDENT AWARDS AND PRIZES
University Medal in Medical Microbiology and Immunology
Laura Cook
University Medal in Microbiology
Gee Chong Ling
University Medal in Medical Microbiology and Immunology
Arthur Chee
Jackson Prize for best overall performance in Honours year
Laura Cook
Jackson Prize for the best performance in Microbiology and
Immunology
Gee Chong Ling
Beckman Coulter Prize for the best performance in the Year 4
Biochemistry Honours
Tamar Kapterian
GE Healthcare Prize in Biotechnology for the best performance in
BIOT3061 Biopharmaceuticals
Wooi Fang Lim
Shelston IP Prize for the best performance in BIOT3091 Professional
Issues in Biotechnology
Keith Friedlander
Invitrogen Prize for the best performance in BIOC3281 Recombinant
DNA Techniques and Eukaryotic Biology
Eliza Kate Courtney
School of Biotechnology and Biomolecular Sciences Prize for the best
performance in Level 3 Biochemistry
Eliza Kate Courtney
School of Biotechnology and Biomolecular Sciences Prize for the best
performance in BIOC3111 Molecular Biology of Proteins
Marie Josephine Kidd
School of Biotechnology and Biomolecular Sciences Prize for the best
performance in Examinations in Level 2 Biochemistry courses
Sarah Finlayson
Clinical Microbiology Update Program Prize for the best performance
in MICR3081 Bacteria and Disease
Abhinav Rajkumar
Garry King Prize for the the best Honours thesis in Molecular Biology
or Genetics
Elizabeth Blaber
School of Biotechnology and Biomolecular Sciences Talented Student
Scholarship for Outstanding Achievement in Year 1 ($1,000)
Shady M El-Wahsh
School of Biotechnology and Biomolecular Sciences Talented Student
Scholarship for Outstanding Achievement in Year 2 ($1,000)
Amanda Jane Lawson
School of Biotechnology and Biomolecular Sciences Talented Student
Scholarship for Outstanding Achievement in Year 3 ($1,200)
Samantha Zhiying Chia
49
BIOTECHNOLOGY AND
BIOMOLECULAR STUDENTS
SOCIETY
Building and sustaining community and pride
amongst students is the mission of BABSOC
(Biotechnology and Biomolecular Sciences
Student Society). Any student enrolled in a BABSadministered undergraduate or postgraduate
subject or program is nominally a member of the
BABSOC. Each year, Wallace Bridge and Tim Ellis
mentor the BABSOC management team, made
up of third-year undergrads, through the planning
and organisation of the society’s annual events.
BABSOC achieves their mission by hosting a
series of social (fun) and professional (serious)
networking events throughout the year.
The 2009 calendar was a great success for
BABSOC, despite a short 12-week semester. In
light of the global financial crisis, sponsorship
money was scarce at best. This only strengthened
the resolve of BABSOC, and its President Marc
Barker, which secured $1000 from Crown Scientific
and $750 from ResMed – truly a great effort! In
addition to this, sponsorship was secured through
competing for competitive Arc Student Society
Grants. This met expenses for all the events
throughout the year, where Arc members (a
proportion of BABS students) were involved.
Events in 2009 involved participating in and
hosting the Meet the Entrepreneur Event (Titled
‘The Biotech Way’). This was held in conjunction
with the Australian School of Business and the
Centre for Innovation and Entrepreneurship. This
saw distinguished Biotech professionals discuss
their careers with students. A series of BBQs were
also hosted by BABSOC to enhance interactions
between senior staff and students.
A source of positive feedback from the
participating students involved two Careers Nights
organised by BABSOC. One focused on the recent
graduates sharing their experience and passing
on wisdom, with the second focused on employers
and what they see in potential graduates – a
positive experience for all involved.
Again the highlight event of the year that was most
talked about was the Annual Ball. This year’s Ball,
with a Masquerade theme, was held at Darling
Harbour at The Star Room in the IMAX building.
Guests attended with their best mask and a
fantastic night of food, drink, and dancing was had
by all.
