53542-BABS Annual Report 2012_0627.indd

School of Biotechnology and
Biomolecular Sciences
Annual Report 2012
Never Stand Still
Faculty of Science
School of Biotechnology and Biomolecular Sciences
School of Biotechnology and Biomolecular Sciences
Biological Sciences Building
The University of New South Wales
Kensington NSW 2033 Australia
www.babs.unsw.edu.au
Tel: 61 2 9385 2029
Fax: 61 2 9385 1483
Production Editor: Michele Potter
Designer: Eva Wong, UNSW P3 Design Studio, R53542
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.
© 2013 The University of New South Wales
Published June 2013
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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:
ƒ be nationally and internationally
recognised as a source of scholarship
ƒ apply cutting-edge biotechnology to
capitalise on biomolecular discoveries
ƒ train and enthuse students
ƒ further interdisciplinary research
ƒ positively interact with researchers
and students across the university,
the state, the nation and the globe
Contents
FOREWORD FROM HEAD OF SCHOOL
4
2012 SCHOOL MANAGEMENT
5
Executive Committee Members
5
SCHOOL SNAPSHOT
7
Research
7
Learning and Teaching
9
OUR PEOPLE
10
Academic Staff
10
Professional & Technical Staff
10
Research Staff
10
Visiting Staff
11
M0LECULAR MEDICINE GROUP
12
Understanding Haemophilia B Leyden: curious investigators never give up
13
Space – the final frontier: gravitational effects on cell behaviour and its
implications for life on Earth
14
Soluble hydrogenases as biocatalysts for fuel cells
16
SYSTEMS AND CELLULAR BIOLOGY GROUP
17
Cholesterol through the looking-glass
18
Tiny switches that control interactions: the role of protein methylation
in the interactome
20
Identification of a new protein that directs cholesterol traffic
22
Yang Lab: multicultural array
23
ENVIRONMENTAL MICROBIOLOGY
Microbial biotechnologies for environmental health
26
The genetic basis for cyanotoxin biosynthesis and beyond
27
Biological soil crusts – nature’s icing on the soil cake
28
INFECTIOUS DISEASE
2
25
29
Genomics and evolution of human bacterial pathogens
30
The role and function of non-coding RNAs in epigenetic modes
of gene regulation
31
How liquefied zombies help us understand microbial evolution
32
SPECIALISED EQUIPMENT, FACILITIES AND SERVICES
34
Seahorse Extracellular Flux (XF) Analyser
34
C1Si Confocal Microscope
34
Single-Cell Analysis Facility
34
UNSW Recombinant Products Facility
34
Molecular and Image Analysis Facility (MIAF)
35
Other specialised instruments and amenities in BABS
35
EXTERNAL PARTNER ORGANISATIONS
36
MEMBERSHIPS IN SOCIETIES & ASSOCIATIONS
38
PROFILE
40
Faculty of Science Visiting Research Fellow
Professor Moustapha Kassem
RESEARCH CENTRES
40
42
The Ramaciotti Centre for Gene Function Analysis
43
Centre for Marine Bio-Innovation
45
Australian Centre for Astrobiology
46
Evolution & Ecology Research Centre
47
LEARNING AND TEACHING
48
PROFILE
52
Australia’s First EMBL PhD Candidate Simone Li
52
2012 STUDENT AWARDS AND PRIZES
54
BABSOC
56
2012 HONOURS PROJECTS
58
2012 PHD COMPLETIONS
60
RESEARCH FUNDING
62
Grants announced in 2012 commencing in 2013
62
Grants commencing or in operation during 2012
63
2012 PUBLICATIONS
68
3
Foreword from Head of School
It is my pleasure to introduce this Annual
Report, the last during my tenure as Head of
School. Every year when writing this foreword,
I am pleased to look back at what the School
has accomplished. It is a privilege for me
e to
acknowledge the work of all staff in whatt has
been another busy and productive year.
Over the past 5 years, BABS has grown into a
School that constantly strives to deliver. This is
evidenced by an increase in research output,
t,
illustrated by the number of HERDC publications
tions
increasing from 158 in 2008 to 202 in 2012.
Rationalisation of the School’s financial position has
allowed an increase in the CAPEX budget, enabling
purchase of new pieces of equipment and welcome
improvements to the quality of research, teaching
ching
and administration spaces.
Following a number of years of significant
challenges and substantial internal change,
e,
2012 was a year of consolidation. The School’s
hool’s
financial position continued to be strong,
and our recruitment strategy to attract highperforming early career researchers resulted
ed in
the appointment of three first-rate academics.
ics.
Applications for these positions came from
m all
corners of the globe, an endorsement of the
he
growing recognition of BABS internationally.
y.
Associate Professor Kevin Morris joined BABS
ABS
from the Scripps Institute, and Senior Lecturers
urers
Irina Voineagu and Paul Waters were appointed,
ointed,
relocating from the Riken Institute in Japan
n and
the ANU respectively.
Four years on since the 2008 Research, Teaching,
eaching,
Administration (RAT) Review of BABS, it was
as
considered timely to reflect on how the School
hool
had fared in the intervening period. To assess
ess
progress from an external perspective, a followollowup RAT Review was held in October. A report
port was
produced that provided an overview of where
ere
the School currently sat in relation to each of the
2008 recommendations, and this also provided
an opportunity to evaluate the School’s current
rrent
strengths and weaknesses and identify new
w
challenges and opportunities.
During 2012, the School’s academic staff
continued to be acknowledged for their
excellence, with Professor Brett Neilan being
ng
awarded a UNSW Scientia Professorship.
Andrew Brown, Peter White and Rob Yang were
promoted to Professor, and Torsten Thomas
4
and Scott Rice were promoted
oted to Associate
Professor, effective 1 January
Marc
y 2013. Professor M
rc
Wilkins was awarded the 2012
Beckman
2 ASBMB Beckm
n
Coulter Discovery Science Award, and Associate
ate
Professor John Foster was elected
cted a Member
of the American Society for Laser Medicine and
o
Surgery. Associate Professor
Su
or Andrew Brown was
awarded the 2012 Vice-Chancellor’s
awa
hancellor’s Award for
Teaching Excellence (Postgraduate
Teac
ostgraduate Research
Supervision)
Anne
Sup
vision) and Dr An
e Galea was awarded the
2012
Staff Excellence award for
20
2 Science Faculty St
Teaching.
T
aching.
Itt was gratifying to learn dur
during 2012 that The
Genetics
AustralAsia
established an
enetics Society of Austral
sia has establish
Award
Associate
Alan
ard to honour the late A
sociate Professor A
Wilton,
years
W
n, a key member of our
ur School for many yea
2011.
who passed
assed away in 2
1.
Our teaching
Ou
aching facilities again
gain benefited from
investment,
second cutting-edge teaching
in
ment, with a secon
lab coming on line to assi
assist in maintaining the
School’s
teaching
hool’s excellence in teac
ng and learning.
The
revamped and
he School’s website was rev
now
ow features more usability as well as clearly
communicating
education programs and
c
mmunicating our educa
research
res
arch facilities.
After considerable uncertainty over the past 5
years, planning is now well under way for a major
year
upgrade to the UNSW BioSciences precinct, which
up
currently includes the proposed construction of
c
an additional building. This will be built along the
Botany Street boundary of the campus and will
be followed by a major renovation
existing
ion of the existin
Biological Sciences building.
B
would like to extend thanks
I wo
nks to my dedicated
colleagues on the Executive
collea
utive Committee and in
School
the S
hool Office for tthe support I have received
as Head
ead of School, and wish
ish the incoming Head
and the School communi
community the best of success in
an
the
e future.
Professor
rofessor JWO (Bill) Ballard
2012 School Ma
Management
ent
The School is le
led by the Head of Sch
School, assisted by the Deputy Head of
comprise the BABS Executive Committee,
School and six academics who compr
together with various other committees rresponsible for key areas
eas of the
School’s operations.
ations.
Professor Bill Bal
Ballard
Head of School
A/Professor Noel Whitaker
D
Deputy Head of School
Executive Committee Members
Executiv
Mem
A/Professor And
Andrew Brown
A/Professor
essor Ruiting Lan
Dr Louise Lutz
Lutze-Mann
ann
A/Professor Vince
Vincent Murray
urray
P
Professor
fessor Brett Neilan
Professor Marc Wilkins
5
6
School Snapshot
The School of Biotechnology and Biomolecular
Sciences (BABS) was formed in January 2002
following the amalgamation of the School of
Biochemistry and Molecular Genetics, the
School of Microbiology and Immunology, and the
Department of Biotechnology (part of the School
of Applied Biosciences). It is one of the largest
Schools in the Faculty of Science at The University
of New South Wales, and is proud to be one of the
largest and most prestigious schools of scientific
research in Australia.
UNSW is renowned for the quality of its graduates
and its world-class research, demonstrated by:
ƒ scoring the maximum five-star rating for nine
key performance indicators in the 2013 Good
Universities Guide
ƒ being ranked 85th worldwide in the 2012/13
The Times Higher Education world rankings
ƒ being awarded Five Stars+ in the 2012
QS Stars rating system, which measures
performance against international benchmarks
ƒ being a founding member of the G08, a
coalition of Australia’s leading researchintensive universities.
Research
In BABS we aim to achieve a balance of pure
basic, strategic, applied and experimental
development research and have a solid track
record in linking fundamental research to tangible,
commercially orientated outcomes.
The School has strong links with a range of high
profile external research institutions, including
the Garvan Institute, the Victor Chang Cardiac
Research Institute and Prince of Wales Hospital,
with 32 researchers currently having adjunct or
visiting appointments.
During 2012, the School had 36 academic staff
engaging in research spanning fundamental to
applied sciences, including human bacterial
and viral pathogens, tissue engineering, cancer,
bioinformatics, functional genomics, astrobiology,
extremophiles and biofuels.
Research in BABS is aligned into four
Discipline Areas:
„Environmental Microbiology
This discipline addresses the globally
relevant research themes of water, climate,
remediation, biodiversity and drug discovery.
The latest enabling technologies in
bioanalytical chemistry, genomics, imaging,
and informatics are being broadly applied
to address societal and economic issues,
including drinking water quality, biofouling, the
health of Australian ecosystems, biofuels and
other novel biomolecules.
„Infectious Disease
The Infectious Disease group focuses on
bacterial and viral pathogenesis and/or
carcinogenesis, pathogen evolution and
adaptation, molecular epidemiology and the
pathogenomics of emerging and re-emerging
blood-borne, respiratory and intestinal
pathogens. There are extensive research
collaborations within the group as well as
strong international collaborations.
„Molecular Medicine
The Molecular Medicine group has a unique
strength in combining fundamental biological
and biomolecular sciences with a strong
applied biotechnology and medical focus. The
School facilitates collaborative research efforts
across discipline boundaries for fundamental
discoveries, generation of commercial
opportunities and clinical research.
„Systems and Cellular Biology
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.
7
BABS is home to a number of significant research
centres that are leaders in their respective fields.
These centres provide cutting-edge services to
BABS, UNSW and other Australian and international
researchers. The School also has affiliations with a
number of research initiatives.
„Australian Centre for Astrobiology
The ACA was established in 2011. It is one
of the few organisations in the world that is
truly inter- and multidisciplinary, reflective of
astrobiology. The ACA is also affiliated with
BABS and the School of Biological, Earth and
Environmental Sciences (BEES).
„Centre for Marine Bio-Innovation
The CMB was established in 1994. It
is internationally know as a focal point
for interdisciplinary basic and applied
research into chemically mediated
interactions between organisms. The
CMB is affiliated with BABS and BEES.
„Evolution and Ecology Research Centre
The centre was established in 2007 with the
generous support of the University of New
South Wales. It builds on a desire to provide
a cohesive and cooperative environment for
the University’s effort in evolution and ecology
research and research training.
Research productivity in BABS has increased
substantially over the past five years and
the School aims to grow further by strongly
supporting existing academics and attracting
talented new staff. Recruitment is currently
limited by space, but the planned development
of the Biosciences precinct that includes the
construction of a new building will allow the
School a higher rate of growth in future years.
Faculty Research Grants and Early Career
Research grants help researchers through lean
funding periods, and a proportion of Faculty
funding derived from publications and grant
funding flows through to individual academics in
the form of SPF02 funding. The School funds half
the cost of a publication in high ranked journals
and there is a Paper of the Month award for the
paper with the highest impact factor.
The BABS Annual Research Day Out (BARDO)
is held off-site in October each year, with a
different group of researchers presenting an
overview of their work. This event helps to foster
good communication and enhance collegiality in
the School.
A regular BABS seminar series sees a range
of prominent local and international speakers
presenting their research topic to the School
community, including Honours and PhD students.
„New South Wales Systems Biology Initiative
The SBI was established in mid-2008. It is a notfor-profit facility that aims to become Australia’s
foremost centre for systems biology.
„Ramaciotti Centre for Gene Function
Analysis
The Ramaciotti Centre for Gene Function
Analysis was established in August 2000 as a
focus for the development and application of
functional genomics in NSW.
„UNSW Environmental Microbiology Initiative
The EMI was established in 2007 to formalise a
UNSW research area that has for decades been
recognised for its internationally competitive
advantage. The underlying philosophy of this
consortium is to take fundamental discoveries
through to application.
8
The School’s website had further design
changes during 2012 to bring it into line with
new UNSW branding guidelines, aimed at
achieving a clear identity and consistency
across all UNSW websites and providing
School researchers with a web presence in
addition to the UNSW Research Gateway.
Learning and Teaching
Undergraduate
The School offers a comprehensive range of
undergraduate and postgraduate degrees and
caters for a variety of career paths. A culture of
teaching excellence for both undergraduate and
postgraduate students is reflected by exceptional
internal CATEI scores for our academics. The
number of undergraduate students enrolled in
BABS courses (including Honours) increased from
3,031 in 2008 to 3,408 in 2012.
A new PC1 teaching lab with increased student
capacity and preparation area was opened during
2012, and two further new PC1 labs are expected
to be completed in early 2014. All newly renovated
labs are air-conditioned and feature state-of-the-art
AV systems. Provision has been made for students
with disabilities in these labs with the installation
of hearing loops and wheelchair accessible
lab benches. New equipment purchases have
significantly enhanced and updated items in the
teaching and preparation areas, with funding
sourced from School CAPEX and building
renovation funds.
Postgraduate
BABS offers Doctor of Philosophy (PhD), Master
of Science (MSc) research-based degrees, and
the Master of Philosophy in Biotechnology and
Biomolecular Sciences (MPhil BABS), which
provides students with an emphasis on research
training supplemented by a substantial coursework
component.
BABS is one of the main recruiters of PhD students
at UNSW, and among the Schools with the highest
number of postgraduate students in the Faculty of
Science. A large number of our PhD students are
supervised by eminent visiting or adjunct staff.
In 2012, BABS continued its PhD Scholarship
Supplement Scheme for eligible students. Each
package comprises a $7,500 per annum stipend
for new and continuing students, and $5,000 in
travel support over the duration of their PhD.
