2014 Annual Report - The School of Biotechnology and

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2014 Annual Report - The School of Biotechnology and
School of Biotechnology and Biomolecular Sciences
Annual Report 2014
Never Stand Still
Faculty of Science
School of Biotechnology and Biomolecular Sciences
School of Biotechnology and Biomolecular Sciences
Biological Sciences Building
Room 229 Level 2
UNSW Australia
Kensington NSW 2033 Australia
babs.unsw.edu.au
Tel: 61 2 9385 2029
Fax: 61 2 9385 1483
Production Editor: Michele Potter
Graphic Design: Jane Gascoigne – gascoignedesign
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. UNSW Australia
assumes no responsibility for the accuracy of information provided by third parties.
© 2015 UNSW Australia
Published July 2015
CRICOS Provider Number 00098G
Contents
Foreword from Head of School
2
2014 School Management
3
Executive committee members
3
Our People
4
School at a Glance
6
A New Home for BABS
8
2014 Highlights
9
BABS Research Group – Environmental Microbiology
13
BABS Research Group – Infectious Disease
16
BABS Research Group – M'$-$Ǐ*3!!&33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333A9
BABS Research Group – Systems and Cellular Biology
24
Profile – Dr Richard Edwards, New Senior Lecturer
27
Profile – Dr Kyle Hoehn, New Senior Lecturer
28
Profile – Dr Jai Tree, New Senior Lecturer
29
Profile – Ruben Meerman, ABC Surfing Scientist and BABS PhD Candidate
30
Affiliated Research Organisations
32
The Ramaciotti Centre for Genomics
33
NSW Systems Biology Initiative
36
Centre for Marine Bio-Innovation
37
Specialised Facilities, Services and Equipment
38
External Partner Organisations
40
Memberships in Societies and Associations
42
Learning and Teaching
43
Innovations in teaching
43
Modern facilities
44
Outreach and supporting students
44
Undergraduate degrees
44
Majors
45
Honours
45
Postgraduate degrees
45
Teaching students how science can make a difference
46
Learning and Teaching Prizes and Scholarships
47
2014 undergraduate student awards
47
BABS PhD scholarship supplement scheme
48
BABSOC
49
2014 Honours Completions
51
2014 PhD Completions
53
Research Funding
55
Grants awarded in 2014 commencing in 2015
55
Grants current in 2014 (awarded prior to 2014)
57
2014 Publications
61
Our Vision
Our ambition is to be the best School of molecular biosciences in Australia, performing
excellent research and attracting and retaining high-calibre staff and students. Towards
this end, we encourage an engaged and collegial atmosphere, where advancement
is based on merit and staff members’ efforts are recognised. We strive to foster an
environment where research excellence can thrive, and where quality and innovative
teaching is valued. We strive to manage ourselves in a fair, transparent and efficient way.
Our Mission
We aim to create a community dedicated to achieving national and international levels of
scholarship in the fields of biotechnology and biomolecular sciences.
Our Aims
The School of Biotechnology and Biomolecular Sciences aims to:
„
be nationally and internationally recognised as a source of scholarship
„
apply cutting-edge biotechnology to capitalise on biomolecular discoveries
„
train and enthuse students
„
further interdisciplinary research
„
positively interact with researchers and students across the university, the state, the
nation and the globe.
Foreword from Head of School
Welcome to the 2014 Annual Report for the School
of Biotechnology and Biomolecular Sciences (BABS)
at UNSW, one of Australia’s premier science and
technology universities. We study life at a molecular
level (biomolecular sciences), and strive to put that
knowledge to good use in terms of commercial
applications (biotechnology). We have core strengths
in molecular medicine (particularly in cancer,
metabolism and brain research), environmental
biology (both freshwater and marine environs)
and infectious diseases, with a particular focus on
diseases of the gastrointestinal tract. Underpinning
much of what we do is a systems-based approach to
biology, embracing the latest technologies yielded by
the omics revolution. We are therefore proud to host
the Ramaciotti Centre for Genomics within BABS,
which is going from strength to strength under the
directorship of Professor Marc Wilkins.
As this is my first Annual Report as Head of School,
I would like to thank my predecessors, Professor Bill
Ballard and Associate Professor Noel Whitaker. Bill
presided over some of the greatest changes in BABS
since our inception and pushed through the most
extensive renovations that the School has seen. As
Acting HOS, Noel thankfully was not content to take
just a caretaker role, but initiated a number of new
initiatives of his own that we have continued.
I took over as HOS in July 2013, and it is certainly
a great privilege to lead such a talented and
dynamic team. I’m also fortunate to have Dr Louise
Lutze-Mann as my Deputy Head of School and
Director of Teaching. Louise is a fine and innovative
teacher, winning several teaching awards, including
a prestigious national award in 2014. We have
begun a host of initiatives aimed at providing our
students with a richer and more fulfilling experience,
including introducing more research opportunities
to undergraduates. We also re-purposed an old
lab to create an informal student learning space,
called BiBS (BABS Interactive Breakout Space),
which is being very well utilised, giving our students
a welcoming home in BABS to hang out and study.
Thanks to the ongoing review of our curriculum, we
are now taking concrete steps towards revamping
our course offerings (a big job!) and I am grateful to
Louise for driving this and to all of the staff who have
been actively engaged in these discussions.
BABS is a large and diverse School. This can be a
strength but also a challenge, so several initiatives
have been directed at increasing contacts and
cohesion within the School. For example, we
reinstated PhD exit seminars, mixing them up with
both external and internal speakers so that we all
|2
catch up on everyone’s latest research findings.
These Friday afternoon seminars followed by a
Happy Hour have proved very popular, with some
of the seminars being standing room only. We have
also had a very successful renaissance of the end-ofyear BABS Research Symposium, with our research
students and postdocs showcasing the richly diverse
science being conducted within the School. In the
past two years, Dr Wallace Bridge and his BABSOC
team have done a wonderful job organising the
symposium – even going to the trouble of coaching
the presenters to ensure high-quality and accessible
presentations.
Since the last Annual Report (2012), we have had
a big injection of fresh talent into the School, being
joined by Dr Paul Waters (from ANU), Dr Irina
Voineagu (RIKEN Omics Science Center, Japan), Dr
Richard Edwards (University of Southampton), Dr
Kyle Hoehn (University of Virginia) and Dr Jai Tree
(University of Melbourne). Several of our continuing
academic staff also became Research Fellows in the
last couple of years: Dr Irina Voineagu (ARC DECRA),
Associate Professors Kevin Morris, Torsten Thomas,
and Mark Tanaka (ARC Future Fellowships) and
Professor Rob Yang, who managed to nimbly leap
from an ARC Future Fellowship to an NHMRC Senior
Research Fellowship. Securing such Fellowships in
the current climate is no mean feat, and indeed, is a
great achievement. Congratulations to all!
Towards the end of 2014 there was some nostalgia
mixed with lots of excitement as the Biomed Lecture
Theatres were demolished. The nostalgia was due to
many of us having spent much time lecturing there,
and the excitement because out of the rubble our
new Biosciences Building will rise, ready for us to
occupy in 2017.
Thanks to Michele Potter for producing yet another
highly polished and professional Annual Report.
And finally thank you, the reader, for looking over
this report and sharing in the excitement of just a
selection of our recent discoveries.
Professor Andrew Brown
2014 School Management
The operations of the School are managed by the Head of School, assisted by the Deputy Head of School
and six members of the BABS Executive Committee, together with various other committees responsible
for key areas of the School’s operations.
Professor Andrew Brown
Head of School
Dr Louise Lutze-Mann
Deputy Head of School
Executive committee members
Dr Brendan Burns
Dr Chris Marquis
A/Professor Vincent Murray
Professor Brett Neilan
A/Professor Mark Tanaka
Professor Marc Wilkins
3|
Our People
Academic Staff
Senior Lecturers
Professors
Wallace Bridge
Bill Ballard
Brendan Burns
Andrew Brown
(Head of School)
Richard Edwards
BSc Hons PhD (UNSW)
Belinda Ferrari
Rick Cavicchioli
Professional Officer
Infrastructure
Kyle Hoehn
Merlin Crossley
(Dean, Faculty of Science)
Michael Janitz
Michele Potter
BA (USYD)
Staffan Kjelleberg
(Scientia Professor)
Louise Lutze-Mann
(Deputy Head of School)
Chris Marquis
Hazel Mitchell
Vladimir Sytnyk
Brett Neilan
(Scientia Professor)
Irina Voineagu
(ARC DECRA Fellow)
Peter White
Paul Waters
Marc Wilkins
Li Zhang
Malcolm Walter
(ARC Professorial Fellow)
H Robert Yang
(NHMRC Senior Research
Fellow)
Lecturers
John Foster
Ruiting Lan
Michael Manefield
(ARC Future Fellow)
Kevin Morris
(ARC Future Fellow)
Vincent Murray
Mark Tanaka
Torsten Thomas
Noel Whitaker
William Whitfield
Finance Officer
Technical Officers
Ned Elkaid
Daud Khaled
BSc Hons MSc (Dhaka)
PhD (UNSW)
Elessa Marendy
BSc Hons, PhD (JCU)
Sharon Murarotto
BAppSc (UTS)
Kim Nguyen
BSc (UNSW)
Rebecca LeBard
Shamima Shirin
John Wilson
Owen Sprod
BSc Hons PhD (U Tasmania)
Professional and Technical
Staff
Lily Zhang
BEng (Tianjin)
Administration
Adam Abdool
Administrative Officer (50%)
Jenny Campbell
Administrative Assistant
Kylie Jones
Administrative Officer
Geoff Kornfeld
Professional Officer
Infrastructure
Terry Law
WHS Manager
Jani O’Rourke
BSc (USYD) PhD (UNSW)
Professional Officer (Laboratory
Manager)
|4
Jeff Welch
Anne Galea
Associate Professors
Andrew Collins
School Manager
Research Staff
Research Fellows
Frances Byrne
(Hope Funds for Cancer
Research Fellow)
Nadeem Kaakoush
(NHMRC Postdoctoral
Training Fellow)
Federico Lauro
(ARC DECRA Research Fellow)
Senior Research Associates
Leanne Pearson
Suhelen Egan
(ARC Future Fellow)
Jacob (Yanfei) Qi
Richard Pearson
Kate Quinlan
Bettina Rosche
Tim Williams
Research Associates
Michelle Allen
Sabrina Beckman
Mark Brown
Frances Byrne
Rocky Chau
Zhiliang Chen
Matt Clemson
Susan Corley
Paul D’Agostino
Nandan Deshpande
Robin (Ximing) Du
Melissa Erce
Jim (Zhi Ming) Fang
David Fung
Alister Funnell
Rajesh Ghai
Gene Hart-Smith
Katherine Jackson
John Kalaitzis
Andrew Kelly
Iryna Leshchynska
Ruby Lin
Cassie Mak
Rabia Mazmouz
Sophie Octavia
Sarah Ongley
Martin Pagac
Laura Sharpe
Nidhi Sodhi
Aiden Tay
Shafagh Waters
Jason Woodhouse
Research Assistants
Cindy (Yi Ning) Gao
Alyce Hancock
Sarah Payne
Helene Lebhar
Winnie Luu
Natalie Twine
Young J Jeon
(Visiting Fellow)
James Krycer
(Conjoint)
James Lawson
(Emeritus Professor)
Ruby Lin
(Adjunct Senior Lecturer)
Karen MacKenzie
(Conjoint)
Kerensa McElroy
(Conjoint)
Anne Mai-Prochnow
(Adjunct Lecturer)
William Rawlinson AM
(Professorial Visiting Fellow)
Yan Wang
Laurent Rivory
(Visiting Associate Professor)
Visiting and Adjunct Staff
Peter Rogers
(Emeritus Professor)
Kevin Barrow
(Professorial Visiting Fellow)
Emmanuelle Botte
(Visiting Fellow)
Andrew Burgess
(Conjoint)
Antony Cooper
(Visiting Fellow)
Anuruddhika Dadigamuwage
(Visiting Fellow)
Ian Dawes FAA
(Emeritus Professor)
Michael Edwards
(Honorary Associate Professor)
Susanne Erdmann
(Visiting Fellow)
Carly Rosewarne
(Adjunct Lecturer)
Stuart Tangye
(Visiting Fellow)
Nai Tran-Dinh
(Visiting Fellow)
Alison Todd
(Senior Visiting Fellow)
Mark Van Asten
(Adjunct Senior Lecturer)
Sheila Van Holst Pellekaan
(Visiting Fellow)
Pieter Visscher
(Senior Visiting Fellow)
Martin Zarka
(Adjunct Lecturer)
Haluk Ertan
(Professorial Visiting Fellow)
Michelle Gehringer
(Visiting Fellow)
Wendy Glenn
(Honorary Lecturer)
Iggy (Chi Nam) Pang
5|
School at a Glance
The School of Biotechnology and Biomolecular
Sciences (BABS) is one of the largest Schools in
the Faculty of Science at UNSW Australia. UNSW
is a member of the prestigious Group of Eight, a
coalition of Australia’s leading research-intensive
universities. Our University is renowned for the
quality of its graduates and world-class research.
This is clearly demonstrated by:
„
being ranked 48th in the 2014/15 QS World
University Rankings
„
being awarded the maximum QS Five Star
Plus rating in the 2014 rankings, one of only 13
universities in the world to do so
„
being voted one of the top performing
universities in the 2014 Global Employability
University Ranking
„
UNSW researchers being awarded the highest
amount of Australian Research Council (ARC)
funding in Australia for 2015
„
being recognised as the Australian university
with the strongest links to industry: in 2014
UNSW received $10.5 million in Linkage
Project grants from the ARC, the highest level
of funding in the country.
The School of BABS is a powerhouse of
biomolecular research, employing 33 academics,
50 research associates and 16 technical and
administrative staff. At any point in time, BABS
is training over 150 Higher Degree by Research
students, and teaches approximately 2,000
full-time undergraduate students each year.
BABS consistently attracts extensive government
and industry funding and top-tier academic
accolades. Our achievements in technology
development are underpinned by excellence in
fundamental research.
Research
The School is recognised as one of the largest
and most prestigious schools of scientific
research and teaching in Australia. With
distinguished academic staff, an innovative
teaching program and state-of-the-art facilities,
BABS is producing graduates and scientific
discoveries of international renown. We aim
to achieve a balance of pure basic, strategic,
applied and experimental development research.
We have strong links with a range of high
profile external research institutions, including
the Garvan Institute of Medical Research, the
Victor Chang Cardiac Research Institute and
the Prince of Wales Hospital, and a solid track
record in linking fundamental research to tangible
outcomes.
Researchers in the School are aligned into four
research discipline areas:
Environmental Microbiology
Environmental Microbiology forms a top-level
research grouping at UNSW. Coupled with the
biotechnology sector, we have a strong presence
in the pure and applied biosciences. BABS
addresses globally relevant research themes in
environmental health and sustainability, microbial
processes, biomaterials and nanotechnology,
environmental genomics, biodiversity and
conservation, and bioprospecting for enzyme
and drug discovery. Current research projects
encompass numerous national and international
networks with Asian, European and US-based
research institutes and universities.
Infectious Disease
Infectious diseases are responsible for around
one-third of annual deaths worldwide. The BABS
Infectious Disease research group focuses
on molecular epidemiology, with an aim to
combat microbes that remain a huge biological
challenge affecting both human and animal
health. The group brings together a wide range
of internationally recognised research expertise
to investigate the microbiological factors affecting
a range of vital health issues, including tracking
norovirus pandemics, molecular evolution and
population structure of bacterial pathogens
(Bordetella, Salmonella, Shigella and Vibrio),
immune evasion by hepatitis, inflammatory bowel
disease, and viruses in cancer.
|6
Molecular Medicine
Molecular Medicine within BABS 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. Major
research strengths of the group currently exist in
biomaterials, immunology, bioinformatics, cancer
and genetics. The group uses a wide range of
cutting-edge molecular and bioinformatic tools
to understand and combat genetic disease and
cancer. Specific research foci include cancer,
immunogenetics and biomaterials.
Systems and Cellular Biology
The Systems and Cellular Biology (SCB)
group undertakes research in the biology of
eukaryotes. SCB groups are active users of
high-technology facilities, with researchers being
highly successful in attracting regular competitive
Category 1 funding, particularly from the ARC
and National Health & Medical Research Council
(NHMRC). The group has also been active in
securing infrastructure funding in genomics,
proteomics and systems biology. Research
areas for this group include cholesterol and
sterols, cell stress and aging, genetic mapping
of phenotypes and disease, protein interaction
networks and systems biology.
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.
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.