2009 STUDENT AWARDS AND PRIZES // BABSOC
BABSOC
50 // BABS ANNUAL REPORT 2009
2009 PHD COMPLETIONS
LAST NAME
FIRST NAME/S
SUPERVISOR
THESIS TITLE
CAVALIERE
Rosalia
Brett Neilan
The regulation of Saxitoxin production in Cyanobacteria
COWLEY
Mark J
Peter Little
The effects of regulatory variation in multiple mouse tissues
GINN
Hannah P
Brett Neilan
Transcription regulation of hepatotoxins microcystin and
nodularin from cyanobacteria
HOANG
Thi KL
Noel Whitaker
Investigation of some infectious and genetic factors involved in
cervical cancer
IWASENKO
Jenna M
William
Rawlinson
Genetic factors of cytomegalovirus and other herpesviruses that
influence outcomes of antiviral therapy in transplantation
LAM
Yuen T
Ian Dawes
Oxidative stress and effects of glucose metabolism on
mitochondrial morphology in cell ageing of Saccharomyces
cerevisiae
LY
Linda
Valerie Wasiner
Development of selective electrophoresis for proteins and
peptides within proteomes
MAK
Jennifer KY
Peter White
Integrons, resistance genes and their dissemination (in GramNegative Bacteria)
MATALLANA SURGET
Sabine A
Rick Cavicchioli
Physiological and molecular responses of the marine
oligotrophic ultramicrobacterium Sphingopyxis Alaskensis
rb2256 to visible light and ultraviolet radiation
MOHD YATIM
Abdul R
John Foster
Biotransformation of palm olein into sophorolipid biosurfactant
MORGAN
Charlotte A
Peter White
Development of precise microbiological reference materials
NG
Foong LY
David James
Insulin action: unravelling Akt signalling in adipocytes
ROBERTS
Alexandra A
Brett Neilan
Unnatural production of natural products: Heterologous
expression and combinatorial biosynthesis of cyanobacterialderived compounds
SCOTT
Melissa ME
Steve Mahler
Determination of the Mechanisms of Immune System Regulation
of Inflammation by the Human Protein, Chaperonin 10
SHAHIN
Kifah
Pauline Doran
In Vitro Production of Human Hyaline Cartilage Using Tissue
Engineering
SUWANDI
Ronald
Alison Todd
The applications of multi-component nucleic acid enzymes
(MNAzymes)
TAN
Shixiong
Ian Dawes
Cellular mechanisms affecting redox homeostasis in response
to stress in Saccharomyces cerevisiae
TRAINI
Mathew
Ian Dawes
Modelling aspects of neurodegeneration in Saccharomyces
cerevisiae
TU
Elise TV
Peter White
Molecular Epidemiology and Detection of Norovirus
YIP
Ming F
David James
The Role of Myo1c Phosphorylation in GLUT4 Translocation
51
LAST NAME
FIRST NAME
SUPERVISOR/S
HONOURS THESIS TITLE
ABD HAPIZ
Shafini
Mike Manefield
The role of quorum sensing in electron shuttle production and
biofilm formation
APLIN
Meagan L
Andrew Brown
Development of a bioassay to detect androgen production in
androgen refractory prostate cancer cells
ASHLEY
Jasper O
Peter Robers
Xylitol production from candida tropcalis
BLABER
Elizabeth
Brendan Burns
Bioastronautics: The influence of simulated microgravity on human
stem cells
BREULING
Luke T
Wallace Bridge
In vitro determination of bioavailability of ®
-glutamyl cysteine and
glutathione replenishment
BROWN
Tallulah M
Mike Manefield
The effect of electron shuttles on complex microbial communities
BUDIMAN
Vanna
Li Zhang
Isolation and detection of Campylobacter concisus from the saliva
of healthy individuals and children with Crohn’s disease
CHAN
Rodman TH
John Foster
Blends of polyhydroxybutyrate (PHB) and cellulose derivatives as
biomaterials
CHEE
Arthur
Peter White
Hepatitis C virus RNA-dependent RNA polymerase and its role in
viral evolution
CHI
Fei
Louise Lutze-Mann
Antipsychotics and statins: Potential treatments for malignant
gliomas
CHOO
Foong L
Charles MacKay/
Frederick Sierro
The chemokine receptor CXCR7 as a target to prevent cancer
progression
COLLEY
Brendan
Staffan Kjelleberg/
Jason Klebensberger
Signal transduction and gene regulation in response to surfactant
stress in Pseudomonas aeruginosa
COOK
Laura
Anthony Kelleher
Generation and characterisation of a human antigen specific CD4+
regulatory T cell clone
COUPLAND
Kirsten G
Mike Manefield
Electron shuttle activity from natural environments and their
application to bioremediation
DIETRICH
Philipp A
Karen MacKenzie
E2F transcription factors and the upregulation of survivin during
immortalisation of human fibroblasts
DJAFAR
Shaheera
Staffan Kjelleberg/
Diane McDougald
The effect of salinity on biofilm formation, EPS production and
resistance to protozoan grazing in vibrio cholerae
DUNN
Nathan S
Brett Neilan
Combinatorial biosynthesis of microcystin-derived peptides for
heterologous expression in Synechocystis sp. PCC6803
FAN
Sabrina PY
John Foster
The evaluation of antibiotic loading in chitosanbased SurgiLux®
film
GENINSON
Greta
Richard Lock
Regulation of Bcl-2 family expression by glucocorticoids in acute
lymphoblastic leukaemia
HAMILTON
Stuart T
William Rawlinson/
Jonathan Howard
The role of human cytomegalovirus in stillbirth
HO
Sonia
John Foster
Manipulation of process parameters in SurgiLux®
HOLMES
Julie K
Hazel Mitchell
Detection of helicobacter species in patients with Crohn’s disease
HURON
Vanessa AA
Staffan Kjelleberg/
Scott Rice
The role of the Pf4 filamentous prophage of Pseudomonas
aeruginosa in mediating virulence
JAHJA
Krisandra F
Ruiting Lan
Nutritional requirements and metabolomics of shigella
KAPTERIAN
Tamar S
Robert Yang
The role of essential genes in the cellular dynamics of lipid droplets
