2014 Annual Report - The School of Biotechnology and
Transcription
2014 Annual Report - The School of Biotechnology and
School of Biotechnology and Biomolecular Sciences Annual Report 2014 Never Stand Still Faculty of Science School of Biotechnology and Biomolecular Sciences School of Biotechnology and Biomolecular Sciences Biological Sciences Building Room 229 Level 2 UNSW Australia Kensington NSW 2033 Australia babs.unsw.edu.au Tel: 61 2 9385 2029 Fax: 61 2 9385 1483 Production Editor: Michele Potter Graphic Design: Jane Gascoigne – gascoignedesign Disclaimer: The information contained in this publication is correct at the time of printing but may be subject to change without notice. Please check the School’s website for the latest information. UNSW Australia assumes no responsibility for the accuracy of information provided by third parties. © 2015 UNSW Australia Published July 2015 CRICOS Provider Number 00098G Contents Foreword from Head of School 2 2014 School Management 3 Executive committee members 3 Our People 4 School at a Glance 6 A New Home for BABS 8 2014 Highlights 9 BABS Research Group – Environmental Microbiology 13 BABS Research Group – Infectious Disease 16 BABS Research Group – M'$-$Ǐ*3!!&33333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333A9 BABS Research Group – Systems and Cellular Biology 24 Profile – Dr Richard Edwards, New Senior Lecturer 27 Profile – Dr Kyle Hoehn, New Senior Lecturer 28 Profile – Dr Jai Tree, New Senior Lecturer 29 Profile – Ruben Meerman, ABC Surfing Scientist and BABS PhD Candidate 30 Affiliated Research Organisations 32 The Ramaciotti Centre for Genomics 33 NSW Systems Biology Initiative 36 Centre for Marine Bio-Innovation 37 Specialised Facilities, Services and Equipment 38 External Partner Organisations 40 Memberships in Societies and Associations 42 Learning and Teaching 43 Innovations in teaching 43 Modern facilities 44 Outreach and supporting students 44 Undergraduate degrees 44 Majors 45 Honours 45 Postgraduate degrees 45 Teaching students how science can make a difference 46 Learning and Teaching Prizes and Scholarships 47 2014 undergraduate student awards 47 BABS PhD scholarship supplement scheme 48 BABSOC 49 2014 Honours Completions 51 2014 PhD Completions 53 Research Funding 55 Grants awarded in 2014 commencing in 2015 55 Grants current in 2014 (awarded prior to 2014) 57 2014 Publications 61 Our Vision Our ambition is to be the best School of molecular biosciences in Australia, performing excellent research and attracting and retaining high-calibre staff and students. Towards this end, we encourage an engaged and collegial atmosphere, where advancement is based on merit and staff members’ efforts are recognised. We strive to foster an environment where research excellence can thrive, and where quality and innovative teaching is valued. We strive to manage ourselves in a fair, transparent and efficient way. Our Mission We aim to create a community dedicated to achieving national and international levels of scholarship in the fields of biotechnology and biomolecular sciences. Our Aims The School of Biotechnology and Biomolecular Sciences aims to: be nationally and internationally recognised as a source of scholarship apply cutting-edge biotechnology to capitalise on biomolecular discoveries train and enthuse students further interdisciplinary research positively interact with researchers and students across the university, the state, the nation and the globe. Foreword from Head of School Welcome to the 2014 Annual Report for the School of Biotechnology and Biomolecular Sciences (BABS) at UNSW, one of Australia’s premier science and technology universities. We study life at a molecular level (biomolecular sciences), and strive to put that knowledge to good use in terms of commercial applications (biotechnology). We have core strengths in molecular medicine (particularly in cancer, metabolism and brain research), environmental biology (both freshwater and marine environs) and infectious diseases, with a particular focus on diseases of the gastrointestinal tract. Underpinning much of what we do is a systems-based approach to biology, embracing the latest technologies yielded by the omics revolution. We are therefore proud to host the Ramaciotti Centre for Genomics within BABS, which is going from strength to strength under the directorship of Professor Marc Wilkins. As this is my first Annual Report as Head of School, I would like to thank my predecessors, Professor Bill Ballard and Associate Professor Noel Whitaker. Bill presided over some of the greatest changes in BABS since our inception and pushed through the most extensive renovations that the School has seen. As Acting HOS, Noel thankfully was not content to take just a caretaker role, but initiated a number of new initiatives of his own that we have continued. I took over as HOS in July 2013, and it is certainly a great privilege to lead such a talented and dynamic team. I’m also fortunate to have Dr Louise Lutze-Mann as my Deputy Head of School and Director of Teaching. Louise is a fine and innovative teacher, winning several teaching awards, including a prestigious national award in 2014. We have begun a host of initiatives aimed at providing our students with a richer and more fulfilling experience, including introducing more research opportunities to undergraduates. We also re-purposed an old lab to create an informal student learning space, called BiBS (BABS Interactive Breakout Space), which is being very well utilised, giving our students a welcoming home in BABS to hang out and study. Thanks to the ongoing review of our curriculum, we are now taking concrete steps towards revamping our course offerings (a big job!) and I am grateful to Louise for driving this and to all of the staff who have been actively engaged in these discussions. BABS is a large and diverse School. This can be a strength but also a challenge, so several initiatives have been directed at increasing contacts and cohesion within the School. For example, we reinstated PhD exit seminars, mixing them up with both external and internal speakers so that we all |2 catch up on everyone’s latest research findings. These Friday afternoon seminars followed by a Happy Hour have proved very popular, with some of the seminars being standing room only. We have also had a very successful renaissance of the end-ofyear BABS Research Symposium, with our research students and postdocs showcasing the richly diverse science being conducted within the School. In the past two years, Dr Wallace Bridge and his BABSOC team have done a wonderful job organising the symposium – even going to the trouble of coaching the presenters to ensure high-quality and accessible presentations. Since the last Annual Report (2012), we have had a big injection of fresh talent into the School, being joined by Dr Paul Waters (from ANU), Dr Irina Voineagu (RIKEN Omics Science Center, Japan), Dr Richard Edwards (University of Southampton), Dr Kyle Hoehn (University of Virginia) and Dr Jai Tree (University of Melbourne). Several of our continuing academic staff also became Research Fellows in the last couple of years: Dr Irina Voineagu (ARC DECRA), Associate Professors Kevin Morris, Torsten Thomas, and Mark Tanaka (ARC Future Fellowships) and Professor Rob Yang, who managed to nimbly leap from an ARC Future Fellowship to an NHMRC Senior Research Fellowship. Securing such Fellowships in the current climate is no mean feat, and indeed, is a great achievement. Congratulations to all! Towards the end of 2014 there was some nostalgia mixed with lots of excitement as the Biomed Lecture Theatres were demolished. The nostalgia was due to many of us having spent much time lecturing there, and the excitement because out of the rubble our new Biosciences Building will rise, ready for us to occupy in 2017. Thanks to Michele Potter for producing yet another highly polished and professional Annual Report. And finally thank you, the reader, for looking over this report and sharing in the excitement of just a selection of our recent discoveries. Professor Andrew Brown 2014 School Management The operations of the School are managed by the Head of School, assisted by the Deputy Head of School and six members of the BABS Executive Committee, together with various other committees responsible for key areas of the School’s operations. Professor Andrew Brown Head of School Dr Louise Lutze-Mann Deputy Head of School Executive committee members Dr Brendan Burns Dr Chris Marquis A/Professor Vincent Murray Professor Brett Neilan A/Professor Mark Tanaka Professor Marc Wilkins 3| Our People Academic Staff Senior Lecturers Professors Wallace Bridge Bill Ballard Brendan Burns Andrew Brown (Head of School) Richard Edwards BSc Hons PhD (UNSW) Belinda Ferrari Rick Cavicchioli Professional Officer Infrastructure Kyle Hoehn Merlin Crossley (Dean, Faculty of Science) Michael Janitz Michele Potter BA (USYD) Staffan Kjelleberg (Scientia Professor) Louise Lutze-Mann (Deputy Head of School) Chris Marquis Hazel Mitchell Vladimir Sytnyk Brett Neilan (Scientia Professor) Irina Voineagu (ARC DECRA Fellow) Peter White Paul Waters Marc Wilkins Li Zhang Malcolm Walter (ARC Professorial Fellow) H Robert Yang (NHMRC Senior Research Fellow) Lecturers John Foster Ruiting Lan Michael Manefield (ARC Future Fellow) Kevin Morris (ARC Future Fellow) Vincent Murray Mark Tanaka Torsten Thomas Noel Whitaker William Whitfield Finance Officer Technical Officers Ned Elkaid Daud Khaled BSc Hons MSc (Dhaka) PhD (UNSW) Elessa Marendy BSc Hons, PhD (JCU) Sharon Murarotto BAppSc (UTS) Kim Nguyen BSc (UNSW) Rebecca LeBard Shamima Shirin John Wilson Owen Sprod BSc Hons PhD (U Tasmania) Professional and Technical Staff Lily Zhang BEng (Tianjin) Administration Adam Abdool Administrative Officer (50%) Jenny Campbell Administrative Assistant Kylie Jones Administrative Officer Geoff Kornfeld Professional Officer Infrastructure Terry Law WHS Manager Jani O’Rourke BSc (USYD) PhD (UNSW) Professional Officer (Laboratory Manager) |4 Jeff Welch Anne Galea Associate Professors Andrew Collins School Manager Research Staff Research Fellows Frances Byrne (Hope Funds for Cancer Research Fellow) Nadeem Kaakoush (NHMRC Postdoctoral Training Fellow) Federico Lauro (ARC DECRA Research Fellow) Senior Research Associates Leanne Pearson Suhelen Egan (ARC Future Fellow) Jacob (Yanfei) Qi Richard Pearson Kate Quinlan Bettina Rosche Tim Williams Research Associates Michelle Allen Sabrina Beckman Mark Brown Frances Byrne Rocky Chau Zhiliang Chen Matt Clemson Susan Corley Paul D’Agostino Nandan Deshpande Robin (Ximing) Du Melissa Erce Jim (Zhi Ming) Fang David Fung Alister Funnell Rajesh Ghai Gene Hart-Smith Katherine Jackson John Kalaitzis Andrew Kelly Iryna Leshchynska Ruby Lin Cassie Mak Rabia Mazmouz Sophie Octavia Sarah Ongley Martin Pagac Laura Sharpe Nidhi Sodhi Aiden Tay Shafagh Waters Jason Woodhouse Research Assistants Cindy (Yi Ning) Gao Alyce Hancock Sarah Payne Helene Lebhar Winnie Luu Natalie Twine Young J Jeon (Visiting Fellow) James Krycer (Conjoint) James Lawson (Emeritus Professor) Ruby Lin (Adjunct Senior Lecturer) Karen MacKenzie (Conjoint) Kerensa McElroy (Conjoint) Anne Mai-Prochnow (Adjunct Lecturer) William Rawlinson AM (Professorial Visiting Fellow) Yan Wang Laurent Rivory (Visiting Associate Professor) Visiting and Adjunct Staff Peter Rogers (Emeritus Professor) Kevin Barrow (Professorial Visiting Fellow) Emmanuelle Botte (Visiting Fellow) Andrew Burgess (Conjoint) Antony Cooper (Visiting Fellow) Anuruddhika Dadigamuwage (Visiting Fellow) Ian Dawes FAA (Emeritus Professor) Michael Edwards (Honorary Associate Professor) Susanne Erdmann (Visiting Fellow) Carly Rosewarne (Adjunct Lecturer) Stuart Tangye (Visiting Fellow) Nai Tran-Dinh (Visiting Fellow) Alison Todd (Senior Visiting Fellow) Mark Van Asten (Adjunct Senior Lecturer) Sheila Van Holst Pellekaan (Visiting Fellow) Pieter Visscher (Senior Visiting Fellow) Martin Zarka (Adjunct Lecturer) Haluk Ertan (Professorial Visiting Fellow) Michelle Gehringer (Visiting Fellow) Wendy Glenn (Honorary Lecturer) Iggy (Chi Nam) Pang 5| School at a Glance The School of Biotechnology and Biomolecular Sciences (BABS) is one of the largest Schools in the Faculty of Science at UNSW Australia. UNSW is a member of the prestigious Group of Eight, a coalition of Australia’s leading research-intensive universities. Our University is renowned for the quality of its graduates and world-class research. This is clearly demonstrated by: being ranked 48th in the 2014/15 QS World University Rankings being awarded the maximum QS Five Star Plus rating in the 2014 rankings, one of only 13 universities in the world to do so being voted one of the top performing universities in the 2014 Global Employability University Ranking UNSW researchers being awarded the highest amount of Australian Research Council (ARC) funding in Australia for 2015 being recognised as the Australian university with the strongest links to industry: in 2014 UNSW received $10.5 million in Linkage Project grants from the ARC, the highest level of funding in the country. The School of BABS is a powerhouse of biomolecular research, employing 33 academics, 50 research associates and 16 technical and administrative staff. At any point in time, BABS is training over 150 Higher Degree by Research students, and teaches approximately 2,000 full-time undergraduate