Postgraduate
BABS offers Doctor of Philosophy (PhD) and
Master of Science (MSc) research-based
degrees, and the School is one of the highest
recruiters of PhD students at UNSW. A number
of our PhD students are supervised by visiting or
adjunct staff located at external organisations,
including the Garvan Institute of Medical
Research and the Prince of Wales Hospital.
The School offers a PhD Scholarship Supplement
Scheme for eligible new and continuing students,
comprising a $5,000 one-off annual payment.
Research facilities
BABS is home to a number of significant research
facilities that are leaders in their respective fields,
providing cutting-edge services to researchers
within BABS, across UNSW and other Australian
and international institutions. These include
the Ramaciotti Centre for Genomics, Centre
for Marine Bio-Innovation, New South Wales
Systems Biology Initiative and School staff
are also members of the UNSW Evolution &
Ecology Research Centre and the Environmental
Microbiology Initiative.
7|
A New Home for BABS
New Biological Sciences Building to complete
UNSW Biomedical Precinct
Planning and initial construction is under way
for a new 16,900m² building to house UNSW’s
biological and environmental sciences, which
includes many of the research labs in BABS. The
new Biological Sciences Building will complete
UNSW’s Biomedical Precinct, which comprises
the Lowy Cancer Research Centre and the
recently redeveloped Wallace Wurth Building,
home to the Faculty of Medicine.
The project aims to deliver world-class facilities,
with the building designed to support current
research as well as providing infrastructure to
support future technological advances. The
main features of the design include flexible
research laboratory spaces, specialised research
equipment, staff accommodation and large
loading dock, stores, workshop and utilities. The
building is expected to have capacity for more
than 400 staff and PhD students.
The key objectives of the project are to:
„
provide a contemporary, world class research
and teaching environment as part of the
UNSW Biomedical Precinct
„
provide modern infrastructure for training the
next generation of researchers and technically
qualified graduates who will help maintain
Australia’s connectivity and competitiveness in
a rapidly advancing world
„
create flexible and adaptable space for
strategic recruitment, taking into account
trends in technology, research infrastructure,
and national and UNSW priority areas
„
enhance effectiveness and interdisciplinary
teamwork by efficiently connecting biologists,
environmental, earth and biomedical scientists
and reinforcing research synergies between
the research groups, Schools and Faculties.
A complete refurbishment of the current Biological Sciences Building, which was built circa 1960, will take
place after the new building is complete. The current forecast completion date is late 2017.
|8
2014 Highlights
Deputy HOS and Director of Teaching
Dr Louise Lutze-Mann
Louise’s teaching expertise was recognised at the highest
level in Australia when she won the Award for Teaching
Excellence for Biological Sciences, Health and Related
Studies in the discipline of Biological Sciences as part of the
2014 Australian Government Awards for University Teaching.
The award was presented at Parliament House Canberra in
December, with Louise receiving a congratulatory letter from
UNSW Vice-Chancellor Professor Fred Hilmer.
In addition, the Dean of Science Professor Merlin Crossley
announced Louise the winner of the Best Lecturer in Science as
voted by students in the Faculty of Science Excellence Awards
for 2014.
Louise receiving her award at Parliament House, Canberra.
BABS HDR students excel in Faculty of Science
Research Competition
BABS again demonstrated the excellent quality of its students
and their skills in presenting their research, with three of
the seven awards on offer in the 2014 Faculty of Science
Postgraduate Research Competition going to BABS students.
Alex Knights (pictured, supervisor Professor Merlin Crossley)
was the winner in the Health, Lifestyle & Ageing category;
Angela Chilton (supervisor Professor Brett Neilan) runnerup in the Cutting-Edge Discovery category; and Lifu Sheng
(supervisor Dr Vladimir Sytnyk) took out the People’s Choice
award for best poster.
This hotly contested competition saw more than 70 research
students entering in 2014, being judged on the quality of
the poster, an abstract about their project as well as a oneminute long talk describing their topic. The competition judges
included Robyn Williams, presenter of The Science Show on
ABC Radio National, and astronomer and author Professor
Fred Watson, who joined more than 30 UNSW researchers to
assess the students’ presentations.
Alex at the bench
BABS alumnus awarded 2014 ASMR Medal
In addition to being named in Time Magazine’s 2014 Top
100 Influential People, Professor David Sinclair was the
recipient of the 2014 Australian Society for Medical Research
(ASMR) medal. This annual prestigious award recognises a
researcher’s career contributions to medical research. David
did Honours and then completed his PhD in BABS under the
supervision of Professor Ian Dawes (now Emeritus at UNSW
Australia), in whose lab he also met his future wife. As part of
the award events, David was the keynote speaker at a series of
Gala Dinners around Australia during Medical Research Week.
The School booked a table at the Sydney dinner, and during
his presentation, David warmly praised BABS and UNSW, and
invited Ian on stage to express his appreciation.
Ian Dawes accepting a tribute from David Sinclair.
9|
Emeritus Professor Ian Dawes and Professor Merlin Crossley, Dean of Science
Ian and Merlin were elected Honorary Fellows of The Royal Society of NSW in 2014. The Society is the
oldest learned society in the Southern Hemisphere and traces its origin back to 1821.The Society’s main
function is to promote science in all its aspects, and to link the disciplines of science to each other and to
other elements of human endeavour.
Ian Dawes, back row second from right; Merlin Crossley, front row second from right.
New BABS student breakout space BiBS
Conversion of an old lab to the BABS Interactive Breakout Space created a much-needed
multifunctional space for our large student cohort. The aim was to provide an informal learning space
for student activities, including tutoring, group work and pre-lab studies. Computers and wi-fi are
available, along with a substantial library, and kitchen facilities have been provided. Students were
encouraged to submit ideas and decoration suggestions for the space, with the official launch taking
place in Semester 2.
| 10
Joint Academic Microbiology Seminars (JAMS)
The JAMS initiative is a networking and ideas exchange forum, bringing together microbiologists from
five universities across Sydney on a regular basis. It provides a platform for large funding bids and a
shopfront for access to a wide array of microbiology expertise available locally and internationally.
JAMS also represents a strong link between BABS and the Australian Museum, where the events are
held. Website: jams.org.au
Annual BABS Research Symposium
The 2014 BABS Research Symposium was held at Royal Randwick racecourse. Reintroduced by
Head of School Professor Andrew Brown, the aim of this symposium is to generate more awareness
amongst the School community of the breadth of research being carried out by postdocs, research
fellows, HDR and Honours students. With the assistance of the BABSOC/EISSOC student society, led
by Dr Wallace Bridge, the day was a great success, with many opportunities to strengthen collegiality
among the School community.
11 |
BABS Research Seminar Series
The School’s fortnightly seminar series features a range of prominent international researchers together
with specialists from within Australia, together with School academics, postdocs and exiting PhD students
presenting their research topic to the School community. External speakers during 2014 included:
„
Dr Jeremy Webb, Director, Graduate
School of Biological Sciences, University of
Southampton, UK
„
Professor Amitabha Chattopadhyay, Centre for
Cellular and Molecular Biology, Uppal Road,
Hyderabad, India
„
„
„
Dr Gursharan Chana, Joint Head, Stem Cells
and Disease Modelling Laboratory, Centre
for Neural Engineering, The University of
Melbourne
Dr Vicky Schneider, The Genome Analysis
Centre, Norwich, UK
Professor Ryan Lister, ARC Future Fellow
& Professor ARC Centre of Excellence in
Plant Energy Biology, School of Chemistry &
Biochemistry, University of Western Australia
„
Associate Professor Marianne Farnebo,
Department Of Oncology/Pathology,
Karolinska Hospital, Stockholm, Sweden
„
Associate Professor Leonard Lipovich, Center
for Molecular Medicine and Genetics and
Department of Neurology, School of Medicine,
Wayne State University, Detroit, USA
| 12
„
Professor David Levens, Chief, Gene
Regulation Section, Laboratory of Pathology,
National Cancer Institute, Center for Cancer
Research, National Institutes of Health, USA
„
Professor Paul Thomas, School of Molecular &
Biomedical Science, University of Adelaide
„
Professor Kevin Lynch, Professor and Vice
Chair of Pharmacology, University of Virginia
„
Professor Junying Yuan, Elizabeth D Hay
Professor of Cell Biology, Harvard Medical
School
„
Associate Professor Jon Whitehead,
Translational Research Institute, Brisbane
„
Professor Ofer Biham, Racah Institute of
Physics, Hebrew University, Jerusalem, Israel
„
Professor Francis Stewart, Director,
Biotechnology Center of TU, Dresden,
Germany
„
Professor Steven Djordjevic, Professor of
Infectious Diseases, ithree Institute, University
of Technology Sydney
Environmental Microbiology
Academic Staff
Professor Rick Cavicchioli
Professor Staffan Kjelleberg
Scientia Professor Brett Neilan
Associate Professor Torsten Thomas
Associate Professor Michael Manefield
Senior Lecturer Dr Brendan Burns
Senior Lecturer Dr Belinda Ferrari
Lecturer Dr Rebecca LeBard
BABS Research Group –
Environmental Microbiology
13 |
Rocking the cradle of life – microbiology of early earth
ecosystems
Dr Brendan Burns, Senior Lecturer
To understand the biology of an ecosystem,
a time separation of billions of years seems to
present an insurmountable hurdle. In Australia,
there exist a few modern analog ecosystems that
can act as a worm-hole to the past, allowing us to
bring a contemporary arsenal of tools to the field
site.
One of the most famous and extensive of these
anywhere in the world are the stromatolites of
Shark Bay in Western Australia, a World Heritage
site. Stromatolites are biogeological ecosystems
resulting from the metabolic activity of resident
microbial communities. The excitement stems
from the fact that there is a clear fossil record of
such structures for more than 3 billion years.
Dr Brendan Burns and his research team have
worked on various aspects of these ecosystems
in a bid to comprehensively charcterise their
functional complexity. The goal is to thoroughly
understand the diversity, biogeochemistry and
key interactions of the microorganisms forming
the Shark Bay stromatolites. In addition to
identifying potentially novel microbial activities
vital to ecosystem function, this will provide a
rational focus when seeking biosignatures that
will ultimately help interpret the fossil record. By
using a combination of diverse and cutting-edge
techniques, it will afford more rational predictions
on past environments and build useful models
to further our understanding of early earth
communities.
Most recently and for the first time in relation
to these ecosystems, the group has employed
high-throughput next generation sequencing
platforms – omics. This has begun to decipher
at the millimetre scale the intricate dance
between microorganisms: who is where and
what are they doing. Data suggest ancient forms
of carbon fixation could be active in modernday stromatolite systems, and that archaea in
particular may be key players at multiple levels.
Combinations of analyses are providing estimates
of the flow of key metabolites in these microbial
systems, and enabling creation of a 3-D
reconstruction of key metabolic activities. This
is critical to be able to relate specific activities
to resulting biosignatures that can be detected
in the fossil record. Through the application
of an ecosystems biology approach, some of
| 14
the mysteries surrounding these early Earth
communities are being gradually unravelled.
Through collaborations with NASA, for this
project Dr Burns is also employing a state-of-theart imager that utilises technology developed for
the Mars Rover mission.
This year Dr Burns was invited to take part in
an ambitious global effort – Ocean Sampling
Day – to sample and analyse the world’s oceans
simultaneously at the same point in time during
the 2015 summer/winter solstice. This campaign
aims to analyse marine microbial biodiversity
and function, and will incorporate work by ‘citizen
scientists’. It will also contribute to The Blue
Economy (10 years; 10 innovations; 100 million
jobs) through the identification of novel, oceanderived biotechnologies of benefit to a wide
range of stakeholders.
Finally, this research group’s findings have
provided information vital to the conservation
of these unique resources (identified as under
threat by climate change), carefully monitoring
changes in biological diversity that could indicate
possible threats to these evolutionally significant
systems.
Exploring Antarctica’s unique soil microbial biodiversity
Dr Belinda Ferrari, Senior Lecturer
The Ferrari lab integrates next-generation
sequencing technologies with novel cultivation
approaches to explore the microbial diversity
in polar soils of Antarctica. During the last two
years, Belinda has been developing communitywide microbial ecotoxicity assays in collaboration
with the Australian Antarctic Division, which has
funded the majority of this work.
Several sites in Antarctica and sub-Antarctic
Macquarie Island are currently undergoing
bioremediation due to diesel fuel spills. Belinda’s
research is aimed at using bacterial communities
as potential indicators of soil health, monitoring
the communities throughout the bioremediation
process and aiding the development of sitespecific guidelines. Belinda believes that
community-wide models are more representative
of an environment compared to single species
toxicity assays, and her future goal includes the
development of a rapid chip array for assessing
hydrocarbon toxicity.
Belinda’s team is gaining information on
what species are stimulated by petroleum
hydrocarbons. As part of this work, Dr Josie van
Dorst provided valuable EC20 targets that are
being used for the development of site-specific
remediation guidelines for Macquarie Island. Aside
from this major aim, the Ferrari lab isolated an
array of novel soil polar fungi and bacteria, some
of which are capable of degrading hydrocarbons,
even at low temperatures. Ongoing research
is now aimed at characterising cold-adapted
fungal enzymes involved in the biodegradation
of hydrocarbons; and in a separate project,
Sub-Antarctic Macquarie Island
investigating the biotechnological potential of
the lab’s polar library by screening for novel
secondary metabolites genes.
A primary focus of Belinda’s research is to
explore the diversity of bacteria and fungi in the
Windmill Islands region of Eastern Antarctica.
Mitchell Peninsula, one of the remote sites under
investigation, is a nutrient-poor polar desert, and
the team recently found that it harbours a unique
microbial taxonomic composition not previously
observed in any reported polar or temperate
ecosystem. Belinda believes this region is a
potential microbial biodiversity hotspot, as it
contains rare yet-to-be cultured lineages of
bacteria in unusually high abundances.
With the utilisation of a new differential binning
technique and in collaboration with the Australian
Centre for Genomics, PhD student Mukan Ji
reconstructed 18 near-complete genomes from
Mitchell Peninsula soil, including for the first time,
genomes for both Candidate Division WPS-2 and
AD3. Through this exciting research the Ferrari
team discovered that the majority of bacterial
genomes recovered contain RuBisCO genes,
indicative of carbon fixation. However, very little
evidence for photosynthesis exists.
These findings suggest that alternative
strategies for survival are dominant in this hostile
environment and as this work moves forward, the
Ferrari team hopes to exploit these new genomic
insights to develop cultivation strategies for these
yet-to-be cultured groups of bacteria.
Streptomyces – PhD student Nicole Benaud
15 |
Infectious Disease
Academic Staff
Professor Hazel Mitchell
Professor Peter White
Associate Professor Ruiting Lan
Associate Professor Kevin Morris
Associate Professor Mark Tanaka
Associate Professor Noel Whitaker
Senior Lecturer Dr Jai Tree
Senior Lecturer Dr Li Zhang
BABS Research Group –
Infectious Disease
| 16
Paleovirology; mining the cane toad genome for
biocontrol viruses
Professor Peter White
I would like to describe one of our wackier
projects that we have been working on in the
Molecular Microbiology Laboratory over the last
year and a half. The study of ancient viruses is
termed paleovirology. The genomes of animals
and insects contain traces of past viral infections
through the integration of viral genetic material
into the host genome, termed endogenous viral
elements (EVEs). These viral fossils can be used
to look at viruses that once existed hundreds of
thousands of years ago. Around 1% of the human
genome is comprised of EVEs, the vast majority
being retroviruses that naturally insert their
genomes into the host genome as part of their life
cycle. For other viruses, germ line integration is
rare, but has been identified in many organisms.
The most surprising viral fossils originate from
RNA viruses; for example, in humans, everyone
has a small trace on chromosome 10 of a
bornavirus, which is an RNA virus.
The genome of the Aedes aegyptii mosquito
contains numerous endogenised viruses. In fact,
through work by Dr Andrew Kelly in the lab to
date, we have discovered the remnants of 241
different RNA viruses in the A. aegyptii genome.
This is a lot more than we were expecting.
Perhaps the most interesting one of these viral
fossils is an ancient insect specific flavivirus,
which we estimate to be 129,000 years old. The
genome of this virus is scattered and duplicated
in 55 fragments across the mosquito genome. We
have re-built the genome of this virus to a level
of 89% completion (see figure). Given the rapid
advance in viral reverse genetics in recent times
(you can make fully infectious viral particles out of
only RNA or DNA), this raises the very interesting
concept of the resurrection and propagation of
ancient extinct viruses.