2009 PHD COMPLETIONS // 2009 HONOURS PROJECTS
2009 HONOURS PROJECTS
52 // BABS ANNUAL REPORT 2009
LAST NAME
FIRST NAME
SUPERVISOR/S
HONOURS THESIS TITLE
KELSO
Emma V
Hazel Mitchell
The immune response to helicobactre pylori in patients with gastric
cancer
KOW
Siew C
Volga Bulmus
In vitro investigation of PEG conjugated dicer-substrate small
interfering RNA
KOWALCZYK
Paulina
Alan Wilton
Genetic diseases in the Australian Cattle Dog
KRISHNA
MOORTHY
Manju L
Vincent Murray
The interaction of cisplatin with telomeric sequence
LAMB
Sarah L
Hazel Mitchell
The role of non-jejuni campylobacters in inflammatory bowel
disease
LEDGER
Scott
Torsten Thomas
Antibiotic resistance and gene transfer in marine bacteria
LEE
Terry HY
Callia Catzel/Chris
Marquis/ K Bryant
Production of LILRA3 in Pichia pastoris
LEE
Yin E
Robert Yang
Oxysterol binding protein-related proteins and cholesterol
trafficking
LIM
Han Fui
Peter White
Development of a multiplex polymerase chain reaction assay for the
detection of human enteric viruses
LING
Gee C
Staffan Kjelleberg
The effects of micro-fabricated surfaces on microbial attachment
LOW
An AC
Stuart Tangye
Revertant somatic mosaicism in X-linked lymphoproliferative
disease
LU
Jamie F
Brett Neilan
Identification and characterisation of genes responsible for the
biosynthesis of secondary metabolites in Lyngbya wollei
LUTZ
Carla M
Staffan Kjelleberg/
Suhelen Egan
The effect of environmental stress on the development of bacterial
biofilm dispersal cells
LUU
Winnie
Andrew Brown
Investigating the involvement of Akt in cholesterol metabolism
M RAJAN
Sandhya N
Maria Craig/ KinChuen Leung
Enterovirus regulation of cytokine/chemokine expression in insulinproducing cells
MA
Chao H
Staffan Kjelleberg/
Torsten Thomas
Nitric oxide-controlled biofilm dispersal from reverse osmosis
membranes
MAJOR
Joelene A
Li Zhang
The role of non-jejuni Campylobacter species in inflammatory bowel
disease
MOONEY
Anne-Marie M
Ruiting Lan
Differentiation and virulence variation in Shigella spp. and
enteroinvasive Escherichia coli
MUSCAT
Rita Ann
Ruiting Lan
Genomic variability and molecular typing of bordetella pertussis
NGO
Siu ME
Bill Ballard/Wallace
Bridge
Dietary J-glutamylcysteine in Drosophila simulans: A potential
precursor for glutathione replenishment
NICHOLSON
Elizabeth M
Bettina Rosche
Traditional Chinese herbs - Inhibition of quorum sensing
NIKOLAYSEN
Stina T
Vanessa Hayes
The androgen receptor gene and prostate cancer risk
NORIZAN
Siti NM
Staffan Kjelleberg
Investigation of the relationship between the global regulatory
systems of quorum sensing and nitric oxide in control of dispersal
of Pseudomonas Aeruginosa biofilm
OLIVER
Michael
Brendan Burns
An investigation of acylated homoserine lactone production in
stromatolites of Shark Bay Western Australia
53
FIRST NAME
SUPERVISOR/S
HONOURS THESIS TITLE
POON
Yan Y
Wallace Bridge
The uptake and conversion of exogenous GGC in Saccharomyces
cerevisiae and its effect on oxidative stress resistance in
comparison with other thiols
PRATT
Eleanor
Andrew Collins/B
Sewell/John Wilson
An investigation of tissue IgE antibody sequences
SHAHBAZI
Jeyran
John Foster
Experimental evaluation of SurgiLux® as a chitosan-based
adhesive for ophthalmic applications
STEVENS
Maxwell
Volga Bulmus
In vitro investigation of targeted magnetic nanoparticles for siRNA
delivery
TAN
Cheng C
Brett Neilan
Expression and characterisation of SxtG, an enzyme involved in
biosynthesis of saxitoxin in cylindrospermopsis raciborskii T3
TAYLOR
Katie A
Wallace Bridge
Exogenous g-glutamylcysteine and its ability to protect against
reactive oxygen species-induced mitochondrial dysfunction and
paracetamol toxicity
THORP
Samuel TM
Antony Cooper
Mitochondrial dysfunction and oxidative stress in alpha-synuclein
models of Parkinson’s disease
TIAN
Chen
Ian Dawes/Joyce
Chiu
The involvement of Swi6p and Yap1p in the paraquat-induced G1
arrest in Saccharomyces cerevisiae
TNG
Jie LT
John Whitelock
Investigating perlecan turnover in human colon carcinoma cells
VAN DORST
Josie M
Belinda Ferrari
Assessment of Viable Bacterial Assemblages in Petroleum
Contaminated Sub Antarctic Soils
VERMA
Arjun
Rick Cavicchioli/
Torsten Thomas
Analysis of microbioal diversity in acid mine drainage sites in New
South Wales using 16S rDNA sequence analysis
WALPOLE
Emily A
Andrew Collins/John
Wilson
IgG3 expression, mutation and selection in Papua New Guinean
individuals
WALSH
Corrina
Melody Caramins
Haplotype analysis of ACTN3 in West African athletes
WILKINS
David
Rick Cavicchioli/
Federico Lauro
Characterisation of the Y-shaped element, a novel intergenic
transposable element in bacteria
WU
Zi Cong
Alan Wilton
Differentiating dingoes from dogs using molecular markers
ZERENTURK
Eser
Andrew Brown
The regulation and membrane topology of Seladin-1
ZHANG
Wenyu
Pablo Silveira
The role of CTLA-4 on B cells in Type 1 diabetes
ZHANG
Yuxi
Robert Yang
Phospholipids in lipid droplet fusion
2009 HONOURS PROJECTS
LAST NAME
54 // BABS ANNUAL REPORT 2009
PUBLICATIONS
Alagappan A, Bergquist P and
Ferrari BC. (2009) ‘Development
of a two-color fluorescence in situ
hybridization technique for specieslevel identification of human-infectious
Cryptosporidium spp’. Applied and
Environmental Microbiology. 75: 59965998.