students each year. BABS consistently attracts extensive government and industry funding and top-tier academic accolades. Our achievements in technology development are underpinned by excellence in fundamental research. Research The School is recognised as one of the largest and most prestigious schools of scientific research and teaching in Australia. With distinguished academic staff, an innovative teaching program and state-of-the-art facilities, BABS is producing graduates and scientific discoveries of international renown. We aim to achieve a balance of pure basic, strategic, applied and experimental development research. We have strong links with a range of high profile external research institutions, including the Garvan Institute of Medical Research, the Victor Chang Cardiac Research Institute and the Prince of Wales Hospital, and a solid track record in linking fundamental research to tangible outcomes. Researchers in the School are aligned into four research discipline areas: Environmental Microbiology Environmental Microbiology forms a top-level research grouping at UNSW. Coupled with the biotechnology sector, we have a strong presence in the pure and applied biosciences. BABS addresses globally relevant research themes in environmental health and sustainability, microbial processes, biomaterials and nanotechnology, environmental genomics, biodiversity and conservation, and bioprospecting for enzyme and drug discovery. Current research projects encompass numerous national and international networks with Asian, European and US-based research institutes and universities. Infectious Disease Infectious diseases are responsible for around one-third of annual deaths worldwide. The BABS Infectious Disease research group focuses on molecular epidemiology, with an aim to combat microbes that remain a huge biological challenge affecting both human and animal health. The group brings together a wide range of internationally recognised research expertise to investigate the microbiological factors affecting a range of vital health issues, including tracking norovirus pandemics, molecular evolution and population structure of bacterial pathogens (Bordetella, Salmonella, Shigella and Vibrio), immune evasion by hepatitis, inflammatory bowel disease, and viruses in cancer. |6 Molecular Medicine Molecular Medicine within BABS has a unique strength in combining fundamental biological and biomolecular sciences with a strong applied biotechnology and medical focus. The School facilitates collaborative research efforts across discipline boundaries for fundamental discoveries, generation of commercial opportunities and clinical research. Major research strengths of the group currently exist in biomaterials, immunology, bioinformatics, cancer and genetics. The group uses a wide range of cutting-edge molecular and bioinformatic tools to understand and combat genetic disease and cancer. Specific research foci include cancer, immunogenetics and biomaterials. Systems and Cellular Biology The Systems and Cellular Biology (SCB) group undertakes research in the biology of eukaryotes. SCB groups are active users of high-technology facilities, with researchers being highly successful in attracting regular competitive Category 1 funding, particularly from the ARC and National Health & Medical Research Council (NHMRC). The group has also been active in securing infrastructure funding in genomics, proteomics and systems biology. Research areas for this group include cholesterol and sterols, cell stress and aging, genetic mapping of phenotypes and disease, protein interaction networks and systems biology. Research productivity in BABS has increased substantially over the past five years and the School aims to grow further by strongly supporting existing academics and attracting talented new staff. Recruitment is currently limited by space, but the planned development of the Biosciences precinct that includes the construction of a new building will allow the School a higher rate of growth in future years. Learning and teaching Undergraduate The School offers a comprehensive range of undergraduate and postgraduate degrees and caters for a variety of career paths. A culture of teaching excellence for both undergraduate and postgraduate students is reflected by exceptional internal CATEI scores for our academics. Postgraduate BABS offers Doctor of Philosophy (PhD) and Master of Science (MSc) research-based degrees, and the School is one of the highest recruiters of PhD students at UNSW. A number of our PhD students are supervised by visiting or adjunct staff located at external organisations, including the Garvan Institute of Medical Research and the Prince of Wales Hospital. The School offers a PhD Scholarship Supplement Scheme for eligible new and continuing students, comprising a $5,000 one-off annual payment. Research facilities BABS is home to a number of significant research facilities that are leaders in their respective fields, providing cutting-edge services to researchers within BABS, across UNSW and other Australian and international institutions. These include the Ramaciotti Centre for Genomics, Centre for Marine Bio-Innovation, New South Wales Systems Biology Initiative and School staff are also members of the UNSW Evolution & Ecology Research Centre and the Environmental Microbiology Initiative. 7| A New Home for BABS New Biological Sciences Building to complete UNSW Biomedical Precinct Planning and initial construction is under way for a new 16,900m² building to house UNSW’s biological and environmental sciences, which includes many of the research labs in BABS. The new Biological Sciences Building will complete UNSW’s Biomedical Precinct, which comprises the Lowy Cancer Research Centre and the recently redeveloped Wallace Wurth Building, home to the Faculty of Medicine. The project aims to deliver world-class facilities, with the building designed to support current research as well as providing infrastructure to support future technological advances. The main features of the design include flexible research laboratory spaces, specialised research equipment, staff accommodation and large loading dock, stores, workshop and utilities. The building is expected to have capacity for more than 400 staff and PhD students. The key objectives of the project are to: provide a contemporary, world class research and teaching environment as part of the UNSW Biomedical Precinct provide modern infrastructure for training the next generation of researchers and technically qualified graduates who will help maintain Australia’s connectivity and competitiveness in a rapidly advancing world create flexible and adaptable space for strategic recruitment, taking into account trends in technology, research infrastructure, and national and UNSW priority areas enhance effectiveness and interdisciplinary teamwork by efficiently connecting biologists, environmental, earth and biomedical scientists and reinforcing research synergies between the research groups, Schools and Faculties. A complete refurbishment of the current Biological Sciences Building, which was built circa 1960, will take place after the new building is complete. The current forecast completion date is late 2017. |8 2014 Highlights Deputy HOS and Director of Teaching Dr Louise Lutze-Mann Louise’s teaching expertise was recognised at the highest level in Australia when she won the Award for Teaching Excellence for Biological Sciences, Health and Related Studies in the discipline of Biological Sciences as part of the 2014 Australian Government Awards for University Teaching. The award was presented at Parliament House Canberra in December, with Louise receiving a congratulatory letter from UNSW Vice-Chancellor Professor Fred Hilmer. In addition, the Dean of Science Professor Merlin Crossley announced Louise the winner of the Best Lecturer in Science as voted by students in the Faculty of Science Excellence Awards for 2014. Louise receiving her award at Parliament House, Canberra. BABS HDR students excel in Faculty of Science Research Competition BABS again demonstrated the excellent quality of its students and their skills in presenting their research, with three of the seven awards on offer in the 2014 Faculty of Science Postgraduate Research Competition going to BABS students. Alex Knights (pictured, supervisor Professor Merlin Crossley) was the winner in the Health, Lifestyle & Ageing category; Angela Chilton (supervisor Professor Brett Neilan) runnerup in the Cutting-Edge Discovery category; and Lifu Sheng (supervisor Dr Vladimir Sytnyk) took out the People’s Choice award for best poster. This hotly contested competition saw more than 70 research students entering in 2014, being judged on the quality of the poster, an abstract about their project as well as a oneminute long talk describing their topic. The competition judges included Robyn Williams, presenter of The Science Show on ABC Radio National, and astronomer and author Professor Fred Watson, who joined more than 30 UNSW researchers to assess the students’ presentations. Alex at the bench BABS alumnus awarded 2014 ASMR Medal In addition to being named in Time Magazine’s 2014 Top 100 Influential People, Professor David Sinclair was the recipient of the 2014 Australian Society for Medical Research (ASMR) medal. This annual prestigious award recognises a researcher’s career contributions to medical research. David did Honours and then completed his PhD in BABS under the supervision of Professor Ian Dawes (now Emeritus at UNSW Australia), in whose lab he also met his future wife. As part of the award events, David was the keynote speaker at a series of Gala Dinners around Australia during Medical Research Week. The School booked a table at the Sydney dinner, and during his presentation, David warmly praised BABS and UNSW, and invited Ian on stage to express his appreciation. Ian Dawes accepting a tribute from David Sinclair. 9| Emeritus Professor Ian Dawes and Professor Merlin Crossley, Dean of Science Ian and Merlin were elected Honorary Fellows of The Royal Society of NSW in 2014. The Society is the oldest learned society in the Southern Hemisphere and traces its origin back to 1821.The Society’s main function is to promote science in all its aspects, and to link the disciplines of science to each other and to other elements of human endeavour. Ian Dawes, back row second from right; Merlin Crossley, front row second from right. New BABS student breakout space BiBS Conversion of an old lab to the BABS Interactive Breakout Space created a much-needed multifunctional space for our large student cohort. The aim was to provide an informal learning space for student activities, including tutoring, group work and pre-lab studies. Computers and wi-fi are available, along with a substantial library, and kitchen facilities have been provided. Students were encouraged to submit ideas and decoration suggestions for the space, with the official launch taking place in Semester 2. | 10 Joint Academic Microbiology Seminars (JAMS) The JAMS initiative is a networking and ideas exchange forum, bringing together microbiologists from five universities across Sydney on a regular basis. It provides a platform for large funding bids and a shopfront for access to a wide array of microbiology expertise available locally and internationally. JAMS also represents a strong link between BABS and the Australian Museum, where the events are held. Website: jams.org.au Annual BABS Research Symposium The 2014 BABS Research Symposium was held at Royal Randwick racecourse. Reintroduced by Head of School Professor Andrew Brown, the aim of this symposium is to generate more awareness amongst the School community of the breadth of research being carried out by postdocs, research fellows, HDR and Honours students. With the assistance of the BABSOC/EISSOC student society, led by Dr Wallace Bridge, the day was a great success, with many opportunities to strengthen collegiality among the School community. 