I first chatted with Professor Eddie Holmes from
the University of Sydney over lunch about the
idea of mining the cane toad’s genome to find
endogenised viruses. It is a wacky idea, but it has
merit. If we discount the retroviruses (of which
there will be many), we should be able to identify
a number of viruses that the toad was once
infected with, going back hundreds of thousands
of years. The genome, if you like, contains a fossil
record of these past infections.
It is possible to resurrect ancient viruses through reverse
genetics given only the viral genome. Reconstruction of
the relic A. aegypti flaviviral genome, 89% complete.
This is because some infections of the egg or
sperm cells result in the viral genome merging
into the host genome, leaving a trace of the
infection through the generations.
Given the fact that viruses have been very
successful biocontrol agents for controlling rabbit
populations, a toad virus has the potential to be
a biocontrol agent. We could try to reconstruct
these early toad viruses if we find enough
sequence, or alternatively, find the closest match
in a contemporary toad virus, and test them as a
biocontrol agent against the cane toad.
I was dismayed to find that the genome of the
cane toad is not yet available, although people
have tried to sequence it. There is currently no
evidence in any database of any success, but
there are many people in Australia who want
to sequence the genome of the cane toad for
scientific studies.
We have therefore established the Cane Toad
Consortium to explore the mission to “sequence
the cane toad for science”. Consortium members
from UNSW are Professor Peter White (virology),
Professor Marc Wilkins (sequencing), who is also
Director of the Ramaciotti Centre for Genomics
(where the sequencing will take place), Dr Rich
Edwards (sequencing and bioinformatics) and Dr
Andrew Kelly (bioinformatics). Also on board and
willing to help are Dr Lee Ann Rollins from Deakin
University (toad collector and geneticist), and
Professor Eddie Holmes (virology and biocontrol)
and Professor Rick Shine (biology of rapid cane
toad evolution) from the University of Sydney.
17 |
Understanding the role of oral Campylobacter species
Dr Li Zhang, Senior Lecturer
Dr Li Zhang’s group has conducted internationally
pioneering research in understanding the
role of oral Campylobacter species, such as
Campylobacter concisus, in initiating a subgroup
of human inflammatory bowel disease (IBD).
In 2009, Dr Zhang and collaborators reported
an association between C. concisus and Crohn’s
disease (one type of human IBD) for the first time,
and in 2010, Dr Zhang hypothesised that some
oral C. concisus strains are involved in initiating a
subgroup of human IBD. Continuous studies over
the past five years have provided information that
is fundamental to this emerging research field.
The group found that C. concisus uses the
human oral cavity as its natural colonisation site.
C. concisus prefers anaerobic growth; it may
grow under microaerobic conditions only in the
presence of H2 gas. Patients with IBD are often
colonised by multiple oral C. concisus strains;
there are no distinct enteric C. concisus strains.
C. concisus strains detected in the intestinal tract
of patients with IBD originate from oral
C. concisus strains.
C. concisus is very sensitive to low pH and their
growth is greatly inhibited by bile, thus most of
the C. concisus swallowed would have been
killed by the low pH of the gastric acid and would
| 18
Campylobacter
be unlikely to establish long-term colonisation
in the lower parts of the gastrointestinal tract.
However, a small percentage of oral C. concisus
strains have greater abilities in resisting the
antimicrobial effects of low pH and bile. These
oral C. concisus strains may establish short-term
intestinal colonisation before being cleared.
This process may occur repeatedly in some
individuals, which may initiate chronic enteric
inflammatory conditions such as IBD if the
colonised C. concisus strains are virulent.
Dr Zhang’s group has identified a number of
C. concisus prophages and found that some
C. concisus prophages encode zonula occludens
toxin (Zot). Their recent work showed that
C. concisus Zot damages the intestinal epithelial
barrier and has an impact on the immune system.
They are currently investigating how Zot toxin is
released in the intestinal environment and are
developing diagnostic methods to accurately
detect the involvement of C. concisus and its
toxins in individual IBD cases.
The other aspect of Dr Zhang’s research is on
chronic neurological diseases, investigating the
role of human hosted Campylobacter species
in chronic neurological diseases. A link to Dr
Zhang’s publications can be found on the UNSW
Research Gateway.
M'$-$Ǐ*3M!!&
Academic Staff
Professor Merlin Crossley
Associate Professor Andrew Collins
Associate Professor John Foster
Associate Professor Vincent Murray
Senior Lecturer Dr Wallace Bridge
Senior Lecturer Dr Michael Janitz
Senior Lecturer Dr Louise Lutze-Mann
Senior Lecturer Dr Chris Marquis
Senior Lecturer Dr Vladimir Sytnyk
Lecturer Dr Anne Galea
BABS Research Group –
M'$-$Ǐ*3!!&
19 |
Lipases for the production of biodiesel
Dr Christopher Marquis, Senior Lecturer
The Marquis lab undertakes collaborative
research projects across a range of
areas, including protein biotechnology,
nanobiotechnology and bioenergy. Since 2012,
the lab has worked on projects that investigate
the use of enzymes, called lipases, for the
reaction of natural oils (seed and algal, for
example) and waste oils (tallow and used cooking
oil) to produce biodiesel.
Biodiesel describes a heterogeneous
range of biofuel products derived from
the transesterification of plant and animal
triglycerides by reaction with a simple alcohol,
usually methanol. The most commonly reported
processes are catalysed using caustic (in
the form of sodium methoxide). However, this
process is not without problems, which include
soap formation with poorer quality oils (high free
fatty acid content), production of a less valuable
glycerol by-product, and toxicity and explosion
hazards handling sodium methoxide.
Another problem is the source of the oil
feedstock, which is largely food oils (soybean,
canola, palm and coconut oil, for example). Some
biodiesel plants can access waste feedstocks
such as used cooking oils, non-comestible seed
oils (such as jatropha) and tallow. The Scientific
Research Organisation of Samoa (SROS) has
had a biodiesel program since 2009 to develop
biodiesel from coconut oil, and operates a
200L scale pilot plant to produce coconut oil
biodiesel using conventional methods. In 2009,
a collaboration between SROS and UNSW was
established. As part of this collaboration, we
began to develop an enzyme-based process to
produce coconut oil biodiesel.
Current projects have centred on recombinant
expression of lipases for this purpose in the
methylotrophic yeast, Picha pastoris. We aim
to evaluate a “closed-loop” enzyme-based
bioprocess to develop biodiesel from stocks
locally available in Samoa. Glycerol by-product
from transesterification will be assessed
for cultivation of fodder yeast as well as
recombinant yeast-producing lipase enzymes
for transesterification, which is currently under
development in the Marquis lab.
The group is expressing enzymes that have been
reported for use in industry and undertaking
modifications for surface (including cell-surface)
immobilisation and for improved performance,
through directed evolution strategies. The
lab continues to produce lipase-mediated
coconut oil biodiesel for the evaluation of engine
performance of biodiesel blends in advanced
research engines.
This project is a collaboration with Dr Shawn
Kook, Director of the UNSW Engine Research
Laboratory based in the UNSW School of
Mechanical Engineering and Samania Tupufua at
SROS.
Separation of biodiesel from glycerol after immobilized enzyme transesterification
| 20
Looking towards addressing oxidative stress in ageing and
chronic disease
Dr Wallace Bridge, Senior Lecturer
It is a never-ending message that can be literally
forced down our throats “if a food contains heaps
of antioxidants then it must be good for you”. We
are led to believe by marketers that it doesn’t
matter what type of antioxidant it might be, as
long as it can wipe out a free radical then you
need it; and if you take antioxidant supplements
you will live longer, be healthier and maybe even
be cured of disease.
There is a myriad of antioxidant forms and all
have different biologic modes of activity. They
should therefore not be all lumped together when
considering whether they are beneficial or not. It
should also be noted that no human clinical trials
to date have demonstrated any clinical benefit in
taking any form of antioxidant supplement.
So how has this immense marketing push
come to be, if there is no evidence of benefit?
From a science perspective, the majority of
reactive oxygen species (ROS) are produced
as a by-product of mitochondrial oxidative
phosphorylation, which involves oxygen acting
as an electron acceptor. Some of these ROS
are harnessed for normal cellular functions
and the remainder are mopped up by the cell’s
antioxidant system. This involves enzymes
and chemical entities that act as co-factors
for the enzymes or directly neutralise ROS
and other forms of free radicals. Insufficient or
overwhelmed cellular antioxidant capacity will
lead to an excess of oxidants that will damage
nucleic acids, protein and lipids, leading to
mitochondrial or cellular dysfunction and
ultimately cell death. It is from this oxidative stress
perspective that the consumption of antioxidants
is thought to be of benefit.
Often referred to as the master antioxidant,
glutathione is almost ubiquitous in aerobic
organisms, from bacteria, yeast and plants to
humans. It is a tripeptide comprising glutamate,
cysteine and glycine, with the –SH moiety of the
cysteine being responsible for the antioxidant
activity. Glutathione is produced in all cells within
the body by two sequential ATP-dependent
enzymes, with homeostasis being dictated
by feedback inhibition exerted by glutathione
on the first enzyme, glutamate cysteine ligase
(GCL), which catalyses the synthesis of gammaglutamylcysteine (GGC).
21 |
It has been reported in many models that cellular
glutathione levels progressively decline during
ageing and are substantially lower in tissues
affected by many age related and chronic
disorders. Our research over the last 10 years
has been focused on exploring the potential for
GGC administration to elevate glutathione levels,
with the long-term objective of investigating
its potential to treat or even prevent/delay age
glutathione depletion-associated conditions. The
mechanistic basis is that either through damage
or down regulation, the GCL enzyme has
become ineffective at producing sufficient GGC
to maintain adequate homeostatic glutathione
levels.
Since commencing the project, we have
developed and patented (triadic granted) a
process for GGC manufacture that we licensed to
Biospecialties International P/L, a company that
was formed to commercialise GGC manufacture.
The production process was initially validated at
pilot scale with the assistance of a $1.16 million
federal government grant.
On the basis of our published animal studies
performed according to OECD guidelines and
other evidence relating to GGC’s presence in
many foods, we have been successful in having
GGC given GRAS (Generally Recognised as
Safe) status according to the US FDA regulations.
Recently, we conducted a UNSW-sponsored
human clinical trial that demonstrated that orally
administered GGC could significantly and
systemically increase cellular glutathione levels in
healthy volunteers. Many other compounds have
been tested previously in similar trials but none
has been credibly successful.
The production factory in Newcastle, NSW
has recently been upgraded to a commercial
production facility in readiness for a 2015 GGC
(Glyteine™) product launch in the US. Future
human clinical trials are being planned to
investigate GGC’s potential to be of therapeutic
benefit in select disorders.
Commercial production facility, Newcastle.
| 22
Identification of the new regulators of neuronal growth
Dr Vladimir Sytnyk, Senior Lecturer
In the developing brain, neurons must grow long
and extensively branched axons and dendrites to
establish numerous contacts with other neurons.
This process is required for formation of the
elaborated networks of neurons interconnected
by synaptic contacts, which play a critical role
in all brain functions, including information
processing, learning and memory formation.
To reach their targets in the immature neuronal
network, axons and dendrites have to grow
through a complex extracellular environment,
which significantly influences the direction and
speed of the growth. Cell adhesion molecules
are the proteins at the cell surface of axons
and dendrites, which bind to the molecules in
the extracellular space. This binding results
in increased or reduced growth of axons and
dendrites and their branching. Cell adhesion
molecules thus function as recognition molecules,
which recognise the growth promoting and
inhibiting cues in the extracellular environment of
developing neurons.
Levels of NCAM2 are increased in brains of
Down syndrome patients. Mutations in the
NCAM2 gene were also found in autistic patients.
How changes in the levels of this protein
result in mental abnormalities remains poorly
understood. The results from the lab’s recent
work suggest that altered levels of NCAM2 can
induce abnormalities in development of neurons,
affecting the formation and functioning of
neuronal networks in the brain.
The lab is now investigating whether changes
in levels of NCAM2 and other cell adhesion
molecules affect neurotransmission between
neurons and excitability of neuronal networks.
The results of this work will help to understand
the molecular mechanisms of brain disorders
and identify new molecular targets, which can
be used to design novel treatments of these
disorders.
Dr Vladimir Sytnyk’s laboratory is interested in
how cell adhesion molecules induce changes in
neuronal growth at the molecular level. We are
particularly interested in cell adhesion molecules,
expression of which is altered in brain disorders.
In a recent study completed by the group, a
cell adhesion molecule called the Neural Cell
Adhesion Molecule 2 (NCAM2) was shown to be
an important regulator of the branching of axons
and dendrites.
Growth of axons and dendrites depends on the
activation of a number of enzymes in the cytosol
of neurons. These enzymes regulate changes
required for building of a new axon or dendrite,
such as switching on the expression of gene
coding for structural proteins or inducing the
remodelling of the cytoskeleton.
Ca2+ ions are important regulators of the
activity of intracellular enzymes involved in
growth regulation (Sheng et al., 2013). By using
genetically encoded reporters of the intracellular
Ca2+ concentration, the lab demonstrated
that binding of NCAM2 to molecules in the
extracellular environment induced transient
increases in the levels of intracellular Ca2+, which
promoted formation and stabilisation of new
branches in developing neurons.
NCAM2 induces changes in neuronal morphology by inducing
transient increases in intracellular Ca2+ levels.
A – images of a control neuron with non-active NCAM2 and a neuron
treated to activate NCAM2.
B – pseudocolored image of a neuron transfected with a genetically
encoded Ca2+ reporter. Arrow shows a transient NCAM2-induced
increase in intracellular Ca2+ levels.
Adapted from Sheng L, Leshchyns’ka I & Sytnyk V, 2015, ‘Neural cell
adhesion molecule 2 promotes the formation of filopodia and neurite
branching by inducing submembrane increases in Ca2+ levels’,
Journal of Neuroscience, 35(4):1739-52.
23 |
Systems and Cellular Biology
Academic Staff
Professor Bill Ballard
Professor Andrew Brown
Professor Marc Wilkins
Professor Rob Yang
Senior Lecturer Dr Richard Edwards
Senior Lecturer Dr Kyle Hoehn
Senior Lecturer Dr Irina Voineagu
Senior Lecturer Dr Paul Waters
BABS Research Group –
Systems and Cellular Biology
| 24
Autism genetics
Dr Irina Voineagu, Senior Lecturer
Irina is currently an ARC DECRA Fellow. She
established her lab at UNSW in 2013 and her
team has since grown, currently including two
postdoctoral researchers, one PhD student and
several undergraduate students. Her laboratory
investigates the molecular genetic mechanisms
underlying normal brain function and their
perturbation in neurodevelopmental disorders,
using a combination of functional genomic
studies in human brain tissue and neuronal cell
culture systems.
Autism spectrum disorders (ASD) encompass
a range of neurodevelopmental conditions
characterised by language impairments,
deficits of social-reciprocal interaction and
repetitive and restrictive behaviours. As for
other neurodevelopmental disorders such as
intellectual disability and schizophrenia, ASD
are highly heritable. Extensive research into
the genetics of ASD over the last two decades
has demonstrated that the disorders are also
genetically heterogeneous, with hundreds
of genetic loci implicated. Given this genetic
heterogeneity, a challenging yet fundamental
question is whether the wide variety of genetic
changes ultimately dysregulate a common set of
molecular pathways, amenable as therapeutic
targets.
Irina’s work demonstrated that despite genetic
heterogeneity, common gene expression
changes could be identified in a large subset of
ASD cases. A key finding of this study was that
the neuronal splicing factor A2BP1 (Ataxin-2
binding protein 1) was downregulated in a large
subset of ASD brains. While A2BP1 has been
previously implicated in ASD, the mechanisms of
its transcriptional dysregulation and the functional
consequences of altered A2BP1-dependent
splicing in ASD remain unknown.
Genomic diversity in the
human brain
The Voineagu lab is also interested in
investigating somatic instability at trinucleotide
repeats (TNRs) in the normal human brain.
Although genetic variation can potentially occur
anywhere in the genome, certain genomic
regions are particularly susceptible to genetic
changes. These regions are called hotspots of
genomic instability, and are frequently underlied
by repeated DNA sequences.
One class of hotspots of genomic instability
particularly relevant to brain function consists
of expandable DNA repeats. These are tandem
DNA repeats, most often trinucleotide repeats
(TNRs) such as (CGG)n, (CAG)n, (GAA)n, which
have an intrinsic propensity to increase in length
during germline transmission. Unstable DNA
repeats block DNA replication, and replication
stalling at TNRs eludes the cellular checkpoint
machinery, leading to chromosomal fragility.