Allen BJ, So TP, Abbas Rizvi SM,
Song EY, Fernandez HR, Lutze-Mann
L. (2009) ‘Mutagenesis induced by
targeted alpha therapy using 213BicDTPA- 9.2.27 in lacZ transgenic
mice’. Cancer Biology and Therapy. 8:
777-781.
Allen MA, Goh F, Burns BP and Neilan
BA. (2009) ‘Bacterial archaeal and
eukaryotic diversity of smooth and
pustular microbial mat communities in
the hypersaline lagoon of Shark Bay’.
Geobiology. 7: 82-96.
Allen MA, Lauro FM, Williams TJ,
Burg DW, et al. (2009) ‘The genome
sequence of the psychrophilic
archaeon Methanococcoides burtonii:
The role of genome evolution in cold
adaptation’. ISME Journal. 3: 1012
1035.
Ballard JWO, Puslednik L, Wolf JN
Russell RC. (2009) ‘Variation under
nature: A sesquicentennial DNA
barcoding perspective’. Chiang Mai
Journal of Science. 36: 188-199.
Barraud NL, Schleheck DF,
Klebensberger J, Webb JS, et al.
(2009) ‘Nitric oxide signaling in
Pseudomonas aeruginosa biofilms
mediates phosphodiesterase activity
decreased cyclic diguanosine-5’monophosphate levels and enhanced
dispersal’. Journal of Bacteriology. 191:
7333-7342.
Barraud NL, Storey M, Moore ZP, Webb
JS, et al. (2009) ‘Nitric oxide-mediated
dispersal in single- and multi-species
biofilms of clinically and industrially
relevant microorganisms’. Microbial
Biotechnology. 2: 370 378.
Bergquist P, Hardiman E, Ferrari BC
and Winsley T. (2009) ‘Applications
of flow cytometry in environmental
microbiology and biotechnology’.
Extremophiles. 13: 389-401.
Boyer CA, Bulmus V and Davis
TP. (2009) ‘Efficient Usage of
Thiocarbonates for both the production
and the biofunctionalization of
polymers’. Macromolecular Rapid
Communications. 30: 493-497.
Boyer CA, Bulmus V, Davis TP, Ladmiral
V, et al. (2009) ‘Bio-applications of
RAFT polymerization’. Chemical
Reviews. 109: 5402-5436.
Boyer CA, Bulmus V, Priyanto P, Teoh
WY, et al. (2009) ‘The stabilization
and bio-functionalization of iron oxide
nanoparticles using heterotelechelic
polymers’. Journal of Materials
Chemistry. 19: 111-123.
Boyer CA, Granville A, Davis TP and
Bulmus V. (2009) ‘Modification of
RAFT-polymers via thiol-ene reactions:
A general route to functional polymers
and new architectures’. Journal of
Polymer Science Part A-Polymer
Chemistry. 47: 3773-3794.
Boyer CA, Liu J and Bulmus V et al.
(2009) ‘RAFT polymer end-group
modification and chain coupling/
conjugation Via disulfide bonds’.
Australian Journal of Chemistry. 62:
830-847.
Brown AJ. (2009) ‘24(S)25Epoxycholesterol: A messenger for
cholesterol homeostasis’. International
Journal of Biochemistry and Cell
Biology. 41: 744-747.
Brown AJ and Jessup W. (2009)
‘Oxysterols: Sources cellular storage
and metabolism and new insights into
their roles in cholesterol homeostasis’.
Molecular Aspects of Medicine. 30:
111-122.
Brown, AJ, Kristiana, I & Krycer, JR
2009, ‘Cholesterol Homeostasis in two
commonly used human prostate cancer
cell-lines, LNCap and PC-3.’ PLOS
One,.
Burke CM, Kjelleberg S and Thomas T.
(2009) ‘Selective extraction of bacterial
DNA from the surfaces of macroalgae?’.
Applied and Environmental
Microbiology. 75: 252-256.
Burns BP. (2009) Understanding the
Origins of Life on Earth. Journal of
Cosmology. 1:60-62.