11 | BABS Research Seminar Series The School’s fortnightly seminar series features a range of prominent international researchers together with specialists from within Australia, together with School academics, postdocs and exiting PhD students presenting their research topic to the School community. External speakers during 2014 included: Dr Jeremy Webb, Director, Graduate School of Biological Sciences, University of Southampton, UK Professor Amitabha Chattopadhyay, Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India Dr Gursharan Chana, Joint Head, Stem Cells and Disease Modelling Laboratory, Centre for Neural Engineering, The University of Melbourne Dr Vicky Schneider, The Genome Analysis Centre, Norwich, UK Professor Ryan Lister, ARC Future Fellow & Professor ARC Centre of Excellence in Plant Energy Biology, School of Chemistry & Biochemistry, University of Western Australia Associate Professor Marianne Farnebo, Department Of Oncology/Pathology, Karolinska Hospital, Stockholm, Sweden Associate Professor Leonard Lipovich, Center for Molecular Medicine and Genetics and Department of Neurology, School of Medicine, Wayne State University, Detroit, USA | 12 Professor David Levens, Chief, Gene Regulation Section, Laboratory of Pathology, National Cancer Institute, Center for Cancer Research, National Institutes of Health, USA Professor Paul Thomas, School of Molecular & Biomedical Science, University of Adelaide Professor Kevin Lynch, Professor and Vice Chair of Pharmacology, University of Virginia Professor Junying Yuan, Elizabeth D Hay Professor of Cell Biology, Harvard Medical School Associate Professor Jon Whitehead, Translational Research Institute, Brisbane Professor Ofer Biham, Racah Institute of Physics, Hebrew University, Jerusalem, Israel Professor Francis Stewart, Director, Biotechnology Center of TU, Dresden, Germany Professor Steven Djordjevic, Professor of Infectious Diseases, ithree Institute, University of Technology Sydney Environmental Microbiology Academic Staff Professor Rick Cavicchioli Professor Staffan Kjelleberg Scientia Professor Brett Neilan Associate Professor Torsten Thomas Associate Professor Michael Manefield Senior Lecturer Dr Brendan Burns Senior Lecturer Dr Belinda Ferrari Lecturer Dr Rebecca LeBard BABS Research Group – Environmental Microbiology 13 | Rocking the cradle of life – microbiology of early earth ecosystems Dr Brendan Burns, Senior Lecturer To understand the biology of an ecosystem, a time separation of billions of years seems to present an insurmountable hurdle. In Australia, there exist a few modern analog ecosystems that can act as a worm-hole to the past, allowing us to bring a contemporary arsenal of tools to the field site. One of the most famous and extensive of these anywhere in the world are the stromatolites of Shark Bay in Western Australia, a World Heritage site. Stromatolites are biogeological ecosystems resulting from the metabolic activity of resident microbial communities. The excitement stems from the fact that there is a clear fossil record of such structures for more than 3 billion years. Dr Brendan Burns and his research team have worked on various aspects of these ecosystems in a bid to comprehensively charcterise their functional complexity. The goal is to thoroughly understand the diversity, biogeochemistry and key interactions of the microorganisms forming the Shark Bay stromatolites. In addition to identifying potentially novel microbial activities vital to ecosystem function, this will provide a rational focus when seeking biosignatures that will ultimately help interpret the fossil record. By using a combination of diverse and cutting-edge techniques, it will afford more rational predictions on past environments and build useful models to further our understanding of early earth communities. Most recently and for the first time in relation to these ecosystems, the group has employed high-throughput next generation sequencing platforms – omics. This has begun to decipher at the millimetre scale the intricate dance between microorganisms: who is where and what are they doing. Data suggest ancient forms of carbon fixation could be active in modernday stromatolite systems, and that archaea in particular may be key players at multiple levels. Combinations of analyses are providing estimates of the flow of key metabolites in these microbial systems, and enabling creation of a 3-D reconstruction of key metabolic activities. This is critical to be able to relate specific activities to resulting biosignatures that can be detected in the fossil record. Through the application of an ecosystems biology approach, some of | 14 the mysteries surrounding these early Earth communities are being gradually unravelled. Through collaborations with NASA, for this project Dr Burns is also employing a state-of-theart imager that utilises technology developed for the Mars Rover mission. This year Dr Burns was invited to take part in an ambitious global effort – Ocean Sampling Day – to sample and analyse the world’s oceans simultaneously at the same point in time during the 2015 summer/winter solstice. This campaign aims to analyse marine microbial biodiversity and function, and will incorporate work by ‘citizen scientists’. It will also contribute to The Blue Economy (10 years; 10 innovations; 100 million jobs) through the identification of novel, oceanderived biotechnologies of benefit to a wide range of stakeholders. Finally, this research group’s findings have provided information vital to the conservation of these unique resources (identified as under threat by climate change), carefully monitoring changes in biological diversity that could indicate possible threats to these evolutionally significant systems. Exploring Antarctica’s unique soil microbial biodiversity Dr Belinda Ferrari, Senior Lecturer The Ferrari lab integrates next-generation sequencing technologies with novel cultivation approaches to explore the microbial diversity in polar soils of Antarctica. During the last two years, Belinda has been developing communitywide microbial ecotoxicity assays in collaboration with the Australian Antarctic Division, which has funded the majority of this work. Several sites in Antarctica and sub-Antarctic Macquarie Island are currently undergoing bioremediation due to diesel fuel spills. Belinda’s research is aimed at using bacterial communities as potential indicators of soil health, monitoring the communities throughout the bioremediation process and aiding the development of sitespecific guidelines. Belinda believes that community-wide models are more representative of an environment compared to single species toxicity assays, and her future goal includes the development of a rapid chip array for assessing hydrocarbon toxicity. Belinda’s team is gaining information on what species are stimulated by petroleum hydrocarbons. As part of this work, Dr Josie van Dorst provided valuable EC20 targets that are being used for the development of site-specific remediation guidelines for Macquarie Island. Aside from this major aim, the Ferrari lab isolated an array of novel soil polar fungi and bacteria, some of which are capable of degrading hydrocarbons, even at low temperatures. Ongoing research is now aimed at characterising cold-adapted fungal enzymes involved in the biodegradation of hydrocarbons; and in a separate project, Sub-Antarctic Macquarie Island investigating the biotechnological potential of the lab’s polar library by screening for novel secondary metabolites genes. A primary focus of Belinda’s research is to explore the diversity of bacteria and fungi in the Windmill Islands region of Eastern Antarctica. Mitchell Peninsula, one of the remote sites under investigation, is a nutrient-poor polar desert, and the team recently found that it harbours a unique microbial taxonomic composition not previously observed in any reported polar or temperate ecosystem. Belinda believes this region is a potential microbial biodiversity hotspot, as it contains rare yet-to-be cultured lineages of bacteria in unusually high abundances. With the utilisation of a new differential binning technique and in collaboration with the Australian Centre for Genomics, PhD student Mukan Ji reconstructed 18 near-complete genomes from Mitchell Peninsula soil, including for the first time, genomes for both Candidate Division WPS-2 and AD3. Through this exciting research the Ferrari team discovered that the majority of bacterial genomes recovered contain RuBisCO genes, indicative of carbon fixation. However, very little evidence for photosynthesis exists. These findings suggest that alternative strategies for survival are dominant in this hostile environment and as this work moves forward, the Ferrari team hopes to exploit these new genomic insights to develop cultivation strategies for these yet-to-be cultured groups of bacteria. Streptomyces – PhD student Nicole Benaud 15 | Infectious Disease Academic Staff Professor Hazel Mitchell Professor Peter White Associate Professor Ruiting Lan Associate Professor Kevin Morris Associate Professor Mark Tanaka Associate Professor Noel Whitaker Senior Lecturer Dr Jai Tree Senior Lecturer Dr Li Zhang BABS Research Group – Infectious Disease | 16 Paleovirology; mining the cane toad genome for biocontrol viruses Professor Peter White I would like to describe one of our wackier projects that we have been working on in the Molecular Microbiology Laboratory over the last year and a half. The study of ancient viruses is termed paleovirology. The genomes of animals and insects contain traces of past viral infections through the integration of viral genetic material into the host genome, termed endogenous viral elements (EVEs). These viral fossils can be used to look at viruses that once existed hundreds of thousands of years ago. Around 1% of the human genome is comprised of EVEs, the vast majority being retroviruses that naturally insert their genomes into the host genome as part of their life cycle. For other viruses, germ line integration is rare, but has been identified in many organisms. The most surprising viral fossils originate from RNA viruses; for example, in humans, everyone has a small trace on chromosome 10 of a bornavirus, which is an RNA virus. The genome of the Aedes aegyptii mosquito contains numerous endogenised viruses. In fact, through work by Dr Andrew Kelly in the lab to date, we have discovered the remnants of 241 different RNA viruses in the A. aegyptii genome. This is a lot more than we were expecting. Perhaps the most interesting one of these viral fossils is an ancient insect specific flavivirus, which we estimate to be 129,000 years old. The genome of this virus is scattered and duplicated in 55 fragments across the mosquito genome. We have re-built the genome of this virus to a level of 89% completion (see figure). Given the rapid advance in viral reverse genetics in recent times (you can make fully infectious viral particles out of only RNA or DNA), this raises the very interesting concept of the resurrection and propagation of ancient extinct viruses. I first chatted with Professor Eddie Holmes from the University of Sydney over lunch about the idea of mining the cane toad’s genome to find endogenised viruses. It is a wacky idea, but it has merit. If we discount the retroviruses (of which there will be many), we should be able to identify a number of viruses that the toad was once infected with, going back hundreds of thousands of years. The genome, if you like, contains a fossil record of these past infections. It is possible to resurrect ancient viruses through reverse genetics given only the viral genome. Reconstruction of the relic A. aegypti flaviviral genome, 89% complete. This is because some infections of the egg or sperm cells result in the viral genome merging into the host genome, leaving a trace of the infection through the generations. Given the fact that viruses have been very successful biocontrol agents for controlling rabbit populations, a toad virus has the potential to be a biocontrol agent. We could try to reconstruct these early toad viruses if we find enough sequence, or alternatively, find the closest match in a contemporary toad virus, and test them as a biocontrol agent against the cane toad. I was dismayed to find that the genome of the cane toad is not yet available, although people have tried to sequence it. There is currently no evidence in any database of any success, but there are many people in Australia who want to sequence the genome of the cane toad for scientific studies. We have therefore established the Cane Toad Consortium to explore the mission to “sequence the cane toad for science”. Consortium members from UNSW are Professor Peter White (virology), Professor Marc Wilkins (sequencing), who is also Director of the Ramaciotti Centre for Genomics (where the sequencing will take place), Dr Rich Edwards (sequencing and bioinformatics) and Dr Andrew Kelly (bioinformatics). Also on board and willing to help are Dr Lee Ann Rollins from Deakin University (toad collector and geneticist), and Professor Eddie Holmes (virology and biocontrol) and Professor Rick Shine (biology of rapid cane toad evolution) from the University of Sydney. 17 | Understanding the role of oral Campylobacter species Dr Li Zhang, Senior Lecturer Dr Li Zhang’s group has conducted internationally pioneering research in understanding the role of oral Campylobacter species, such as Campylobacter concisus, in initiating a subgroup of human inflammatory bowel disease (IBD). In 2009, Dr Zhang and collaborators reported an association between C. concisus and Crohn’s disease (one type of human IBD) for the first time, and in 2010, Dr Zhang hypothesised that some oral C. concisus strains are involved in initiating a subgroup of human IBD. Continuous studies over the past five years have provided information that is fundamental to this emerging research field. The group found that C. concisus uses the human oral cavity as its natural colonisation site. C. concisus prefers anaerobic growth; it may grow under microaerobic conditions only in the presence of H2 gas. Patients with IBD are often colonised by multiple oral C. concisus strains; there are no distinct enteric C. concisus strains. C. concisus strains detected in the intestinal tract of patients with IBD originate from oral C. concisus strains. C. concisus is very sensitive to low pH and their growth is greatly inhibited by bile, thus most of the C. concisus swallowed would have been killed by the low pH of the gastric acid and would | 18 Campylobacter be unlikely to establish long-term colonisation in the lower parts of the gastrointestinal tract. However, a small percentage of oral C. concisus strains have greater abilities in resisting the antimicrobial effects of low pH and bile. These oral C. concisus strains may establish short-term intestinal colonisation before being cleared. This process may occur repeatedly in some individuals, which may initiate chronic enteric inflammatory conditions such as IBD if the colonised C. concisus strains are virulent. Dr Zhang’s group has identified a number of C. concisus prophages and found that some C. concisus prophages encode zonula occludens toxin (Zot). Their recent work showed that C. concisus Zot damages the intestinal epithelial barrier and has an impact on the immune system. They are currently investigating how Zot toxin is released in the intestinal environment and are developing diagnostic methods to accurately detect the involvement of C. concisus and its toxins in individual IBD cases. The other aspect of Dr Zhang’s research is on chronic neurological diseases, investigating the role of human hosted Campylobacter species in chronic neurological diseases. A link to Dr Zhang’s publications can be found on the UNSW Research Gateway. M'$-$Ǐ*3M!!