9
OUR PEOPLE
Academic Staff
Professors
Bill Ballard
Head of School
Rick Cavicchioli
Merlin Crossley
Dean, Faculty of Science
Staffan Kjelleberg FAA
Scientia Professor
Dr Vladimir Sytnyk
BSc Hons, PhD (UNSW)
Dr Torsten Thomas
Technical Officer
Dr Li Zhang
Mr Ned Elkaid
Technical Officer
Lecturers
Dr Anne Galea
Mr John Wilson
Marc Wilkins
Malcolm Walter FAA
ARC Professorial Fellow
Associate Professors
Dr Sven Delaney
Dr Elessa Marendy
BSc Hons, PhD (JCU)
Dr Rebecca LeBard
Technical Officer
Emeritus Professors
Ms Sharon Murarotto
Ian Dawes FAA
Peter Rogers
Professional &
Technical Staff
Mr William Whitfield
Finance Officer
Mark Tanaka
ARC QEII Fellow
Noel Whitaker
Deputy Head of School
Peter White
Rob Yang
ARC Future Fellow
Senior Lecturers
Mr Adam Abdool
Administrative Officer
Ms Kylie Jones
Administrative Officer
Ms Kim Nguyen BSc (UNSW)
Technical Officer
Ms Shamima Shirin
Technical Officer
Ms Lily Zhang BEng (Tianjin)
Technical Officer
Research Staff
Dr Michelle Allen
Research Associate
Mr Wen Aw
Research Associate
Ms Anita Ayer
Research Associate
Dr Robin Du
Research Associate
Dr John-Sebastian Eden
Research Associate
Dr Melissa Erce
Research Associate
Dr Hazel Farrell
Research Associate
Dr David Fung
Research Associate
Dr Alister Funnell
Research Associate
Dr Steven Hamblin
Research Associate
Dr Gene Hart-Smith
ARC APD Research Fellow
Dr Martin Horan
Research Associate
Ms Karina Huinao
Research Assistant
Dr Katherine Jackson
Research Associate
Dr Nadeem Kaakoush
NHMRC Postdoctoral
Research Fellow
Dr John Kalaitzis
Research Associate
Ms Ika Kristiana
Research Assistant
Ms Sabrina Beckman
Research Associate
Dr Federico Lauro
ARC DECRA Research
Fellow
Administrative Assistant
Dr Mark Brown
ARC QEII Fellow
Ms Helene Lebhar
Research Officer
Ms Alana McHattan
Administrative Assistant
Dr Timothy Charlton
Research Associate
Dr Iryna Leshchynska
Research Associate
Mr Geoff Kornfeld
Professional Officer
Infrastructure
Ms Zhiliang Chen
Research Associate
Dr Ruby Lin
Research Associate
Dr Jani O’Rourke
Ms Cassie Mak
Research Associate
Ms Liz Daly
Administrative Assistant
Ms Penny Hamilton
BA (UNE)
Dr Wallace Bridge
Dr Brendan Burns
BSc (USyd), PhD (UNSW)
Dr Susan Corley
Research Assistant
Dr Belinda Ferrari
Professional Officer Lab
Manager
Mr Matthew DeMaere
Research Associate
Dr Shingo Miyauchi
Research Associate
Dr Jeff Welch
Dr Nandan Deshpande
Research Associate
Dr Julia Muenchhoff
Research Associate
Dr Michael Janitz
10
Technical Officer
BA (USyd)
Ruiting Lan
Vincent Murray
BAppSc (UTS)
Ms Michele Potter
School Manager
Kevin Morris
Dr Helder Marcal
Health & Safety Manager
John Foster
Michael Manefield
ARC Future Fellow
MSc (Dhaka), PhD (UNSW)
Technical Officer
BSc Hons (UNSW), PhD (UTS)
Andrew Brown
Andrew Collins
Dr Daud Khaled BSc Hons,
Associate Lecturers
Hazel Mitchell
Brett Neilan
ARC Federation Fellow
Mr Matt Clemson
Dr Louise Lutze-Mann
BSc Hons, PhD (UNSW)
Dr Chris Marquis
Professional Officer
Infrastructure
Dr Shauna Murray
Research Associate
Dr Nico Wanandy
Research Associate
Dr Sophie Octavia
Research Associate
Mr Yan Wang
Research Assistant
Dr Iggy Pang
Research Associate
Dr Tim Williams
Senior Research Associate
Dr Leanne Pearson
Research Associate
Dr Jonci Wolff
ARC APD Research Fellow
Dr Richard Pearson
Senior Research Associate
Dr Nicolas Pichaud
Research Associate
Dr Jodi Richards
Research Associate
Dr Bettina Rosche
Senior Research Associate
Dr Laura Sharpe
Research Associate
Dr Khawar Siddiqui
Research Associate
Ms Doris Suen
Technical Officer
Ms Natalie Twine
Research Assistant
Mr Arjun Verma
Research Assistant
Visiting Staff
Dr Muhammad Ali
Visiting Fellow
Dr Greg Arndt
Senior Visiting Fellow
A/Prof Kevin Barrow
Professorial Visiting Fellow
Dr Volga Bulmus
Visiting Fellow
Dr Vibeke Catts
Visiting Fellow
Dr Antony Cooper
Visiting Fellow
Dr Anuruddhika
Dadigamuwage
Visiting Fellow
Dr Michael Edwards
Honorary Associate
Professor
Prof Haluk Ertan
Professorial Visiting Fellow
Dr Michelle Gehringer
Visiting Fellow
Ms Clare Saddler
Visiting Fellow
Dr Roger Summons
Professorial Visiting Fellow
Dr Alison Todd
Senior Visiting Fellow
Dr Wendy Glenn
Visiting Fellow
Dr Sheila Van Holst
Pellekaan
Visiting Fellow
Prof David James FAA
Professorial Visiting Fellow
Dr Graham Vesey
Senior Visiting Fellow
Dr Young J Jeon
Visiting Fellow
Irina Voineagu
Visiting Fellow
Dr Moustapha Kassem
Professorial Visiting Fellow
Paul Waters
Visiting Fellow
Dr James Lawson
Professorial Visiting Fellow
Dr Jeremy Webb
Adjunct Senior Lecturer
Dr Greg Neely
Visiting Fellow
A/Prof Thomas Preiss
Senior Visiting Fellow
Dr William Rawlinson AM
Professorial Visiting Fellow
Dr Laurent Rivory
Visiting Associate
Professor
11
M0LECULAR
MEDICINE GROUP
Moleccular Medicine Group
Academic Staff
Professor Me
M rliin Cros
Cros
ro sle
s y
Associate Pr
P ofe
fesso
s or Andr
nd
d ew
w Col
Co
o lin
ns
Associate Pr
P ofessor John Fo
Foste
ste
er
Associate Pr
Profe
ofe
fe
esso
sorr Vinc
so
Vinc
nc
cent
en Mu
Murra
rrra
ay
Senior Lectu
t rer Dr Wa
W lllla
lace Bri
Brid
dge
dge
Senior Lectu
urer Dr Mi
M cha
c el Jan
Janitz
itz
Senior Lectu
ctu
tu
ure
rer
e Dr L
Lo
ouis
ise
is
e Lutz
Lutz
utze-M
e-Mann
e-M
a
ann
Senior Lecturer Dr
D Ch
hris Ma
M rqu
rquis
is
Senior Lecturer
e Dr Vl
Vladi
ad mir Sy
Sytny
tny
yk
Lectur
Lec
turer
tur
er Dr
er
Dr Ann
Anne
e Gale
Gale
alea
a
12
Understanding Haemophilia B Leyden: curious investigators never give up
Professor Merlin Crossley, Dean of Science
Blood clotting is driven by an enzymatic cascade
of clotting factors, ultimately leading to the
formation of a fibrin clot at the wound site.
Mutations in genes coding for a number of these
factors result in haemophilia, a potentially lethal
group of diseases characterised by excessive
bleeding. The Crossley lab’s research focuses on
haemophilia B, also known as the ‘royal disease’,
as it was carried by Queen Victoria and passed
to descendants throughout the royal houses of
Europe. Haemophilia B is an x-linked recessive
genetic disease, which arises from mutations in
the clotting factor 9 (F9) gene. Merlin’s group is
particularly interested in a subtype of this disease,
known as haemophilia B Leyden, which is caused
by mutations in a region of the gene that regulates
F9 expression levels.
The Crossley lab’s interest in this haemophilia B
Leyden began over 20 years ago, during Merlin’s
PhD studies at Oxford University, which were
directed at understanding the regulation of the
F9 gene. Having observed that the disease is
associated with three clusters of mutations in
the F9 gene regulatory region, he deduced that
these mutations most likely affected the interaction
of three DNA-binding proteins, and that these
proteins would be key regulators of F9 expression.
He was able to identify and characterise two
of these factors, C/EBP˟ and HNF4, and show
that they do indeed control levels of F9, and
that specific mutations could be correlated with
binding affinity and severity of the disease. His
research also allows affected families to be informed
of the likelihood of the condition improving at puberty,
following the identification of an additional regulatory
element controlled by factors that respond to levels of
testosterone and growth hormone. However, despite
these discoveries, the identity of the third factor
remained elusive at this time.
In the years following this initial characterisation
of the F9 gene, recombinant F9 protein became
available for therapeutic use, and as a result,
research was redirected to other pressing areas,
leaving behind the identity of the third enigmatic
factor. Twenty years later while marking a PhD
thesis, Merlin noticed that the consensus binding
site for a newly characterised DNA-binding
protein – ONC1/2 – corresponded exactly with
the site in the F9 gene where the third unknown
factor was proposed to bind. To investigate further,
he assembled an international research team,
including laboratories from New Zealand, Belgium
and the UK. This team, led at the bench by
Crossley lab scientist Dr Alister Funnell, confirmed
that ONC1/2 is indeed the final factor and that
the various patient mutations correlate ONC1/2
binding affinity, level of F9 expression and severity
of disease.
Left to Right: Cassie
Mak, Beeke Wienert,
Jasmine Yib, Dr Alister
Funnel, Crisbel Artuz,
Prof Merlin Crossley,
Alexander Knights,
Gabriella Martyn,
Stella Lee, Dr Richard
Pearson, Catheryn Lim
and Laura Norton.
This research, now published in the American
Journal of Human Genetics, completes the
understanding of the regulatory module
controlling F9 gene expression and explains
how clusters of human mutations in this module
lead to haemophilia B Leyden. Furthermore,
understanding the regulation of the F9 gene also
has implications in developing novel therapies for
other blood conditions such as thrombosis.
Above all, this intriguing story also highlights the
tenacity of research scientists, who never let go of
a puzzle until it is solved!
13
Space – the final frontier: gravitational effects on cell
behaviour and its implications for life on Earth
Associate Professor John Foster
Bioastronautics is a specialised multidisciplinary
area of research that incorporates aspects of
behavioural, biological and medical sciences to
study the effects of space travel on biological
systems. Exposure to short- and long-term
absence of gravity during space missions has
degenerative effects on human physiology. Despite
the current credit crunch, investment in spacerelated enterprises has increased. The planned
privatisation of space travel and a proposed trip
to Mars has stimulated increased interest in the
influence that gravity exerts on biological systems.
Low gravity simulation is achieved on Earth using a
National Aeronautical Space Administration (NASA)
designed rotating wall vessel (RWV) bioreactor.
Studies at the Space Station and use of the RWV
have shown that low levels of gravity – microgravity
– influences cells differently.
Associate Professor John Foster and his Bio/
Polymer Research Group (BRG) have investigated
the influence microgravity exerts on the behaviour
of cancer cell lines. Astronauts are not only
exposed to gravity-free conditions, but they also
have a high risk of exposure to ionising radiation,
increasing their chances of developing cancer.
Theo Orfanos, a PhD student in the group, has
shown that human herpatic and pancreatic
cancer cells, from the liver and pancreas
respectively, behave differently when cultivated
under microgravity conditions compared to their
conventionally grown counterparts.
Research using these cell lines and analysis
of their intercellular signalling pathways has
allowed the group to see how microgravity
influences tumorigenesis. Two-dimensional
gel electrophoresis combined with liquid
14
chromatography and mass spectrometry clearly
shows differences in the protein expression
profiles of these cell lines, that is, their proteomes.
Theo’s work has found that a group of proteins
whose expression is switched off in microgravity
are known to interact with one another and are
involved in the shared signal transduction pathway
for the growth of nerve axons.
Already known for its work on the innovative
development of new biomaterials and sutureless
technology, the BRG’s interest in bioastronautics
extends to its more earthly implications. Current
tissue engineering techniques are restricted
to conventional 2D models where cells spread
and proliferate over the surface of a biomaterial
scaffold. In contrast, the RWV permits cells to
exhibit 3D growth. Consequently, the RWV has
been used by other researchers to produce cell
niches that exhibit more tissue-like behaviour.
Another member of the BRG, Honours student
Hayley Cullen, is investigating how cell lines
respond to engineered scaffolds when they are
cultivated together under microgravity conditions.
Her research has shown that just as cell response
can be manipulated by biomaterial chemistry
and scaffold morphology, cell behaviour to the
same biomaterial scaffolds in microgravity can be
significantly different.
Meanwhile, back in space … Hayley’s research
results so far also have tremendous implications
for the manned mission to Mars, space stations,
astronauts and space medicine in general. After all,
who wants a suture that causes cancer in space?
For further information, visit our website:
biopolymers.unsw.edu.au
2D Gel electrophoresis used to produce a map of cancer cell proteins. The BRG has
shown that microgravity switches off some proteins responsible for nerve growth.
Theo using the RWV which permits
simulation of microgravity in cell culture
conditions on earth
Hayley using the TALI Cell Imaging Cytometer
to investigate if cell responses to biomaterials
are different in microgravity
15
Soluble hydrogenases as biocatalysts for fuel cells
Senior Lecturer Dr Chris Marquis
The Marquis lab undertakes collaborative research
projects across a range of areas, including protein
biotechnology, nanobiotechnology and bioenergy.
Over the last two years, the group has begun
working on a soluble hydrogenase produced by
Cupravidus necator (formerly known as Ralstonia
eutropha). This bacterium is capable of switching
between heterotrophic growth and autotrophic
growth, utilising molecular hydrogen as its sole
source of energy.
Hydrogenases are found in a wide range of
archaea, prokaryotes and eukaryotes as soluble
and membrane-bound metalloenzymes, and are
generally classified by the structure of the catalytic
site. These enzymes catalyse the reversible
oxidation of hydrogen. From a biotechnological
perspective, hydrogenases have been examined
for their role in the production of biohydrogen;
for co-factor regeneration in coupled enzyme
reactions; for environmental applications; and
for the electrochemical oxidation of molecular
hydrogen.
Due to their ability to readily oxidise hydrogen
or reduce protons into hydrogen, hydrogenases
have huge potential as biocatalysts in many
emerging technologies that are based on the
use of hydrogen as a clean energy vector. In
particular, there is a great deal of interest in utilising
appropriate uptake hydrogenases for hydrogen
oxidation in hydrogen fuel cells, to replace the
expensive and potentially problematic use of
platinum catalysts.
The soluble hydrogenase of C.necator is
particularly resistant to molecular oxygen
and strongly favours hydrogen oxidation.
Furthermore, the organism uniquely synthesises
this hydrogenase under heterotrophic conditions.
16
Chris’s group is working to generate a bioprocess
to over-produce this enzyme in its native host,
and to also more fundamentally understand
the regulation of its biosynthesis through
transcriptomic studies. Longer term, the team is
looking at engineering the enzyme to enhance
activity and stability, but also to facilitate binding
and stabilisation at electrode surfaces. The lab
currently has the capability to produce the enzyme
in batch and fed-batch processes and has
developed an optimised purification process. They
have also demonstrated functional activity of this
purified enzyme in a hydrogen fuel cell.
ƒ This project is a collaboration with Dr Kondo-Francois
Aguey-Zinsou, leader of the MERLIN group based
in the UNSW School of Chemical Engineering
(merlin.unsw.edu.au).
ƒ Jugder BE, Welch J, Aguey-Zinsou KF & Marquis
CP. (2013) ‘Fundamentals and applications of [Ni-Fe]
uptake hydrogenases’, RSC Advances, 3(22): 81428159.
SYSTEMS AND
CELLULAR BIOLOGY
GROUP
Systems and Cellularr
Bio
ology Group
A ad
Ac
adem
e ic
em
ic Sta
taff
ff
Profes
Pro
fesssor
so Bi
B ll Ballar
lard
d
Profes
Pro
fessor
fes
sor Ma
Marc
r Wil
rc
Wi kin
ns
A oc
As
Ass
ociate
e Pr
Profe
o sso
ofe
sorr Andr
ndrew
ew Bro
ew
Bro
own
Associ
ciiate
t Pr
Profe
ofesso
ofe
sso
sorr Rob
Rob
b Yang
Associate Lecturer Dr Sven Del
elane
a y
17
Cholesterol through the
looking-glass
Associate Professor Andrew Brown
Illustration by Dr Anne Galea
Associate Professor Andrew Brown’s group
studies how our cells control cholesterol. This
notorious molecule is sometimes described as
two-faced, in that it is essential for human health,
but lethal in excess.
In 2012, Andrew’s lab made several new
discoveries about how cholesterol achieves
this delicate balancing act. He collaborated
with a group at the University of California who
laboriously synthesised the mirror image of
cholesterol. This so-called enantiomer affects
membranes just as native cholesterol does, but
cannot specifically bind to proteins – because
the orientation is wrong. His group used this
mirror image of cholesterol to demonstrate that
the cell senses cholesterol to achieve balance
both via specific protein binding (the prevailing
paradigm), as well as by altering membrane
properties1.
The lab has continued to uncover new control
points in cholesterol synthesis, this year
focusing on the final step in the pathway,
catalysed by the enzyme DHCR24. Originally
identified as a selective Alzheimer’s disease
indicator (hence called seladin-1 for short), this
enzyme is generally regarded as being less
expressed in the brains of Alzheimer’s disease
patients. Teaming up with brain researchers
from Neuroscience Research Australia and the
Illawarra Health and Medical Research Institute,
18
the group discovered that this is not in fact the
case, thus overturning a common misconception2.
Nonetheless, this enzyme is important, having
been implicated in a number of other diseases
from Hepatitis C infection to certain cancers.
Andrew’s group has gone on to study the
regulation of this enzyme, demonstrating that it
can be inhibited by physiological regulators of
cholesterol metabolism (oxysterols)3 and is under
the control of the master regulator of cholesterol
metabolism (SREBP)4.
When cells grow and proliferate in cancers, SREBP
is needed to make more cholesterol, which in
turn is needed to make more cell membranes.
Following on from their previous work5, the group
has now demonstrated that a key signalling
molecule (Akt) responsible for controlling cell
growth and proliferation rapidly drives activation
of SREBP6. Moreover, they showed that SREBP
can be targeted to kill prostate cancer cells by
employing a minor form of vitamin E (tocotrienols)7.
This work would not have been possible without
funding from the National Health and Medical
Research Council and the National Heart
Foundation of Australia, and of course, Andrew
advises, his dedicated and talented team of staff
and students.
1. Kristiana I, Luu W, Stevenson J, Cartland S, Jessup
W, Belani JD, Rychnovsky SD & Brown AJ. (2012)
‘ Cholesterol through the looking glass: ability of its
enantiomer also to elicit homeostatic responses’,
Journal of Biological Chemistry, 287: 33897-33904.