TNR expansions have been investigated primarily
as a cause of neurodegenerative disorders,
including Huntington’s disease, Fragile X
syndrome and Friedriech’s ataxia. Irina’s lab is
now asking the fundamental question whether
somatic TNR instability events occur in the normal
human brain, and whether such instability events
affect gene expression.
Now the lab is taking an integrative approach
to investigate the role of A2BP1 and alternative
splicing abnormalities in ASD pathogenesis,
aiming to (a) identify the genetic and epigenetic
causes of A2BP1 transcriptional dysregulation
in ASD brain; (b) elucidate A2BP1-dependent
alternative splicing targets in the human brain;
and (c) investigate the cellular and transcriptional
consequences of A2BP1 dysfunction.
Network of genes dysregulated in autistic brains (from
Voineagu et al. 2011)
25 |
Evolution and structure of mammal sex chromosomes
Dr Paul Waters, Senior Lecturer
In most mammals females have two X
chromosomes, whereas males have just one X
and a gene-poor Y chromosome that determines
maleness. The evolution of sex chromosomes
(the X and Y) has been a hot topic for nearly a
century, because they seem to break the most
fundamental rules of Darwinian selection (i.e. the
“fittest” chromosome does not always persist).
It is now widely accepted that the human X and
Y evolved from an ordinary pair of chromosomes
via a process of gene loss from the male-specific
Y chromosome, and genes that remain on the
Y are generally important to male reproduction.
This same process of sex chromosome evolution
has resulted in differentiated sex chromosomes in
diverse animals (from flies to mammals).
For each species with differentiated sex
chromosomes, unique hurdles need to be
overcome. In humans, females have two copies
of approximately 800 X chromosome proteincoding genes, whereas males have just one
copy of these genes. How are such extreme
dosage differences tolerated between the
sexes, considering that one copy of any other
chromosome is lethal?
Subsequently, this over-expression is
compensated for by transcriptional silencing
of one X chromosome in the somatic cells of
females; a phenomenon called X chromosome
inactivation that is mediated by long non-coding
RNAs.
Since arriving at UNSW in 2013, research in
the Waters lab has focused on the evolution
and structure of mammal sex chromosomes,
along with X chromosome inactivation. Paul was
recently involved in a large-scale project focused
on the evolution of mammal Y chromosomes
(Nature cover story April 2014). This project
employed high-throughput sequencing in 15
mammal-representative species to identify
over 100 new mammalian Y chromosome
genes, analysis of which demonstrated that
sex chromosomes have arisen independently
at least three times in amnoite vertebrates
(i.e. birds, monotremes and the marsupial/
eutherian ancestor). Surprisingly, genes that
persisted on mammal Y chromosomes originally
did so because they were under strict dosage
constraints, and subsequently recruited into
male-specific functions.
It is thought that in male mammals, dosage
compensation is achieved by over-expression of
genes on the X, ultimately resulting in doubled
gene expression from the single X in males.
Because females have two Xs, carry-through of
over-expressed X genes from males to females
would result in a doubled gene dose (functionally
equivalent to four copies of the X – just as bad as
one copy).
More recently, the Waters lab has focused on
understanding how non-coding RNAs mediate
inactivation of the X chromosome in the distantly
related marsupial and eutherian mammals. This
project has provided fascinating insight into
the similarity of interacting protein networks
shared by two long non-coding RNAs, which
evolved independently to mediate arguably the
most iconic example of epigenetic silencing in
mammals – X chromosome inactivation.
Chromosomes from a male kangaroo with one X and one Y
chromosome
In female cells the inactive X chromosome is coated in
non coding RNA (red)
| 26
Profile
Dr Richard Edwards, New Senior Lecturer
I joined BABS in November 2013, relocating
from the Centre of Biological Sciences at the
University of Southampton in the UK. My earlier
research background is in genetics, but since
2002 I have mainly been working on bioinformatic
methods for predicting important sites in protein
function. I was therefore attracted to BABS by
the strength and depth that the School has in
genomics, proteomics and systems biology.
It has been a good move. My research group
now has joint journal clubs with the proteomics
group of Professor Marc Wilkins, and several
new collaborations are making good use of the
Ramaciotti Centre for Genomics, which is hosted
by BABS.
I lead a bioinformatics group that uses
computational tools to analyse biological data.
My research can broadly be described as
hunting for evolutionary footprints of molecular
function, stemming from a fascination with the
molecular basis of evolutionary change and
how we can harness the genetic sequence
patterns left behind to make useful predictions
about biological systems. I consider myself an
evolutionary biologist at heart, and the famous
adage of Theodosius Dobzhansky, “Nothing
in biology makes sense except in the light
of evolution” is particularly true of sequence
analysis. The evolutionary process leaves clues
in the sequences and it is those clues that my lab
seeks to exploit.
recent efforts have concentrated on improving
performance for specific scenarios. The reliability
of its predictions has enabled us to shift the
emphasis from algorithms to applications. A
major research area in the lab is the application
of SLiMFinder to viral-human protein interactions
in order to identify “molecular mimicry”, in which
viral pathogens mimic host motifs to hijack
cellular processes.
Finally, the lab has a number of interdisciplinary
collaborative projects applying bioinformatics
tools and molecular evolution theory to
experimental biology, often using large genomic,
transcriptomic and/or proteomic datasets.
These projects often involve the development of
bespoke bioinformatics pipelines and a number
of open source bioinformatics tools have been
generated as a result.
Joining BABS has also enabled me to return to
my first love, genetics. The Ramaciotti Centre
for Genomics has just received a new PacBio
sequencer, and I am excited about some new
collaborations harnessing the power of long-read
sequencing.
Core research in the lab is the study of Short
Linear Motifs (SLiMs), which are short regions
of proteins that mediate interactions with other
proteins. This research originated with my
postdoctoral work, during which I developed
a bioinformatics (sequence analysis) method
for rational design of biologically active short
peptides. Since then, we have developed a
number of SLiM discovery tools, including
SLiMDisc, one of the first algorithms for
successfully predicting novel SLiMs from
sequence data (coining the term “SLiM” into
the bargain), and SLiMFinder, the first SLiM
prediction algorithm able to estimate the
statistical significance of motif predictions.
SLiMFinder is still the most successful general
SLiM prediction tool on benchmarking data, and
State-of-the-art SLiM prediction tools developed in the Edwards lab.
27 |
Profile
Dr Kyle Hoehn, New Senior Lecturer
I was awarded my PhD in Biochemistry from
Colorado State University in 2005, and trained
as a postdoc at the Garvan Institute of Medical
Research in Sydney from 2005-2009. My
independent research career started in 2009
as an Assistant Professor of Pharmacology at
the University of Virginia. I joined the School of
Biotechnology and Biomolecular Sciences in July
2014 as an academic with both teaching and
research responsibilities.
I coordinate a second-year undergraduate
course entitled Fundamentals of Biochemistry,
and I guest lecture in other courses as needed
(e.g. Human Biochemistry and Molecular
Frontiers). My research lab consists of one
postdoc and one undergraduate student, and
we are currently working on a drug discovery
project.
Our research centres on small molecule drug
discovery for anti-cancer agents, with the
objective of identifying new anti-cancer agents
that kill cancer cells by altering the way they
use glucose. To date, we have identified a small
molecule named BAM10 that reduces melanoma
tumour growth in mice and is selectively toxic to
cancer cells grown in culture (see figure). These
promising results formed the basis of an NHMRC
grant application submitted in 2015.
My first eight months in BABS have been very
intellectually stimulating and have broadened my
understanding of the microbial world and junk
DNA. Importantly, I have developed many new
collaborations both within the School and across
the UNSW campus. These interactions have
helped to secure new School equipment through
the MREII program, and resulted in 9 different
grant applications to date in 2015.
In summary, I’m very happy to be involved in a
School with such diverse talents in both research
and teaching, and I look forward to contributing
to the School’s already sterling reputation.
Cancer cells intake much more glucose than non-cancer cells and they use it to produce building blocks (lipids, DNA, protein) for
cell replication. BAM10 interferes with this pathway by increasing the amount of glucose that is oxidised to carbon dioxide (CO2).
Since non-cancer cells normally oxidise glucose, they are less affected by BAM10. Therefore, BAM10 represents a potential
chemotherapeutic agent that may have less toxicity to healthy cells.
| 28
Profile
Dr Jai Tree, New Senior Lecturer
I joined the School of Biotechnology and Biomolecular
Sciences in March 2015. I completed my postdoctoral
work at the The Roslin Institute and Wellcome Trust
Centre for Cell Biology at the University of Edinburgh,
UK. On returning to Australia in 2014, I joined the Peter
Doherty Institute at the University of Melbourne as a
Research Fellow, but was soon attracted to Sydney
by the opportunity to establish a research group in
BABS at UNSW because of its excellent infrastructure
(including the Ramaciotti Centre for Genomics) and
strength in RNA biology.
We are also applying high-throughput techniques to
study small RNA interactions with messenger RNAs
(mRNAs) in bacterial cells. These approaches will allow
us to map the extent of ncRNA regulation and identify
novel interactions that are not predicted, by extrapolating
our current understanding of ncRNA regulation.
Ultimately, we expect that by understanding this
fundamental layer of gene regulation in bacterial
pathogens, we will provide targets for novel interventions
such as small molecular inhibitors of virulence.
My lab is interested in how bacterial pathogens control
gene expression in response to stress and host
colonisation, with a particular focus on how proteinRNA and RNA-RNA interactions control expression of
virulence genes.
Recent advances in sequencing technologies have
led to the realisation that bacteria encode a panoply of
regulatory RNA, known as non-coding RNA (ncRNA),
that functions in both sensing and responding to
environmental cues and stress. My lab works on an
abundant subclass of ncRNA, termed small RNA, and
seeks to understand how this layer of gene regulation
adapts bacterial pathogens for disease.
Our model system is the human pathogen
enterohaemorhaggic E. coli (EHEC) that has a
“mosaic genome”, consisting of a core genome
shared with commensal E. coli isolates, and an
accessory genome that has been horizontally
acquired on mobile genetic elements such as
plasmids, bacteriophage and transposons. The
accessory genome provides the tools for EHEC to
cause disease in humans. I have shown that the
accessory genome encodes a large number of small
RNAs, and that bacteriophage carry a new class
of ncRNA that represses host small RNA regulation
(termed anti-sRNA), providing a selective advantage
for colonisation of ruminants (the reservoir host) This
work was recently published in Molecular Cell.
We use a broad range of molecular biology tools
to explore how RNAs regulate pathogenesis,
including mutagenesis and transcriptomics,
using high-throughput (HTP) sequencing. We
have demonstrated that UV-crosslinking and HTP
sequencing (known as CRAC or CLIP-Seq) can be
applied to bacteria and are using this technique to
study how small RNAs direct, and are directed by,
protein interactions in the cell.
Mapping protein-RNA interactions transcriptome-wide (top) and within
the 5’UTR of a virulence gene (bottom) using UV-crosslinking (CRAC).
29 |
Profile
Ruben Meerman, ABC Surfing Scientist and
BABS PhD Candidate
When somebody loses weight,
where does it go?
Most people believe the weight turns into energy
or heat, some think it ends up in the toilet, while
others assume it is converted into muscle. These
beliefs are all incorrect!
While scientists have known the true fate of fat for
more than a century, ABC Surfing Scientist Ruben
Meerman and Head of School Professor Andrew
Brown recently completed a survey that revealed
that these misconceptions are common amongst
today’s doctors, dieticians and personal trainers.
“Right now, most of the health professionals
at the frontline of the obesity epidemic have
scientifically impossible ideas about how human
beings lose weight,” says Ruben.
Their survey was published in the British Medical
Journal alongside a novel calculation that shows
that 84% of the mass in a fat molecule is exhaled
as carbon dioxide gas while the remaining 16%
becomes water. The duo’s paper attracted
worldwide attention in December 2014. Ruben is
now a BABS PhD candidate, but his unexpected
| 30
return to academia can be traced back to a 2012
surfing holiday in Fiji.
“Pondering my pot belly in those photos
motivated me to do what doctors and dietitians
have always recommended and, lo and behold,
after eleven weeks of eating less I’d lost 6.5 kg”
said Ruben, “So I did a quick linear regression,
of course, and discovered that I’d been losing 85
grams per day, which meant I would reach my
target weight in just a few months.” That was a
happy moment for Ruben but it was the question
he asked next that would lead him to BABS. “I
wanted to know precisely what proportion of
those 85 grams I had been exhaling every day,”
he explains.
Ruben studied physics at QUT and spent several
years in industry producing optical coatings
using electron beam physical vapour deposition
(EBPVD) for military, medical and industrial
lasers, but has no formal training in biochemistry.
He completed a Graduate Diploma in Science
Communication at the ANU in 1995, which
included a practical component performing
science demonstrations in primary and high
schools as a member of the Shell Questacon
Science Circus. A generation of Aussie kids now
know him as the ABC’s “Surfing Scientist”, and he
became Play School’s first ever resident scientist
in 2012.
He credits one particular demonstration for
sparking his curiosity about weight loss. “I’ve
been using liquid nitrogen to freeze my exhaled
breath inside transparent balloons for years so
when I started losing weight, I had this vivid
image of that solid frozen carbon dioxide you
can see inside,” Ruben explains, “I found it
incredibly motivating to know that I was turning
my fat into gas and water, but I’m a geek so I had
to know the precise proportions of each that it
had become.” The problem is that fat is made
of carbon, hydrogen and oxygen and it is not
clear whether those oxygen atoms are exhaled
as CO2, excreted as H2O, or depart in some
combination of the two.”
After a self-directed crash course in biochemistry,
it dawned on Ruben that the answer had never
been published so he called Professor Andrew
Brown at UNSW Australia for some expert advice.
Unaware that Andrew was on sabbatical in
Finland, Ruben called several other biochemistry
professors across the country but none had
ever contemplated the metabolic fate of a fat
molecule’s oxygen atoms. He finally found the
vital clue in a paper published in the Journal
of Biological Chemistry in 1949. The authors
injected water labelled with heavy oxygen (O18)
into mice and, because some of those atoms
were later exhaled in carbon dioxide, Ruben was
able to deduce that two thirds of the oxygen in fat
ends up in CO2.
“I danced around my lounge room for an hour
when I found that paper,” Ruben recalls, “I could
finally say with certainty that precisely 8.4 out of
every 10 kilograms of fat departs the body as
carbon dioxide.” He presented his calculations at
TEDxQUT soon after and eventually convinced
his producers to air them on ABC Television’s
Catalyst program. By then, Andrew was back at
BABS and still on top of Ruben’s list and the pair
eventually met in March 2014. “Andrew was the
first person who really appreciated the value of
my simple calculation and he emailed the day
after our interview suggesting we co-author a
paper about my work,” Ruben said, “I danced
around the kitchen until the crew made me get
back to work.”
“It is my life’s mission, and now my PhD’s, to make
sure every human being knows how their body
gains and loses weight,” Ruben says, “Once you
understand that we expend kilojoules but exhale
kilograms, you can appreciate why there is only
one way to lose weight – which is to eat fewer
carbon atoms than you exhale. Any diet that
satisfies this simple rule will work.”
Filming Catalyst with Andrew Brown’s HDR students
31 |
Affiliated Research Organisations
| 32
The Ramaciotti Centre for Genomics
The Ramaciotti Centre for Genomics is hosted by
the School of Biotechnology and Biomolecular
Sciences. It is committed to enabling
internationally competitive genomic research
and is funded by the Federal Government NCRIS
(National Collaborative Research Infrastructure
Scheme) and by the State Government of NSW.
Our technology suite includes next-generation
sequencing, Sanger sequencing, single-cell
analysis, microarrays, and high-throughput
qPCR. Services provided to the research
community include:
„
Genome sequencing
„
Transcriptome analysis
„
Single cell analysis
„
Metagenomic profiling
„
Copy number variation analysis
„
Sample/cell line identification
Fluidigm High throughput qPCR system
Highlights from 2014
ARC LIEF grant success
The Ramaciotti Centre Consortium was
successful in its bid to the ARC Linkage
Infrastructure and Equipment Funding (LIEF)
scheme for a PacBio RSII single molecule
sequencer. The grant was led by UNSW. The
PacBio RSII, unlike other next-generation
sequencers that have read lengths of 100 to 400
bases, generates average read lengths of 10,000
bases up to a maximum of >40,000 bases.
Illumina HiSeq 2500 Next Generation Sequencer
The long read lengths generated by the PacBio
RSII will help to simplify and improve the
assembly of genomes, and will facilitate the
analysis of base modifications and transcript
isoforms.
This is the Centre’s fifteenth successful LIEF
grant, bringing the total ARC LIEF funds awarded
to the Ramaciotti Centre Consortium to $9.5
million.