& Academic Staff Professor Merlin Crossley Associate Professor Andrew Collins Associate Professor John Foster Associate Professor Vincent Murray Senior Lecturer Dr Wallace Bridge Senior Lecturer Dr Michael Janitz Senior Lecturer Dr Louise Lutze-Mann Senior Lecturer Dr Chris Marquis Senior Lecturer Dr Vladimir Sytnyk Lecturer Dr Anne Galea BABS Research Group – M'$-$Ǐ*3!!& 19 | Lipases for the production of biodiesel Dr Christopher Marquis, Senior Lecturer The Marquis lab undertakes collaborative research projects across a range of areas, including protein biotechnology, nanobiotechnology and bioenergy. Since 2012, the lab has worked on projects that investigate the use of enzymes, called lipases, for the reaction of natural oils (seed and algal, for example) and waste oils (tallow and used cooking oil) to produce biodiesel. Biodiesel describes a heterogeneous range of biofuel products derived from the transesterification of plant and animal triglycerides by reaction with a simple alcohol, usually methanol. The most commonly reported processes are catalysed using caustic (in the form of sodium methoxide). However, this process is not without problems, which include soap formation with poorer quality oils (high free fatty acid content), production of a less valuable glycerol by-product, and toxicity and explosion hazards handling sodium methoxide. Another problem is the source of the oil feedstock, which is largely food oils (soybean, canola, palm and coconut oil, for example). Some biodiesel plants can access waste feedstocks such as used cooking oils, non-comestible seed oils (such as jatropha) and tallow. The Scientific Research Organisation of Samoa (SROS) has had a biodiesel program since 2009 to develop biodiesel from coconut oil, and operates a 200L scale pilot plant to produce coconut oil biodiesel using conventional methods. In 2009, a collaboration between SROS and UNSW was established. As part of this collaboration, we began to develop an enzyme-based process to produce coconut oil biodiesel. Current projects have centred on recombinant expression of lipases for this purpose in the methylotrophic yeast, Picha pastoris. We aim to evaluate a “closed-loop” enzyme-based bioprocess to develop biodiesel from stocks locally available in Samoa. Glycerol by-product from transesterification will be assessed for cultivation of fodder yeast as well as recombinant yeast-producing lipase enzymes for transesterification, which is currently under development in the Marquis lab. The group is expressing enzymes that have been reported for use in industry and undertaking modifications for surface (including cell-surface) immobilisation and for improved performance, through directed evolution strategies. The lab continues to produce lipase-mediated coconut oil biodiesel for the evaluation of engine performance of biodiesel blends in advanced research engines. This project is a collaboration with Dr Shawn Kook, Director of the UNSW Engine Research Laboratory based in the UNSW School of Mechanical Engineering and Samania Tupufua at SROS. Separation of biodiesel from glycerol after immobilized enzyme transesterification | 20 Looking towards addressing oxidative stress in ageing and chronic disease Dr Wallace Bridge, Senior Lecturer It is a never-ending message that can be literally forced down our throats “if a food contains heaps of antioxidants then it must be good for you”. We are led to believe by marketers that it doesn’t matter what type of antioxidant it might be, as long as it can wipe out a free radical then you need it; and if you take antioxidant supplements you will live longer, be healthier and maybe even be cured of disease. There is a myriad of antioxidant forms and all have different biologic modes of activity. They should therefore not be all lumped together when considering whether they are beneficial or not. It should also be noted that no human clinical trials to date have demonstrated any clinical benefit in taking any form of antioxidant supplement. So how has this immense marketing push come to be, if there is no evidence of benefit? From a science perspective, the majority of reactive oxygen species (ROS) are produced as a by-product of mitochondrial oxidative phosphorylation, which involves oxygen acting as an electron acceptor. Some of these ROS are harnessed for normal cellular functions and the remainder are mopped up by the cell’s antioxidant system. This involves enzymes and chemical entities that act as co-factors for the enzymes or directly neutralise ROS and other forms of free radicals. Insufficient or overwhelmed cellular antioxidant capacity will lead to an excess of oxidants that will damage nucleic acids, protein and lipids, leading to mitochondrial or cellular dysfunction and ultimately cell death. It is from this oxidative stress perspective that the consumption of antioxidants is thought to be of benefit. Often referred to as the master antioxidant, glutathione is almost ubiquitous in aerobic organisms, from bacteria, yeast and plants to humans. It is a tripeptide comprising glutamate, cysteine and glycine, with the –SH moiety of the cysteine being responsible for the antioxidant activity. Glutathione is produced in all cells within the body by two sequential ATP-dependent enzymes, with homeostasis being dictated by feedback inhibition exerted by glutathione on the first enzyme, glutamate cysteine ligase (GCL), which catalyses the synthesis of gammaglutamylcysteine (GGC). 21 | It has been reported in many models that cellular glutathione levels progressively decline during ageing and are substantially lower in tissues affected by many age related and chronic disorders. Our research over the last 10 years has been focused on exploring the potential for GGC administration to elevate glutathione levels, with the long-term objective of investigating its potential to treat or even prevent/delay age glutathione depletion-associated conditions. The mechanistic basis is that either through damage or down regulation, the GCL enzyme has become ineffective at producing sufficient GGC to maintain adequate homeostatic glutathione levels. Since commencing the project, we have developed and patented (triadic granted) a process for GGC manufacture that we licensed to Biospecialties International P/L, a company that was formed to commercialise GGC manufacture. The production process was initially validated at pilot scale with the assistance of a $1.16 million federal government grant. On the basis of our published animal studies performed according to OECD guidelines and other evidence relating to GGC’s presence in many foods, we have been successful in having GGC given GRAS (Generally Recognised as Safe) status according to the US FDA regulations. Recently, we conducted a UNSW-sponsored human clinical trial that demonstrated that orally administered GGC could significantly and systemically increase cellular glutathione levels in healthy volunteers. Many other compounds have been tested previously in similar trials but none has been credibly successful. The production factory in Newcastle, NSW has recently been upgraded to a commercial production facility in readiness for a 2015 GGC (Glyteine™) product launch in the US. Future human clinical trials are being planned to investigate GGC’s potential to be of therapeutic benefit in select disorders. Commercial production facility, Newcastle. | 22 Identification of the new regulators of neuronal growth Dr Vladimir Sytnyk, Senior Lecturer In the developing brain, neurons must grow long and extensively branched axons and dendrites to establish numerous contacts with other neurons. This process is required for formation of the elaborated networks of neurons interconnected by synaptic contacts, which play a critical role in all brain functions, including information processing, learning and memory formation. To reach their targets in the immature neuronal network, axons and dendrites have to grow through a complex extracellular environment, which significantly influences the direction and speed of the growth. Cell adhesion molecules are the proteins at the cell surface of axons and dendrites, which bind to the molecules in the extracellular space. This binding results in increased or reduced growth of axons and dendrites and their branching. Cell adhesion molecules thus function as recognition molecules, which recognise the growth promoting and inhibiting cues in the extracellular environment of developing neurons. Levels of NCAM2 are increased in brains of Down syndrome patients. Mutations in the NCAM2 gene were also found in autistic patients. How changes in the levels of this protein result in mental abnormalities remains poorly understood. The results from the lab’s recent work suggest that altered levels of NCAM2 can induce abnormalities in development of neurons, affecting the formation and functioning of neuronal networks in the brain. The lab is now investigating whether changes in levels of NCAM2 and other cell adhesion molecules affect neurotransmission between neurons and excitability of neuronal networks. The results of this work will help to understand the molecular mechanisms of brain disorders and identify new molecular targets, which can be used to design novel treatments of these disorders. Dr Vladimir Sytnyk’s laboratory is interested in how cell adhesion molecules induce changes in neuronal growth at the molecular level. We are particularly interested in cell adhesion molecules, expression of which is altered in brain disorders. In a recent study completed by the group, a cell adhesion molecule called the Neural Cell Adhesion Molecule 2 (NCAM2) was shown to be an important regulator of the branching of axons and dendrites. Growth of axons and dendrites depends on the activation of a number of enzymes in the cytosol of neurons. These enzymes regulate changes required for building of a new axon or dendrite, such as switching on the expression of gene coding for structural proteins or inducing the remodelling of the cytoskeleton. Ca2+ ions are important regulators of the activity of intracellular enzymes involved in growth regulation (Sheng et al., 2013). By using genetically encoded reporters of the intracellular Ca2+ concentration, the lab demonstrated that binding of NCAM2 to molecules in the extracellular environment induced transient increases in the levels of intracellular Ca2+, which promoted formation and stabilisation of new branches in developing neurons. NCAM2 induces changes in neuronal morphology by inducing transient increases in intracellular Ca2+ levels. A – images of a control neuron with non-active NCAM2 and a neuron treated to activate NCAM2. B – pseudocolored image of a neuron transfected with a genetically encoded Ca2+ reporter. Arrow shows a transient NCAM2-induced increase in intracellular Ca2+ levels. Adapted from Sheng L, Leshchyns’ka I & Sytnyk V, 2015, ‘Neural cell adhesion molecule 2 promotes the formation of filopodia and neurite branching by inducing submembrane increases in Ca2+ levels’, Journal of Neuroscience, 35(4):1739-52. 