5. Du X, Kristiana I, Wong J & Brown AJ. (2006)
‘Involvement of Akt in ER-to-Golgi transport of
SCAP/SREBP: a link between a key cell proliferative
pathway and membrane synthesis’, Molecular
Biology of the Cell, 17: 2735-2745.
2. Sharpe LJ, Wong J, Garner B, Halliday GM & Brown
AJ. (2012) ‘Is seladin-1 really a selective Alzheimer’s
disease indicator?’, Journal of Alzheimer’s Disease,
30(1): 35-39.
6. Luu W, Sharpe LJ, Stevenson J & Brown AJ.
(2012) ‘Akt acutely activates the cholesterogenic
transcription factor SREBP-2’, Biochimica et
Biophysica acta, Molecular Cell Research, 1823(2):
458-464.
3. Zerenturk EJ, Kristiana I, Gill S & Brown AJ. (2012)
‘The endogenous regulator 24(S)25-epoxycholesterol
inhibits cholesterol synthesis at DHCR24 (Seladin-1)’,
Biochimica et Biophysica ACTA - Molecular and Cell
Biology of Lipids, 1821(9): 1269-1277.
7. Krycer JR, Phan L & Brown AJ. (2012) ‘A key
regulator of cholesterol homoeostasis SREBP-2 can
be targeted in prostate cancer cells with natural
products’, Biochemical Journal. 446(2): 191-201.
4. Zerenturk EJ, Sharpe LJ & Brown AJ. (2012) ‘Sterols
regulate 3beta-hydroxysterol Delta24-reductase
(DHCR24) via dual sterol regulatory elements:
cooperative induction of key enzymes in lipid
synthesis by sterol regulatory element binding
proteins, Biochimica et Biophysica acta, Molecular
and Cell Biology of Lipids. 1821(10): 1350-1360.
19
Tiny switches that control interactions: the role of
protein methylation in the interactome
Professor Marc Wilkins
Proteins rarely act by themselves – they interact
with others to form little molecular machines. These
machines deliver all the biological functions that
the cell requires. With recent advances in largescale analyses of protein-protein interactions, the
Wilkins group is gaining the first glimpses into the
totality of protein complexes in a cell – at least in
the model organism of Saccharomyces cerevisiae.
The focus of the research has been to understand
if and how the cell controls protein-protein
interactions through the use of tiny molecular
switches, like the addition of methyl groups to
amino acids such as arginine and lysine, and
thus provide a protein modification-level means
of regulating cellular processes. Marc’s lab has
been exploring this question through a number
of avenues, as outlined below. This work, and
previous research done within his group, was
recognised in 2012 by the Beckman Coulter
Discovery Award from the Australian Society for
Biochemistry and Molecular Biology. This award
recognises distinguished contributions to the field
of biochemistry and molecular biology.
How can we detect protein methylation? The
group’s research found that the methylation of
lysines is stable during tandem mass spectrometry
analysis, and showed that specific fingerprint ions
are present that can help detect the presence
of methyl-lysine in precursor ion scans. The
methylation of arginine, by contrast, is unstable
during standard peptide fragmentation techniques.
It requires the use of electron transfer dissociation
fragmentation to be preserved and thus identified
during mass spectrometry.
20
What is the predominance of protein methylation?
By analysing mass spectra from almost all proteins
in the yeast cell, the researchers predicted that
lysine and arginine methylation was widespread;
this was an important advance for the field.
Subsequently, they used antibody-based
experiments with proteome chips (microarrays with
~4,400 pure proteins spotted thereon, from Prof.
Mike Snyder at Stanford – see figure), to further
confirm this, along with further mass spectrometry
validation of many proteins. This showed that
arginine methylation is found extensively on
proteins associated with RNA processing and
transport, and that lysine methylation is found
on numerous proteins associated with protein
production.
What are the enzymes that control methylation?
Having found that methylation is widespread,
the group sought to understand which enzymes
are responsible for the modification of which
proteins, and at which specific amino acid
sites. Through a series of systematic knockouts
of all known methyltransferases, teamed with
antibody-based screens and mass spectrometry,
they have mapped many enzyme-substrate
protein links. They have also identified two new
methyltransferase enzymes – the first which they
named elongation factor methyltransferase 2
(Efm2). The team is still deciding on a name for
the second new member of the family. These
enzyme-susbtrate links, along with existing protein
interaction network data, allowed the lab to create
the first methyproteome network for any cell.
Does methylation control protein-protein
interactions? Marc’s group developed a new twohybrid system to address this question – called
the Conditional Two Hybrid (C2H) system. In
this, the interactions of two proteins of interest
are tested in the presence or absence of an
enzyme that methylates one or both proteins. With
the C2H system, they have now shown that the
methylation of arginine can act as a tiny switch
to control certain protein-protein interactions and
that methylation increases the strength of many
other interactions. This is now being scaled up to
understand how widespread this effect is in the
eukaryotic cell.
This outstanding work in the lab over the last few
years has been done by postdocs Drs Melissa
Erce, Gene Hart-Smith and Ignatius Pang, and PhD
students Tim Couttas, Jason Low, Lelin Zhang and
Samantha Chia, and Honours student Dhanushi
Abeygunawardena along, with bioinformatics from
Apurv Goel and Simone Li.
A yeast proteome chip. Approximately 4,400 yeast
proteins have been purified and spotted in duplicate onto
a microscope slide (from Mike Snyder, Stanford). The
Wilkins lab has probed with anti-methylation antibodies;
white dots are proteins that carry arginine methylation.
21
Identification of a new protein that directs cholesterol traffic
Associate Professor Rob Yang, ARC Future Fellow
Cholesterol is carried around our bloodstream
packaged in particles called lipoproteins.
Cholesterol from the low-density lipoproteins (LDL,
also known as “bad” cholesterol) enters our cells
and deposits at different locations through a poorly
understood maze of transport routes.
Mis-direction of cholesterol will cause cholesterol
to accumulate in the wrong places in a cell,
resulting in disturbed cholesterol metabolism and
eventual cell death. This will in turn contribute to
the development of heart disease, and a number
of neurological disorders including Alzheimer’s
disease and Parkinson’s disease.
Little is known about how LDL-derived cholesterol
is transported inside the cell. The Yang lab has
identified a protein called Hrs as a key director of
cholesterol traffic1. Reducing the amount of Hrs
causes cholesterol to accumulate in endosomes,
a cellular compartment usually containing little
cholesterol.
22
This discovery provides a better understanding
of how cells handle cholesterol. The Yang
group is now trying to identify additional factors
that may co-operate with Hrs to help direct
cholesterol traffic, that may point towards new
therapeutic strategies to guard against heart and
neurodegenerative diseases.
ƒ Du X, Kazim A, Brown AJ & Yang H. (2012), ‘An
essential role of Hrs/Vps27 in endosomal cholesterol
trafficking’, Cell Reports, 1(1): 29-35.
Yang Lab: multicultural array
Four countries are represented across the group of postdoctoral research
associates currently working in Associate Professor Rob Yang’s lab. Originally
from China, India, Switzerland and Poland, these talented scientists say they
were attracted to UNSW for the opportunity to work in a highly regarded research
institution, to the School of BABS for its state-of-the-art infrastructure, and Rob’s lab
in particular to work on how our cells store fat and move cholesterol.
Dr Robin Du
Dr Rajesh Ghai
Originally from China, I completed my
PhD training under the supervision of
BABS Associate Professor Andrew Brown
in 2006, during which time he made two
important findings on cholesterol trafficking
to the endoplasmic reticulum and the role of
cholesterol in membrane expansion.
After completing my undergraduate degree
in Chennai, India, I undertook my PhD in Dr
Brett Collins’s lab at the Institute for Molecular
Bioscience, University of Queensland, where
I gained experience as a structural biologist.
My PhD was focused on visualisation of the
mechanism that dictates the trafficking of
transmembrane proteins from endosomes to cell
surface at an atomic resolution. To achieve this,
I employed structural methods including X-ray
crystallography and nuclear magnetic resonance
spectroscopy, and biophysical and biochemical
methods such as isothermal titration calorimetry.
This work resulted in two high impact first author
papers that were recently published in PNAS.
I joined the Yang Lab in early 2007, and since
then, my research interests have focused
on how mammalian cells sort and transport
cholesterol between different organelles.
My work in the Yang Lab has identified oxysterol
binding protein-related protein 5 (ORP5) as a
novel protein involved in endosomal cholesterol
trafficking. I have also demonstrated that
Vps27/Hrs and Vps4/SKD1, two key proteins
involved in the endosomal complex required for
the transport (ESCRT) pathway, play important
roles in the exit of cholesterol from late
endosomes/ lysosomes.
I joined the Yang lab to investigate the
mechanistics of lipid transport between different
intracellular organelles, which is critical in
numerous clinical conditions. I am trying to answer
this riddle by working at the interface of cell
and structural biology using a multidisciplinary
approach. This strategy will allow me to utilise the
skills gained during my doctoral studies and also
to learn new cell biology methods to study the
non-vesicular trafficking of various lipids, including
phospholipids and cholesterol.
23
Dr Martin Pagac
Dr Pawel Sadowski
I was born and raised in Switzerland. In 2002
I finished my MSc studies in biochemistry
at the University of Berne. I then worked as
a scientific assistant at the Swiss Federal
Institute of Technology in Zurich to gain some
practical experience. I undertook my PhD in
the lab of Professor Andreas Conzelmann
at the University of Fribourg from 2006 to
2009, followed by a postdoctoral research
position at the Cancer Research Center in
Honolulu, Hawai’i.
I joined the Yang lab in 2012. My research
interests focus on applying cutting-edge
proteomics technologies to study interacting
partners and post-translational modifications
of BSCL2/seipin, important in lipid droplet
formation and adipocyte differentiation.
Originally from Poland, I received extensive
training in proteomics first in the UK where
I obtained my PhD from the Centre for
Proteomics at the University of Cambridge,
and then in the US where I had a postdoctoral
research position in the New York University
Mass Spectrometry Core for Neuroscience.
I have now joined the research group of
Professor Rob Yang, who is among the
world’s leading experts in lipid droplet
biology. My current projects aim to better
understand the biological function of the
BSCL2 protein, its role in lipid droplet
formation and adipogenesis. The School
of BABS at UNSW with its international
reputation provides not only an excellent
infrastructure but also possibilities for
fruitful collaborations to advance our
research projects.
24
What attracted me to come to Sydney, and
UNSW in particular, was the access to state-ofthe-art mass spectrometry instruments at the
BMSF facility, and also the fact that this city is
the birth place of the concept of proteomics.
ENVIRONMENTAL
MICROBIOLOGY
Environmental
Microbiolog
gy Group
Academic Staff
Professor Rick Cavicchio
oli
Professor Staffan Kjellebe
erg
g
Professor Brett Neilan
Professor Malcolm Walte
er
Associate Professor Mic
ch el Mane
chael
efield
Senior Lecturer Dr Bren
ndan Burnss
Senior Lecturer Dr Belin
nda Ferrarri
Senior Lecturer Dr Torstten Tho
T ma
as
Associate Lecturer Dr Rebec
becca LeBard
25
Microbial biotechnologies for environmental health
Associate Professor Michael Manefield, ARC Future Fellow
Associate Professor Mike Manefield is an
Australian Research Council Future Fellow, and
heads a team of over 20 students and staff
focused on the development of environmental
biotechnologies for the remediation, wastewater
and energy resource industries. The team is
primarily funded through the ARC and independent
linkages with industry partners, including Orica
Australia Pty Ltd, Dow Chemicals (Australia) Ltd,
Biogas Energy Pty Ltd, Bluescope Steel Pty Ltd
and Micronovo Pty Ltd.
Since 2005, the team has invested heavily
in the development of biological remediation
technologies to support the Australian groundwater
remediation industry. As with every other
industrialised nation, Australia has had its fair
share of chemical spills adversely affecting
environmental and human health, not to mention
property prices and the reputation of some
major Australian companies. During 2012, the
team (staff members Drs Matthew Lee, Joanna
Koenig, Astrid Michaelsen, Olivier Zemb and
Adrian Low) made major breakthroughs in the
development of bacterial cultures for the cleanup of organochlorine-contaminated groundwater,
including discovery of the world’s first culture that
can completely degrade chloroform to harmless
end products.
In 2012 the team launched the biotech spinoff Micronovo Pty Ltd to provide environmental
diagnostics and cultures to environmental
consulting companies such as Golder Associates
Pty Ltd, Parsons Brinckerhoff Pty Ltd and
Aecom Pty Ltd. The team was responsible for
the first bioaugmentation of an organochlorinecontaminated site on the Australian continent,
and was awarded the 2012 UNSW Innovation
Award for its quality of science and progression
to application. This work was featured on national
television and radio, and BABS Honours student
Eliza Wells was awarded the Jackson Prize
for best Honours performance in microbiology
and immunology. Future directions include the
development of an anaerobic bioreactor for
destruction of the infamous hexachlorobenzene
(HCB) stockpile located on the Botany Industrial
Park – the largest of its kind in the world.
26
In 2009, the team had adopted a new research
portfolio in the area of biogas production, which
is set to become a significant statistic in energy
markets with its potential to reduce greenhouse
gas emissions from electricity generation and
transport industries. While initially focused on the
transformation of non-renewable organic feedstock
such as coal, in collaboration with the UNSW
School of Photovoltaic and Renewable Energy
Engineering this research has now broadened to
include biotransformation of renewable feedstock,
including food waste and algal biomass.
In 2012, the team (staff members Drs Sabrina
Beckmann and Maria-Luisa Gutierrez-Zamora)
made major breakthroughs in the rational
manipulation of complex microbial communities to
enhance biogas production, both in the laboratory
and in field demonstrations, and PhD candidate
Ms Hazlin Hazrin-Chong won the 2012 Faculty of
Science Postgraduate Research Competition for
her work on fungal colonisation of complex organic
substrates.
Future directions for the Manefield lab
include patenting and publishing field-scale
demonstrations of these inventions and further
development of approaches to transform
microbial communities into devices applicable to
improvements in environmental health.
The genetic basis for cyanotoxin biosynthesis and beyond
Professor Brett Neilan, ARC Federation Fellow
The cyanobacteria, or “blue-green algae” as they
are commonly termed, are an ancient group of
photosynthetic autotrophic bacteria responsible
for the oxygenation of Earth’s early atmosphere
more than 3 billion years ago. As a phylum,
the cyanobacteria are morphologically and
metabolically diverse, and inhabit a wide variety
of environmental niches, ranging from desert soil
crusts to polar melt-water ponds. However, it is
their persistence in rivers, lakes and reservoirs that
has gained them notoriety. In addition to imparting
a foul taste and odour to the water in which
they bloom, certain strains of cyanobacteria are
capable of producing toxic secondary metabolites,
which are hazardous to the health of humans and
livestock as well as native fauna.
Cyanobacterial toxins (cyanotoxins) are typically
categorised according to the symptoms they
impart, which include hepatotoxic, neurotoxic,
cytotoxic and dermatoxic effects. These
toxicological groups encompass a wide
variety of chemical structures, including nonribosomal peptides, polyketides, alkaloids and
lipopolysaccharides. Among the most deadly
cyanotoxins are the hepatotoxic non-ribosomal
peptide microcystin and the neurotoxic saxitoxin,
the latter of which is included among the World
Health Organisation’s list of the top ten biological
weapons.
Over the past decade, the Neilan lab’s
Cyanobacterial Research Group has endeavoured
to unravel the genetic basis for cyanotoxin
production and to elucidate the environmental
triggers regulating this process. Following
Brett’s initial discovery of the microcystin
biosynthesis gene cluster, the group identified
the genes responsible for nodularin, saxitoxin
and cylindrospermopsin production. These
break-through studies have paved the way
for subsequent molecular regulation studies,
demonstrating that light, nitrogen and iron levels
play a role in hepatotoxin biosynthesis, while
sodium levels and pH influence neurotoxin
biosynthesis. Characterisation of these gene
clusters has also enabled the development of
rapid early detection protocols for toxigenic
cyanobacteria in drinking water supplies, which
have been implemented world-wide.
Due to their biologically active properties, the
cyanotoxins are also being considered as building
blocks for future therapeutic agents. The targeted
modification and heterologous expression of
cyanotoxin analogues is an area of current focus
in the Neilan lab. Functional expression of the
dermatoxic lyngbyatoxin gene cluster in Escherichia
coli has already been achieved, and future tailoring
of the biosynthesis genes involved in this pathway
promise to offer a proof of concept for the utility of
cyanobacteria as novel drug factories.
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27
Biological soil crusts – nature’s icing on
the soil cake
Professor Brett Neilan, ARC
Federation Fellow
Biological soil crusts (BSC) offer a
unique opportunity to investigate
the ecology and community
interactions of microorganisms in
extreme environments. BSC microbial
communities comprise a varying
assemblage of cyanobacteria, lichen,
fungi, heterotrophic bacteria, algae
and bryophytes, which form an
intimate association with the top few
millimetres of soil. It is the presence
and activity of these microorganisms
that lead to the aggregation of soil
particles, resulting in the formation
of a veritable crust that carpets
the soil surface. BSC occur where
above-ground plant cover is
sparse, and thrive in the harsh and
arid conditions of deserts, which
include low and variable rainfall,
high evapotranspiration, high solar
radiation, extreme temperatures and
low nutrient soils. In essence, BSC
act as a living mulch and are a major
contributor to soil organic matter,
locking in soil moisture, reducing
soil erosion, and actively fixing
atmospheric carbon and nitrogen,
predominantly via cyanobacteria.