Illumina NextSeq 500 Next Generation Sequencer
33 |
National Framework Dataset Program
The Centre continues to work on a number of
federally funded strategic dataset projects,
which involve genome sequencing – including
metagenomics – and transcriptomic analysis.
These projects are building large biomolecular
datasets, which will positively impact on problems
of importance to Australia. They include:
„
Biome of Australian Soil Environments –
metagenomic and amplicon sequencing to
map soil biodiversity
„
DNA Barcoding – sequencing genetic markers
to enable rapid species identification and aid
conservation
„
Koala Consortium – sequencing the koala
genome and transcriptome to protect koalas
from debilitating disease
„
Great Barrier Reef – sequencing coral and
symbionts to protect and preserve the coral
reef
„
Melanoma – genome sequencing to identify
genetic mutations that lead to cancer
„
Wheat – sequencing pathogens to increase
yields and help defend against disease
„
Wine – sequencing chardonnay varieties and
yeast to enhance wine characteristics.
Illumina MiSeq Next Generation Sequencer
| 34
Alliance with the Garvan Institute’s
Kinghorn Centre for Clinical Genomics
On 9 September 2014 the Centre announced
an alliance with the Garvan Institute’s Kinghorn
Centre for Clinical Genomics (KCCG) that will
allow the research community access to the most
powerful available platform for human genome
sequencing, the Illumina HiSeq X Ten.
The X Ten system provides unparalleled
sequencing capacity and is capable of
sequencing around 350 human genomes a
week, or 18,000 per year. The KCCG was one of
the first institutions in the world to acquire the X
Ten platform, and the first in Australia to operate
a purpose-built facility for sequencing clinical
grade human genomes.
By forming this alliance, the Ramaciotti Centre will
allow the broader research community access to
this world-class genomics sequencing facility.
Professional Women in Leadership
Acquisition of an Illumina NextSeq 500
The Centre Manger Dr Helen Speirs was
accepted into the inaugural UNSW Professional
Women in Leadership Program (PWIL). The
program aims to identify, grow and retain a
pool of high potential talented women to take
up leadership roles within UNSW. It supports
the University’s strategic objective of improving
leadership and operational capabilities and seeks
to develop strong female role models.
Next generation sequencing continues to be a
growth area for the Centre. With funding awarded
by the ARC in a successful 2014 LIEF grant, the
Centre expanded its suite of next generation
sequencing instruments by investing in an
Illumina NextSeq 500 sequencer. The NextSeq
is a desktop sequencer that provides great
flexibility allowing us to sequence genomes,
exomes and transcriptomes.
With over 300 eligible candidates for nomination,
Helen was one of 21 Professional staff selected to
be part of the 12-month program.
Oxford NanoPore MinION
The Ramaciotti Centre was selected to be part
of the Oxford NanoPore Technologies (ONT)
MinION access early programme. The MinION
is a new sequencing technology that utilises
protein nanopores. The MinION passes an ionic
current through nanopores in a membrane and
measures the changes in current as molecules
pass through the nanopore, with the information
on the changes in current being used to identify
the molecule.
The Centre is currently beta testing the MinION
system on small genomes such as the bacterial
virus lambda phage and E. coli DNA.
Sanger Sequencer RAMAC
Oxford NanoPore Technolgies MinION
35 |
NSW Systems Biology Initiative
The Systems Biology Initiative (SBI) is a centre for
molecular systems biology. It has deep expertise
in proteomics, genomics and transcriptomics,
and in the bioinformatics that is required to
analyse and integrate omics results and data. It
is funded by the Australian Research Council,
the federal government National Collaborative
Research Infrastructure Scheme (NCIRS),
and the NSW State Government Research
Attraction and Acceleration Program (RAAP). It
is actively involved in the establishment of ‘omics
infrastructure, in genomics, proteomics and high
performance computing, through leading and
participating in ARC LIEF grants.
The SBI has an active program in yeast systems
biology. A focus of this work is to understand the
role that protein methylation has in the regulation
of protein-protein interactions, and to study
this on a global scale in the yeast proteome.
After recent work to define the proteins, and
sites on proteins that are methylated, we have
focused our research on (i) discovery of the
methyltransferases that are responsible for this
methylation and (ii) the use of our ‘conditional
two-hybrid’ system to measure the effect of
methylation on the protein interactions. This has
led to the finding that, for a protein with many
interaction partners, methylation increases
interactions with some partners but not with
others. Methylation thus modulates interaction
specificity. From this work, in 2014 we presented
the general hypothesis of the ‘protein interaction
code’.
Regulation of protein-protein interactions by methylation,
in the yeast interactome. From Erce et al. (2013) Mol Cell
Proteomics 12(11): 3184-98.
| 36
The SBI has a team of bioinformatics researchers
that are funded to develop expertise in the
analysis of omics data and to disseminate this
expertise through collaboration. The team works
closely with users of NCRIS-funded omics
facilities, specifically the Ramaciotti Centre for
Genomics, the Bioanalytical Mass Spectrometry
Facility, and the Australian Proteome Analysis
Facility.
In 2014, the bioinformatics team was involved
in many collaborations, addressing a range of
biological questions. These ranged from de novo
assembly of the koala genome, to understanding
the network-basis of synergistic drug effects,
through to the discovery of osteoblast-specific
markers in stem cells during their differentiation to
osteoblasts.
Stem cell marker genes show hierarchical clustering that
relate to their temporal expression during differentiation.
From Twine et al (2014) Bone ;67: 23-32.
Centre for Marine Bio-Innovation
The CMB is an international focal point for
interdisciplinary basic and applied research
into chemically mediated interactions between
organisms. Located in the Biological Sciences
Building, the Centre integrates research
across microbiology, marine chemical ecology,
ecological theory, chemistry, and organism
and community genomics. The CMB drives
research excellence in studies of microbial
biofilms, bacteria-higher organism interactions,
colonization biology of marine sessile organisms,
experimental marine ecology, biofouling,
biodiversity, bioremediation and inter-kingdom
signalling.
Key research activities in the CMB occur within
and in collaboration with a number of Australian
and international institutions and industries. 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 wide
network.
The CMB has more than 50 full time members,
comprised of research fellows, postdoctoral
research associates and research assistants,
and its members have a strong record in honours
and postgraduate student supervision. A number
of collaborations in Australia and overseas
contribute to the high standard and international
profile of the Centre, which 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. This includes success
in competitive grants, notably the Australian
Research Council, but also from international
bodies, and it has also received considerable
support from relevant industry sources.
Further information is available on the Centre’s
website: cmb.unsw.edu.au/
37 |
Specialised Facilities, Services and
Equipment
UNSW Recombinant
Products Facility
Molecular and Image
Analysis Facility (MIAF)
This facility located in Room 329 of the Biological
Sciences Building provides services in cell
line development, bioprocess design, protein
production services and training to the research
community. Services include
The MIAF is a multiuser facility that is able
to be accessed by researchers from BABS,
other UNSW Science Schools and Faculties
and UNSW-associated 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.
1. Cell line development (choice of host, vector
and gene design)
2. Cell line characterisation
3. Bioprocess development and evaluation
4. Microbial fermentation (E.coli and yeast) to 25
litres
5. Protein and antibody purification using AKTA
systems
6. Protein characterisation and analysis
including protein gel electrophoresis, Western
blotting, HPLC
7. Co-ordination with other UNSW services such
as LC-MS and other proteomic services via
the BMSF
8. Training in Fermentation and purification using
the AKTA systems
Website: proteins.unsw.edu.au
Seahorse Extracellular Flux
(XF) Analyser
The Seahorse Analyser is
cutting-edge technology
that measures the
metabolic activity of
cells in minutes, allowing
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 RPF provides a range of services for upstream
(fermentation), midstream (filtration and centrifugation),
purification and analysis.
| 38
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.
C1Si Confocal Microscope
The C1si is a revolutionary true spectral imaging
confocal laser microscope that can be valuable in
a wide range of applications. It has the capability
to acquire 32 channels of fluorescence spectra
over a 320nm-wide wavelength range in a single
pass. 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.
Other specialised
instruments and
amenities in BABS
„
Beckman Coulter Quanta MPC flow cytometer
„
Bioscreen cell growth monitoring system
„
CLARIOstar microplate reader
„
EnSight Multimode plate reader
„
EVOS-FL digital LED-based fluorescence
microscope
„
Gel documentation systems
„
Low temperature incubators
„
Neon transfection system
„
Nikon TS100-F inverted microscope with an
LED source
„
Olympus BX51 fixed stage fluorescence
microscope equipped with an Eppendorf
microdissector
„
Olympus FSX100 digital imaging system
„
PAM2500 Portable chlorophyll fluorometer
„
Polarstar omega microplate reader
„
Protean IEF system
„
QC1 and QC2 quarantine-approved premises
„
RT PCR systems
„
Security Sensitive Biological Organisms
(SSBA) facility
„
Semi-automatic microtome
„
TissueLyser LT cell lysis apparatus
„
TLC autospotter
„
Various liquid-handling robotic systems
„
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.
39 |
External Partner Organisations
ANZAC Research Institute
Hanze University of Applied Sciences
Arizona State University
Hebrew University of Jerusalem
Atma Jaya University Indonesia
Helmholtz Centre for Infection Research
Australian Antarctic Division
International Society for Microbial Ecology
Australian Coal Association Research Program
J Craig Venter Institute
Australian Coal Mining Industry
James Cook University
Australian Drosophila Biomedical Research
Support Facility
Japanese Border Collie Health Network
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
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
| 40
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
Microbiogen
Murdoch University
Nanyang Environment and Water Research
Institute
Nanyang Technological University
NASA Ames Research Centre
National Centre for Adult Stem Cell Research
Griffith 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
University of Cologne
Orica Australia Pty Ltd
University of Copenhagen
Peking University Health Science Center
University of Heidelberg
Pennsylvania State University
University of Konstanz
Prince of Wales Hospital
University of Leipzig
Queensland Parks and Wildlife Service
University of Manchester
Queensland University
University of Melbourne
Rutgers University
University of Minho Portugal
SA Department of Primary Industries
University of New Mexico
Save Sight Institute
University of Otago
Scripps Institute of Oceanography
University of Ottawa Heart Institute
Seoul National University
University of Papua New Guinea
Singapore Advanced Environmental
Biotechnology Centre
University of Poitiers
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
Universidad Nacional de Quilmes
University College Dublin
University of Adelaide
University of Alberta
University of Amsterdam
University of Auckland
University of British Columbia
University of California, Davis
University of Queensland
University of Salzburg
University of Saskatchewan Canada
University of Southampton
University of Southern California
University of Sussex
University of Sydney
University of Tasmania
University of Technology Sydney
University of Utah
University of Washington
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
University of California, Irvine
University of California, Los Angeles
University of California, San Diego
University of Canberra
University of Cincinnati
41 |
Memberships in Societies and
Associations
Alexander von Humboldt Foundation
American Academy of Microbiology
American Association for Cancer Research
American Society for Biochemistry and Molecular
Biology
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
Buttressing Coalition of the Papua New Guinea
Institute of Medical Research
Chronic Lymphocytic Leukemia Australian
Research Consortium
Council of the Human Proteome Organisation
Endocrine Society of Australia
| 42
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
Learning and Teaching
The School of BABS is advancing cellular and
biomolecular science to make a real difference
in the world. By investigating and understanding
life at the molecular and cellular level, including
life from some of the most extreme environments
on earth, our students help solve real-world
challenges.
Our undergraduate and postgraduate degree
programs offer structured training in scientific
methodology, creative thinking, organisational
skills, problem solving and analysis. Our
programs prepare students for a variety of
career options within and outside the sciences,
with graduates excelling in a wide range of
commercial research pathways, including
medical, environmental and biotechnology.
Communication and information literacy are
emphasised, providing our graduates with
a competitive edge for careers in business
and science communication. They also are
well qualified for employment in government
and privately sponsored industries in areas
ranging from management, policy development,
production and quality control, to education.
Innovations in teaching
New courses in rapidly evolving discipline areas
have been developed in recent years, attracting
significant interest amongst students, with our
majors restructured to align more closely with
the School’s emerging research strengths.
Recognising the importance of research training
and associated skills, BABS has introduced a
number of initiatives to provide undergraduate
students with the opportunity to engage in
authentic research opportunities, both within
traditional courses as well as via an internship
program in our research labs.
While BABS is home to internationally recognised
and innovative researchers, we also leverage
the School’s close collaboration with prominent
centres such as the Ramaciotti Centre for
Genomics and the UNSW Mark Wainwright
Analytical Centre to incorporate cutting-edge
research into undergraduate teaching.
Building on the introduction online resources in
previous years, during 2014 the School:
„
introduced the use of electronic online
laboratory notebooks
„
developed more online resources, including
pre-laboratory quizzes and self-paced tutorial
activities
„
purchased Surface Pro3 tablets to enable
students to investigate laboratory techniques
and contextualise their learning in real time;
this also facilitated their engagement with
bioinformatic data analysis
„
took advantage of resources available in
Moodle, UNSW’s learning management
system, to develop peer-based assessment
strategies that enhance student capabilities to
analyse and critique scientific writing.
43 |
Modern facilities
Renovation of BABS teaching laboratories is now
complete, providing state-of-the-art teaching
facilities for our students, including biochemistry/
molecular biology teaching laboratories to PC1
standard and a microbiology teaching laboratory
to PC2 standard. All labs feature video display
screens, demonstrator-led independent group
areas with video/computer/internet facilities, a
preparation laboratory and real-time microscope
projection.
In conjunction with these improvements, we
converted one of the old laboratories into an
informal learning space christened BiBS (BABS
interactive breakout space), where students are
able to interact with each other as well as with
staff. Amenities include textbook resources,
computers and wi-fi, discussion areas and
kitchen facilities. In addition, a duty tutor is
available for student consultation three days
per week. The facility is frequently used by
students to practice presentations and work
on group projects, and the student society,
BABSOC, makes good use of the space for
functions, including trivia nights and other
fundraising activities.
| 44
Outreach and supporting
students
Academics from the School participate frequently
in outreach activities, including those designed
to engage secondary school students and
encourage them to continue on to science at a
tertiary level. Academic staff act as judges in
high school science competitions and contribute
to the Nura Gili program for indigenous high
school students, and are members of the
CSIRO Scientist in Schools program. BABS also
supports science teachers with mentoring and
provision of learning resources, and remains
actively involved with the Science Teachers
Association of NSW 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, making our
programs ideal for those wishing to pursue
research-oriented careers.
Majors
Postgraduate degrees
The School teaches within the science discipline
areas of biotechnology, genetics, microbiology,
and molecular and cell biology. In conjunction
with the Faculty of Medicine, we also teach
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 specialisation, with study plans provided for
each discipline area.
As the next generation of researchers, our large
cohort of Higher Degree by Research (HDR)
students are an important group in the School.
We offer a range of opportunities for HDR
students from Australia and overseas countries
to work towards a Graduate Diploma, Masters by
Research or PhD Degree. In 2014 the School had
142 HDR students, with 119 progressing towards
a PhD, and 43 HDR students completed their
programs during the year.
Honours
An optional Honours year can be undertaken by
undergraduate students who have maintained
a credit average or above during their 3-year
program. Honours students join a research team
within one of the School’s research labs, working
under the direct supervision of an experienced
academic. They complete a research project and
write a thesis during the year-long program.
45 |
Teaching students how science can
make a difference
Dr Wallace Bridge, Senior Lecturer
Australia’s reputation for producing high quality
scientists is supported by the oft quoted “we have
0.3% of the world’s population but we produce
3% of the world’s peer-reviewed publications”.
Unfortunately, this does not correlate to a similar
capacity to translate that great science into new
products and services that could make the world
a better place, evidenced by our accounting for
only 0.6% of the world’s patenting activity. To
understand this dichotomy, we need to consider
the motivation of our scientists, where they are
employed and how they are educated.
Most early stage high-risk research, which is
where the great scientific discoveries are often
made, occurs in our government-funded research
agencies (GFRAs) such as UNSW Australia. The
majority of GFRA-employed researchers are
financially dependent on federal government
ARC and NHMRC grants, and a researcher’s
competitiveness for these grants is largely
dependent on their publication and grant track
record. There is, however, no career or financial
imperative for researchers to make any real effort
to translate their great research findings into
tangible benefits for society. On the contrary, any
effort to do so may result in catastrophic outcomes
for their career by distracting them from the
mandated “publish or perish” system for funding.
This ongoing reluctance of our funding systems
to demand and reward innovation is further
exacerbated by an education system that generally
has not provided any of the requisite business
skills that a scientist would require to put their
research findings into practice.
