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