In order to further investigate the
importance of BSC communities
in arid ecosystems and provide
information for improved land
management practices, the
Cyanobacterial Research Group in
Brett’s lab is currently investigating
the genetic diversity of BSC from
sites around Australia via high
throughput sequencing technologies.
Results from BSC microbial
communities of the Pilbara Region
of Western Australia were shown
to be dominated by two orders of
cyanobacteria, Nostocales and
Oscillatoriales, and were found
to harbour a diverse range of
heterotrophic bacteria. Interestingly,
a high level of diversity of genes
involved with secondary metabolite
production was also observed.
As society’s need for novel drugs
to treat infections and diseases
intensifies, natural products are
a likely source of such novel
compounds. The production of
secondary metabolites such as
antibiotics by microorganisms has
led to increased interest in mining
microbial communities and genomes
for use in novel natural products.
As a result of having to deal with
harsh environmental conditions, for
example high pH and temperatures,
it is likely that microorganisms
inhabiting extreme environments will
provide a rich source of such novel
natural products.
This area has been a primary focus
of Brett’s lab, which has actively
been bioprospecting for novel natural
products in microbial communities
in extreme environments over the
past decade. Recently, the group
has confirmed antimicrobial and
antitumor properties from bacteria
and fungi isolated from native bee
gut microbiota, the surface of sea
sponges and traditional Chinese and
Indonesian medicinal plants.
The group is yet to open the ‘black
box’ of compounds produced by BSC
that may hold the key to a new suite
of antibiotics or cancer therapies.
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Photo by Leanne Pearson, 2012.
28
INFECTIOUS
DISEASE
Infectiou
us Disseasee Group
Ac
cad
adem
dem
emic
ic
c Sta
taff
ff
Proffes
Pro
fes
essor
sorr Ha
sso
Hazel
zel Mi
M tch
tchell
ell
el
Ass
As
Ass
s
ssociate
e Pr
P ofe
o sso
so
or Ruitting
n La
ng
an
Associate Professor Kev
Kev
evviin Morrris
i
Associate Professor Mark
arrk
a
rk Ta
T nak
akka
aka
Associate Profe
of ssor Noe
ofe
oell Wh
Whita
Whita
taker
ker
Associ
cia Prro
ciate
ci
ofe
esso
esso
ssor
ss
or Pete
Peter
ete
te
er Whit
h e
Senior
Sen
ior
or L
Le
ectu
cture
cture
re Dr Li Zh
rer
Zhang
ang
g
29
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. Ruiting’s lab takes a multi-disciplinary
approach to studying pathogenic bacteria, with
their research addressing how pathogens arise
and cause disease, and how to identify and type
such pathogens. The group works 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.
Ruiting’s team uses genomics and bioinformatics
approaches to seek an understanding of
evolution and molecular epidemiology of bacterial
pathogens. Their research on pertussis gained
considerable media coverage during 2012 due to
a recent epidemic of the disease in Australia.
Pertussis, commonly known as whooping cough, is
caused by Bordetella pertussis and has remained
endemic in Australia despite more than half a
century of vaccination. The research carried out in
Ruiting’s lab has used different molecular markers,
including single nucleotide polymorphisms (SNPs),
to type a large collection of clinical pertussis
isolates, some of which were obtained during the
epidemic period (2008-2011).
30
Based on analysis of 194 B. pertussis isolates,
Ruiting’s group identified a new strain carrying
a new genotype that was responsible for the
pertussis epidemic. Isolates with two closely
related SNP profiles (SP13 and SP14) carrying a
new variant of the pertactin gene (prn2), and a new
variant of the pertussis toxin promoter (ptxP3) from
the recently emerged SNP cluster I, predominated.
The prn2-ptxP3 genotype was responsible for
31 per cent of cases in the 10 years before the
epidemic, but for 84 per cent during the epidemic
– almost a three-fold increase. The data suggest
increasing selection among the B. pertussis
population in Australia in favour of strains carrying
prn2 and ptxP3 under the pressure of acellular
vaccine-induced immunity. The combination of
changes to ptxP3, which controls pertussis toxin
production, and to the pertactin gene (prn), which
encodes a major acellular vaccine component, has
led to fitter variants of B. pertussis. Such findings
are significant in monitoring the global distribution
of B. pertussis, particularly in highly immunised
populations, and in the development of new
prevention strategies.
The role and function of non-coding RNAs in epigenetic
modes of gene regulation
Associate Professor Kevin Morris
It’s beginning to look like a strange new RNA world
exists! Observations by the Morris lab and others
have shown that non-coding RNAs (ncRNAs) play an
under-appreciated role in controlling gene expression
in human cells. Studies have found that in human
cells, both long and short ncRNAs can epigenetically
regulate gene expression and transcriptional manner.
These findings suggest that the once held dogma
that RNA functions as an information transfer medium
between DNA and protein may be incomplete.
Evidence suggests that some RNAs may also be
governing particular protein and DNA interactions,
such as epigenetic states, that may not only guide
natural selective states in the cell but also prove to be
exceptionally valuable and therapeutically relevant
molecules to target.
Ongoing projects in the Morris lab include
mechanistic determination of small and long
ncRNA mediated transcriptional gene silencing
(TGS) and epigenetic gene regulation in human
cells; TGS of HIV-1 and several oncogenes
involved in human cell cancers; transcriptional
gene activation (TGA)/de-repression utilizing
ncRNAs or antisense oligonucleotides targeted
to endogenous regulatory long ncRNAs; and
nucleic acid-based genetic therapy targeted
approaches to delivering regulatory ncRNAs to
cells to treat different diseases. Current methods
involve developing receptor targeted aptamers
and mobilisation of competent lentiviral vectors to
parasitise HIV-1.
ƒ Johnsson P, Ackley A, Vidarsdottir L, Lui WO,
Corcoran M, Grandér N & Morris KV. (2013) ‘A
pseudogene long-non-coding-RNA network regulates
PTEN transcription and translation in human cells’ ,
Nature Structural and Molecular Biology, vol. 20, no.
4, pp. 440-446.
Kevin’s lab is interested in determining how
ncRNAs regulate gene expression and dictate
epigenetic states, and to what extent this
mechanism is operative in shaping the content and
architecture of the human genome. Specifically,
the group wishes to apply this knowledge to
transcriptionally control HIV-1, cancer and
diseases such as cystic fibrosis.
ƒ Turner AM & Morris KV. (2010) ‘Controlling
transcription with noncoding RNAs in mammalian
cells’, Biotechniques, 48(6): ix-xvi.
(D)
(A)
EZH2?
Ago1
DNMT3A
(G)
HDAC-1
EZH2?
(E)
(B)
(H)
5’
Ago1
5’
3’
(C)
CpG
(F)
CpG
CpG
CpG
Figure 1 Mechanism of non-coding RNA directed gene regulation.
ƒ (A-C) The endogenous long noncoding RNA pathway of epigenetic
regulation in human cells is shown,
as it is understood by the Morris lab
(circa 2013).
ƒ The ncRNA interacts with
epigenetic remodelling proteins
DNMT3a1 and possibly other
DNMT3a-associated proteins such
as HDAC1 and EZH2.
ƒ Next, the ncRNA/protein complex
is localised to the homology
containing target loci in the
genome, whereby (C) the targeting
results in histone and DNA
methylation at the targeted loci and,
ultimately, chromatin compaction
and transcriptional gene silencing.
ƒ Conversely, (G-H) suppression
of endogenous long ncRNAs by
(G) antisense oligonucleotides or
siRNAs can result in a loss of long
ncRNA function and ultimately (H)
de-repression of the long ncRNAtargeted locus and subsequent
activation of gene expression.
ƒ (D-F) Small antisense ncRNAs can
be generated to mimic the longer
ncRNAs and drive gene silencing.
31
How liquefied zombies help us understand microbial evolution
Associate Professor Mark Tanaka
In the quest to understand and prevent infectious
disease, there is still much to learn about the basic
evolution and ecology of pathogens. As part of its
mission to understand the evolution of pathogens,
the Tanaka lab has investigated a diverse array
of topics in viral and bacterial evolution, including
the emergence of antimicrobial resistance, the
evolution of mutation rates and the manipulation of
host behaviour by viruses.
Manipulation of host behaviour by pathogens is
a fascinating topic that has been better studied
in complex parasites than in viruses. Among
viral causes of host behavioural change, one
particularly interesting example comes from
a family of viruses known as Baculoviridae.
Baculoviruses, which primarily infect caterpillars,
are known for causing “tree-top disease”. This
disease “zombifies” caterpillars by forcing them
to stop eating and move to top of the tree or plant
they were feeding on. This occurs in the hours
before the viruses kill the host and liquefy its
corpse, thereby spreading liquid virus into the path
of other feeding caterpillars and consequently
increasing transmission.
Viruses, however, are typically constrained by their
small genomes, which must contain all the genes
necessary for replication and transmission to
new hosts. Why, then, would baculoviruses invest
resources in causing this change in caterpillar
behaviour?
organisms change their environments in ways that
feed back into the evolution of the organism itself.
While some biologists may be dismayed at viruses
being regarded as organisms, viruses certainly
alter their hosts, and these hosts clearly form their
environment.
The Tanaka lab’s model aimed to demonstrate
the way in which niche construction could lead
to the behavioural manipulation trait of the virus
(zombification of the caterpillar) becoming linked
to the liquefaction trait. This connection arises
because caterpillars that die on other parts of the
plant will not be as effective at spreading the virus:
the virus increases the reproductive benefit of
liquefying the host by changing the host’s physical
location.
The group’s work on this system has implications
for both the basic and applied science of viral
evolution. Baculoviruses are used as biopesticides
to control pest species of caterpillars, which
destroy crops and defoliate entire forest regions.
Baculoviruses have a long and fascinating
evolutionary history, with links to other viral
families and effects on the evolution of caterpillars
worldwide.
Understanding the rise and maintenance of these
viral traits may help improve such biopesticides as
well as provide new insights into the fundamental
properties of microbial evolution.
Mark’s team has modelled this problem
mathematically and concluded that a possible
explanation for tree-top disease lies in ‘niche
construction’, an evolutionary force by which
Illustration by Dr Steven Hamblin
32
33
Specialised Equipment, Facilities and
Services
Seahorse Extracellular Flux (XF)
Analyser
Single-Cell Analysis Facility
The SCAF contains the following equipment:
The Seahorse is a cutting-edge piece of
technology that measures the metabolic activity
of cells in minutes, offering a physiologic cellbased assay for the determination of basal
oxygen consumption, glycolysis, ATP turnover
and respiratory capacity in a single experiment.
The two major energy producing pathways of the
cell, mitochondrial respiration and glycolysis, are
measured simultaneously and the data generated
provides the most physiologically relevant
bioenergetic assay available for the determination
of mitochondrial function.
The system can be used to study respiratory
malfunction in multiple diseases including cancer,
cardiovascular disease, ageing-associated
disorders, mitochondrial diseases, immunological
disorders, neurodegenerative disease, obesity and
diabetes. Assays are non-invasive, allowing for
further downstream applications to be performed.
ƒ Beckman Coulter Quanta MPC flow cytometer
ƒ BD Biosciences three laser FACSAria llu flow
cytometer
ƒ Olympus BX51 fixed stage fluorescence
microscope equipped with an Eppendorf
microdissector
Website: babs.unsw.edu.au/research/single-cellanalysis-facility
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:
ƒ cell line and hybridoma development
C1Si Confocal Microscope
ƒ cell line characterisation
ƒ bioprocess development and evaluation
The C1si is a revolutionary true spectral imaging
confocal laser microscope system with the
amazing capability to acquire 32 channels
of fluorescence spectra over a 320 nm wide
wavelength range in a single pass. The C1si
is useful for a wide range of applications. By
cleanly unmixing overlapping spectra of different
fluorescent labels, the C1si dramatically improves
dynamic observations of live cells and facilitates
the acquisition of detailed data.
ƒ microbial fermentation (e.coli and yeast) to 25
litres
ƒ mammalian cell culture to 10 litres
ƒ protein and antibody purification
ƒ protein characterisation and analysis including
ƒ protein gel electrophoresis, Western blotting,
Biacore SPF
ƒ LC-MS and other proteomic services via the
BMSF
ƒ cell line storage (-80°C and liquid nitrogen)
Website: proteins.unsw.edu.au
34
Molecular and Image Analysis
Facility (MIAF)
Other specialised instruments and
amenities in BABS
The MIAF is a multiuser facility that is able to be
accessed by researchers from BABS, other Faculty
of Science Schools and other Faculties and UNSWassociated institutions. The facility contains Fujifilm
FLA-5000 and a GE Typhoon FLA-9500 (including
a 685 nm red laser) biomolecular imaging systems
for fluorescence, phosphorimaging, digitisation,
and chemiluminescence detection. The scanning
area is as large as 40 x 46 cm at a pixel size as low
as 10 microns. The MIAF also has Fujifilm LAS3000 and GE LAS-500 imaging systems, which
use a CCD camera with very high sensitivity for
detection of chemiluminescent Western blots,
imaging of fluorescent protein and DNA gel stains,
and white light imaging of colourimetric stains and
markers. An ImageScanner III for densitometric
applications completes the unit, and offers high
resolution with a wide optical density range to scan
gels, blots, membranes, and slides.
ƒ QC1 and QC2 quarantine-approved premises
ƒ Security Sensitive Biological Organisms (SSBA)
facility
ƒ Gel documentation systems
ƒ FACSAria II
ƒ Neon transfection system
ƒ Nikon TS100-F inverted microscope with an
LED source
ƒ Olympus FSX100 digital imaging system
ƒ PAM2500 Portable chlorophyll fluorometer
ƒ Polarstar omega microplate reader
ƒ Protean IEF system
ƒ Bioscreen cell growth monitoring system
ƒ Various liquid-handling robotic systems
ƒ Genetix QPix-II colony-picking robot
ƒ Low temperature incubators
ƒ RT PCR systems
ƒ Semi-automatic microtome
ƒ TissueLyser LT cell lysis apparatus
ƒ TLC autospotter
ƒ Whitley DG250 workstation for culturing
anaerobes
There is also a wide variety of standard biomedical
instrumentation in the School, including HPLCs,
FPLCs, GCs, thermocyclers, centrifuges,
ultracentrifuges, plate-, drop-, and cuvette- based
spectrophotometers and fluorimeters, scintillation
counters, fluorescence and light microscopes and
electrophoresis equipment.