Although BABS cannot change the current grant
systems, it can influence the education of our
future research scientists. Since 1999, BABS has
been offering professional business and science
translation-oriented courses for its students, and
in 2001, the Diploma in Innovation Management
was launched as a separate add-on program to
be taken concurrently by science students. The
rationale for the Diploma was to teach the business
aspects of science without necessarily diluting the
science.
The 36UOC Diploma comprised the two BABS
professional courses (BABS3071 and BABS3091),
a formal work placement, and three other courses
| 46
that focused on entrepreneurship, strategic
communication and finance. BABS3091, a
capstone course for both the Diploma and the BSc
(Biotech) program, teaches financial accounting
and guides student teams through the preparation
of business plans for opportunities based on real
intellectual property. The accounting content is
tailored for science students, who usually have no
underlying interest or background in business.
Throughout the course we awaken and reinforce
the principle that the ability to understand business
and to communicate in its language will be a major
determinant of their future professional success.
We constantly remind students that science is
actually hard, and business is really easy. To
reinforce and hopefully validate this, we encourage
them to enter the UNSW Business School’s
Business Planning competition (currently known as
the Peter Farrell Cup) that is open to all students
from across UNSW.
Teams from BABS have historically excelled in this
highly applauded and acknowledged competition,
winning it 8 times and taking out minor placings
another 34 times. In 2014, this success continued:
of the 42 entrants, 9 were from BABS3071 and 6
of these made the final 10. At the finals, the teams
pitched their plans to an 8-member judging panel,
and claimed first and third places, also winning 2
Honourable Mentions and the Most Popular vote.
They took away $7,500 of the $10,000 prize money
on offer, lifting the BABS3071 progressive cash
winnings to $112,250.
Over 250 BABS students now have “UNSW
Business School Business Planning Competition
Finalist” on their resumes, with 140 as placegetters
and 32 as winners. These BABS students have
learnt business skills, often with some initial
reluctance, developed ability and confidence in
communicating how science can be translated,
and have gained confidence from senior business
professionals that they can excel in the field.
Perhaps one day it will be former BABS3091
students who stem the tide of Australia’s poor
innovation performance!
Learning and Teaching Prizes and
Scholarships
2014 undergraduate student awards
University medallists
UNSW University Medal in Biotechnology
Farzana Kastury
UNSW University Medal in Microbiology
Sophie Holland
School prizes
Jackson Prize for Honours Year for best overall performance in
Honours year
Sophie Holland
Jackson Prize in Microbiology and Immunology for the best
performance in Microbiology and Immunology
Daniel Enosi Tuipulotu
Garry King Prize for the best Honours thesis in Molecular Biology or
Genetics major
Beth Caruana
The School of Biotechnology and Biomolecular Sciences Prize
for the best overall performance in Level 3 Professional Issues in
Biotechnology courses BABS3071 and BABS3091
Eddie Ip
School of Biotechnology and Biomolecular Science Prize for the best
performance in BIOC3111 Molecular Biology of Proteins
Medha Sengupta
School of Biotechnology and Biomolecular Science Prize in Level 2
Biochemistry for the best performance in the examinations in Level 2
Biochemistry courses in the Bachelor of Science program
Kimberley Hanssen
School of Biotechnology and Biomolecular Science Prize in Level
3 Biochemistry for the best performance in Level 3 Biochemistry
courses in the Bachelor of Science program
Akshay Flora
Talented student scholarships
School of Biotechnology and Biomolecular Sciences Talented
Student Scholarship for outstanding achievement in Year 1
Asma Hossain
School of Biotechnology and Biomolecular Sciences Talented
Student Scholarship for outstanding achievement in Year 2
Jessica Horton
School of Biotechnology and Biomolecular Sciences Talented
Student Scholarship for outstanding achievement in Year 3
Tracy Mak
47 |
BABS PhD scholarship supplement scheme
BABS offers a PhD Scholarship Supplement scheme as a School-funded initiative
to provide support to PhD students and encourage them to publish their work.
Candidates must hold a primary competitive postgraduate scholarship, and not have
been awarded any other top-up scholarship.
Selection criteria include number of papers published or accepted where the student
is first author (journals must generally have an impact factor of 2 or higher).
Each top-up package comprises a $5,000 per annum stipend for new and continuing
students ($2,500 for 4th year students).
Awardees during 2014:
„
Bakir Al-Sinawi (supervisor Brett Neilan)
„
Wen Aw (supervisor Bill Ballard)
„
Giampiero Batani (supervisor Torsten Thomas)
„
Jugder Bat-Erdene (supervisor Chris Marquis)
„
Jose Burgos-Portugal (supervisor Hazel Mitchell)
„
Jesse Cain (supervisor Brett Neilan)
„
Natalia Castano-Rodriguez (supervisor Hazel Mitchell)
„
Long Chung (supervisor Vincent Murray)
„
Caio Damski (supervisor Kevin Morris)
„
Joshua Hamey (supervisor Marc Wilkins)
„
Nicholas Lister (supervisor Kevin Morris)
„
Fang Lu (supervisor Li Zhang)
„
Jennifer Lun (supervisor Peter White)
„
Laurence Luu (supervisor Ruiting Lan)
„
James Mills (supervisor Michael Janitz)
„
Jadranka Nappi (supervisor Suhelen Egan)
„
Anika Prabhu (supervisor Andrew Brown)
„
Jeyran Shahbazi (supervisor Tao Liu, CCIA)
„
Angela Soeriyadi (supervisor Brett Neilan)
„
Jessica Taylor (supervisor Torsten Thomas)
„
Daniel Winter (supervisor Marc Wilkins)
| 48
BABSOC
BABSOC is the student-run society that caters for all
undergraduate and postgraduate students enrolled
in BABS courses and programs. Its objective is to
facilitate the development of and interaction within the
BABS community by providing a stream of social and
professional events throughout the academic year.
The society is affiliated with and financially supported
by the UNSW-wide student organisation, Arc.
The 2014 BABSOC Executive mentored by BABS
academic Dr Wallace Bridge comprised two fresh
first-years (Wendy and Elizabeth), one keen secondyear (James), two talented third-years (Rhys and
Alex), four passionate Honours students (Farzana,
Nush, Akira and Jess), and one indispensable PhD
student (Josh).
One of the aims of the year was to give BABSOC
an identity to set it apart from the 200-odd clubs
competing for student attention at UNSW. The
executive achieved this by creating a new logo for
the society that depicts BABS as a tree nourished by
the roots of BABSOC (the BABS community), with the
branches representing the School’s output via its four
research disciplines. The logo was incorporated into
T-shirts for the executives to wear during events, as
well as mugs and stubby holders reserved for gifts at
special occasions.
This not only helped make BABSOC identifiable
to all its members, but also served as an effective
advertisement of its existence and value to the
School.
BABSOC organised many great events in 2014,
including barbeques for students and staff, a Careers
Night, a meet-and-greet for prospective Honours
students to chat with academics and potential
supervisors, the Great Debate, and assisted with the
management of the BABS Research Symposium.
Feedback from all these activities reconfirmed the
successful addressing of the BABSOC mission:
encouraging students to undertake Honours,
informing career choices, providing platforms
for networking between students, academics
and professionals, and above all, showing off the
excellent research carried out in BABS.
Two free barbeques held in the Wilton room were
overwhelmingly successful, with well over 100
students and staff attending each event. The
BABSOC team was actually overwhelmed, running
out of sausages both times and having to dispatch
runners to the local supermarket to replenish
supplies. The barbeques were a great means to
promote awareness of BABSOC and provide an
opportunity for students to mingle with staff outside
of an academic atmosphere and, in doing so, help
develop that sense of community we are so keen to
achieve within the School.
The annual BABSOC Careers Night was held in
September with the theme “Where can Honours take
you?”. A panel of recent BABS graduates told stories
of how they secured their first job, and demonstrated
how a BABS Honours degree could enable many
career paths, from research, product development
and finance, through to business. The night wrapped
up with a pizza networking session, with the
speakers being flocked by enthusiastic enquiring
attendees.
Something new for BABSOC in 2014 was the
inaugural Great Debate, towards the end of Semester
2 during one of the regular bi-weekly Friday
afternoon research seminar timeslots. The topic was
“Use of Experimental Drugs is Ethical in the Case of
Ebola”, and the contesting teams were selected from
undergraduate BABS student applicants. To ensure
the quality of the debate, DebSoc (UNSW Debating
Society) kindly agreed to train the speakers and
adjudicate on the day. Following a splendid to and
fro, the winner was declared to be the ‘Aye’ team. It
was a great success for all involved and provided
an excellent opportunity for the students to develop
49 |
Bachelor of Science student Rhys Keirle cooking up a storm.
valuable communication skills and network with
academics and researchers.
with non-scientists – as well as the very important
role of selfies!
Finally, after the success of the inaugural event
in 2013, the greatly anticipated annual BABS
Research Symposium was held at the stunning
Randwick Racecourse. The event, which BABSOC
assisted to organise and deliver, was a highlight
of the BABS year and drew in over 200 people
from the BABS community. They could not have
been disappointed, as every speaker had worked
diligently through practice sessions to ensure that
their presentations were free from unnecessary
jargon so that they could be readily understood by a
broad audience.
Head of School Professor Andrew Brown closed the
event, commenting on how successful the day had
been, and thanking Dr Bridge and the BABSOC
executive for their great work in organising such
a wonderful event. It was then time for what was
possibly another highlight for some delegates, a
happy hour at the nearby Doncaster Hotel.
The Symposium commenced with eight talented
Honours students presenting their research
findings. With the high standard of the day already
set, the next two sessions for PhD students and
postdoctoral researchers built on this, as they
continued to share the great work that they and their
labs were undertaking. Delegates heard topics from
a wide array of research areas, including molecular
medicine, environmental microbiology, infectious
disease and systems biology. Over 30 posters
that had been presented at conferences within
the previous year, both locally and internationally,
added to the already sensational day.
The 2014 Symposium also saw a presentation
on science communication by the ABC’s Surfing
Scientist and Catalyst presenter Ruben Meerman,
who wowed the audience after exploding a balloon
within a balloon using just a class IIIB laser. He
spoke on the importance of trying to make research
sound relevant and interesting when communicating
| 50
2014 Honours Completions
Name
Supervisor
Project Title
Akerman,
Anouschka
Louise Lutze-Mann/Noel
Whitaker
The role of human papillomavirus-encoded miRNAs in
HPV transformation.
Araghi, Hamid
Richard Lock/Marc
Wilkins/Sibasish Dolai)
Targeting insulin-signalling pathway in high-risk B-cell
precursor acute lymphoblastic leukaemia
Bainbridge, Emily
Hazel Mitchell
The role of the Campylobacter concisus virulence
plasmid in autophagy manipulation.
Benaud, Nicole
Belinda Ferrari/John
Kalaitzis
Polar soil aActinobacteria: a potential source of novel
antibiotic secondary metabolites.
Caruana, Beth
Louise Lutze-Mann
Targeting site-1 protease as a novel therapeutic for
glioblastoma.
Chadwick, Justin
John Foster
Genetic response of Human Adult Dermal Fibroblasts
(HDFa) to novel biomaterials for wound healing
applications.
Chan, William
Torsten Thomas/Nicholas
Barraud
Nitric oxide-mediated regulation of bacterial biofilm
dispersal and virulence in plant hosts.
Chen, Jieqiong
Michael Janitz
Molecular analysis of long intervening non-coding RNAs
highly expressed in the white matter of the human brain.
Davis, Sarah
Antony Cooper
Novel long non-coding RNAs as Parkinson’s Disease
blood biomarkers.
Dutton, Rosanna
Kevin Morris
The identification and characterisation of DNAmethyltransferase 3A associated long non-coding RNAs.
Enosi Tuipulotu,
Daniel
Peter White
Recognition sequences and template specificity of viral
polymerases.
FigueroaCrisostomo, Carah
Bill Rawlinson/Maria
Craig/Ammir Al-Shabeeb
Circulating microRNAs distinguish enterovirus infection in
type 1 diabetes patients: potential biomarkers?
Gana, Christine
Andrew Brown
Post-translational regulation of DHCR7, the terminal
enzyme of cholesterol synthesis.
Gaweda, Yvette
Brett Neilan
Biotic and abiotic factors influencing toxic cyanobacterial
blooms in an urban and residential freshwater
environment.
Gokoolparsadh,
Akira
Irina Voineagu
Functional role of IMMP2L in human astrocytes and
implications for Tourette Syndrome.
Hegarty, Narelle
Rebecca Lebard
The aflatoxin mystery.
Holland, Sophie
Mike Manefield
Organochlorine metabolism in chloroform-respiring
cultures.
Kastury, Farzana
Mike Manefield
Ecotoxicology of neutral red for environmental
applications.
Kotevski, Damian
Rob Yang
The role of FLD1 in the regulation of yeast GPAT and
AGPAT activity.
Lee, Sandra
Li Zhang
The investigation of the biological effects of toxins
produced by Campylobacter concisus CON_phi2
prophage.
51 |
Name
Supervisor
Project Title
Liew, Heng
Brett Neilan/Brendan
Burns
Shark Bay microbial mats: key to reveal UV adaptation
strategies of archaean life.
Luk, Alison
Mike Manefield
Quantification of microbial groups involved in subsurface
biogas production.
Lun, Jennifer
Peter White
Epidemiologic surveillance of Norovirus in NSW, 20132014.
Marczuk, Jevira
Marc Wilkins/Boris
Martinac
Engineering E.coli MscL for x-ray crystallography.
Moreau, Alexandre
Torsten Thomas
Utilisation of biochar by soil bacteria.
Ng, Hong
Noel Whitaker
Impact of HPV-infection on hu-miR-145 and transcription
factor KLF4 expression.
Nguyen, Kim
Stuart Tangye
Impact of a mutation in phosphatidylinositol 3-kinase
(PI3K) on B cell development and function.
Nicholls, Laura
Irina Voineagu
Gene expression profiling of Rett syndrome brain tissue.
Pontifex, Ashleigh
Brendan Burns
A day in the life of a stromatolite: innovative
metaproteomic analyses of early Earth microbial
communities.
Poon, James
Rob Yang/Daniel
Hesselson
A new pink1-deficient zebrafish PD model to investigate
gene X environment interactions.
Ray, Jason
Chris Marquis
Isolation and characterisation of a lesser chlorinated
benzene degrading community
Stewart, Shannan
Marc Wilkins
Construction of a switchable two-hybrid system for
detecting PTM-mediated protein-protein interactions.
Tam, Hon
Belinda Ferrari
Partners of candidate division TM7 in soil.
Tan, Hao
Torsten Thomas/Shaun
Neilsen
Isolation and characterisation of biochar-utilising bacteria
from soil.
Tan, Jessica
Bettina Rosche/John
Kalaitzis
The effect of the traditional Chinese medicine Jie Geng
on Pseudomonas aeruginosa biofilm development and
integrity.
Tan, Amanda
Vladimir Sytnyk
Regulation of synaptic activity in hypothalamic neurons
by NEGR1.
Wang, Zichen
Kevin Morris
Investigating the effects of RNA-directed transcriptional
gene silencing on BIRC5 (Survivin)
Wong, Alan
Brendan Burns
Depth profiling of microorganisms in Hamelin Pool
microbial mats
Yao, Pu
Irina Voineagu
Comparsion of brain and LCL transcriptome profilling by
RNA-seq and CAGE.
Yap, Samantha
Marc Wilkins/S ven
Delaney
Genetic variation in mitochondrial and nuclear DNA of
Wollemi pine.
Yee, Mon
Mike Manefield
Manipulating electron flow in methanogenic microbial
communities using semiconductive phenazine crystals.
| 52
2014 PhD Completions
Name
Supervisor
Title
Ballestriero, Francesco
Suhelen Egan/ Staffan
Kjelleberg
Combining microbial functional metagenomics and
Caenorhabditis elegans genetics to uncover and
characterise novel bioactive compounds.
Blaber, Elizabeth
Brendan Burns
Stem cell-based tissue regeneration in space.
Bone, Simon
Alison Todd
The development of signal amplification detection
technology utilising dnazymes.
Burdach, Jonathan
Merlin Crossley
Insights into in vivo transcription factor targeting
through studies of the archetypal zinc finger protein
KLF3.
Castãno Rodriguez,
Natalia
Hazel Mitchell
The role of innate immunity in helicobacter pylorirelated gastric cancer.
Chan, Carmen
Mark Tanaka
Developing new mathematical models of the
evolutionary dynamics of viruses.