Burns BP, Anitori R, et al. (2009)
‘Modern analogues and the early
history of microbial life’. Precambrian
Research. 173: 10-18.
Cairns M, Thomas T, Beltran C and
Tillett D. (2009) ‘Primer fabrication using
polymerase mediated oligonucleotide
synthesis’. BMC Genomics. 10: 344.
Cairns MJ, Carland M, McFadyen WD,
Denny WA, et al. (2009) ‘The DNA
sequence selectivity of maltolatocontaining cisplatin analogues in
purified plasmid DNA and in intact
human cells’. Journal of Inorganic
Biochemistry. 103: 1151-1155.
Cairns MJ, Thomas T, Beltran C and
Tillett D. (2009) ‘Primer fabrication
using polymerase mediated
oligonucleotide synthesis’. BMC
Genomics. 10: 1012-1035.
Cavicchioli R and Lauro FM. (2009)
‘Effects of climate change on polar
microbes’. Microbiology Australia. 30:
72-74.
Chan W, Maharjan RP, Reeves PR,
Sintchenko V, et al. (2009) ‘Rapid and
accurate typing of Bordetella pertussis
targeting genes encoding acellular
vaccine antigens using real time PCR
and High Resolution Melt analysis’.
Journal of Microbiological Methods. 77:
326-329.
Chen AK, Gelling CL, Rogers PL,
Dawes IW, and et al. (2009) ‘Response
of Saccharomyces cerevisiae to
stress-free acidification’. Journal of
Microbiology. 47: 1-8.
Chionh Y, Walduck A, Mitchell HM
and Sutton P. (2009) ‘A comparison
of glycan expression and adhesion of
mouse-adapted strains and clinical
isolates of Helicobacter pylori’. FEMS
Immunology and Medical Microbiology.
57: 25-31.
Chong S, Chandrawati R, Stadler
B, Park J, et al. (2009) ‘Stabilization
of polymer-hydrogel capsules via
ThiolDisulfide exchange’. Small. 5:(22)
2601-2610.
Cowley MJ, Cotsapas C, Williams RB,
Chan EK, et al. (2009) ‘Intra- and interindividual genetic differences in gene
expression’. Mammalian Genome. 20:
281-295.
55
Gaucci VJ, Beckhouse AG, Lyons V,
Eric J Beh,et al. (2009), ‘The Zap1pindependent zinc response is mediated
by the Msn2/Msn4p transcriptional
activator’. FEMS Yeast Research. 9:
1187-1195.
De Leon EJ, Yuan F, Pearson HA,
Marquis C, et al. (2009) ‘Evidence
of heterogeneity in the antibody
response against the platelet antigen
3a: Recognition of an 11-mer peptide
carrying the HPA-3a polymorphic
determinant’. Vox Sanguinis. 96: 252255.
Ginn H, Pearson LA and Neilan BA.
(2009) ‘Hepatotoxin biosynthesis
and regulation in cyanobacteria- The
putative involvement of nitrogen and
iron homeostasis mechanisms’. Chiang
Mai Journal of Science. 36 : 200-223.
Dore, G. J., M. Hellard, P. Haber,
G. Matthews, B. Yeung, P. Marks,
K. Petoumenos, I. van Beek, G.
McCaughan, P. A. White, R. Ffrench W.
Rawlinson, A. Lloyd and J. M. Kaldor.
2009. Hepatitis C virus (HCV) treatment
outcomes in acute and early chronic
HCV infection in a predominantly
injecting drug user cohort: the
Australian Trial in Acute Hepatitis C
(ATAHC) study. Clinical Infectious
Disease. 48:650–658.
Erce MA, Low J, March PE, Wilkins
MR, et al. (2009) ‘Identification and
functional analysis of RNase E of Vibrio
angustum S14 and two-hybrid analysis
of its interaction partners’. Biochimica
et Biophysica ACTA-Proteins and
Proteomics. 1794: 1107-1114.
Fei W, Wang H, Fu X, Christopher B, et
al. (2009) ‘Conditions of endoplasmic
reticulum stress stimulate lipid
droplet formation in Saccharomyces
cerevisiae’. Biochemical Journal. 424:
61-67.
Ferrari BC and Gillings M. (2009)
‘Cultivation of fastidious bacteria by
viability staining and micromanipulation
in a soil substrate membrane
system’. Applied and Environmental
Microbiology. 75: 3352-3354.
Foster LJ and Tighe BJ. (2009)
‘In vitro hydrolytic degradation of
centrifugally-spun polyhydroxybutyratepectin composite fibres’. Polymer
International. 58: 1442-1451.
Goh F, Allen MA, Leuko S, Kawaguchi
T, et al. (2009) ‘Determining the specific
microbial populations and their spatial
distribution within the stromatolite
ecosystem of Shark Bay’. ISME. 3:
383-396.
Gunawan C, Teoh WY, Marquis C, Lifia
J, et al. (2009) ‘Reversible antimicrobial
photoswitching in nanosilver’. Small. 5:
341-344.