23 | Systems and Cellular Biology Academic Staff Professor Bill Ballard Professor Andrew Brown Professor Marc Wilkins Professor Rob Yang Senior Lecturer Dr Richard Edwards Senior Lecturer Dr Kyle Hoehn Senior Lecturer Dr Irina Voineagu Senior Lecturer Dr Paul Waters BABS Research Group – Systems and Cellular Biology | 24 Autism genetics Dr Irina Voineagu, Senior Lecturer Irina is currently an ARC DECRA Fellow. She established her lab at UNSW in 2013 and her team has since grown, currently including two postdoctoral researchers, one PhD student and several undergraduate students. Her laboratory investigates the molecular genetic mechanisms underlying normal brain function and their perturbation in neurodevelopmental disorders, using a combination of functional genomic studies in human brain tissue and neuronal cell culture systems. Autism spectrum disorders (ASD) encompass a range of neurodevelopmental conditions characterised by language impairments, deficits of social-reciprocal interaction and repetitive and restrictive behaviours. As for other neurodevelopmental disorders such as intellectual disability and schizophrenia, ASD are highly heritable. Extensive research into the genetics of ASD over the last two decades has demonstrated that the disorders are also genetically heterogeneous, with hundreds of genetic loci implicated. Given this genetic heterogeneity, a challenging yet fundamental question is whether the wide variety of genetic changes ultimately dysregulate a common set of molecular pathways, amenable as therapeutic targets. Irina’s work demonstrated that despite genetic heterogeneity, common gene expression changes could be identified in a large subset of ASD cases. A key finding of this study was that the neuronal splicing factor A2BP1 (Ataxin-2 binding protein 1) was downregulated in a large subset of ASD brains. While A2BP1 has been previously implicated in ASD, the mechanisms of its transcriptional dysregulation and the functional consequences of altered A2BP1-dependent splicing in ASD remain unknown. Genomic diversity in the human brain The Voineagu lab is also interested in investigating somatic instability at trinucleotide repeats (TNRs) in the normal human brain. Although genetic variation can potentially occur anywhere in the genome, certain genomic regions are particularly susceptible to genetic changes. These regions are called hotspots of genomic instability, and are frequently underlied by repeated DNA sequences. One class of hotspots of genomic instability particularly relevant to brain function consists of expandable DNA repeats. These are tandem DNA repeats, most often trinucleotide repeats (TNRs) such as (CGG)n, (CAG)n, (GAA)n, which have an intrinsic propensity to increase in length during germline transmission. Unstable DNA repeats block DNA replication, and replication stalling at TNRs eludes the cellular checkpoint machinery, leading to chromosomal fragility. TNR expansions have been investigated primarily as a cause of neurodegenerative disorders, including Huntington’s disease, Fragile X syndrome and Friedriech’s ataxia. Irina’s lab is now asking the fundamental question whether somatic TNR instability events occur in the normal human brain, and whether such instability events affect gene expression. Now the lab is taking an integrative approach to investigate the role of A2BP1 and alternative splicing abnormalities in ASD pathogenesis, aiming to (a) identify the genetic and epigenetic causes of A2BP1 transcriptional dysregulation in ASD brain; (b) elucidate A2BP1-dependent alternative splicing targets in the human brain; and (c) investigate the cellular and transcriptional consequences of A2BP1 dysfunction. Network of genes dysregulated in autistic brains (from Voineagu et al. 2011) 25 | Evolution and structure of mammal sex chromosomes Dr Paul Waters, Senior Lecturer In most mammals females have two X chromosomes, whereas males have just one X and a gene-poor Y chromosome that determines maleness. The evolution of sex chromosomes (the X and Y) has been a hot topic for nearly a century, because they seem to break the most fundamental rules of Darwinian selection (i.e. the “fittest” chromosome does not always persist). It is now widely accepted that the human X and Y evolved from an ordinary pair of chromosomes via a process of gene loss from the male-specific Y chromosome, and genes that remain on the Y are generally important to male reproduction. This same process of sex chromosome evolution has resulted in differentiated sex chromosomes in diverse animals (from flies to mammals). For each species with differentiated sex chromosomes, unique hurdles need to be overcome. In humans, females have two copies of approximately 800 X chromosome proteincoding genes, whereas males have just one copy of these genes. How are such extreme dosage differences tolerated between the sexes, considering that one copy of any other chromosome is lethal? Subsequently, this over-expression is compensated for by transcriptional silencing of one X chromosome in the somatic cells of females; a phenomenon called X chromosome inactivation that is mediated by long non-coding RNAs. Since arriving at UNSW in 2013, research in the Waters lab has focused on the evolution and structure of mammal sex chromosomes, along with X chromosome inactivation. Paul was recently involved in a large-scale project focused on the evolution of mammal Y chromosomes (Nature cover story April 2014). This project employed high-throughput sequencing in 15 mammal-representative species to identify over 100 new mammalian Y chromosome genes, analysis of which demonstrated that sex chromosomes have arisen independently at least three times in amnoite vertebrates (i.e. birds, monotremes and the marsupial/ eutherian ancestor). Surprisingly, genes that persisted on mammal Y chromosomes originally did so because they were under strict dosage constraints, and subsequently recruited into male-specific functions. It is thought that in male mammals, dosage compensation is achieved by over-expression of genes on the X, ultimately resulting in doubled gene expression from the single X in males. Because females have two Xs, carry-through of over-expressed X genes from males to females would result in a doubled gene dose (functionally equivalent to four copies of the X – just as bad as one copy). More recently, the Waters lab has focused on understanding how non-coding RNAs mediate inactivation of the X chromosome in the distantly related marsupial and eutherian mammals. This project has provided fascinating insight into the similarity of interacting protein networks shared by two long non-coding RNAs, which evolved independently to mediate arguably the most iconic example of epigenetic silencing in mammals – X chromosome inactivation. Chromosomes from a male kangaroo with one X and one Y chromosome In female cells the inactive X chromosome is coated in non coding RNA (red) | 26 Profile Dr Richard Edwards, New Senior Lecturer I joined BABS in November 2013, relocating from the Centre of Biological Sciences at the University of Southampton in the UK. My earlier research background is in genetics, but since 2002 I have mainly been working on bioinformatic methods for predicting important sites in protein function. I was therefore attracted to BABS by the strength and depth that the School has in genomics, proteomics and systems biology. It has been a good move. My research group now has joint journal clubs with the proteomics group of Professor Marc Wilkins, and several new collaborations are making good use of the Ramaciotti Centre for Genomics, which is hosted by BABS. I lead a bioinformatics group that uses computational tools to analyse biological data. My research can broadly be described as hunting for evolutionary footprints of molecular function, stemming from a fascination with the molecular basis of evolutionary change and how we can harness the genetic sequence patterns left behind to make useful predictions about biological systems. I consider myself an evolutionary biologist at heart, and the famous adage of Theodosius Dobzhansky, “Nothing in biology makes sense except in the light of evolution” is particularly true of sequence analysis. The evolutionary process leaves clues in the sequences and it is those clues that my lab seeks to exploit. recent efforts have concentrated on improving performance for specific scenarios. The reliability of its predictions has enabled us to shift the emphasis from algorithms to applications. A major research area in the lab is the application of SLiMFinder to viral-human protein interactions in order to identify “molecular mimicry”, in which viral pathogens mimic host motifs to hijack cellular processes. Finally, the lab has a number of interdisciplinary collaborative projects applying bioinformatics tools and molecular evolution theory to experimental biology, often using large genomic, transcriptomic and/or proteomic datasets. These projects often involve the development of bespoke bioinformatics pipelines and a number of open source bioinformatics tools have been generated as a result. Joining BABS has also enabled me to return to my first love, genetics. The Ramaciotti Centre for Genomics has just received a new PacBio sequencer, and I am excited about some new collaborations harnessing the power of long-read sequencing. Core research in the lab is the study of Short Linear Motifs (SLiMs), which are short regions of proteins that mediate interactions with other proteins. This research originated with my postdoctoral work, during which I developed a bioinformatics (sequence analysis) method for rational design of biologically active short peptides. Since then, we have developed a number of SLiM discovery tools, including SLiMDisc, one of the first algorithms for successfully predicting novel SLiMs from sequence data (coining the term “SLiM” into the bargain), and SLiMFinder, the first SLiM prediction algorithm able to estimate the statistical significance of motif predictions. SLiMFinder is still the most successful general SLiM prediction tool on benchmarking data, and State-of-the-art SLiM prediction tools developed in the Edwards lab. 27 | Profile Dr Kyle Hoehn, New Senior Lecturer I was awarded my PhD in Biochemistry from Colorado State University in 2005, and trained as a postdoc at the Garvan Institute of Medical Research in Sydney from 2005-2009. My independent research career started in 2009 as an Assistant Professor of Pharmacology at the University of Virginia. I joined the School of Biotechnology and Biomolecular Sciences in July 2014 as an academic with both teaching and research responsibilities. I coordinate a second-year undergraduate course entitled Fundamentals of Biochemistry, and I guest lecture in other courses as needed (e.g. Human Biochemistry and Molecular Frontiers). My research lab consists of one postdoc and one undergraduate student, and we are currently working on a drug discovery project. Our research centres on small molecule drug discovery for anti-cancer agents, with the objective of identifying new anti-cancer agents that kill cancer cells by altering the way they use glucose. To date, we have identified a small molecule named BAM10 that reduces melanoma tumour growth in mice and is selectively toxic to cancer cells grown in culture (see figure). These promising results formed the basis of an NHMRC grant application submitted in 2015. My first eight months in BABS have been very intellectually stimulating and have broadened my understanding of the microbial world and junk DNA. Importantly, I have developed many new collaborations both within the School and across the UNSW campus. These interactions have helped to secure new School equipment through the MREII program, and resulted in 9 different grant applications to date in 2015. In summary, I’m very happy to be involved in a School with such diverse talents in both research and teaching, and I look forward to contributing to the School’s already sterling reputation. Cancer cells intake much more glucose than non-cancer cells and they use it to produce building blocks (lipids, DNA, protein) for cell replication. BAM10 interferes with this pathway by increasing the amount of glucose that is oxidised to carbon dioxide (CO2). Since non-cancer cells normally oxidise glucose, they are less affected by BAM10. Therefore, BAM10 represents a potential chemotherapeutic agent that may have less toxicity to healthy cells. | 28 Profile Dr Jai Tree, New Senior Lecturer I joined the School of Biotechnology and Biomolecular Sciences in March 2015. I completed my postdoctoral work at the The Roslin Institute and Wellcome Trust Centre for Cell Biology at the University of Edinburgh, UK. On returning to Australia in 2014, I joined the Peter Doherty Institute at the University of Melbourne as a Research Fellow, but was soon attracted to Sydney by the opportunity to establish a research group in BABS at UNSW because of its excellent infrastructure (including the Ramaciotti Centre for Genomics) and strength in RNA biology. We are also applying high-throughput techniques to study small RNA interactions with messenger RNAs (mRNAs) in bacterial cells. These approaches will allow us to map the extent of ncRNA regulation and identify novel interactions that are not predicted, by extrapolating our current understanding of ncRNA regulation. Ultimately, we expect that by understanding this fundamental layer of gene regulation in bacterial pathogens, we will provide targets for novel interventions such as small molecular inhibitors of virulence. My lab is interested in how bacterial pathogens control gene expression in response to stress and host colonisation, with a particular focus on how proteinRNA and RNA-RNA interactions control expression of virulence genes. Recent advances in sequencing technologies have led to the realisation that bacteria encode a panoply of regulatory RNA, known as non-coding RNA (ncRNA), that functions in both sensing and responding to environmental cues and stress. My lab works on an abundant subclass of ncRNA, termed small RNA, and seeks to understand how this layer of gene regulation adapts bacterial pathogens for disease. Our model system is the human pathogen enterohaemorhaggic E. coli (EHEC) that has a “mosaic genome”, consisting of a core genome shared with commensal E. coli isolates, and an accessory genome that has been horizontally acquired on mobile genetic elements such as plasmids, bacteriophage and transposons. The accessory genome provides the tools for EHEC to cause disease in humans. I have shown that the accessory genome encodes a large number of small RNAs, and that bacteriophage carry a new class of ncRNA that represses host small RNA regulation (termed anti-sRNA), providing a selective advantage for colonisation of ruminants (the reservoir host) This work was recently published in Molecular Cell. We use a broad range of molecular biology tools to explore how RNAs regulate pathogenesis, including mutagenesis and transcriptomics, using high-throughput (HTP) sequencing. We have demonstrated that UV-crosslinking and HTP sequencing (known as CRAC or CLIP-Seq) can be applied to bacteria and are using this technique to study how small RNAs direct, and are directed by, protein interactions in the cell. Mapping protein-RNA interactions transcriptome-wide (top) and within the 5’UTR of a virulence gene (bottom) using UV-crosslinking (CRAC). 