Chan, Rodman
John Foster
Natural synthetic composites of
poly(hydroxybutyrate) poly(ethylene glycol) as
potential scaffolds for nerve repair.
Chenu, Jeremy
Julian Cox
A (semi-) quantitative approach towards a better
understanding of the ecological dynamics of
Campylobacter spp. in a commercial broiler chicken
operation.
Correa Ospina, Claudia
Bill Ballard
Evolution of cytoplasmic genetic variation: studying
Wolbachia from a mitochondrial perspective.
Eltahla, Auda
Peter White
Non-nucleoside inhibitors of viral RNA polymerases;
scaffolds for rational drug design.
Flannery, David
Malcolm Walter
Palaeobiology of the Neoarchean Fortescue Group.
Gardiner, Melissa
Suhelen Egan
Molecular determinants of bacteria colonisation on
macroalgal surfaces.
Hazrin Chong, Nur Hazlin
Mike Manefield
Microbial cell attachment, colonisation and
degradation of coal.
Hui, Janice
Scott Rice
The genes and factors that drive the conversion of
the Pseudomonas aeruginosa Pf4 prophage into the
superinfective form.
Kapterian, Tamar
Robert Yang
The characterisation of CDP-Diacylglycerol
synthases in lipid droplet dynamics and adipocyte
development.
Kohli, Gurjeet
Brett Neilan/Shauna
Murray
Diversity and genetics of Australasian
dinoflagellates, including Gambierdiscus spp., the
causative agent of ciguatera fish poisoning.
Lam, Connie
Ruiting Lan
Effects of vaccine selection pressure on the genetic
diversity and evolution of Bordetella pertussis.
Linardy, Evelyn
Alison Todd
The development of nuclease-mediated
amplification technology for analyte detection.
53 |
Name
Supervisor
Title
Luu, Winnie
Andrew Brown
The role of signalling and sensing in cellular
cholesterol homeostasis.
Mohd Omar, Suhaila
Rick Cavicchioli
Utilising Antarctic metagenomic resources for the
identification of hydrolases.
Moradi Manesh, Donya
Richard Lock
Molecular determinants of T-cell acute Iymphoblastic
Ieukaemia sensitivity to the pre-prodrug PR-104.
Ongley, Sarah
Brett Neilan
Development of a system for the heterologous
expression of cyanobacterial natural products.
Sach, Roy
Malcolm Walter
Containing space warfare in the early decades of
the twenty-first century.
Stevenson, Julian
Andrew Brown
Cholesterol-dependent degradation and unsaturated
fatty acid-dependent stabilisation of squalene
monooxygenase in the control of cholesterol
synthesis.
Taleb, Imam
Mike Manefield
Linking the degradation of model saturated
and aromatic crude oil components to specific
marine microbial taxa during biostimulation and
bioaugmentation using RNA-stable isotope probing.
Timms, Verlaine
Brett Neilan
The mycobacteriology of inflammatory bowel
disease.
Van Dorst, Josie
Belinda Ferrari
Microbial indicators of diesel fuel toxicity in polar
soils
Wijenayake, B Nirmani
Louise Lutze-Mann
Investigation of psychotropic drugs for the treatment
of glioblastoma.
Winsley, Tristrom
Belinda Ferrari
An Investigation into the bacterial phylum, candidate
division TM7.
Woodhouse, Jason
Brett Neilan
The microbial and metabolic diversity associated
with cyanobacteria-dominated consortia.
Zerenturk, Eser
Andrew Brown
The regulation and membrane topology of DHCR24,
a key enzyme in cholesterol synthesis.
Zhang, Yuxi
Robert Yang
Molecular analysis of lipid storage and trafficking.
Zhang, Lelin
Marc Wilkins
Discovery and characterisation of novel protein
methyltransferases in Saccharomyces cerevisiae.
| 54
4
Research Funding
Grants awarded in 2014 commencing in 2015
Australian Research Council
ARC Discovery Project
Ballard JWO & Wade CM. Defining unconscious
and artificial selection. 2015-2017: $374,900.
Brown MV, Ostrowski ML, Bodrossy L, Beman
JM & Fuhrman JA. Mapping and modelling
the ocean’s unseen biodiversity. 2015-2017:
$532,200.
Cavicchioli R, Raftery MJ & Papke RT. How
do microbes grow in high salt at very cold
temperatures? 2015-2019: $835,200.
Crossley M & Mackay JP. The role of DNA
methylation in transcription factor activity. 20152017: $428,100
National Health and Medical
Research Council
NHMRC Project Grant
Yang HR. Molecular characterization of SEIPIN
function: implications for lipogenesis and
adipogenesis. 2015-2018: $737,660.
Early Career Fellowship
Palmer A. Understanding the mechanisms of
drug-drug synergy in combination chemotherapy.
2015-2019: $375,932.
Man SM. The role of interferon-regulatory factors
in the host defense against bacterial infection.
2015-2018: $334,284. Plus associated NHMRC
RG Menzies Fellowship 2015-2018: $40,000.
ARC Linkage Project
Neilan BA & Van Asten M. Heterologous
expression of cyanobacterial compounds of
analytical and therapeutic value. 2014-2017:
$401,219.
ARC Linkage Infrastructure and Equipment
Facilities
Wilkins MR, Cavicchioli R, Morris KV, Thomas
T, Charles IG, Djordjevic SP, Darling A, Petty
NK, Paulsen IT, Gillings MR, Holmes EC, James
DE, Wade CM & Dinger ME. PacBio long
read sequencer for the Ramaciotti Genomics
Consortium of NSW. 2015: $630,000. [UNSW
Central contribution $160,000.]
ARC Future Fellowship
Tanaka M. How microbes build their environments
through evolutionary feedback. 2015-2018:
$808,160.
Other National Schemes
Autism Cooperative Research Centre Innovation
Project
Voineagu I. Transcriptome analyses of human
ASD brain tissue as a complementary method to
aid the identification of ASD susceptibility genes.
2014-2015: $50,000.
Ramaciotti Australia Foundation
Voineagu I. Functional genomic studies in autism
spectrum disorders. 2014-2015: $74,000.
International Schemes
Hope Funds for Cancer Research (US)
Postdoctoral Fellowship
Byrne FL. Reversing Warburg metabolism to treat
cancer. 2014-2017: $176,962.
Thomas T. The dynamics of evolution: How
horizontal gene transfer drives the diversification
and adaptation of complex, bacterial
communities. 2015-2018: $892,402.
ARC DECRA Fellowship
Hart-Smith GO, Protein network regulation: A
systems-level analysis of methylation. 2015-2017:
$352,000.
55 |
UNSW Internal Schemes
Faculty of Science Research Grant
Major Research Equipment Infrastructure
Initiative (MREII)
Galea A. Investigating the interaction of cisplatin
and cisplatin analogues with different human
genomic DNA targets. 2015: $12,000.
Brown AJ & Hoehn KL. Fluorescent screening
facility for cellular drug discovery. 2015: $111,947.
Brown AJ & Marquis C. HPLC for peptides and
proteins. 2015: $145,908.
UNSW Goldstar (ARC)
Brown AJ. Uncovering new regulatory programs
in sterol production. 2015: $40,000.
Crossley PM. A new generation of designer DNAbinding factors. 2015: $40,000.
Tanaka M. The evolutionary dynamics of hostassociated microbial communities. 2015:
$40,000.
UNSW Goldstar (NHMRC)
Ballard JWO. Can dietary modification that
minimises mitochondrial stress reduce cellular
and organismal dysfunction caused by mutations
in the fly homologue of a gene known to cause
familial Parkinsonism? 2015: $40,000.
Lan R. Elucidating the role and mechanisms
of Bordetella pertussis adaptation to vaccine
selection pressure in the 2008-2012 pertussis
epidemic in Australia. 2015: $40,000.
Ferrari B. Landscape connectivity and microbial
community assembly in terrestrial Antarctica.
2015: $10,000.
Burns B. Correlating population dynamics and
elemental cycling in modern stromatolites. 2015:
$10,000.
Zhang L. Examination of the impact of
polymorphic Campylobacter concisus zonula
occludens toxin on the intestinal epithelial barrier.
2015: $12,000.
Lutze-Mann L. Site 1 Protease as a
chemotheraputic target in cancer. 2015: $8,000.
Janitz M. The role of long intervening non-coding
RNA 00263 in regulation of oligodendrocyte
maturation. 2015: $12,000.
Waters P. Sex chromosome dosage
compensation – novel insights gained from the
genome to proteome. 2015: $14,000.
Murray V. The precise location of DNA adducts
caused by the anti-tumour drug Cisplatin in the
entire human genome. 2015: $14,000.
Morris KV. Activating cystic fibrosis conductance
regulator expression: the therapeutic potential of
RNA directed gene activation. 2015: $40,000.
Sytnyk V. Mechanisms of abnormal neuronal
differentiation induced by hyperactivation of
the Junctional Adhesion Molecule B (JAMB):
implications for Down syndrome. 2015: $12,000.
Faculty of Science Silverstar (ARC)
Faculty of Science Early Career Researcher Grant
Wilkins M. Methylation of glutamic acid: a new
switch for protein-protein interactions. 2015:
$35,000.
Erce M. Code of conduct: are all hub proteins
governed by an interaction code? 2015: $13,200.
Faculty of Science Silverstar (NHMRC)
Nil.
| 56
Ghai R. The mechanism of lipid trafficking
orchestrated by oxysterol binding proteins. 2015:
$13,200.
Grants current in 2014 (awarded prior to 2014)
Australian Research Council
ARC Discovery Project
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. What do microorganisms do
season by season, year after year in the frigid
Antarctic wilderness? 2013-2016: $240,000.
Dawes IW. How do cells regulate redox
environment at the subcellular level? 2010-2014:
$420,000.
Manefield MJ, Deppenmeier U & Juhasz A.
Synthetic phenazines for enhanced biogas
production from renewable and non-renewable
resources. 2014-2016: $330,000.
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.
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.
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.
White, PA. Maintaining fidelity in viral Ribonucleic
acid (RNA) polymerases. 2012-2014: $215,000.
Wilkins MR. Does phosphorylation regulate the
methylation of proteins? 2013-2015: $315,000.
Yang, HR. Characterisation of novel gene
products that regulate phospholipid metabolism
and lipid droplet formation in the yeast
saccharomyces cerevisiae. 2012-2014: $310,000.
Yang HR & Dawes IW. The role of Fld1p protein
in lipid droplet formation and growth in the yeast
Saccharomyces cerevisiae. 2013-2015: 285,000.
ARC Linkage Project
Manefield, MJ, Gooding, JJ & Lam, D. Partner
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.
Manefield MJ, Marquis CP, Lee MJ, Adrian L &
Stening R. Partner organisation: Orica Australia
Pty Ltd. Development of an anaerobic bioprocess
for hexachlorobenzene destruction. 2013-2015:
$164,780.
Neilan BA. Partner 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.
Neilan BA, Burford MA, Jex AR, Orr PT &
Azevedo SM. Partner organisations: South East
Queensland Water, Federal University of Rio
De Janeiro. Adaptive ecotyping of the toxic
cyanobacterium Cylindrospermopsis raciborskii
to predict its invasive capacity. 2013-2016:
$612,756.
Thomas T, Munroe PR & Joseph SD. Partner
organisation: Renewed Carbon Pty Ltd.
Development of the next generation of organomineral fertilisers utilising domestic and
commercial waste products. 2012-2015: 340,000.
ARC Linkage Infrastructure and Equipment
Facilities
Manefield MJ, Paulsen IT, Neilan BA, Gillings
MR, Conibeer GJ, Ralph PJ, Anderson IC, Lauro
F, Seymour JR, Singh BK, Mazard SL, Uddin A,
Bissett AP, Richardson AE, Barrett LG & White
RG. Partner organisations: Macquarie University,
University of Western Sydney, University of
Technology, Sydney, Commonwealth Scientific
and Industrial Research Organisation. A time of
flight secondary ion mass spectrometer facility
for elemental and isotopic imaging of ultra-fine
features. 2014: $1,000,000.
Wilkins MR, Cavicchioli R, Neilan BA, Scott RJ,
Foster PS, Dickson PW, Paulsen IT, Packer NH,
Gillings MR, Charles IG, Harry EJ, Djordjevic
SP & Whitchurch CB. Expanding the genomic
frontier from species to strains and individuals to
populations. 2014: $475,000.
57 |
ARC Future Fellowship
Egan S. Chemical warfare in the marine
environment: the role of surface-associated
bacteria and their antibiotics. 2013-2017:
$753,690.
Manefield MJ. Harnessing microbial respiration
for pollutant degradation and natural gas
production. 2011-2015: $808,000.
Morris KV. Is ‘junk DNA’ involved in gene editing
in human cells. 2013-2017: $821,640.
ARC DECRA Fellowship
Lauro, F. The role of deep-sea microorganisms in
nutrient cycling in the Southern Ocean. 20122014: $375,000.
Voineagu I. Genomic diversity in the human brain:
the functional role of expandable DNA repeats.
2014-2016: $315.220.
National Health and Medical
Research Council
Yang HR. The role of seipin in adipocyte
development and lipid droplet formation. 20122014: $363,510.
Yang HR & Brown AJ. Identification and
characterization of novel proteins in endosomal
cholesterol transport. 2013-2015: $521,976.
Yang HR. The role of phosphatidic acid in lipid
storage and obesity. 2014-2016: $479,838.
NHMRC Senior Research Fellowship
Yang HR. Lipid storage and trafficking in human
diseases. 2014-2018: $664,515.
NHMRC Training (Postdoctoral) Fellowship
Kaakoush N. Australian Based Biomedical
Category. 2011-2014: $290,032.
Other National Schemes
Bioplatforms Australia/CRIS Bioplatforms
Australia Research Infrastructure Scheme
Emerging Biomolecular Platforms and Informatics
Project (shared grant):
NHMRC Project Grant
„
Brown AJ. Characterising an important control
point in cholesterol synthesis beyond HMG-CoA
reductase. 2014-2016: $464,916.
School of Biotechnology & Biomolecular
Sciences Systems Biology Initiative
Component. Wilkins M. 2013-2015: $300,000.
„
Ramaciotti Centre for Gene Function Analysis
Component. Wilkins M & Speirs HJ. 20132015: $287,000.
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.
Foster LJR. Development of an ocular adhesive
film with local drug delivery to prevent infection
and inflammation in corneal wounds. 2014-2016:
$358,447.
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.
Voineagu I. (New Investigator Grant). The role
of the neuronal splicing factor A2BP1 in autism
spectrum disorders. 2014-2016: $383,447.
| 58
Brain Foundation/Research Gifts Program
Janitz M. Identifying the transcriptional cause of
multiple system atrophy. 2013-2014: $34,000.
Brain and Behaviour Foundation/NARSAD
Young Investigator Grant
Voineagu I. Brain transcriptome sequencing
and non-coding RNA characterisation in autism
spectrum disorders. 2013: $29,029.
Department of Sustainability, Environment,
Water, Population and Communities/Australian
Antarctic Division
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.
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.
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.
NSW Department of Trade and Investment/
NSW Research Attraction and Acceleration
Program - Collaborative Research Infrastructure
Scheme
Emerging Biomolecular Platforms and Informatics
Project (shared grant):
„
Ramaciotti Centre for Gene Function Analysis
Component. Wilkins, M. 2013-2015: $100,000.
„
School of Biotechnology & Biomolecular
Sciences Systems Biology Initiative
Component. Wilkins M. 2013-2015: $102,000.
„
University of New South Wales/CRIS Central
Contribution. Wilkins M. 2013-2015: $75,000.
International Schemes
UNSW/Go8 German Joint Research Cooperation
Scheme
UNSW Goldstar (ARC)
Ballard WJO. Differentiating unconscious and
artificial selection. 2014: $40,000.
Brown AJ. Uncovering new programs of
regulation in sterol synthesis. 2014: $40,000.
Morris KV. Is it possible to parasitise human
immunodeficiency virus and drive it towards a
symbiotic state in human cells? 2014: $40,000.
UNSW Goldstar (NHMRC)
Kaakoush NO & Mitchell HM. Does faecal
transplantation lead to improved outcomes for
patients with ulcerative colitis by modulating their
intestinal microbiota. 2014: $40,000.
Kaakoush NO, Lemberg DA & Mitchell HM.
Investigation of the interplay between host
genetics, immune response and the intestinal
microbiota in children newly diagnosed with
Crohn’s disease and ulcerative colitis. 2014:
$40,000.
Leshchynska I & Sytnyk V. Molecular
mechanisms of neurotransmission abnormalities
induced by disruptions of the functions of the
neural cell adhesion molecule in bipolar disorder
and schizophrenia. 2014: $40,000.