Gurvitz A, Suomi F, Rottensteiner H,
Hiltunen J, et al. (2009) ‘Avoiding
unscheduled transcription in shared
promoters: Saccharomyces cerevisiae
Sum1p represses the divergent
gene pair SPS18-SPS19 through a
midsporulation element’. FEMS Yeast
Research. 9: 821-831.
Gutierrez T, Learmonth R and
Couperwhite I. (2009) ‘Analysis
of benzene-induced effects on
Rhodococcus sp. 33 reveals that
constitutive processes play a major role
in conferring tolerance’. The Scientific
World Journal. 9 : 209-223.
Heng B, Glenn WK ,Ye Y, Tran B,
Delprado W, Lutze-Mann L, Lawson
JS and Whitaker NJ. (2009) ‘Human
papilloma virus is associated with
breast cancer’. British Journal of
Cancer. 101: 1345-1350.
Hu Y, Lehrach H, Janitz M. (2009)
‘Apoptosis screening of human
chromosome 21 proteins reveals
novel cell death regulators’. Molecular
Biology Reports. Nov 29. [Epub ahead
of print].
Fukuda Y, Ohmura ST, Sano Y,
Nakabayashi N, Takahashi R, Fujioka
T, Mitchell HM, Shimoyama T. (2009)
Characterization and application of a
new monoclonal antibody with high
specificity for Helicobacter hepaticus.
Helicobacter 14: 66-71.
Hu Y, Lehrach H, Janitz M. (2009)
‘Comparative analysis of an
experimental subcellular protein
localization assay and in silico
prediction methods’. Journal of
Molecular Histology. 40: 343-52.
Galea AM and Brown AJ. (2009)
‘Special relationship between sterols
and oxygen: Were sterols an adaptation
to aerobic life?’. Free Radical Biology
and Medicine. 47: 880-889.
Huang K, Filarsky M, Padula M, Raftery
MJ, et al. (2009) ‘Micropreparative
fractionation of the complexome
by blue native continuous elution
electrophoresis’. Proteomics. 9: 24942502.
Iwasenko J, Scott GM, Rawlinson WD,
Keogh AM, et al. (2009) ‘Successful
valganciclovir treatment of posttransplant cytomegalovirus infection in
the presence of UL97 mutation N597D’.
Journal of Medical Virology. 81: 507510.
Jia Z, Boyer CA, Davis TP and
Bulmus V. (2009) ‘Functional disulfidestabilized polymer-protein particles’.
Biomacromolecules. 10: 3253-3258.
Jia, Z, Liu, J, Davis, TP, & Bulmus, V
2009, ‘RAFT polymerization and thiolene modification of 2-vinyloxyethyl
methacrylate: Towards functional
branched polymers’, Polymer, 50, pp.
5928 – 5932.
Jin D, Ferrari BC, et al. (2009) ‘Timegated flow cytometry: An ultra-high
selectivity method to recover ultra-rareevent u-targets in high background
samples’. Journal of Biomedical Optics.
14: 024023-1 024023-10.
Johal H, Scott GM, Jones RF, Camaris
C, et al. (2009) ‘Mouse mammary
tumour virus-like virus. (MMTV-LV)
is present within the liver in a wide
range of hepatic disorders and
unrelated to nuclear p53 expression
or hepatocarcinogenesis’. Journal of
Hepatology. 50: 548-554.
Johal H, Scott GM, Riordan SM and
Rawlinson WD. (2009) ‘The need
for hypothesis testing in MMTV-like
virus. (MMTV-LV)studies’. Journal of
Hepatology. 51: 414-415.
Jungblut A, Allen MA, Burns BP and
Neilan BA. (2009) ‘Lipid biomarker
analysis of cyanobacteria-dominated
microbial mats in meltwater ponds on
the McMurdo Ice Shelf Antarctica’.
Organic Geochemistry. 40: 258 269.
Kalaitzis J, Lauro FM and Neilan
BA. (2009) ‘Mining cyanobacterial
genomes for genes encoding complex
biosynthetic pathways’. Natural Product
Reports. 26: 1447-1465.
Kautto L, Grinyer J ,Birch D, Kapur A,
et al. (2009) ‘Rapid purification method
for the 26S proteasome from the
filamentous fungus Trichoderma reesei’.
Protein Expression and Purification. 67:
156-163.
Klebensberger J, Birkenmaier
A, Geffers R, Kjelleberg S, et al.
(2009) ‘SiaA and SiaD are essential
for inducing autoaggregation as
a specific response to detergent
stress in Pseudomonas aeruginosa’.
Environmental Microbiology. 11: 30733086.
PUBLICATIONS
Cristescu R, Cahill V, Sherwin WB,
Handasyde K, et al. (2009) ‘Inbreeding
and testicular abnormalities in a
bottlenecked population of koalas.
(Phascolarctos cinereus)’. Wildlife
Research. 36: 299-308.
56 // BABS ANNUAL REPORT 2009
Krycer JR and Brown AJ. (2009)
‘Putative fat fighter hits the middle man’.
Chemistry and Biology. 16: 798 800.
Krycer JR, Brown AJ, Kristiana I.
(2009) ‘Cholesterol homeostasis in two
commonly used human prostate cancer
cell-lines LNCap and PC-3.’ PLOS One.