Green fluorescent protein is a biosensor often used in
molecular biology
35
ANZAC Research Institute
Arizona State University
Atma Jaya University Indonesia
Australian Antarctic Division
Australian Coal Association Research Program
Australian Coal Mining Industry
Australian Drosophila Biomedical Research
Support Facility
Australian Geographic Society
Australian Institute of Marine Science
Australian National University
Australian Nuclear Science & Technology
Organisation
Baker IDI Institute
Bar Ilan University
BASF The Chemical Company
Centenary Institute
Centre for Vascular Research
Centre of Marine Biotechnology
Charles Sturt University
Chinese Center for Disease Control and Prevention
Christchurch Hospital
Concord Hospital
CSIRO Entomology
Denmark National Environmental Research Institute
Desert Research Institute Nevada
DHI Singapore
Diagnostic Technology Pty Ltd
DOE Joint Genome Institute
Dow Chemical Company
Environmental Biotechnology Cooperative
Research Centre
Garvan Institute
Hamburg University Center for Molecular
Neurobiology
36
Hanze University of Applied Sciences
Hebrew University of Jerusalem
Helmholtz Centre for Infection Research
International Society for Microbial Ecology
J Craig Venter Institute
James Cook University
Japanese Border Collie Health Network
Kamaishi Marine Biotechnology Institute
Karolisnka Institute Department of Microbiology
La Trobe University
Laboratoire d’Oceanologie Biologique de Banyuls
Universite Paris
Landcare Research New Zealand
Laurentian University Canada
Lowy Cancer Research Centre
Macquarie University
Massachusetts Institute of Technology
Massey University New Zealand
Max Planck Institute for Chemical Ecology
McGowan Institute for Regenerative Medicine
Murdoch University
Nanyang Environment and Water Research
Institute
Nanyang Technological University
NASA Ames Research Centre
National Centre for Adult Stem Cell Research Griffi
th University
National Centre in HIV Epidemiology & Clinical
Research
National University of Singapore
Neuroscience Research Australia
Northwestern University Chicago
Norwegian Veterinary College
NSW Department of Primary Industries (Fisheries)
NSW Food Authority
NSW National Parks and Wildlife Service
Optigen
Orica Australia Pty Ltd
Peking University Health Science Center
Pennsylvania State University
Prince of Wales Hospital
Queensland Parks and Wildlife Service
Queensland University
Rutgers University
SA Department of Primary Industries
Scripps Institute of Oceanography
Seoul National University
Singapore Advanced Environmental Biotechnology
Centre
Singapore Centre on Environmental Life Sciences
Engineering
Singapore Institute of Molecular and Cell Biology
Singapore Tropical Marine Science Institute
Southern Cross University
Stanford University
Stockholm Royal Institute of Technology
Sydney Children’s Hospital
Sydney Institute of Marine Science
Sydney Royal Botanic Gardens and Domain Trust
Tasmanian Department of Health
Tsinghua University China
University of Alberta
University of Auckland
University of British Columbia
University of California, Davis
University of California, Irvine
University of California, Los Angeles
University of California, San Diego
University of Cincinnati
University of Cologne
University of Copenhagen
University of Heidelberg
University of Konstanz
University of Manchester
University of Melbourne
University of Minho Portugal
University of New Mexico
University of Otago
University of Ottawa Heart Institute
University of Papua New Guinea
University of Queensland
University of Salzburg
University of Saskatchewan Canada
University of Southampton
University of Southern California
University of Sydney
University of Tasmania
University of Technology Sydney
University of Utah
University of Western Australia
University of Western Sydney
University of Wollongong
US National Institutes of Health
Victor Chang Institute
Victoria University Wellington
Wake Forest Institute for Regenerative Medicine
Weizmann Institute of Science Israel
Westmead Hospital
37
Memberships in Societies &
Associations
Alexander von Humboldt Foundation
American Academy of Microbiology
American Association for Cancer Research
Chronic Lymphocytic Leukemia Australian
Research Consortium
American Society for Biochemistry and Molecular
Biology
Council of the Human Proteome Organisation
American Society for Microbiology
American Society for Pharmacognosy
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
Australia and New Zealand Society for Cell and
Developmental Biology
Australian Academy of Science
Australian Atherosclerosis Society
Australian Centre for Hepatitis Virology
Australian Institute of Dangerous Goods
Consultants
Australian Institute of Policy & Science
Australian Neuroscience Society
Australian Society for Biochemistry & Molecular
Biology
Australian Society for Medical Research
Australian Society for Microbiology
BioEnvironmental Polymer Society
Bioinformatics Australia
38
Buttressing Coalition of the Papua New Guinea
Institute of Medical Research
Endocrine Society of Australia
Forum for European-Australian Science and
Technology Cooperation
Fulbright Alumni Association
Genetics Society of AustralAsia
Geological Society of Australia
High Blood Pressure Research Council of Australia
Institute of Biology
International Society for Microbial Ecology
International Society for Microbiology
International Society for the Study of Harmful Algae
International Society of Animal Genetics
NASA Astrobiology Institute
Pacific Institutes of Marine Science
Royal Society of Victoria
Safety Institute of Australia
Society for General Microbiology (UK)
Society for Neuroscience (USA)
Tissue Engineering & Regenerative Medicine
International Society
39
PROFILE
Faculty of Science Visiting Research Fellow
Professor Moustapha Kassem
In 2011, the Faculty of Science launched a Visiting
Research Fellowship scheme with the aims
of initiating and developing collaboration with
researchers of high standing both in Australia and
overseas, and facilitating interaction with Faculty
staff and students.
Under this scheme, Professor Moustapha Kassem
was hosted by Professor Marc Wilkins for a yearlong research sabbatical in the NSW Systems
Biology Initiative in the School of BABS. Moustapha
is Professor of Molecular Endocrinology at the
University Hospital of Odense in Denmark, and
Professor of Stem Cell Research at the Danish
Stem Cell Center located at the University of
Copenhagen.
Moustapha advises he chose the Wilkins lab for
his sabbatical due to its enormous expertise in
sophisticated bioinformatics analysis, biological
network analysis and the ability to integrate results
obtained from genomic and proteomic platforms.
His focus during this Fellowship was to learn about
bioinformatics and systems biology approaches to
studying biological systems, very promising areas
of research with respect to understanding disease
processes and providing novel ideas for therapy.
Stromal (mesenchymal) stem cells (MSC) are
multipotent cells that present in the stromal
compartment of bone marrow and can
differentiate into mesoderm-type cells, including
Heatmap and
dendrogram showing
clustering of 123
osteoblast (OB)
marker profiles during
differentiation from
MSC to OB. The OB
markers cluster in a
differentiation-stage
specific manner
40
During 2012, the following visitors were also hosted by BABS
academics under the Faculty of Science Visiting Research
Fellowships scheme:
ƒ
Professor James Fox, Massachusetts Institute of Technology,
host Professor Hazel Mitchell
ƒ
Professor Neale Ridgway, Dalhousie University Nova Scotia,
host Associate Professor Rob Yang
ƒ
Professor Steven Siciliano, University of Saskatchewan,
host Dr Belinda Ferrari
ƒ
Professor Roger Summons, Massachusetts Institute of Technology,
host Professor Brett Neilan
osteoblasts, chondrocytes and adipocytes. MSC
hold great promise for clinical use in a wide variety
of clinical settings, including bone and cartilage
regeneration. Currently, over 300 clinical trials are
being conducted worldwide to investigate the
therapeutic benefits of MSC administration in a
large number of disease conditions.
Moustapha has studied the biology of MSC
relevant for clinical use for more than 20 years,
and has described novel methods for their
isolation from bone marrow. He has also studied
the mechanisms that control their proliferation and
differentiation and, in particular, the differentiation
potential of MSC into bone forming cells
(osteoblasts). The aim is to identify novel genes
and proteins to be targeted pharmacologically
to enhance bone formation in low bone-mass
diseases, including osteoporosis. In addition,
Moustapha has initiated and participated in several
clinical trials employing MSC for regeneration
of damaged heart muscle following myocardial
infarction, and brain tissue following cerebral
haemorrhage and stroke.
In addition, the RNA-seq data will be integrated
with a large amount of proteomic data obtained
in his lab regarding changes in MSC membrane
proteome and secretome during MSC
differentiation.
Moustapha received his medical degree from
Cairo University in Egypt, and completed
postgraduate training in Internal Medicine and
Endocrinology in Denmark and the US. He
obtained his PhD degree and DSc degrees
from the University of Aarhus, Denmark and
completed a postdoctoral fellowship at the Mayo
Clinic in the US. Moustapha has published over
220 original papers and reviews in the field of
bone biology, stem cell biology and osteoporosis
pathophysiology. He has received several awards,
including the prestigious 2012 Marie and August
Krogh Prize from the Danish Medical Association
and the Novo Nordisk Foundation.
During his sabbatical, Moustapha collaborated
with the Wilkins group on a project using
RNA-Seq technology to investigate the mRNA
changes associated with MSC differentiation into
osteoblasts. The aim of the project is to delineate
genetic changes occurring in MSC as they
develop from undifferentiated to fully differentiated
osteoblastic cells, and identify intracellular
signalling networks that control MSC osteoblast
lineage fate.
Professor Moustapha Kassem and Professor Marc Wilkins
41
RESEARCH
CENTRES
42
The Ramaciotti Centre for Gene Function Analysis
The Ramaciotti Centre is a high throughput
functional genomics facility, offering expertise in
sequencing and microarray technology. It supports
genomics research throughout UNSW and its
associated research institutes by offering a range
of services and access to specialised equipment.
The following services are offered:
ƒ Next-generation sequencing: Illumina HiSeq
2000 & MiSeq, Roche GS FLX+
ƒ Microarray: Affymetrix, Agilent, Exiqon and
Illumina
ƒ Sanger Sequencing
ƒ Bioanalyser
Highlights from 2012
Acquisition of second HiSeq 2000
As the demand for sequencing data continued
to grow, the Centre focused on the application
of next-generation sequencing technology.
With funding from the Australian Government’s
Education Investment Fund Super Science
Scheme, the Centre purchased a second Illumina
HiSeq 2000 sequencer, doubling our sequencing
capacity. We continue to provide a number of
services on the Illumina platform for an increasingly
diverse range of customers. Research projects
ranged from human transcriptome sequencing to
metatranscriptome sequencing of coral from the
Great Barrier Reef.
New technology –
MiSeq Personal Sequencer
The School of BABS and the Ramaciotti Centre
were successful in their application to the UNSW
Major Research Equipment and Infrastructure
scheme for funding for an Illumina MiSeq. The
MiSeq is a personal sequencer that provides a fast
turnaround on small-scale sequencing projects.
The MiSeq will facilitate rapid, cost-effective
sequencing of amplicons and small genomes,
such as those from viruses and bacteria.
Ramaciotti Centre
Staff
(Front row L-R:)
Zhiliang Chen,
Kristin Miller, Marc
Wilkins, Helen Speirs,
Bronwyn Robertson,
Ruby Lin.
(Back row L-R:)
Nandan Deshpande,
Tonia Russell, Jason
Koval, Hannah Ginn,
Jackie Chan, Helena
Mangs, Erika Becker
Melanoma Sequencing Project
As part of the Bioplatforms Australia Melanoma
Biomolecular Datasets project, during 2012
the Centre sequenced its first complete human
genomes, 26 in total. The project aims to sequence
both normal and cancer samples from 75
individuals to 40x and 70x coverage respectively.
It is collaborative project utilising sequencing
capacity across Australia, with contributions from
all three nodes of Genomics Australia (ANU, AGRF
& RAMAC).
FIELD trial –
Genome-wide association study
The Centre completed a genome-wide association
study for the NHMRC Clinical Trials Centre. The
study, which is aimed at discovering genetic
factors that predict complications in Type 2
diabetes, used the Centre’s GeneTitan robot to
genotype 5,760 individuals. This is the largest
study that the Centre has ever undertaken.
43
Bioinformatics
Publications
The Centre continued its collaboration with the
NSW Systems Biology Initiative (SBI) in the
analysis of data. This collaboration has provided
a capacity for the assembly and annotation of
genomes, and for analysis of RNA-seq data from
the next-generation sequencers. These capacities
are of benefit for users of the Centre who do not
necessarily have strengths in bioinformatics. Some
of the first projects have now been completed and
have been published. This includes the genome
sequencing of a new Campylobacter, and the
RNA-seq analysis of an Alzheimer’s brain.
The Centre supports research across a broad
range of areas. Below are selected publications
from researchers who have used the Centre’s
services:
ƒ Bernardo BC, Gao X, Winbanks C, Boey E, Tham
YK, Kiriazis H, Gregorevic P, Obad S, Kauppinen S,
Du X, Lin RCY & McMullen JR. (2012) ‘Therapeutic
inhibition of the miR-34 family attenuates pathological
cardiac remodeling and improves heart function’,
Proceedings of the National Academy of Sciences
of the United States of America-Biological Sciences,
109: 17615-17620.
ƒ Cowley M, Weinberg A, Zammit N, Walters SN,
Hawthorne WJ, Loudovaris T, Thomas H, Kay T,
Gunton JE, Alexander SI, Kaplan W, Chapman J,
O’Connell PJ & Grey ST. (2012) ‘Human islets express
a marked pro-inflammatory molecular signature prior
to transplantation, Cell Transplantation, 21: 20632078.
ƒ Funnell AP, Norton LJ, Mak, KS, Burdach J, Artuz
CM, Twine NA, Wilkins MR, Power C, Hung TT,
Perdomo JS, Bell-Anderson K, Orkin SH, Pearson RC
& Crossley M. (2012) ‘The CACCC-binding protein
KLF3/BKLF represses a subset of KLF1/EKLF target
genes and is required for proper erythroid maturation
in vivo’, Molecular and Cellular Biology, 32: 32813292.
MiSeq Personal Sequencer
ƒ Hook SE & Osborn HL. (2012) ‘Comparison of toxicity
and transcriptomic profiles in a diatom exposed to
oil, dispersants, dispersed oil’, Aquatic Toxicology,
124-125: 139-151.
ƒ Lane A, Cheng Y, Wright B, Hamede R, Levan L,
Jones M, Ujvari B & Belov K. (2012) ‘New insights
into the role of MHC diversity in devil facial tumour
disease’, PLOS ONE, 7(6):e36955.
ƒ Swaminathan, S, Suzuki K, Seddiki N, Kaplan W,
Cowley M, Hood CL, Clancy JL, Murray DD, Méndez
C, Gelgor L, Anderson B, Roth N, Cooper DA &
Kelleher AD. (2012) ‘Differential regulation of the
Let-7 family of microRNAs in CD4+ T cells alters IL-10
expression’, Journal of Immunology, 188: 6238–6246.
HiSeq 2000 Next-Generation Sequencing System
44
For further information, please visit our website:
ramaciotti.unsw.edu.au
Centre for Marine Bio-Innovation
The CMB is located in the Biological Sciences
Building at the University of New South Wales. The
Centre integrates research across microbiology,
marine chemical ecology, ecological theory,
chemistry and genomics, in its home Schools
of Biotechnology & Biomolecular Sciences and
Biological, Earth & Environmental Sciences.
Key research activities in the CMB also occur
within and in collaboration with a number of
Australian and international institutions and is a
focal point for interdisciplinary basic and applied
research. With research platforms based on
the integration of marine chemical ecology and
microbiology, the CMB has grown to include a
diversity of research capabilities, and is a key
node across a network of national and international
institutions and industries. It drives research
excellence in studies of microbial biofilms, and
bacteria/higher organism interactions including
disease, colonisation biology of marine sessile
organisms, experimental marine ecology,
biofouling, biodiversity, bioremediation and
environmental engineering.
CMB personnel and expertise contribute to a
number of undergraduate lectures and laboratory
classes in the Schools of BABS and BEES,
bringing the latest research advances into the
classroom. The CMB is also very active in training
research students, who are directly involved in the
Centre’s main research areas. Supervision occurs
within the Centre and via different collaborations
with external researchers, resulting in high calibre
graduates that go on to work in academia and
industry both in Australia and overseas.
The CMB has more than 50 full time members,
comprised of research fellows, postdocs,
research assistants and postgraduate and
Honours students, and due to collaborations
in Australia and overseas, routinely welcomes
visiting researchers from around the world. Since
its creation, the Centre has attracted funding
from a variety of sources both within and outside
Australia. It includes success in competitive grants,
notably the ARC but also from international bodies,
and has also received considerable support from
relevant industry sources.
For further information, please visit our website:
cmb.unsw.edu.au
45
Australian Centre for Astrobiology
46
The Australian Centre for Astrobiology is the only
centre of astrobiological research in Australia. It is
an Associate Member of the NASA Astrobiology
Institute and has close links with the European
Space Agency and other international space
agencies and institutions.
Astrobiology is a relatively new field of study,
developing at the crossroads of astronomy,
biology, geology, paleontology, physics and other
disciplines. Recent discoveries in this field are
rapidly changing our view of the potential for life
elsewhere in the Universe.
The Centre’s key goals include contributing to the
understanding of the origin of life on Earth. It has
strong media, education and outreach programs
and It provides a highly visible flagship program
that is able to attract quality science and science
communication PhD students to pursue such
research programs. All doctoral students have
the opportunity to spend time at NASA in some
capacity during their PhD studies.
For further information, please visit our website:
aca.unsw.edu.au
Evolution & Ecology Research Centre
The EERC was established in 2007 and draws
together diverse strengths of academic staff,
independent research fellows, and a large number
of postgraduate students from the UNSW Schools
of Biological, Earth and Environmental Sciences,
Biotechnology and Biomolecular Sciences,
Mathematics and Statistics, and Medical Sciences,
Evolution is responsible for all of the biological
diversity in the natural world and the fossil
record. Evolution occurs within the context of
ecological interactions between an organism and
its environment. The most exciting research in
whole organism biology is at the intersection of
how organisms interact with their biological and
physical environment (Ecology) and the way in
which these interactions effect adaptive change
across generations (Evolutionary Biology).
The EERC provides a cohesive and cooperative
environment for the University’s effort in evolution
and ecology research and research training, and
maintains a vibrant seminar and visitor program.
It provides seed funding for innovative new
research collaborations, recognises excellence
in research, learning and supervision, engages in
public outreach relating to evolution and ecology,
and runs the innovative Graduate Program in
Evolution & Ecology.
For further information, please visit our website:
eerc.unsw.edu.au
47
LEARNING AND TEACHING
Undergraduate and postgraduate degree
programs in the School of BABS prepare
students for a variety of career paths within and
outside the sciences. Our graduates work in a
variety of research areas, including medical and
environmental, as well as biotechnology.
Recognising rapid changes in research, and taking
advantage of the expertise of new academic
staff, a revitalisation program for our third year
course offerings has been initiated, starting with
BABS3281, which has elicited strong student
support.
They also find employment in government and
privately sponsored industries, in areas ranging
from management, policy development, production
and quality control, 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 emphasised, providing
our graduates with a competitive edge for careers
in journalism, business and management.
While BABS is home to internationally recognised
innovative researchers, it also has many members
of staff who are innovators in teaching and
learning. In a collaboration with and utilising
considerable support from centres such as the
Ramaciotti Centre for Gene Function Analysis and
the UNSW Mark Wainwright Analytical Centre,
the School continues to incorporate cutting-edge
research into undergraduate teaching.