Pearson R & Crossley M. The insulin-sensitising
factor adipolin: a new target for metabolic health.
2014: $40,000.
Faculty of Science Silver Star (ARC)
Neilan BA & Muenchhoff J. The regulation and
role of toxin production in cyanobacteria. 20132014: $18,750.
Foster LJR. What gives Chitosan its antimicrobial
properties? - Relating Polymer Chain
Conformation to Bactericidal Activity. 2014:
$30,000.
UNSW Internal Schemes
Morris KV. Do non-coding ribonucleic acids
function as cellular sensors to the outside
environment in human cells? 2014: $30,000.
Major Research Equipment Infrastructure
Initiative (MREII)
Brown AJ & Yang HR. Microscale
Thermophoresis Monolith NT.115. 2014: $152,000.
Faculty of Science Silver Star (NHMRC)
Nil
Cavicchioli R, Charles IG, Dickson PW, Djordjevic
SP, Foster PS, Gillings, MR, Harry EJ, Neilan BA,
Packer NH, Paulsen IT, Scott RJ, Whitchurch CB
& Wilkins M. Expanding the Genomic Frontier
– From Species to Strains and Individuals to
Populations. 2014: $180,000.
59 |
Faculty of Science Research Grant
Burns BP. A day in the life of a stromatolite:
innovative metaproteomic analyses of early Earth
microbial communities. 2014: $12,000.
Ferrari BC. Culture independent and dependent
approaches to characterise microbial diversity in
Mitchell Peninsula, Antarctica: A biodiversity “hot
spot”. 2014: $12,000.
Galea AM. Investigating the interaction of
cisplatin and cisplatin analogues with different
human genomic DNA targets. 2014: $10,000.
Janitz M. Investigating the role of hemoglobin
genes overexpression in a-synuclein
aggregation. 2014: $10,500.
Lutze-Mann L. Targeting SCAP as a novel cancer
chemotherapeutic. 2014: $8,000.
Murray V. The precise location of DNA adducts
caused by the anti-tumour drug Cisplatin in the
entire human genome. 2014: $10,000.
Waters PD. Long non-coding RNAs: shaping
the evolution of mammalian transcriptomes and
dosage compensation. 2014: $12,000.
Whitaker NJ. Exosome medicated cell signalling
in Human Papillomavirus (HPV) associated
cancer. 2014: $12,000.
Zhang L. Characterisation of the biological
activities of zonula occludens toxin produced by
Campylobacter concisus. 2014: $12,000.
Faculty of Science Early Career Researcher Grant
Erce M. Cracking the post-translational
modification code of the yeast Npl3 protein. 2014:
$ 9,635.
Hart-Smith G. No project title. 2014: $9,635
Octavia S. Adaptation of Salmonella to different
hosts and environments: a genomic and
transcriptomic illumination. 2014: $9,635.
| 60
SJTU-UNSW Collaborative Research and
Development Fund
Brown AJ, Du X, Li B, Zhang D & Yang HR. Lipid
metabolism and its implications in plant and
human development. 2013-2014: $14,500.
Burns B, Deng Z, He Y, Li Z, Neilan BA, Xu P,
Zhang Z & Manefield M. Establishing a conjoint
SJTU-UNSW research initiative on water and
wastewater microbiology. 2013-2014: $13,500.
Gonzalez P, Huang D, Munroe PR, Nielsen S,
Yang H, Ye J, Zhang L, Zhang R & Thomas T.
Improving food production: Evaluation of biochar
for stimulating the microbial nitrogen cycle in
agricultural soil Improving food production:
Evaluation of biochar for stimulating the microbial
nitrogen cycle in agricultural soil. 2013-2014:
$11,000.
2014 Publications
Aandahl RZ, Stadler T, Sisson
SA & Tanaka MM, 2014, ‘Exact
vs. approximate computation:
reconciling different estimates
of Mycobacterium tuberculosis
epidemiological parameters’,
Genetics, 196(4): 1227-1230.
Aislabie JM, Novis PM &
Ferrari BC, 2014, ‘Microbiology
of eutrophic (ornithogenic
and hydrocarboncontaminated) soil’, in Cowan
DA (ed), Antarctic Terrestrial
Microbiology, Springer,
Heidelberg, ch. 6: 91-113.
Alvin A, Miller KI & Neilan
BA, 2014, ‘Exploring the
potential of endophytes
from medicinal plants as
sources of antimycobacterial
compounds’, Microbiological
Research,
169: 483-495.
Andrisic L, Collinson
EJ, Tehlivets O, Perak E,
Zarkovic T, Dawes IW,
Zarkovic N & Gasparovic AC,
2014, ‘Transcriptional and
antioxidative responses to
endogenous polyunsaturated
fatty acid accumulation in
yeast’, Molecular and Cellular
Biochemistry,
399(1-2): 27-37.
Ballester B, Medina-Rivera
A, Schmidt D, GonzàlezPorta M, Carlucci M, Chen
X, Chessman K, Faure AJ,
Funnell APW, Goncalves A,
Kutter C, Lukk M, Menon
S, McLaren WM, Stefflova
K, Watt S, Weirauch MT,
Crossley M, Marioni JC, Odom
DT, Flicek P & Wilson MD,
2014, ‘Multi-species, multitranscription factor binding
highlights conserved control
of tissue-specific biological
pathways’, eLife, 3:e02626.
Ballestriero F, Daim M,
Penesyan A, Nappi J,
Schleheck D, Bazzicalupo
P, Di Schiavi E & Egan S,
2014, ‘Antinematode activity
of violacein and the role of
the insulin/IGF-1 pathway in
controlling violacein sensitivity
in Caenorhabditis elegans’,
PLoS ONE, 9(10): e109201.
Barnes RJ, Bandi RR, Chua
F, Low JH, Aung T, Barraud
N, Fane AG, Kjelleberg S &
Rice SA, 2014, ‘The roles of
Pseudomonas aeruginosa
extracellular polysaccharides
in biofouling of reverse
osmosis membranes and
nitric oxide induced dispersal’,
Journal of Membrane Science,
466: 161-172.
Barraud N, Kelso M, Rice S
& Kjelleberg S, 2014, ‘Nitric
oxide: a key mediator of biofilm
dispersal with applications in
infectious diseases’, Current
Pharmaceutical Design, 21(1):
31-42.
Barraud N, Moscosco JA,
Ghigo JM & Filloux A, 2014,
‘Methods for studying biofilm
dispersal in Pseudomonas
aeruginosa’, in Filloux A &
Ramos J-L (eds), Methods in
Molecular Biology, vol. 1149,
ch. 49: 643-651.
Bart MJ, Harris SR, Advani
A, Arakawa Y, Bottero D,
Bouchez V, Cassiday PK,
Chiang C-S, Dalby T, Fry NK,
Gaillard ME, van Gent M,
Guiso N, Hallander HO, Harvill
ET, He Q, van der Heide
HGJ, Heuvelman K, Hozbor
DF, Kamachi K, Karataev GI,
Lan R, Luty ska A, Maharjan
RP, Mertsola J, Miyamura T,
Octavia S, Preston A, Quail
MA, Sintchenko V, Stefanelli
P, Tondella ML, Tsang RSW,
Xu Y, Yao S-M, Zhang S,
Parkhill J & Mooi FR, 2014,
‘Global population structure
and evolution of Bordetella
pertussis and their relationship
with vaccination’, mBio, 5(2):
e01074-14.
Basha J, Iwasenko JM,
Robertson P, Craig ME
& Rawlinson WD, 2014,
‘Congenital cytomegalovirus
infection is associated with
high maternal socio-economic
status and corresponding low
maternal cytomegalovirus
seropositivity’, Journal of
Paediatrics and Child Health,
50(5): 368-372.
Beard MR, Ffrench R, Gowans
EJ, Helbig KJ, Eyre NM,
Douglas MMW, Grebely J,
Ahlenstiel G, Locarnini S,
George J, Shackel NA, White
PA, Thompson AJ & Drummer
HE, 2014, ‘A summary
of the 20th International
Symposium on Hepatitis C
Virus and Related Viruses’,
Gastroenterology, 147(1):
e1-e4.
Beckmann S & Manefield
M, 2014, ‘Acetoclastic
methane formation from
Eucalyptus detritus in
pristine hydrocarbonrich river sediments by
Methanosarcinales’, FEMS
Microbiology Ecology, 90(3):
587-598.
Bernardo BC, Gao X-M, Tham
YK, Kiriazis H, Winbanks CE,
Ooi JYY, Boey EJH, Obad S,
Kauppinen S, Gregorevic P,
Du X-J, Lin RCY & McMullen
JR, 2014, ‘Silencing of
miR-34a attenuates cardiac
dysfunction in a setting of
moderate, but not severe,
hypertrophic cardiomyopathy’,
PLoS ONE, 9(2): e90337.
61 |
Bernardo BC, Nguyen SS,
Winbanks CE, Gao X-M, Boey
EJH, Tham YK, Kiriazis H,
Ooi JYY, Porrello ER, Igoor S,
Thomas CJ, Gregorevic P, Lin
RCY, Du X-J & McMullen JR,
2014, ‘Therapeutic silencing
of miR-652 restores heart
function and attenuates
adverse remodeling in a setting
of established pathological
hypertrophy’, The FASEB
Journal, 28(12): 5097-5110.
Bissett A, Abell GCJ, Brown
M, Thrall PH, Bodrossy
L, Smith MC, Baker GH &
Richardsson AE, 2014, ‘Landuse and management practices
affect soil ammonia oxidiser
community structure, activity and
connectedness’, Soil Biology and
Biochemistry, 78: 138-148.
Blaber EA, Dvorochkin N,
Torres ML, Yousuf R, Burns BP,
Globus RK & Almeida EAC,
2014, ‘Mechanical unloading of
bone in microgravity reduces
mesenchymal and hematopoietic
stem cell-mediated tissue
regeneration’, Stem Cell
Research, 13(2): 181-201.
Bone SM, Hasick NJ, Lima
NE, Erskine SM, Mokany E
& Todd AV, 2014, ‘DNA-only
Cascade: a universal tool for
signal amplification, enhancing
the detection of target analytes’,
Analytical Chemistry, 86(18):
9106-9113.
Bone SM & Todd AV, 2014,
‘MNAzymes provide a universal
mechanism for triggering
DNAzyme synthesis cascades’,
Chemical Communications,
50(87): 13243-13246.
Brown MV, Ostrowski M,
Grzymski JJ & Lauro FM, 2014,
‘A trait based perspective
on the biogeography of
common and abundant marine
bacterioplankton clades’, Marine
Genomics, 15: 17-28.
| 62
Burford MA, Davis TW, Orr
PT, Sinha R, Willis A & Neilan
BA, 2014, ‘Nutrient-related
changes in the toxicity of field
blooms of the cyanobacterium,
Cylindrospermopsis raciborskii’,
FEMS Microbiology Ecology,
89(1): 135-148.
Burgos-Portugal JA, Mitchell
HM, Castaño-Rodríguez N &
Kaakoush NO, 2014, ‘The role
of autophagy in the intracellular
survival of Campylobacter
concisus’, FEBS Open Bio, 4:
301-309.
Byrne FL, Poon IKH, Modesitt
SC, Tomsig JL, Chow JDY,
Healy ME, Baker WD, Atkins
KA, Lancaster JM, Marchion
DC, Moley KH, Ravichandran
KS, Slack-Davis JK & Hoehn KL,
2014, ‘Metabolic vulnerabilities
in endometrial cancer’, Cancer
Research, 74(20): 5832-5845.
Cannon MJ, Griffiths PD, Aston
V & Rawlinson WD, 2014,
‘Universal newborn screening
for congenital CMV infection:
what is the evidence of potential
benefit?’, Reviews in Medical
Virology, 24(5): 291-307.
Carter A, Lai YW, Pang CNI,
Campbell LT, Truong M,
Chen S & Wilkins M, 2014,
‘Understanding synergy
between iron chelators
and antifungals using gene
co-expression networks’,
MYCOSES, 57: 107.
Castaño-Rodriguez N, Kaakoush
NO & Mitchell HM, 2014,
‘Pattern-recognition receptors
and gastric cancer’, Frontiers in
Immunology, 5:336.
Castaño-Rodriguez N, Kaakoush
NO, Goh K-L, Fock KM &
Mitchell HM, 2014, ‘The NODlike receptor signalling pathway
in helicobacter pylori infection
and related gastric cancer: a
case-control study and gene
expression analyses’, PLoS ONE,
9(6): e98899.
Castaño-Rodríguez N, Kaakoush
NO, Pardo AL, Goh K-L, Fock
KM & Mitchell HM, 2014,
‘Genetic polymorphisms in
the Toll-like receptor signalling
pathway in Helicobacter pylori
infection and related gastric
cancer’, Human Immunology,
75(8): 808-815.
Chan RTH, Russell RA, Marçal
H, Lee TH, Holden PJ & Foster
LJR, 2014, ‘BioPEGylation of
polyhydroxybutyrate promotes
nerve cell health and migration’,
Biomacromolecules, 15(1):
339-349.
Chen C, Upton C, Braidy N,
Khalil J, Fang Z-M, Xu Y-H &
Chan DKY, 2014, ‘Association
between leukocyte telomere
length and vascular dementia
and cancer mortality in an
elderly population’, Letter to the
Editor, Journal of the American
Geriatrics Society, 62(7): 13841386.
Chew SC, Kundukad B, Seviour
T, van der Maarel JRC, Yang L,
Rice SA, Doyle P & Kjelleberg
S, 2014, ‘Dynamic remodeling of
microbial biofilms by functionally
distinct exopolysaccharides’,
mBio, 5(4): e01536-14.
Chin LS, Lim M, Hung TT,
Marquis CP & Amal R, 2014,
‘Perfluorodecalin nanocapsule
as an oxygen carrier and
contrast agent for ultrasound
imaging’, RSC Advances,
4(25): e13052.
Chow JDY, Lawrence RT, Healy
ME, Dominy JE, Liao JA, Breen
DS, Byrne FL, Kenwood BM,
Lackner C, Okutsu S, Mas VR,
Caldwell SH, Tomsig JL, Cooney
GJ, Puigserver PB, Turner N,
James DE, Villén J & Hoehn
KL, 2014, ‘Genetic inhibition of
hepatic acetyl-CoA carboxylase
activity increases liver fat and
alters global protein acetylation’,
Molecular Metabolism, 3(4):
419-431.
Chua SL, Liu Y, Yam JKH,
Chen Y, Vejborg RM, Tan BGC,
Kjelleberg S, Tolker-Nielsen
T, Givskov M & Yang L, 2014,
‘Dispersed cells represent a
distinct stage in the transition
from bacterial biofilm to
planktonic lifestyles’, Nature
Communications, 5: 4462.
Chung PP, Chu I & Ballard
JWO, 2014, ‘Assessment of
temporal genetic variability
of two epibenthic amphipod
species in an eastern Australian
estuarine environment and their
suitability as biological monitors’,
Australian Journal of Zoology,
62(3): 206.
Clifton MK, Westman BJ, Thong
SY, O’Connell MR, Webster
MW, Shepherd NE, Quinlan KG,
Crossley M, Blobel GA & Mackay
JP, 2014, ‘The identification
and structure of an N-Terminal
PR domain show that FOG1 is
a member of the PRDM family
of proteins’, PLoS ONE, 9(8):
e106011.
Cogger VC, Svistounov D,
Warren A, Zykova S, Melvin
RG, Solon-Biet SM, O’Reilly JN,
McMahon AC, Ballard JWO,
De Cabo R, Le Couteur DG
& Lebel M, 2014, ‘Liver aging
and pseudocapillarization in a
Werner Syndrome mouse model’,
The Journals of Gerontology
Series A: Biological Sciences
and Medical Sciences, 69(9):
1076-1086.
Correa CC & Ballard JWO, 2014,
‘What can symbiont titres tell us
about co-evolution of Wolbachia
and their host?’, Journal of
Invertebrate Pathology, 118:
20-27.
Cortez D, Marin R, ToledoFlores D, Froidevaux L, Liechti
A, Waters PD, Grützner F &
Kaessmann H, 2014, ‘Origins
and functional evolution of Y
chromosomes across mammals’,
Nature, 508(7497): 488-493.
Dafforn KA, Baird DJ, Chariton
AA, Sun MY, Brown MV, Simpson
SL, Kelaher BP & Johnston
EL, 2014, ‘Faster, higher and
stronger? The pros and cons
of molecular faunal data for
assessing ecosystem condition’,
Advances in Ecological
Research, 51(1): 40.
D’Agostino PM, Song X,
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