29 | Profile Ruben Meerman, ABC Surfing Scientist and BABS PhD Candidate When somebody loses weight, where does it go? Most people believe the weight turns into energy or heat, some think it ends up in the toilet, while others assume it is converted into muscle. These beliefs are all incorrect! While scientists have known the true fate of fat for more than a century, ABC Surfing Scientist Ruben Meerman and Head of School Professor Andrew Brown recently completed a survey that revealed that these misconceptions are common amongst today’s doctors, dieticians and personal trainers. “Right now, most of the health professionals at the frontline of the obesity epidemic have scientifically impossible ideas about how human beings lose weight,” says Ruben. Their survey was published in the British Medical Journal alongside a novel calculation that shows that 84% of the mass in a fat molecule is exhaled as carbon dioxide gas while the remaining 16% becomes water. The duo’s paper attracted worldwide attention in December 2014. Ruben is now a BABS PhD candidate, but his unexpected | 30 return to academia can be traced back to a 2012 surfing holiday in Fiji. “Pondering my pot belly in those photos motivated me to do what doctors and dietitians have always recommended and, lo and behold, after eleven weeks of eating less I’d lost 6.5 kg” said Ruben, “So I did a quick linear regression, of course, and discovered that I’d been losing 85 grams per day, which meant I would reach my target weight in just a few months.” That was a happy moment for Ruben but it was the question he asked next that would lead him to BABS. “I wanted to know precisely what proportion of those 85 grams I had been exhaling every day,” he explains. Ruben studied physics at QUT and spent several years in industry producing optical coatings using electron beam physical vapour deposition (EBPVD) for military, medical and industrial lasers, but has no formal training in biochemistry. He completed a Graduate Diploma in Science Communication at the ANU in 1995, which included a practical component performing science demonstrations in primary and high schools as a member of the Shell Questacon Science Circus. A generation of Aussie kids now know him as the ABC’s “Surfing Scientist”, and he became Play School’s first ever resident scientist in 2012. He credits one particular demonstration for sparking his curiosity about weight loss. “I’ve been using liquid nitrogen to freeze my exhaled breath inside transparent balloons for years so when I started losing weight, I had this vivid image of that solid frozen carbon dioxide you can see inside,” Ruben explains, “I found it incredibly motivating to know that I was turning my fat into gas and water, but I’m a geek so I had to know the precise proportions of each that it had become.” The problem is that fat is made of carbon, hydrogen and oxygen and it is not clear whether those oxygen atoms are exhaled as CO2, excreted as H2O, or depart in some combination of the two.” After a self-directed crash course in biochemistry, it dawned on Ruben that the answer had never been published so he called Professor Andrew Brown at UNSW Australia for some expert advice. Unaware that Andrew was on sabbatical in Finland, Ruben called several other biochemistry professors across the country but none had ever contemplated the metabolic fate of a fat molecule’s oxygen atoms. He finally found the vital clue in a paper published in the Journal of Biological Chemistry in 1949. The authors injected water labelled with heavy oxygen (O18) into mice and, because some of those atoms were later exhaled in carbon dioxide, Ruben was able to deduce that two thirds of the oxygen in fat ends up in CO2. “I danced around my lounge room for an hour when I found that paper,” Ruben recalls, “I could finally say with certainty that precisely 8.4 out of every 10 kilograms of fat departs the body as carbon dioxide.” He presented his calculations at TEDxQUT soon after and eventually convinced his producers to air them on ABC Television’s Catalyst program. By then, Andrew was back at BABS and still on top of Ruben’s list and the pair eventually met in March 2014. “Andrew was the first person who really appreciated the value of my simple calculation and he emailed the day after our interview suggesting we co-author a paper about my work,” Ruben said, “I danced around the kitchen until the crew made me get back to work.” “It is my life’s mission, and now my PhD’s, to make sure every human being knows how their body gains and loses weight,” Ruben says, “Once you understand that we expend kilojoules but exhale kilograms, you can appreciate why there is only one way to lose weight – which is to eat fewer carbon atoms than you exhale. Any diet that satisfies this simple rule will work.” Filming Catalyst with Andrew Brown’s HDR students 31 | Affiliated Research Organisations | 32 The Ramaciotti Centre for Genomics The Ramaciotti Centre for Genomics is hosted by the School of Biotechnology and Biomolecular Sciences. It is committed to enabling internationally competitive genomic research and is funded by the Federal Government NCRIS (National Collaborative Research Infrastructure Scheme) and by the State Government of NSW. Our technology suite includes next-generation sequencing, Sanger sequencing, single-cell analysis, microarrays, and high-throughput qPCR. Services provided to the research community include: Genome sequencing Transcriptome analysis Single cell analysis Metagenomic profiling Copy number variation analysis Sample/cell line identification Fluidigm High throughput qPCR system Highlights from 2014 ARC LIEF grant success The Ramaciotti Centre Consortium was successful in its bid to the ARC Linkage Infrastructure and Equipment Funding (LIEF) scheme for a PacBio RSII single molecule sequencer. The grant was led by UNSW. The PacBio RSII, unlike other next-generation sequencers that have read lengths of 100 to 400 bases, generates average read lengths of 10,000 bases up to a maximum of >40,000 bases. Illumina HiSeq 2500 Next Generation Sequencer The long read lengths generated by the PacBio RSII will help to simplify and improve the assembly of genomes, and will facilitate the analysis of base modifications and transcript isoforms. This is the Centre’s fifteenth successful LIEF grant, bringing the total ARC LIEF funds awarded to the Ramaciotti Centre Consortium to $9.5 million. Illumina NextSeq 500 Next Generation Sequencer 33 | National Framework Dataset Program The Centre continues to work on a number of federally funded strategic dataset projects, which involve genome sequencing – including metagenomics – and transcriptomic analysis. These projects are building large biomolecular datasets, which will positively impact on problems of importance to Australia. They include: Biome of Australian Soil Environments – metagenomic and amplicon sequencing to map soil biodiversity DNA Barcoding – sequencing genetic markers to enable rapid species identification and aid conservation Koala Consortium – sequencing the koala genome and transcriptome to protect koalas from debilitating disease Great Barrier Reef – sequencing coral and symbionts to protect and preserve the coral reef Melanoma – genome sequencing to identify genetic mutations that lead to cancer Wheat – sequencing pathogens to increase yields and help defend against disease Wine – sequencing chardonnay varieties and yeast to enhance wine characteristics. Illumina MiSeq Next Generation Sequencer | 34 Alliance with the Garvan Institute’s Kinghorn Centre for Clinical Genomics On 9 September 2014 the Centre announced an alliance with the Garvan Institute’s Kinghorn Centre for Clinical Genomics (KCCG) that will allow the research community access to the most powerful available platform for human genome sequencing, the Illumina HiSeq X Ten. The X Ten system provides unparalleled sequencing capacity and is capable of sequencing around 350 human genomes a week, or 18,000 per year. The KCCG was one of the first institutions in the world to acquire the X Ten platform, and the first in Australia to operate a purpose-built facility for sequencing clinical grade human genomes. By forming this alliance, the Ramaciotti Centre will allow the broader research community access to this world-class genomics sequencing facility. Professional Women in Leadership Acquisition of an Illumina NextSeq 500 The Centre Manger Dr Helen Speirs was accepted into the inaugural UNSW Professional Women in Leadership Program (PWIL). The program aims to identify, grow and retain a pool of high potential talented women to take up leadership roles within UNSW. It supports the University’s strategic objective of improving leadership and operational capabilities and seeks to develop strong female role models. Next generation sequencing continues to be a growth area for the Centre. With funding awarded by the ARC in a successful 2014 LIEF grant, the Centre expanded its suite of next generation sequencing instruments by investing in an Illumina NextSeq 500 sequencer. The NextSeq is a desktop sequencer that provides great flexibility allowing us to sequence genomes, exomes and transcriptomes. With over 300 eligible candidates for nomination, Helen was one of 21 Professional staff selected to be part of the 12-month program. Oxford NanoPore MinION The Ramaciotti Centre was selected to be part of the Oxford NanoPore Technologies (ONT) MinION access early programme. The MinION is a new sequencing technology that utilises protein nanopores. The MinION passes an ionic current through nanopores in a membrane and measures the changes in current as molecules pass through the nanopore, with the information on the changes in current being used to identify the molecule. The Centre is currently beta testing the MinION system on small genomes such as the bacterial virus lambda phage and E. coli DNA. Sanger Sequencer RAMAC Oxford NanoPore Technolgies MinION 35 | NSW Systems Biology Initiative The Systems Biology Initiative (SBI) is a centre for molecular systems biology. It has deep expertise in proteomics, genomics and transcriptomics, and in the bioinformatics that is required to analyse and integrate omics results and data. It is funded by the Australian Research Council, the federal government National Collaborative Research Infrastructure Scheme (NCIRS), and the NSW State Government Research Attraction and Acceleration Program (RAAP). It is actively involved in the establishment of ‘omics infrastructure, in genomics, proteomics and high performance computing, through leading and participating in ARC LIEF grants. The SBI has an active program in yeast systems biology. A focus of this work is to understand the role that protein methylation has in the regulation of protein-protein interactions, and to study this on a global scale in the yeast proteome. After recent work to define the proteins, and sites on proteins that are methylated, we have focused our research on (i) discovery of the methyltransferases that are responsible for this methylation and (ii) the use of our ‘conditional two-hybrid’ system to measure the effect of methylation on the protein interactions. This has led to the finding that, for a protein with many interaction partners, methylation increases interactions with some partners but not with others. Methylation thus modulates interaction specificity. From this work, in 2014 we presented the general hypothesis of the ‘protein interaction code’. Regulation of protein-protein interactions by methylation, in the yeast interactome. From Erce et al. (2013) Mol Cell Proteomics 12(11): 3184-98. | 36 The SBI has a team of bioinformatics researchers that are funded to develop expertise in the analysis of omics data and to disseminate this expertise through collaboration. The team works closely with users of NCRIS-funded omics facilities, specifically the Ramaciotti Centre for Genomics, the Bioanalytical Mass Spectrometry Facility, and the Australian Proteome Analysis Facility. In 2014, the bioinformatics team was involved in many collaborations, addressing a range of biological questions. These ranged from de novo assembly of the koala genome, to understanding the network-basis of synergistic drug effects, through to the discovery of osteoblast-specific markers in stem cells during their differentiation to osteoblasts. Stem cell marker genes show hierarchical clustering that relate to their temporal expression during differentiation. From Twine et al (2014) Bone ;67: 23-32. Centre for Marine Bio-Innovation The CMB is an international focal point for interdisciplinary