Innovations in teaching
New courses in rapidly evolving discipline areas
were developed in 2011, and attracted significant
interest amongst our students in 2012. The BABS
discipline majors were restructured to align more
closely with the School’s emerging research
strengths. As a consequence of the restructure, a
first year introductory biotechnology course was retailored to provide an integrated path for students
from Years 1 to 3. In light of student feedback,
some second year courses were also modified.
48
During 2012, advances in virtual and online
learning activities included:
ƒ development of new online virtual laboratories
to train students in the essential skills of PCR
and building genetic pedigrees
ƒ development of genetic breeding simulations
ƒ adoption of a new learning management
system for online communication in our large
first year courses
In addition to the introduction of new materials,
the School also regularly reviews its learning and
assessment practices in all courses and programs.
The School continues to use the formal online
course and teaching evaluation tool (CATEI) and
informal focus groups to evaluate the teaching of
and innovations to courses. In addition, we have
continued our review of undergraduate assessment
with the support of the University and the Faculty
of Science, and Professor Jan Orrell (educational
consultant from Flinders University).
Recognition of BABS teaching staff
The quality of the teaching programs in the
School is widely recognised within and outside
UNSW, with many individual academics being
acknowledged in recent years for their outstanding
contributions to learning and teaching.
In yet another exceptional year for recognition
of her educational excellence, Dr Louise LutzeMann was awarded a 2012 Australian Society of
Biochemistry and Molecular Biology (ASBMB)
Outstanding Education Award for innovation and
creativity.
Professor Andrew Brown was awarded the Vice
Chancellor’s Award for Teaching Excellence
(Postgraduate Research Supervision), and
postgraduate research student Mr Gee Chong
Ling was awarded the Vice Chancellor’s Award for
Teaching Excellence (Sessional Teaching).
Associate Lecturer Dr Sven Delaney was invited
to present at the UNSW Learning and Teaching
Forum on using simulations in large group
teaching. Other members of academic staff
continue to work closely with the UNSW Learning
and Teaching Unit to promote the development and
adoption of new technologies to aid learning and
teaching, as well as to develop new courses and
new approaches to teaching and assessment.
Outreach and supporting students
The School recognises its responsibility for
outreach and raising public awareness of the
institution and the Science discipline. Academics
continue to contribute to activities designed for
secondary school students and science teachers.
The popularity of biotechnology and molecular
sciences continues to increase. This is in turn
increasing the demand for support and training
for secondary school science teachers. Dr Jani
O’Rourke and Dr Anne Galea continue the School’s
support of local high schools and high school
students, and A/Professor Noel Whitaker and Dr
Louise Lutze-Mann remain actively involved with
the NSW Teachers Professional Development
program.
Undergraduate degrees
Our undergraduate programs in the biomolecular
sciences are designed to provide students with
rigorous training in the modern sciences and
are aimed at fostering an analytical approach
to problem solving. Students gain a strong
foundation in biology, chemistry and mathematics,
establishing a solid base of knowledge for
advanced coursework relevant to each specialised
program. The flexibility of our integrated
programs provides undergraduate students with
opportunities to interact with eminent researchers
in a variety of disciplines. Students develop
communication and information retrieval skills
necessary to stay up-to-date in rapidly evolving
areas of science, and so our programs are ideal for
those wishing to pursue research-oriented careers.
Bachelor programs
We offer the following Bachelor programs:
Modern facilities
A program of renovation of BABS teaching
laboratories has begun, providing state-of-theart laboratory teaching facilities for our students.
Renovation of our microbiology teaching laboratory
to PC2 standard and the biochemistry/molecular
biology teaching laboratory to PC1 standard has
been completed. Both now feature video display
screens, demonstrator-led independent group
areas with video/computer/internet facilities, a
preparation laboratory and real-time microscope
projection.
ƒ Biotechnology (UNSW code 3052)
ƒ Bioinformatics (UNSW code 3647)
ƒ Science (UNSW code 3970)
ƒ Advanced Science (UNSW code 3972)
ƒ Medical Sciences (UNSW code 3991)
Biotechnology (3052) offers a comprehensive
education in all aspects of this multidisciplinary
field, leading to the award of a Bachelor of Science
Degree in Biotechnology with Honours. Starting
with an introduction to biotechnology, second-year
studies cover molecular biology and microbiology
with choices in chemistry or physiology. Third
49
year specialisations include biopharmaceuticals
and immunology, with optional environmental
biotechnology, environmental microbiology and
microbial genetics. The fourth year comprises
a research project and studies in commercial
biotechnology and professional issues.
Bioinformatics (3647) is jointly administered by
BABS and the School of Computer Science and
Engineering. Bioinformatics is a new and rapidly
expanding discipline at the convergence of
computing and the life sciences, and is focused
on the development of technologies for storing,
extracting, organising, analysing, interpreting and
utilising biological information. Bioinformatics has
recently come to prominence with the analysis
of huge amounts of data generated by genome
projects and postgenomic biology.
For Science (3970), Advanced Science (3972)
and Medical Science (3991) programs, students
may choose to specialise in the disciplines of
biochemistry, biotechnology, genetics, medical
microbiology and immunology or microbiology and
molecular biology.
Majors
The School teaches within the Science discipline
areas of biotechnology, genetics, microbiology
and molecular & cell biology. In conjunction with
the Faculty of Medicine, we also participate in
the teaching of medical and science students in
the Bachelor of Medical Science program. In this
program students can study towards a major and
a minor in a particular specialisation, with study
plans provided for each discipline area.
Combined degrees
ƒ Science/Arts
(UNSW code 3930, 4 years full time)
ƒ Advanced Science/Arts
(UNSW code 3931, 5 years full time)
ƒ Bioinformatics/Science
(UNSW code 3755, 5 years full time)
ƒ Science/Education
(UNSW code 4075, 4 years full time)
ƒ Commerce/Science
(UNSW code 3529, 4 years full time)
ƒ Science/Law
(UNSW code 4770, 5 years full time)
50
Honours
An optional Honours year can be undertaken by
students who have maintained a credit average
or above. Honours students become part of a
research team within one of the research labs in
the School, and complete a supervised research
project and thesis during the year-long program.
Postgraduate degrees
BABS has a strong international reputation for
quality research in fundamental and applied
science. In 2012 the School had 144 Higher
Degree by Research students. Of these, 124 were
progressing towards a PhD, and 20 PhD students
completed during the year.
Doctor of Philosophy (PhD) and Master of Science
(MSc) research-based degrees are offered
to qualified students who have completed a
four-year undergraduate Science degree with
Honours or the equivalent. The BABS Graduate
Diploma comprises a specialised one-year period
of full-time study and research. It is designed
for graduates from overseas universities and
those wanting to change their career direction
to encompass biotechnology and molecular
biological techniques.
The Master of Philosophy in Biotechnology and
Biomolecular Sciences is an alternative research
degree for students considering undertaking
Honours. The MPhil (BABS) is designed to be
taken over three semesters, and comprises three
coursework subjects and a supervised research
project. The program provides students with
a stronger qualification through emphasis on
research training, and provides access to modern,
sophisticated facilities and techniques that apply
to a wide range of biotechnology and molecular
biology fields.
51
PROFILE
Australia’s First EMBL PhD Candidate
Simone Li
The European Molecular Biology Laboratory
(EMBL) is a publicly funded non-profit institute
housed at five sites in Europe, with expertise
covering the whole spectrum of molecular biology.
In 2012, Simone Li headed off to EMBL Heidelberg
to commence her PhD as the first Australian student
to participate in the EMBL International PhD Program,
considered to be one of most competitive PhD
training schemes in the world.
As part of the rigorous selection procedure, which
involved more than 2,000 applicants worldwide,
Simone was shortlisted and in late 2011 was invited
to travel to the EMBL’s Heidelberg headquarters for
the final application round. This part of the process
involved scientific discussions of her research with
a panel of EMBL group leaders, as well as one-onone interviews. Simone advises that “It was great
ATC Building at EMBL Heidelberg, summer
52
to meet fellow candidates from all over Europe
but also from the US, Guatemala, Mexico, Brazil,
China, Japan ... in fact, it almost felt like a Miss
Universe contest!”
After completing her bioinformatics Honours
year in BABS, Simone became the first
employee of the NSW Systems Biology Initiative,
which is headed up by Professor Marc Wilkins.
Simone’s PhD is being co-supervised by Marc
and EMBL’S Dr Peer Bork, joint head of the
Structural and Computational Biology Unit
and Strategic Head of Bioinformatics. Peer’s
group focuses on predicting function and
comparative analysis of complex molecular data
at scales ranging from genes to ecosystems.
Heidelberg by the river Neckar
Simone’s PhD project will focus on using
metagenomics – the study of genetic material
from environmental samples – to understand how
faecal microbiota transplantation therapy can
be used as a treatment and potential cure for
diseases of the digestive system. Many of these
diseases, such as ulcerative colitis, are believed
to arise from imbalances of microorganisms in the
gut. It is hoped that findings from this project will
increase the success rate of the treatment, and
reduce the number of sufferers of these diseases.
Simone’s PhD will be jointly awarded by EMBL and
UNSW.
PhD student life for Simone began with a 2-month
core course in molecular systems biology,
aimed at providing students with an overview of
state-of-the-art developments in the field. “The
lectures were given by group leaders, so it was
ATC Building at EMBL Heidelberg, winter
a nice way to find out what the current trends
in molecular biology are, in areas very much
outside our own expertise. I had the opportunity
to learn about technologies and techniques that I
wouldn’t have otherwise known about. And being a
bioinformatician, getting back into the wet lab was
a definite highlight” says Simone.
Amongst other opportunities offered to PhD
students at EMBL, Simone is also co-ordinating the
EMBL International PhD Symposium this year. “It is
a conference fully organised by the first-year PhD
students – we came up with the theme and the
program, invited the speakers – and we also have
to source the funding!”
“I have really enjoyed my time at EMBL so far. It has been an eye-opening
experience – making friends from all over the world, seeing renowned
scientists in the corridor every day … and living it up in Europe, of course!”
53
2012 Student Awards and Prizes
School of Biotechnology and Biomolecular Sciences Prize
Best performance in BIOC3111 Molecular Biology of Proteins
Dennis Lawrence
Cheung
School of Biotechnology and Biomolecular Sciences Prize
in Level 2 Biochemistry
Best performance in the examinations in Level 2 Biochemistry courses in
the Bachelor of Science Program
Alan Truong
School of Biotechnology and Biomolecular Sciences Prize
in Level 3 Biochemistry
Best performance in the examinations in Level 3 Biochemistry courses in
the Bachelor of Science Program
Gabriella Martyn
Garry King Prize
Best Honours thesis in a Molecular Biology or Genetics Major
Lisa Phan
Jackson Prize in Microbiology and Immunology
Best performance in Microbiology and Immunology Honours
Eliza Wells
Jackson Prize for Honours Year
Best overall performance in Honours year
Zara Sharane Ali
Meat and Livestock Australia Prize
Best performance in INOV4101-INOV4301 Innovation in Practice A-C
Daniel Vieites
Clinical Microbiology Update Program Prize
Claudia Jade
Stocks
Best performance in BABS3081 Bacteria and Disease
54
55
BABSOC
BABSOC/EISSOC (Biotechnology and
Biomolecular Science Students Society/
Entrepreneurship and Innovation Student
Society) is a jointly managed student society
that represents students from BABS and those
enrolled in the UNSW Diploma in Innovation
Management.
The big event for the Outreach team was the annual
UNSW Open Day held in September, where the team
staffed a stall in the Scientia Building. The pitch to
high school leavers is that as it is unique to UNSW,
the Diploma provides a point of difference for them
to choose this university over others for their primary
degree studies.
All students taking undergraduate or
postgraduate BABS courses are automatically
members of BABSOC, with students enrolled in
the Diploma becoming members of EISSOC. A
single executive is elected each year to manage
the interests of both sets of students.
Led by President Bernard Wai, throughout the
year the society held numerous social functions,
including meet & greets, BBQs, pub crawls and
dinners, culminating in the big one, the annual
ball. For 2012, the theme was the “Mad Hatter’s
Ball” in memory of the late Associate Professor
Alan Wilton, who was a great supporter of student
initiatives and never missed the annual ball.
The Diploma was initially designed by BABS
academic Dr Wallace Bridge to teach bioscience
undergraduates about the processes involved
in commercialising scientific discovery. In 2011,
program authority moved from the Faculty of
Science to the Australian School of Business,
where it is now offered as a combined study
program to students from across UNSW. Wallace
still maintains an active role in teaching many
of the Diploma courses, advising on program
management issues and acting as a mentor for
BABSOC/EISSOC.
In 2012, the society had the largest executive
membership (46 students) in its 7-year history.
Given the vast peoplepower available, the 2012
BABSOC/EISSOC executive was structured into
four separate teams with different responsibilities:
Careers & Networking (C&N), Outreach, Social,
and Treasury, Sponsorship & Marketing.
56
The sold-out night of revelry held in The Tea Room
at the Queen Victoria Building in the city would
have made Alan proud, with its excellent food (the
best ever according to Wallace), drinks, music by
DJ Tiger Lilly and, of course, the 110 well-dressed
(some flamboyantly so) guests. All had a great time
showing off their many varied interpretations of the
headwear theme – some elegant, some otherwise
so. BABS staff members who joined the students
in their celebrations were Jeff Welch (who hasn’t
missed a ball in 15 years), Anne Galea, Brendan
Burns, Noel Whitaker and Elessa Marendy. The
prize for the best hat was a Bondi beach parachute
jump, kindly donated by Skydive the Beach
Sydney, and was won by Noel for his court jester
take on the evening.
Two catered careers nights were held during
Semester 2. The first was themed “Road to
Success” and involved 5 guest speakers from
various industries who engaged the audience with
advice, backed up by tales of their experiences,
on how to make the transition from university to that
first job, and progress to a successful career path.
Tragedy almost struck when the pizza order was
mistakenly diverted to a Queensland pizzeria, but
sustained panic and phone calls by the C&N team
saved the day, with the voracious student audience
eventually being fed.
The second evening was themed “Transforming
ideas into Reality – Optimal Priming for
Entrepreneurship”. This event saw a panel of four
Entrepreneurs/CEOs tell their stories of how they
jumped from the safety of corporate careers to
start up their own businesses, and was followed by
discussions with the audience on tips and secrets
to surviving the process. Learning from past
experience, this time there were no issues with the
delivery of the pizzas.
Sponsorship efforts during the year were
successful in gaining external financial support to
assist in funding marketing, catering and delivery
of the societies’ activities. Funding included a
$1,000 Arc grant for the annual ball and $500
generously provided by each of Resmed, CSL and
Halfords IP.
The wide array of the BABSOC/EISSOC activities
during 2012 have been documented in an Annual
Report. If you would like a digital copy (even if it’s
just for the photos) please contact Wallace.
Although all members of the executive played
a valued role in BABSOC/EISSOC’s success in
2012, there were some standout contributions that
deserve special mention.
Thanks and appreciation go to Rajesh Mottey
(sponsorship), Ashleigh Thomas (annual
ball), and the Annual Report subcommittee:
Tim Fang, Treasurer; Noëllie Garand, C&N
Secretary; Colin Fong, Chief Editor; Marco Chau,
http://babsoc.com; Jason Ngo, Arc Delegate; and
Curran Liu, Media.
57
2012 Honours Projects
58
Name
Supervisor/s
Project Title
Abeygunawardena,
Dodampe
Marc Wilkins
A conditional two-hybrid system to study the role of arginine
methylation
Ali, Zara
Merlin Crossley/Richard Pearson
Engineering next-generation artificial transcription factors for
improved chromatin access
Ankulkar, Radhikar
Louise Lutze-Mann
Statins as potential anti-cancer therapeutics
Atmadibrata, Bernard
Tatyana Chtanova
Establishing a system to investigate immune cell interations with
tumours
Baker, Laura
Alex Swarbrick/Radhika Nair
Investigating the role of ID4 in mammary tumorigenesis
Bournazos, Adam
Suhelen Egan/Staffan Kjelleberg
Proteomic profiling of the marine macroalgal pathogen, Nautellasp.