4(12): e8496.
Lan R, Reeves PR and Octavia S.
(2009) ‘Population structure origins
and evolution of major Salmonella
enterica clones’. Infection Genetics and
Evolution. 9: 996-1005.
Lauro FM, McDougald D, Thomas T,
Williams TJ, et al. (2009) ‘The genomic
basis of trophic strategy in marine
bacteria’. Proceedings of the National
Academy of Sciences of the United
States of America-Biological Sciences.
106: 15527-15533.
Lawson JS, Glenn WK, Heng B, Ye Y,
Tran B, Lutze-Mann L and Whitaker
NJ. (2009) Koilocytes indicate a role
for human papilloma virus in breast
cancer. British Journal of Cancer. 101:
1351-1356.
Leuko S, Raftery MJ, Burns BP, Walter
MR, et al. (2009) ‘Global proteinlevel responses of Halobacterium
salinarum NRC-1 to prolonged
changes in external sodium chloride
concentrations’. Journal of Proteome
Research. 8: 2218-2225.
Lillioja SA and Wilton AN. (2009)
‘Agreement among type 2 diabetes
linkage studies but a poor correlation
with results from genome-wide
association studies’. Diabetologia. 52:
1061-1074.
Lin FP, Coiera E, Lan R and Sintchenko
V. (2009) ‘In silico prioritisation of
candidate genes for prokaryotic gene
function discovery: an application
of phylogenetic profiles’. BMC
Bioinformatics. 10: p. 86.
Little PF, Williams RB and Wilkins MR.
(2009) ‘Inter-individual variation in
expression: A missing link in biomarker
biology?’. Trends in Biotechnology. 27:
5-10.
Liu J, Liu H, Boyer CA, Bulmus V, et al.
(2009) ‘Approach to peptide decorated
micelles via RAFT polymerization’.
Journal of Polymer Science Part
A-Polymer Chemistry. 47: 899-912.
Luciani F, Sisson SA, Jiang H, Francis
A, et al. (2009) ‘The epidemiological
fitness cost of drug resistance
in Mycobacterium tuberculosis’.
Proceedings of the National Academy
of Sciences of the United States of
America Biological Sciences. 106:
14711-14715.
Maddocks S, Scandurra G, Nourse C,
Bye C, et al. (2009) ‘Gene expression
in HIV-1/Mycobacterium tuberculosis
co-infected macrophages is dominated
by M. tuberculosis’. Tuberculosis. 89:
285-293.
Maharjan RP, Gu C, Reeves PR,
Sintchenko V, et al. (2009) ‘Genomewide analysis of single nucleotide
polymorphisms in Bordetella
pertussis using comparative genomic
sequencing’. Research in Microbiology.
159: 602-608.
Mak JK, Kim M, Pham JN, Tapsall
JW, et al. (2009) ‘Antibiotic resistance
determinants in nosocomial strains
of multidrug-resistant Acinetobacter
baumannii’. Journal of Antimicrobial
Chemotherapy. 63: 47-54.
Manos J, Arthur JF, Rose B, Bell S, et al.
(2009) ‘Gene expression characteristics
of a cystic fibrosis epidemic strain
of Pseudomonas aeruginosa during
biofilm and planktonic growth’. FEMS
Microbiology Letters. 292: 107-114.
Matallana-Surget S Douki T Cavicchioli
R and Joux F. (2009) ‘Remarkable
resistance to UVB of the marine
bacterium Photobacterium angustum
explained by an unexpected role
of photolyase’ Photochemical and
Photobiological Sciences 8: 1313-1320.
Matallana-Surget S, Joux F, Raftery MJ
and Cavicchioli R. (2009) ‘The response
of the marine bacterium Sphingopyxis
alaskensis to solar radiation
assessed by quantitative proteomics’.
Environmental Microbiology. 11: 26602675.
McIver CJ, Rismanto N, Smith C,
Naing Z, et al. (2009) ‘Multiplex PCR
testing detection of higher-thanexpected rates of cervical Mycoplasma
ureaplasma and Trichomonas and
viral agent infections in sexually active
Australian women’. Journal of Clinical
Microbiology. 47: 1358-1363.
Mihali TK, Kellmann R and Neilan
BA. (2009) ‘Characterisation of the
paralytic shellfish toxin biosynthesis
gene clusters in Anabaena circinalis
AWQC131C and Aphanizomenon sp.
NH-5’. BMC Biochemistry. 10: 1-13.
Morris BJ, Lin RC, Wang XL, Dalziel
B, et al. (2009) ‘Central obesity is
associated with glucocorticoid receptor
N363S variant: Big picture sheds light’.
Obesity Research. 11: 1607-1609.
Murray SA, O’Connor W, Alvin A,
Mihali TK, et al. (2009) ‘Differential
accumulation of paralytic shellfish
toxins from Alexandrium minutum in
the pearl oyster Pinctada imbricata’.
Toxicon. 54: 217-223.
Netting AG. (2009) ‘Limitations within
“the limits to tree height” ’. American
Journal of Botany. 96: 542-544.