basic and applied research into chemically mediated interactions between organisms. Located in the Biological Sciences Building, the Centre integrates research across microbiology, marine chemical ecology, ecological theory, chemistry, and organism and community genomics. The CMB drives research excellence in studies of microbial biofilms, bacteria-higher organism interactions, colonization biology of marine sessile organisms, experimental marine ecology, biofouling, biodiversity, bioremediation and inter-kingdom signalling. Key research activities in the CMB occur within and in collaboration with a number of Australian and international institutions and industries. With research platforms based on the integration of marine chemical ecology and microbiology, the CMB has grown to include a diversity of research capabilities, and is a key node across a wide network. The CMB has more than 50 full time members, comprised of research fellows, postdoctoral research associates and research assistants, and its members have a strong record in honours and postgraduate student supervision. A number of collaborations in Australia and overseas contribute to the high standard and international profile of the Centre, which routinely welcomes visiting researchers from around the world. Since its creation, the Centre has attracted funding from a variety of sources both within and outside Australia. This includes success in competitive grants, notably the Australian Research Council, but also from international bodies, and it has also received considerable support from relevant industry sources. Further information is available on the Centre’s website: cmb.unsw.edu.au/ 37 | Specialised Facilities, Services and Equipment UNSW Recombinant Products Facility Molecular and Image Analysis Facility (MIAF) This facility located in Room 329 of the Biological Sciences Building provides services in cell line development, bioprocess design, protein production services and training to the research community. Services include The MIAF is a multiuser facility that is able to be accessed by researchers from BABS, other UNSW Science Schools and Faculties and UNSW-associated institutions. The facility contains Fujifilm FLA-5000 and a GE Typhoon FLA-9500 (including a 685 nm red laser) biomolecular imaging systems for fluorescence, phosphorimaging, digitisation, and chemiluminescence detection. The scanning area is as large as 40 x 46 cm at a pixel size as low as 10 microns. The MIAF also has Fujifilm LAS3000 and GE LAS-500 imaging systems, which use a CCD camera with very high sensitivity for detection of chemiluminescent Western blots, imaging of fluorescent protein and DNA gel stains, and white light imaging of colourimetric stains and markers. An ImageScanner III for densitometric applications completes the unit, and offers high resolution with a wide optical density range to scan gels, blots, membranes, and slides. 1. Cell line development (choice of host, vector and gene design) 2. Cell line characterisation 3. Bioprocess development and evaluation 4. Microbial fermentation (E.coli and yeast) to 25 litres 5. Protein and antibody purification using AKTA systems 6. Protein characterisation and analysis including protein gel electrophoresis, Western blotting, HPLC 7. Co-ordination with other UNSW services such as LC-MS and other proteomic services via the BMSF 8. Training in Fermentation and purification using the AKTA systems Website: proteins.unsw.edu.au Seahorse Extracellular Flux (XF) Analyser The Seahorse Analyser is cutting-edge technology that measures the metabolic activity of cells in minutes, allowing a physiologic cellbased assay for the determination of basal oxygen consumption, glycolysis, ATP turnover and respiratory capacity in a single experiment. The two major energy producing pathways of the cell, mitochondrial respiration and glycolysis, are measured simultaneously and the data generated provides the most physiologically relevant bioenergetic assay available for the determination of mitochondrial function. The RPF provides a range of services for upstream (fermentation), midstream (filtration and centrifugation), purification and analysis. | 38 The system can be used to study respiratory malfunction in multiple diseases including cancer, cardiovascular disease, ageing-associated disorders, mitochondrial diseases, immunological disorders, neurodegenerative disease, obesity and diabetes. Assays are non-invasive, allowing for further downstream applications to be performed. C1Si Confocal Microscope The C1si is a revolutionary true spectral imaging confocal laser microscope that can be valuable in a wide range of applications. It has the capability to acquire 32 channels of fluorescence spectra over a 320nm-wide wavelength range in a single pass. By cleanly unmixing overlapping spectra of different fluorescent labels, the C1si dramatically improves dynamic observations of live cells and facilitates the acquisition of detailed data. Other specialised instruments and amenities in BABS Beckman Coulter Quanta MPC flow cytometer Bioscreen cell growth monitoring system CLARIOstar microplate reader EnSight Multimode plate reader EVOS-FL digital LED-based fluorescence microscope Gel documentation systems Low temperature incubators Neon transfection system Nikon TS100-F inverted microscope with an LED source Olympus BX51 fixed stage fluorescence microscope equipped with an Eppendorf microdissector Olympus FSX100 digital imaging system PAM2500 Portable chlorophyll fluorometer Polarstar omega microplate reader Protean IEF system QC1 and QC2 quarantine-approved premises RT PCR systems Security Sensitive Biological Organisms (SSBA) facility Semi-automatic microtome TissueLyser LT cell lysis apparatus TLC autospotter Various liquid-handling robotic systems Whitley DG250 workstation for culturing anaerobes There is also a wide variety of standard biomedical instrumentation in the School, including HPLCs, FPLCs, GCs, thermocyclers, centrifuges, ultracentrifuges, plate-, drop-, and cuvette- based spectrophotometers and fluorimeters, scintillation counters, fluorescence and light microscopes and electrophoresis equipment. 39 | External Partner Organisations ANZAC Research Institute Hanze University of Applied Sciences Arizona State University Hebrew University of Jerusalem Atma Jaya University Indonesia Helmholtz Centre for Infection Research Australian Antarctic Division International Society for Microbial Ecology Australian Coal Association Research Program J Craig Venter Institute Australian Coal Mining Industry James Cook University Australian Drosophila Biomedical Research Support Facility Japanese Border Collie Health Network Australian Geographic Society Australian Institute of Marine Science Australian National University Australian Nuclear Science & Technology Organisation Baker IDI Institute Bar Ilan University BASF The Chemical Company Centenary Institute Centre for Vascular Research Centre of Marine Biotechnology Charles Sturt University Chinese Center for Disease Control and Prevention Chinese Center for Disease Control and Prevention Christchurch Hospital Concord Hospital CSIRO Entomology Denmark National Environmental Research Institute Desert Research Institute Nevada DHI Singapore Diagnostic Technology Pty Ltd DOE Joint Genome Institute Dow Chemical Company Environmental Biotechnology Cooperative Research Centre Garvan Institute Hamburg University Center for Molecular Neurobiology | 40 Kamaishi Marine Biotechnology Institute Karolisnka Institute Department of Microbiology La Trobe University Laboratoire d’Oceanologie Biologique de Banyuls Universite Paris Landcare Research New Zealand Laurentian University Canada Lowy Cancer Research Centre Macquarie University Massachusetts Institute of Technology Massey University New Zealand Max Planck Institute for Chemical Ecology McGowan Institute for Regenerative Medicine Microbiogen Murdoch University Nanyang Environment and Water Research Institute Nanyang Technological University NASA Ames Research Centre National Centre for Adult Stem Cell Research Griffith University National Centre in HIV Epidemiology & Clinical Research National University of Singapore Neuroscience Research Australia Northwestern University Chicago Norwegian Veterinary College NSW Department of Primary Industries (Fisheries) NSW Food Authority NSW National Parks and Wildlife Service Optigen University of Cologne Orica Australia Pty Ltd University of Copenhagen Peking University Health Science Center University of Heidelberg Pennsylvania State University University of Konstanz Prince of Wales Hospital University of Leipzig Queensland Parks and Wildlife Service University of Manchester Queensland University University of Melbourne Rutgers University University of Minho Portugal SA Department of Primary Industries University of New Mexico Save Sight Institute University of Otago Scripps Institute of Oceanography University of Ottawa Heart Institute Seoul National University University of Papua New Guinea Singapore Advanced Environmental Biotechnology Centre University of Poitiers Singapore Centre on Environmental Life Sciences Engineering Singapore Institute of Molecular and Cell Biology Singapore Tropical Marine Science Institute Southern Cross University Stanford University Stockholm Royal Institute of Technology Sydney Children’s Hospital Sydney Institute of Marine Science Sydney Royal Botanic Gardens and Domain Trust Tasmanian Department of Health Tsinghua University China Universidad Nacional de Quilmes University College Dublin University of Adelaide University of Alberta University of Amsterdam University of Auckland University of British Columbia University of California, Davis University of Queensland University of Salzburg University of Saskatchewan Canada University of Southampton University of Southern California University of Sussex University of Sydney University of Tasmania University of Technology Sydney University of Utah University of Washington University of Western Australia University of Western Sydney University of Wollongong US National Institutes of Health Victor Chang Institute Victoria University Wellington Wake Forest Institute for Regenerative Medicine Weizmann Institute of Science Israel Westmead Hospital University of California, Irvine University of California, Los Angeles University of California, San Diego University of Canberra University of Cincinnati 41 | Memberships in Societies and Associations Alexander von Humboldt Foundation American Academy of Microbiology American Association for Cancer Research American Society for Biochemistry and Molecular Biology American Society for Microbiology American Society for Pharmacognosy American Society of Human Genetics Association of Vibrio Biologists AusBiotech Australasian Microarray & Associated Technologies Association Australasian Proteomics Society Australasian Society for Immunology Australasian Society for Phycology and Aquatic Botany Australia and New Zealand Society for Cell and Developmental Biology Australian Academy of Science Australian Atherosclerosis Society Australian Centre for Hepatitis Virology Australian Institute of Dangerous Goods Consultants Australian Institute of Policy & Science Australian Neuroscience Society Australian Society for Biochemistry & Molecular Biology Australian Society for Medical Research Australian Society for Microbiology BioEnvironmental Polymer Society Bioinformatics Australia Buttressing Coalition of the Papua New Guinea Institute of Medical Research Chronic Lymphocytic Leukemia Australian Research Consortium Council of the Human Proteome Organisation Endocrine Society of Australia | 42 Forum for European-Australian Science and Technology Cooperation Fulbright Alumni Association Genetics Society of AustralAsia Geological Society of Australia High Blood Pressure Research Council of Australia Institute of Biology International Society for Microbial Ecology International Society for Microbiology International Society for the Study of Harmful Algae International Society of Animal Genetics NASA Astrobiology Institute Pacific Institutes of Marine Science Royal Society of Victoria Safety Institute of Australia Society for General Microbiology (UK) Society for Neuroscience (USA) Tissue Engineering & Regenerative Medicine International Society Learning and Teaching The School of BABS is advancing cellular and biomolecular science to make a real difference in the world. By investigating and understanding life at the molecular and cellular level, including life from some of the most extreme environments on earth, our students help solve real-world challenges. Our undergraduate and postgraduate degree programs offer structured training in scientific methodology, creative thinking, organisational skills, problem solving and analysis. Our programs prepare students for a variety of career options within and outside the sciences, with graduates excelling in a wide range of commercial research pathways, including medical, environmental and biotechnology. Communication and information literacy are emphasised, providing our graduates with a competitive edge for careers in business and science communication. They also are well qualified for employment in government and privately sponsored industries in areas ranging from management, policy development, production and quality control, to education. Innovations in teaching New courses in rapidly evolving discipline areas have been developed in recent years, attracting significant interest amongst students, with our majors restructured to align more closely with the School’s emerging research strengths. Recognising the importance of research training and associated skills, BABS has introduced a number of initiatives to provide undergraduate students with the opportunity to engage in authentic research opportunities, both within traditional courses as well as via an internship program in our research labs. While BABS is home to internationally recognised and innovative researchers, we also leverage the School’s close collaboration with prominent centres such as the Ramaciotti Centre for Genomics and the UNSW Mark Wainwright Analytical Centre to incorporate cutting-edge research into undergraduate teaching. Building on the introduction online resources in previous years, during 2014 the School: introduced the use of electronic online laboratory notebooks developed more online resources, including pre-laboratory quizzes and self-paced tutorial activities purchased Surface Pro3 tablets to enable students to investigate laboratory techniques and contextualise their learning in real time; this also facilitated their engagement with bioinformatic data analysis took advantage of resources available in Moodle, UNSW’s learning management system, to develop peer-based assessment strategies that enhance student capabilities to analyse and critique scientific writing. 