R11, under disease inducing conditions
Burns, Vicky
Andrew Brown
Investigating ABCG1 epitope tagging, dimerisation and interspecies isoform homology
Charlesworth, James
Brendan Burns
Archaea join the conversation: putative identification of quorum
sensing in the halophilic archaea
Chen, Tiffany
Rebecca LeBard/Brett Neilan
Design of a multiplex PCR using Bacteroides sp. for microbial
source tracking studies
Daim, Malak
Suhelen Egan
Characterising the antinematodal activity of the marine
bacterium Pseudoalteromonas tunicata when screened against
Caenorhabditis elegans
De Leon, Emilio
Vincent Murray
The interaction of bleomycin and cisplatin with mitochondrial
sequences
Demirbas, Omer
Li Zhang
Genetic analysis of oral Campylobacter concisus strains isolated
from patients with inflammatory bowel disease and controls
Gorgievski, Elizabeth
Rebecca LeBard/Brendan Burns
Characterisation of plasmid stability systems in Haloarchaea
Hardie, Megan
Anne Galea/Vincent Murray
Investigating the cleavage pattern of cisplatin damage using T4
endonuclease VII
Karsten, Elisabeth
John Foster
The application of SurgiLux® in the treatment and prevention of
corneal infectious disease
Lam, Ivy
Bettina Rosche
Effects of traditional Chinese medicinal herbs on bacterial
sensitivity towards antibiotics
Lavrencic, Peter
Hazel Mitchell
Investigation of the motility and biofilm formation of Campylobacter
concisus strains
M.D.Jamil, Farhana
Anne Galea/Vincent Murray
The interaction of cisplatin, cisplatin analogues and bleomycin with
gene promoters and mitochondrial DNA sequences
Mak, Michelle
Noel Whitaker
Human papillomavirus involvement in human breast cancer
transformation
Minchin, Thomas
Torsten Thomas
The effect of enhanced biochar on microbial communities in soil
Nguyen, Peter
Suhelen Egan/John Kalaitzis
Characterisation of a nonribosomal peptide synthetase gene
cluster linked to anti-diatom activity in the marine bacterium
Pseudoalteromonas tunicate
Ooi, Chi Yan
Rob Yang
Identification and characterisation of novel proteins involved in
endosomal cholesterol transport
Parry, Benjamin
Peter White
A study into norovirus molecular epidemiology and RNAdependant RNA polymerase 2012
Phan, Lisa
Andrew Brown
Regulation and membrane topology of squalene monooxygenase
Name
Supervisor/s
Project Title
Ponto, Aditya
Mike Manefield
(co-supps Dr Patricia Conway/
Dr Meera Esvaran)
Effects of pre-treatments on improving viability of Lactobacillus
fermentum PC1
Prabhu, Anika
Andrew Brown
Cholesterol and the Warburg effect in prostate cancer setting
Pratama, Ryanbi
Brett Neilan
Expression of a cyanobacterial non ribosomal peptide in
Escherichia coli
Rajan, Melvin
Rick Cavicchioli/Tim Williams
Establishing a gene transfer system for psychrophilic haloarchaea
from Deep Lake, Antarctica
Rapadas, Melissa
Brett Neilan
Transcriptional mechanisms regulating the biosynthesis of the
cyanobacterial toxin cylindrospermopsin
Restuccia, Dominic
Kuldip Sidhu
A human LHX8 stem cell reporter line for the detection of basal
forebrain cholinergic neurons
Ricafort, Lawrence
Ruiting Lan
Molecular genotyping of Queensland bordetella pertussis
Saputro, Brian
Graham Vesey
Cell-based assays for in vitro measurements of cytokine function
Sia, Chang
Richard Lock
Determinants of acute lymphoblastic leukaemia cell sensitivity to
small molecule inhibitors of Janus Kinases
Small, Lewin
Rob Yang
An investigation into the function of Stomatin-like Protein 1
Swift, Joshua
Louise Lutze-Mann
The effectiveness of psychotropic agents and statins in the
treatment of non-small cell lung cancer
Tan, Ye Sing
Li Zhang
Investigation of the possible role of specific oral Campylobacter
concisus strains in inflammatory bowel disease
Wai, Pun
Dianne McDougald/Staffan
Kjelleberg
Effect of nutrient limitation and developmental stage of manrine
bacterial biofilms on susceptibility to predation by heterotrophic
protists
Wang, Henry
Antony Cooper
Investigation into Alpha-Synuclein externalisation in Parkinson’s
disease
Wells, Eliza
Matthew Lee/Mike Manefield
Chlorinated methane bioremediation
Wibowo, Jessica
Kuldip Sidhu
Cholinergic neuronal differentiation using neuroprogenitor cells
derived from human induced pluripotent stem cells for Alzheimer’s
disease treatment
Wilton, Annabel
Richard Lock
Mechanisms of glucocorticoid-induced BIMtranscriptional
regulation in acute lymphoblastic leukaemia
Wong, Natalie
Stuart Tangye
Characterisation of circulating CD4+ T cell subsets in normal and
disease settings
Yang, Chen
Karen MacKenzie
The role of dyskerin in proliferation, survival and maliganant
phenotype of neuroblastoma
Yeo, Nicole
Noel Whitaker
Exosomes and their role in HPV-infected cells
Young, Renee
Vladimir Sytnyk
Investigating the protein-protein interactions of neural adhesion
molecule 2 at synapses
59
2012 PhD Completions
60
Name
Supervisor/s
Thesis Title
Al Tebrineh, Jamal
Brett Neilan
Development of Molecular Genetic Techniques for the
Determination of Major Toxic Cyanobacteria from Environmental
Water Sources
Ayer, Anita
Ian Dawes/ Gabriel Perrone
Genetic and environmental factors influencing redox homeostasis
in Saccharomyces cerevisiae
Bebek, Filip
Laurent Rivory
Towards the identification of novel interferon-alpha induced antiHepatitis C virus effectors
Chen, Shih-Ching
Ian Dawes
The intron-mediated gene regulation in Saccharomyces cerevisiae
Couttas, Timothy
Marc Wilkins
Lysine methylation in the interactome of Saccharomyces cerevisiae
Cuddy, William
Brett Neilan
Diversity, nitrogenase activity and salt physiology of Australian
cyanobacteria isolated from agricultural and non-agricultural soils
Eden, John-Sebastian
Peter White
The evolutionary dynamics of Norovirus
Fan, Lu
Torsten Thomas
Phylogenetic Diversity, Functional Convergence, and Stress
Response of the Symbiotic System Between Sponges and
Microorganisms
Han, Sangha
Julian Cox
Quantitative ecology of salmonella in poultry production and
processing
Ismail, Yazan
Li Zhang
Campylobacter concisus and its possible role in inflammatory
bowel disease
Keam, Simon
Catherine Suter
Studies on the mammalian piRNA pathway in cancer cells
Krycer, James
Andrew Brown
Studies on cholesterol metabolism in prostate cancer cells
Li, Richard
Bettina Rosche
Application of microbial biofilms for the production of chemicals
Liu, Yizhe
Staffan Kjelleberg
Metagenomic and metaproteomic analysis of the microbial
communities in marine sponges
Low, Adrian
Staffan Kjelleberg/Mike
Manefield
Generation of a low pH 1,2-dichloroethane enrichment culture for
enhanced bioremediation
Low, Keng
Marc Wilkins
Proteome-wide analysis of arginine methylation in Saccharomyces
cerevisiae
Mak, Cassie
Merlin Crossley
Transcriptional regulators of haematopoiesis
McElroy, Kerensa
Torsten Thomas/Fabio Luciani
Applications of next-generation sequencing to microbial evolution
Nair, Suresh
Ian Dawes
Cellular mechanisms affecting Alzheimer’s amyloid-beta
aggregation in Saccharomyces cerevisiae
Pang, Stanley
Ruiting Lan
Bacterial genomics and its applications in molecular epidemiology
of Salmonella enterica serovar Typhimurium
Pham, Son
Peter White
Infection dynamics of hepatitis C virus
Ramadas, Radhika
Greg Arndt
Identification of Modulators of Chemotherapeutic Resistance Using
a Random shRNA Library
Sodhi, Nidhi
Staffan Kjelleberg
Identifying mechanisms for enhanced bacterial granulation using
pure culture isolates and bench scale batch reactor systems
Sun, Shuyang
Staffan Kjelleberg
Anti-protozoal mechanisms of Vibrio cholerae biofilms
Woolford, Michelle
Sally Dunwoodie
Exploring the function of glutamine fructose-6-phosphate
transaminase (Gfpt2) in embryonic development
A/Prof Peter White and Dr John-Sebastian Eden
Dr James Krycer
Dr Cassie Mak
Dr Tim Couttas
61
Research funding
Grants announced in 2012
commencing in 2013
International Schemes
Australian Research Council
Neilan BA & Muenchhoff J. The regulation and role
of toxin production in cyanobacteria. 2013-2014:
$18,750.
ARC Discovery Projects
Neilan BA. Australia’s freshwater ecosystems:
how microbial diversity and functionality influence
harmful cyanobacterial blooms. 2013-2015:
$349,000.
Thomas T. To eat or not to eat? How symbiotic
bacteria manipulate the phagocytic behaviour of
their eukaryotic host. 2013-2015: $349,000.
UNSW/Go8 German Joint Research
Cooperation Scheme
UNSW Internal Schemes
Major Research Equipment Infrastructure
Initiative (MREII)
Cavicchioli R. GE Typhoon FLA9500 Fluoro/
Phosphoimager. $135,250.
Neilan BA. Buchi Syncore Analyst. $73,179.
Wilkins MR. Does phosphorylation regulate the
methylation of proteins? 2013-2015: $315,000.
Yang HR & Dawes IW. The role of Fld1p protein
in lipid droplet formation and growth in the yeast
Saccharomyces cerevisiae. 2013-2015: 285,000.
Ballard JWO. Is mitochondrial DNA a selectively
neutral marker? $40,000.
Brown AJ. How do mammals maintain cholesterol
homeostasis? $40,000.
National Health & Medical Research
Council
UNSW Goldstar (NHMRC)
NHMRC Project Grants
Mitchell HM. Investigation of the pathogenesis of
the emergent pathogen Campylobacter concisus.
$40,000.
Lan R, Sintchenko V, Tanaka M & Octavia S.
Molecular epidemiology and high resolution
surveillance of Salmonella enterica serovar
Typhimurium in Australia. 2013-2015: $563,052.
Yang HR & Brown AJ. Identification and
characterization of novel proteins in endosomal
cholesterol transport. 2013-2015: $521,976.
Rawlinson WR, Scott G & Alain S. Improved
treatment of congenital cytomegalovirus disease
through study of placental models of pathogenesis.
2013-2015: 652.025.
Other National Schemes
Gordon and Betty Moore Foundation
Thomas T, Kjelleberg S & Steinberg P. Molecular
mechanism of bacteria-sponge symbiosis: Have
bacteria acquired eukaryotic-like proteins to
control their interactions with a host? 2013-2015:
$1,292,000.
62
UNSW Goldstar (ARC)
Neilan BA. Discovery and characterisation of
anti-mycobacterials from bioactive endophytes.
$40,000.
Sytnyk V. Molecular mechanisms of abnormal
synaptic vesicle recycling induced by disruptions
of the functions of the neural cell adhesion
molecule (NCAM). $40,000.
Faculty of Science Silver Star (ARC)
Crossley M. Engineering next generation designer
transcription factors for improved chromatin
access. $35,000.
Morris KV. Parasitizing HIV-1; the evolutionary
dynamics required to drive HIV-1 to a nonpathogenic state. $35,000.
White P. Evolution of pandemic noroviruses.
$35,000.
Grants commencing or in
operation during 2012
Faculty of Science Research Grant (FRG)
Australian Research Council
Burns B. Archaea join the conversation: signalling
in the third domain of life. $10,000.
ARC Discovery Projects
Faculty of Science Silver Star (NHMRC)
Ferrari B. Targeted isolation of Candidate Division
TM7: a ubiquitous bacterial phylum recalcitrant to
traditional cultivation methods. $10,000.
Galea A. Investigating cisplatin and cisplatin
analogue damage targets in different human DNA
sequence elements. $10,000.
Janitz M. Synucleins isoform expression analysis in
multiple system atrophy brain. $10,000.
Lutze-Mann L. Psychotropic drug repositioning for
the treatment of glioblastoma. $10,000.
Murray V. Cisplatin global DNA screening: the
precise location of cisplatin adducts in the entire
human genome. $10,000.
Ballard JWO, Wolff JN (APD) & Sutovsky P.
Challenging current dogma on the inheritance of
mitochondrial DNA. 2011-2013: $370,000.
Cavicchioli R, Lauro F, Guilhaus M, Raftery MJ,
Rintoul SR & Riddle MJ. Microbial genomics of the
southern ocean: monitoring environmental health.
2010-2014: $950,000.
Cavicchioli R. Understanding protein-nucleic-acid
interaction networks in cold-adapted archaea.
2011-2013: $360,000.
Dawes IW. How do cells regulate redox
environment at the subcellular level? 2010-2014:
$420,000.
Whitaker N. Impact of human papillomavirus on
breast cancer exosome. $10,000.
Murray, SA & John, U. Can lateral gene transfer
lead to ecological innovation in eukaryotes?
The role of saxitoxin in the diversification of
Alexandrium. 2012-2014: $230,000.
Zhang L. Investigation of the impact of H2 and
intestinal H2-consuming bacteria on growth and
protein expressions of Campylobacer concisus
and other Campylobacter species that colonize the
human oral cavity. $10,000.
Preiss T & Beilharz TH (ARF). Role of mRNA
polyadenylation control in gene expression. 20082012: $685,000.
Faculty of Science Early Career (ECR) Grant
Hart-Smith G. Comprehensive mass spectrometry
based protein quantification of yeast HMT1
knockout mutants for the study of protein-protein
interaction network dynamics. $8,938.
Kaakoush N. Microbial variations and metabolic
biomarkers in patients with Inflammatory Bowel
Disease. $10,000.
Tanaka MM, White PA, Koelle KV & Regoes RR.
Understanding mutation and genetic reassortment
in viruses: new mathematical models of viral
dynamics and evolution. 2011-2013: $378,000.
Waite TD, Collins RN, Neilan BA, Sinclair G &
Ring RJ. Biogeochemical controls on efficacy and
sustainability of uranium heap leaching. 20102013: $300,000.
Walter MR (APF), Neilan BA, George SC, Summons
RE & Schopf JW. Oxygenating the Earth: Using
innovative techniques to resolve the timing of the
origin of oxygen-producing photosynthesis in
cyanobacteria. 2010-2014: $715,000.
63
White, PA. Maintaining fidelity in viral Ribonucleic
acid (RNA) polymerases. 2012-2014: $215,000.
Wilkins MR, Molloy MP & Hart-Smith GO (APD).
The role and regulation of protein methylation: a
study using the recently developed methylation
network of yeast. 2011-2013: $300,000.
Wilkins MR. Protein methylation: A fundamental
regulator of the interactome. 2010-2012: $285,000.
Yang, HR. Characterisation of novel gene products
that regulate phospholipid metabolism and lipid
droplet formation in the yeast saccharomyces
cerevisiae. 2012-2014: $310,000.
ARC Federation Fellowship
Neilan BA. The toxins of water-borne
cyanobacteria: regulation and exploitation of their
biosynthesis, 2008-2013: $1,640,000.
ARC QEII Fellowship
Brown MV. Towards a predictive model for coastal
marine microbial assemblages. 2009-2013:
$695,000.
Tanaka MM. Mathematical models and
bioinformatic analyses of bacterial genome
evolution. 2009-2013: $614,870.
ARC Future Fellowship
ARC Linkage Projects
Manefield MJ, Thomas T, Kjelleberg SL & Steinberg
PD. In situ microbial conversion of coal to methane:
Biotechnology development for clean use of
Australian coal. 2010-2013: $1,237,600.
Manefield, MJ, Gooding, JJ & Lam, D,
Collaborating Organisations: Coffey Environments
Australia Pty Ltd, Dow Chemical (Australia) Limited,
Orica Australia Pty Ltd. In situ bioremediation
solutions for Australia’s organochlorine
contaminated aquifers. 2011-2015: $773,000.
Murray SA, O’Connor WA & Seebacher F.
Differential accumulation of algal biotoxins within
diploid and triploid Pacific Oysters and Sydney
Rock Oysters. 2011-2013: $115,000.
Neilan BA. Collaborating organisation: Diagnostic
Technology P/L. Discovery of bioactive natural
substances from uncultured bacteria and
their production using photosynthetic reactor
technology. 2011-2014: $1,058.000.
Thomas T, Munroe PR & Joseph SD. Development
of the next generation of organo-mineral fertilisers
utilising domestic and commercial waste products.
2012-2015: 340,000.
ARC Linkage Infrastructure and Equipment
Facilities
Crossley, M, Ward, RL, Kelleher, AD, Gunning, PW,
Haber, M, King, NJ, Sedger, LM & Martiniello-Wilks,
R. Collaborating Organisations: USYD, UTS. A five
laser multichannel flow cytometry cell sorter for
the University of New South Wales as part of an
advanced flow cytometry network. 2012: $250,000.
64
Manefield MJ. Harnessing microbial respiration for
pollutant degradation and natural gas production.
2011-2015: $808,000.
Yang HR. The cellular dynamics of lipid droplets:
implications for obesity and biodiesel production,
2009-2013,: $788,800.
ARC DECRA Fellowship
Lauro, F. The role of deep-sea microorganisms in
nutrient cycling in the Southern Ocean. 2012-2014:
$375,000.
National Health & Medical Research
Council
NHMRC Project Grants
Brown AJ. Novel control points in cholesterol
synthesis. 2011-2013: $354,208.
Collins AM. Immunoglobulin germline genes, BCR
repertoire development and disease susceptibility.
An investigation of haplotypic variation between
individuals. 2012-2014: $502,215.
Crossley M. Transcriptional control of
megakaryopoiesis. 2012-2014: $651,010.
Crossley M. Transcriptional regulation of globin
genes. 2012-2014: $636,325.
Lan R, Sintchenko V, Gilbert G, McIntyre P,
Marshall H & Wood N. Evolution of pertussis
epidemics and effect of genotypes on infection
outcomes and immunisation. 2011-2013: $638,100.