Octavia S and Lan R. (2009) ‘Multiplelocus variable-number tandem-repeat
analysis of Salmonella enterica serovar
Typhi’. Journal of Clinical Microbiology.
47: 2369-2376.
Oehler D, Robert F, Walter MR, Sugitani
K, et al. (2009) ‘NanoSIMS: Insights to
biogenicity and syngeneity of Archaean
carbonaceous structures’. Precambrian
Research. 173: 70-78.
Orde M, Whitaker NJ and Lawson JS.
(2009) ‘High prevalence of prostate
neoplasia in Australian men’. Pathology.
41:433-435
Penesyan A, Marshall-Jones Z,
Holmstrom CG, Kjelleberg S, et al.
(2009) ‘Antimicrobial activity observed
among cultured marine epiphytic
bacteria reflects their potential
as a source of new drugs’. FEMS
Microbiology Ecology. 69: 113-124.
Pretorius L, Du X-J, Woodcock EA,
Kiriazis H, Lin RCY, Marasco S,
Medcalf RL, Ming Z, Head GA, Tan
JW, Cemerlang N, Sadoshima J, Shioi
T, Izumo S, Lukoshkova E, Dart AM,
Jennings GL, McMullen JR. Reduced
phosphoinositide 3 – kinase (p110a)
activation increases the susceptibility to
atrial fibrillation. The American Journal
of Pathology. 2009 175: 998-1008.
Rechter S, Scott GM, Eickhoff
J, Zielke K, et al. (2009) ‘Cyclindependent kinases phosphorylate the
cytomegalovirus RNA export protein
pUL69 and modulate its nuclear
localization and activity’. The Journal of
Biological Chemistry. 284: 8605-8613.
Rice SA, Tan C, Mikkelsen P, Kung V,
et al. (2009) ‘The biofilm life cycle and
virulence of Pseudomonas aeruginosa
are dependent on a filamentous
prophage’. ISME Journal. 3: 271-282.
Roberts A, Copp JN, Marahiel
M and Neilan BA. (2009) ‘The
Synechocystis sp. PCC6803 Sfp-type
phosphopantetheinyl transferase does
not possess characteristic broad-range
activity’. Chembiochem. 10: 1869-1877.
Rollins LA, Woolnough A, Wilton AN,
Sinclair R, et al. (2009) ‘Invasive
species can`t cover their tracks: Using
microsatellites to assist management of
starling (Sturnus vulgaris) populations
in Western Australia’. Molecular
Ecology. 18: 1560-1573.
Rosche B, Li XZ, Hauer B, Schmid A, et
al. (2009) ‘Microbial biofilms: A concept
for industrial catalysis?’ .Trends in
Biotechnology. 27: 636-643.
57
Schleheck DF, Barraud N,
Klebensberger J, et al. (2009)
‘Pseudomonas aeruginosa PAO1
preferentially grows as aggregates in
liquid batch cultures and disperses
upon starvation’. PLOS One. 4: e5513378.
Stapelberg M, Williams RB, Byrne
S and Halliday GM. (2009) ‘The
alternative complement pathway
seems to be a UVA sensor that leads to
systemic immunosuppression’. Journal
of Investigative Dermatology. 129: 2694
2701.
Schmidt HMA, Andres S, Kaakoush
NO, Engstrand L, Eriksson L, Goh KL,
Fock KM, Hilmi I, Dhamodaran S, David
D, Mitchell HM. (2009) The prevalence
of the duodenal ulcer promoting gene
(dupA) in Helicobacter pylori isolates
varies by ethnic group and is not
universally associated with disease
development: A case-control study. Gut
Pathogens. 2009: 1: 5.
Stevenson J and Brown AJ. (2009)
‘How essential is cholesterol?’.
Biochemical Journal. 420: 217-223.
Schmidt HMA, Goh KL, Fock KM,
Hilmi I, Dhamodaran S, Forman D and
Mitchell HM. (2009) Distinct cagA
EPIYA motifs are associated with ethnic
diversity in Malaysia and Singapore.
Helicobacter 14: 256-263.
Shih SM and Doran PM. (2009) ‘Foreign
protein production using plant cell
and organ cultures: Advantages and
limitations’. Biotechnology Advances.
27: 1036-1042.
Shih SM and Doran PM. (2009) ‘In
vitro propagation of plant virus using
different forms of plant tissue culture
and modes of culture operation’.
Journal of Biotechnology. 143: 198-206.
Siddiqui KS, Parkin DM, Curmi PM,
De Francisci D, et al. (2009) ‘A novel
approach for enhancing the catalytic
efficiency of a protease at low
temperature: Reduction in substrate
inhibition by chemical modification’.
Biotechnology and Bioengineering.
103: 676-686.
Siebenga J, Vennema H, Zheng D,
Vinje J, et al. (2009) ‘Norovirus illness
is a global problem: Emergence and
spread of norovirus gii.4 variants 20012007’. Journal of Infectious Diseases.
200: 802-812.
Skindersoe M, Zeuthen L, Brix S, Fink L,
et al. (2009) ‘Pseudomonas aeruginosa
quorum-sensing signal molecules
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T-cell proliferation’. FEMS Immunology
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60 // BABS ANNUAL REPORT 2009
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