Sytnyk V. The impact of the changes in levels
of adhesion molecules NCAM2 and DsCAM on
synapse formation and function: implications for
Down syndrome. 2011-2013: $322,524.
Yang HR. The role of seipin in adipocyte
development and lipid droplet formation. 20122014: $363,510.
NHMRC Training (Postdoctoral) Fellowship
Kaakoush N. Australian Based Biomedical
Category. 2011-2014: $290,032.
Other National Schemes
Australian Institute of Nuclear Science and
Engineering Research Award
Foster LJ, Russell RA & Holden PJ. Why is chitosan
antimicrobial? Relating polymer chain conformation
to bactericide activity. 2012: $26,000.
Neilan BA. Deuterium labelling of a novel
N-hydroxylase responsible for cyanobacterial
toxin production for NMR structural studies. 2012:
$34,857.
Australian National Data Service
Wilkins MR. Validation of genomes and
transcriptomes with proteomic data. 2012:
$246,000.
Cure Cancer
Catts V. Anti cancer effects of cholesterol trafficking
and synthesis inhibitors in glioblastoma. 2012:
$90,000.
National Breast Cancer Foundation Novel
Concept Awards
Lawson J, Whitaker NJ & Glenn WK. Viruses and
breast cancer: Normal patient follow up project.
2011-2012: $200,000.
National Heart Foundation of Australia
Brown AJ. Taking Advantage of an endogenous
regulator to improve statin therapy. 2012-2013:
$130,000.
Noah Foundation (Australia) Genetic Control
of Obesity Fund
Yang H. 2011-2013: $80,000.
NSW State Government Science Leveraging Fund
Wilkins MR & Molloy M. Systems biology in NSW.
2011-2013: $656,000.
Prostate Cancer Foundation of Australia/
Project Grants
Brown AJ. Exploiting cholesterol metabolism to
fight prostate cancer. 2012-2013: $250,000.
Sydney Catchment Authority
Neilan BA & Mihali T. Determination of the factors
responsible for the regulation of cyanobacterial
genes to produce toxins. 2010-2012: $187,680.
International Schemes
Dept of Sustainability, Environment, Water,
Population & Communities/Australian Antarctic
Division
Fulbright Alumni Initiative Grant
Cavicchioli R, Abdool AA, DeMaere MZ, Wilkins D,
Willias TJ & Yau S. Monitoring ecosystem stability
in model marine-derived Antarctic lake systems.
2012-2014: $97,875.
UNSW Internal Schemes
Department of the Environment, Water,
Heritage and the Arts/National Taxonomy
Research Grant
Brown MV & Murray SA. Identifying and describing
new lineages of benthic marine alveolates
(Alveolata) from the Indian Ocean, Western
Australia. 2010-2013: $30,000.
EIF Super Science Project/Bioplatforms
Australia
Wilkins MR & Systems Biology Initiative. Foundation
datasets and technology in the major -omics
facilities of NSW. 2010-2014: $2.0M.
Foster LJ. Australian-American technology for
tissue engineering. 2012: $10,000.
Major Research Equipment Infrastructure
Initiative (MREII)
Foster, J. Electrospin for biomedical
nanotechnology. 2012: $139,685.
Neilan, B. High Performance Liquid
Chromatographic (HPLC) system with semipreparative pump, autosampler and automatic
fraction collector linked to complementary
detection modes of spectroscopic Photodiodide
Array Detection (PDA) and Evaporative Light
Scattering Detection (ELSD) or Charged Aerosol
Detector (CAD). 2012: $115,000.
65
Wilkins, M. MiSeq sequencing platform - next
generation nucleic acid sequencer. FastPrep24
sample preparation system. 2012: $159,471.
UNSW Learning and teaching Grant Seed
Funding
Foster LJ. OH&S: A new graduate attribute? 2012:
$1,760.
Faculty of Science Research Grant (FRG)
Burns B. Listening in: communication as a driver
for stromatolite microbial diversity and function.
$10,000.
Ferrari B. Towards a geospatial analysis of
microbial communities in terrestrial Antarctic and
sub-Antarctic regions through analysis of fungal
and bacterial biodiversity. $10,000.
UNSW Goldstar Award (NHMRC)
Brown AJ. Taking advantage of an endogenous
regulator to improve statin therapy. $40,000.
Mitchell HM. Investigation of the role of the
intestinal microflora in the aetiology of Crohn’s
Disease. $40,000.
Sytnyk V. Analysis of the molecular mechanisms
of abnormal synaptic vesicle recycling induced
by disruption of the functions of the neural
cell adhesion molecule (NCAM) as a possible
mechanism contributing to mood disorders and
schizophrenia. $40,000.
Yang H. Oxysterol binding proteins, AAA ATPases
and endosomal cholesterol trafficking. $40,000.
Faculty of Science Silverstar Award (ARC)
Neilan B. The genetics and chemical ecology of
marine symbioses as a basis for drug discovery.
$35,000.
Dawes IW. Global mechanisms affecting heat
stress survival and their implications for cell
ageing. $35,000.
Lutze-Mann L. An evaluation of gene expression
in cellular (in vitro) and a rat (in vivo) model of
glioblastoma multiforme. $5,000.
Murray V. Cisplatin global DNA screening: the
precise location of cisplatin adducts in the entire
human genome. $10,000.
Whitaker N. Human Papillomavirus in breast cancer
– is there a causal link? $10,000.
Zhang L. Investigation of the possible role of
Campylobacter concisus in Crohn’s disease.
$10,000.
Faculty of Science Early Career (ECR) Grant
Galea A. Investigating the DNA targets of cisplatin
and related analogues in human telomeric,
promoter and guanine-rich DNA sequence
elements. $7,500
Ballard JWO. Is mitochondrial DNA a selectively
neutral marker? $35,000.
Hart-Smith G. Selected reaction monitoring
of peptides with multiple post-translational
modifications. $7,500.
Cooper A. Discovering cellular pathways to reduce
Endoplasmic Reticulum (ER) stress and recover
valuable proteins from degradation in the ER.
$35,000.
Kaakoush N. Microbial variations and metabolic
biomarkers in patients with inflammatory bowel
diseases. $7,354.
Faculty of Science Silverstar Award (NHMRC)
Mitchell HM. Investigation of the pathogenesis of
the emergent pathogen Campylobacter concisus.
$35,000.
Foster LJ. A band-aid for the eye: treatment of
corneal wounds and ulcers. $35,000.
66
Janitz M. Discovering new levels of human brain
complexity: determination of alternative splicing
and gene expression patterns within distinct
cerebral regions. $10,000.
Lebard R. Determining the transcriptional and
bioenergetic effects of the invader-host relationship
between the clinically significant Wolbachia variant
popcorn and its host. $7,354.
Wolff J. Revealing transcriptional and bioenergetic
consequences of infections with the medically
important microbe Wolbachia in the host organism.
$7,354.
67
2012 Publications
Aandahl R, Reyes JF, Sisson SA
& Tanaka M. (2012) ‘A modelbased Bayesian estimation of the
rate of evolution of VNTR loci in
Mycobacterium tuberculosis’, PLoS
Computational Biology, 8: e1002573.
Abramovich RS, Pomati F, Jungblut
AD, Guglielmin M & Neilan B.
(2012) ‘T-RFLP fingerprinting
analysis of bacterial communities
in debris cones, Northern Victoria
Land, Antarctica’, Permafrost and
Periglacial Processes, 23: 244-248.
Al Tebrineh J, Merrick C, Ryan
D, Humpage A, Bowling LC &
Neilan B. (2012) ‘Community
composition, toxigenicity, and
environmental conditions during
a cyanobacterial bloom occurring
along 1,100 kilometers of the Murray
River’, Applied and Environmental
Microbiology, 78: 263-272.
Al Tebrineh J, Pearson LA, Yasar
SA & Neilan BA. (2012) ‘A multiplex
qPCR targeting hepato- and
neurotoxigenic cyanobacteria of
global significance’, Harmful Algae,
15: 19-25.
Ardalan A, Oskarsson, M,
Natanaelsson, C, Wilton AN,
Ahmadian A & Savolainen P. (2012)
‘Narrow genetic basis for the
Australian dingo confirmed through
analysis of paternal ancestry’,
Genetica, Published online 23 May:
1-9.
Aung MT, Ayer A, Breitenbach M
& Dawes IW. (2012) ‘Oxidative
stresses and ageing’, in Breitenbach
M, Jazwinski SM & Laun P (eds),
Aging Research in Yeast, Springer
Science+Business Media B.V.,
Dordrecht, ch. 2: 13-54.
68
Aw WC, Dowell FE & Ballard
JWO. (2012) ‘Using near-infrared
spectroscopy to resolve the species,
gender, age, and the presence of
Wolbachia infection in laboratoryreared Drosophila’, G3: Genes,
Genomes, Genetics, 2: 1057-1065.
Ayer A, Fellermeier S, Li SS, Fife
C, Smits G, Jeyer AJ, Dawes IW &
Perrone G. (2012) ‘A genome-wide
screen in yeast identifies specific
oxidative stress genes required for
the maintenance of sub-cellular
redox homeostasis’, PLoS ONE, 7:
e44278.
Bai L, Xia S, Lan R, Liu L, Ye C, Wang
Y, Jin D, Cui Z, Jing H, Xiong Y, Bai
X, Sun H, Zhang J, Wang L & Xu J.
(2012) ‘Isolation and characterization
of cytotoxic,aggregative Citrobacter
freundii‘, PLoS One, 7: e33054.
Barraud N, Kardak B, Yepuri N,
Howlin R, Webb JS, Faust S,
Kjelleberg S, Rice SA & Kelso
MJ. (2012) ‘Cephalosporin-3’diazeniumdiolates: targeted
NO-donor prodrugs for dispersing
bacterial biofilms’, Angewandte
Chemie (International Edition), 51:
9057-9060.
Bazylinski D, Williams TJ, Lefevre
C, Berg RJ, Zhang CL, Bowser SS,
Dean AJ & Beveridge TJ. (2012)
‘Magnetococcus marinus gen. nov.,
sp. nov., a marine, magnetotactic
bacterium that represents a novel
lineage (Magnetococcaceae fam.
nov.; Magnetococcales ord. nov.) at
the base of the Alphaproteobacteria’,
International Journal of Systematic
and Evolutionary Microbiology, 63:
801-808.
Bazylinski D, Williams TJ, Lefevre C,
Trubitsyn, D, Fang J. Beveridge TJ,
Moskowitz BM, Ward B. Schubbe
S, Dubbels BL & Simpson B. (2012)
‘Magnetovibrio blakemorei, gen.
nov. sp. nov., a new magnetotactic
bacterium (Alphaproteobacteria:
Rhodospirillaceae) isolated from a
salt marsh’, International Journal
of Systematic and Evolutionary
Microbiology, published online 14
September.
Bernardo BC, Gao X, Winbanks
C, Boey E, Tham YK, Kiriazis H,
Gregorevic P, Obad S, Kauppinen
S, Du X, Lin RCY & McMullen JR.
(2012) ‘Therapeutic inhibition of the
miR-34 family attenuates pathological
cardiac remodeling and improves
heart function’, Proceedings of the
National Academy of Sciences of the
United States of America-Biological
Sciences, 109: 17615-17620.
Breit SN, Carrero JJ, Tsai VWW,
Yagoutifam N, Luo XW, Kuffner
T, Bauskin AR, Wu L, Jiang L,
Baranyi P, Heimburer O, Murikami
M, Apple F, Marquis C, Macia L,
Lin S, Sainsbury-Salis A, Herzog
H, Law MG, Stenvinkel P & Brown
DA. (2012) ‘Macrophage inhibitory
cytokine-1 (MIC-1/GDF15) and
mortality in end-stage renal disease’,
Nephrology Dialysis Transplantation,
27: 70-75.
Breitenbach M, Laun P, Dickinson
JR, Klinger H, . (2012) ‘The role of
mitochondria in the aging processes
of yeast’, in in Breitenbach M,
Jazwinski SM & Laun P (eds),
Aging Research in Yeast, Springer
Science+Business Media B.V.,
Dordrecht, ch. 3: 55-78.
Bridge WJ, Chandler SD, Zarka
M, Vinaya Babu S, Suhas Y &
Raghunatha Reddy K. (2012)
‘Safety assessment of gammaglutamylcysteine sodium salt’,
Regulatory Toxicology and
Pharmacology, 64: 17-25.
Brown AJ. (2012) ‘Cholesterol versus
other sterols: how do they compare
as physiological regulators of
cholesterol homeostasis?’, European
Journal of Lipid Science and
Technology, 114: 617-623.
Chesterfield D, Rogers PL, Al-Zaini
E & Adesina AA. (2012) ‘Production
of biodiesel via ethanolysis of waste
cooking oil using immobilised lipase’,
Chemical Engineering Journal, 2078: 701-710.
Brown MV, Lauro FM, Demaere MZ,
Muir L, Wilkins D, Thomas, T, Riddle
M, Fuhrman J, Andrews-Pfannkoch
C, Hoffman JM, McQuaid J, Allen
A, Rintoul & Cavicchioli R. (2012)
‘Global biogeography of SAR11
marine bacteria’, Molecular Systems
Biology, 8: 595.
Chiu AS, Gehringer MM, Braidy N,
Guillemin GJ, Welch JH & Neilan BA.
(2012) ‘Excitotoxic potential of the
cyanotoxin methyl-amino-l-alanine
(BMAA) in primary human neurons’,
Toxicon, 60: 1159-1165.
Burdach J, O’Connell M, Mackay
JP & Crossley M. (2012) ‘Twotiming zinc finger transcription
factors liaising with RNA’, Trends in
Biochemical Sciences, 37: 199-205.
Burgos-Portugal J, Kaakoush
NO, Raftery MJ & Mitchell HM.
(2012) ‘Pathogenic potential of
Campylobacter ureolyticus’, Infection
and Immunity, 80: 883-890.
Burns BP, Gudhka RK & Neilan BA.
(2012) ‘Genome sequence of the
halophilic archaeon Halococcus
hamelinensis’, Journal of
Bacteriology, 194: 2100-2101.
Burns V, Sharpe LJ, Gelissen IC &
Brown AJ. (2012) ‘Species variation
in ABCG1 isoform expression:
Implications for the use of animal
models in elucidating ABCG1
function’, Atherosclerosis, 226: 408411.
Castano-Rodriguez N, Kaakoush NO,
Schmidt HA, Goh K, Fock KM, Sutton
P, Chionh Y & Mitchell HM. (2012)
‘PAR-1 polymorphisms and risk of
Helicobacter pylori-related gastric
cancer in a Chinese population’,
Anticancer Research, 32: 3715-3721.
Catts VS & Shannon Weickert C.
(2012) ‘Gene expression analysis
implicates a death receptor pathway
in schizophrenia pathology’, PLoS
One, 7: Article number e35511.
Chiu J & Dawes IW. (2012) ‘Redox
control of cell proliferation’, Trends in
Cell Biology, 22: 592-601.
Chong GH, Kimyon O, Rice SA,
Kjelleberg S & Manefield MJ. (2012)
‘The presence and role of bacterial
quorum sensing in activated sludge’,
Microbial Biotechnology, 5: 621-633.
Chong HS, Campbell LT, Padula
MP, Hill CJ, Harry EJ, Li SS, Wilkins
MR, Herbert BR & Carter DA. (2012)
‘Time-course proteome analysis
reveals the dynamic response
of cryptococcus gattii cells to
fluconazole’, PLoS One, 7: e42835.
Chuang CY, Shahin K, Lord MS,
Melrose J, Doran PM & Whitelock J.
(2012) ‘The cartilage matrix molecule
components produced by human
foetal cartilage rudiment cells within
scaffolds and the role of exogenous
growth factors’, Biomaterials, 33:
4078-4088.
Chung HCY, Lin RCY, Logan GJ,
Alexander I, Sachdev PS & Sidhu K.
(2012) ‘Human induced pluripotent
stem cells derived under feeder-free
conditions display unique cell cycle
and DNA replication gene profiles’,
Stem Cells and Development, 21:
206-216.
Chung PP, Hyne RV & Ballard JWO.
(2012) ‘It’s all in the genes: How
genotype can impact upon response
to contaminant expose and the
implications for biomonitoring in
acquatic systems, in Srivastava JK
(ed), Environmental Contamination,
InTech, ch.7: doi: 10.5772/30911.
Cooley N, Cowley MJ, Lin RCY,
Marasco S, Wong C, Kaye DM,
Dart AM & Woodwock EA. (2012)
‘Influence of atrial fibrillation on
microrna expression profiles in left
and right atria from patients with
valvular heart disease’, Physiological
Genomics, 44: 211-219.
Correa CC & Ballard JWO. (2012)
‘Wolbachia gonadal density in female
and male Drosophila vary with
laboratory adaptation and respond
differently to physiological and
environmental challenges’, Journal
of Invertebrate Pathology, 111: 197204.
Correa CC, Aw WC, Melvin RG,
Pichaud N. & Ballard JWO.
(2012) ‘Mitochondrial DNA
variants influence mitochondrial
bioenergetics in Drosophila
melanogaster’, Mitochondrion, 12:
459-464.
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