43 | Modern facilities Renovation of BABS teaching laboratories is now complete, providing state-of-the-art teaching facilities for our students, including biochemistry/ molecular biology teaching laboratories to PC1 standard and a microbiology teaching laboratory to PC2 standard. All labs feature video display screens, demonstrator-led independent group areas with video/computer/internet facilities, a preparation laboratory and real-time microscope projection. In conjunction with these improvements, we converted one of the old laboratories into an informal learning space christened BiBS (BABS interactive breakout space), where students are able to interact with each other as well as with staff. Amenities include textbook resources, computers and wi-fi, discussion areas and kitchen facilities. In addition, a duty tutor is available for student consultation three days per week. The facility is frequently used by students to practice presentations and work on group projects, and the student society, BABSOC, makes good use of the space for functions, including trivia nights and other fundraising activities. | 44 Outreach and supporting students Academics from the School participate frequently in outreach activities, including those designed to engage secondary school students and encourage them to continue on to science at a tertiary level. Academic staff act as judges in high school science competitions and contribute to the Nura Gili program for indigenous high school students, and are members of the CSIRO Scientist in Schools program. BABS also supports science teachers with mentoring and provision of learning resources, and remains actively involved with the Science Teachers Association of NSW program. Undergraduate degrees Our undergraduate programs in the biomolecular sciences are designed to provide students with rigorous training in the modern sciences and are aimed at fostering an analytical approach to problem solving. Students gain a strong foundation in biology, chemistry and mathematics, establishing a solid base of knowledge for advanced coursework relevant to each specialised program. The flexibility of our integrated programs provides undergraduate students with opportunities to interact with eminent researchers in a variety of disciplines. Students develop communication and information retrieval skills necessary to stay up-to-date in rapidly evolving areas of science, making our programs ideal for those wishing to pursue research-oriented careers. Majors Postgraduate degrees The School teaches within the science discipline areas of biotechnology, genetics, microbiology, and molecular and cell biology. In conjunction with the Faculty of Medicine, we also teach medical and science students in the Bachelor of Medical Science program. In this program students can study towards a major and a minor in a specialisation, with study plans provided for each discipline area. As the next generation of researchers, our large cohort of Higher Degree by Research (HDR) students are an important group in the School. We offer a range of opportunities for HDR students from Australia and overseas countries to work towards a Graduate Diploma, Masters by Research or PhD Degree. In 2014 the School had 142 HDR students, with 119 progressing towards a PhD, and 43 HDR students completed their programs during the year. Honours An optional Honours year can be undertaken by undergraduate students who have maintained a credit average or above during their 3-year program. Honours students join a research team within one of the School’s research labs, working under the direct supervision of an experienced academic. They complete a research project and write a thesis during the year-long program. 45 | Teaching students how science can make a difference Dr Wallace Bridge, Senior Lecturer Australia’s reputation for producing high quality scientists is supported by the oft quoted “we have 0.3% of the world’s population but we produce 3% of the world’s peer-reviewed publications”. Unfortunately, this does not correlate to a similar capacity to translate that great science into new products and services that could make the world a better place, evidenced by our accounting for only 0.6% of the world’s patenting activity. To understand this dichotomy, we need to consider the motivation of our scientists, where they are employed and how they are educated. Most early stage high-risk research, which is where the great scientific discoveries are often made, occurs in our government-funded research agencies (GFRAs) such as UNSW Australia. The majority of GFRA-employed researchers are financially dependent on federal government ARC and NHMRC grants, and a researcher’s competitiveness for these grants is largely dependent on their publication and grant track record. There is, however, no career or financial imperative for researchers to make any real effort to translate their great research findings into tangible benefits for society. On the contrary, any effort to do so may result in catastrophic outcomes for their career by distracting them from the mandated “publish or perish” system for funding. This ongoing reluctance of our funding systems to demand and reward innovation is further exacerbated by an education system that generally has not provided any of the requisite business skills that a scientist would require to put their research findings into practice. Although BABS cannot change the current grant systems, it can influence the education of our future research scientists. Since 1999, BABS has been offering professional business and science translation-oriented courses for its students, and in 2001, the Diploma in Innovation Management was launched as a separate add-on program to be taken concurrently by science students. The rationale for the Diploma was to teach the business aspects of science without necessarily diluting the science. The 36UOC Diploma comprised the two BABS professional courses (BABS3071 and BABS3091), a formal work placement, and three other courses | 46 that focused on entrepreneurship, strategic communication and finance. BABS3091, a capstone course for both the Diploma and the BSc (Biotech) program, teaches financial accounting and guides student teams through the preparation of business plans for opportunities based on real intellectual property. The accounting content is tailored for science students, who usually have no underlying interest or background in business. Throughout the course we awaken and reinforce the principle that the ability to understand business and to communicate in its language will be a major determinant of their future professional success. We constantly remind students that science is actually hard, and business is really easy. To reinforce and hopefully validate this, we encourage them to enter the UNSW Business School’s Business Planning competition (currently known as the Peter Farrell Cup) that is open to all students from across UNSW. Teams from BABS have historically excelled in this highly applauded and acknowledged competition, winning it 8 times and taking out minor placings another 34 times. In 2014, this success continued: of the 42 entrants, 9 were from BABS3071 and 6 of these made the final 10. At the finals, the teams pitched their plans to an 8-member judging panel, and claimed first and third places, also winning 2 Honourable Mentions and the Most Popular vote. They took away $7,500 of the $10,000 prize money on offer, lifting the BABS3071 progressive cash winnings to $112,250. Over 250 BABS students now have “UNSW Business School Business Planning Competition Finalist” on their resumes, with 140 as placegetters and 32 as winners. These BABS students have learnt business skills, often with some initial reluctance, developed ability and confidence in communicating how science can be translated, and have gained confidence from senior business professionals that they can excel in the field. Perhaps one day it will be former BABS3091 students who stem the tide of Australia’s poor innovation performance! Learning and Teaching Prizes and Scholarships 2014 undergraduate student awards University medallists UNSW University Medal in Biotechnology Farzana Kastury UNSW University Medal in Microbiology Sophie Holland School prizes Jackson Prize for Honours Year for best overall performance in Honours year Sophie Holland Jackson Prize in Microbiology and Immunology for the best performance in Microbiology and Immunology Daniel Enosi Tuipulotu Garry King Prize for the best Honours thesis in Molecular Biology or Genetics major Beth Caruana The School of Biotechnology and Biomolecular Sciences Prize for the best overall performance in Level 3 Professional Issues in Biotechnology courses BABS3071 and BABS3091 Eddie Ip School of Biotechnology and Biomolecular Science Prize for the best performance in BIOC3111 Molecular Biology of Proteins Medha Sengupta School of Biotechnology and Biomolecular Science Prize in Level 2 Biochemistry for the best performance in the examinations in Level 2 Biochemistry courses in the Bachelor of Science program Kimberley Hanssen School of Biotechnology and Biomolecular Science Prize in Level 3 Biochemistry for the best performance in Level 3 Biochemistry courses in the Bachelor of Science program Akshay Flora Talented student scholarships School of Biotechnology and Biomolecular Sciences Talented Student Scholarship for outstanding achievement in Year 1 Asma Hossain School of Biotechnology and Biomolecular Sciences Talented Student Scholarship for outstanding achievement in Year 2 Jessica Horton School of Biotechnology and Biomolecular Sciences Talented Student Scholarship for outstanding achievement in Year 3 Tracy Mak 47 | BABS PhD scholarship supplement scheme BABS offers a PhD Scholarship Supplement scheme as a School-funded initiative to provide support to PhD students and encourage them to publish their work. Candidates must hold a primary competitive postgraduate scholarship, and not have been awarded any other top-up scholarship. Selection criteria include number of papers published or accepted where the student is first author (journals must generally have an impact factor of 2 or higher). Each top-up package comprises a $5,000 per annum stipend for new and continuing students ($2,500 for 4th year students). Awardees during 2014: Bakir Al-Sinawi (supervisor Brett Neilan) Wen Aw (supervisor Bill Ballard) Giampiero Batani (supervisor Torsten Thomas) Jugder Bat-Erdene (supervisor Chris Marquis) Jose Burgos-Portugal (supervisor Hazel Mitchell) Jesse Cain (supervisor Brett Neilan) Natalia Castano-Rodriguez (supervisor Hazel Mitchell) Long Chung (supervisor Vincent Murray) Caio Damski (supervisor Kevin Morris) Joshua Hamey (supervisor Marc Wilkins) Nicholas Lister (supervisor Kevin Morris) Fang Lu (supervisor Li Zhang) Jennifer Lun (supervisor Peter White) Laurence Luu (supervisor Ruiting Lan) James Mills (supervisor Michael Janitz) Jadranka Nappi (supervisor Suhelen Egan) Anika Prabhu (supervisor Andrew Brown) Jeyran Shahbazi (supervisor Tao Liu, CCIA) Angela Soeriyadi (supervisor Brett Neilan) Jessica Taylor (supervisor Torsten Thomas) Daniel Winter (supervisor Marc Wilkins) | 48 BABSOC BABSOC is the student-run society that caters for all undergraduate and postgraduate students enrolled in BABS courses and programs. Its objective is to facilitate the development of and interaction within the BABS community by providing a stream of social and professional events throughout the academic year. The society is affiliated with and financially supported by the UNSW-wide student organisation, Arc. The 2014 BABSOC Executive mentored by BABS academic Dr Wallace Bridge comprised two fresh first-years (Wendy and Elizabeth), one keen secondyear (James), two talented third-years (Rhys and Alex), four passionate Honours students (Farzana, Nush, Akira and Jess), and one indispensable PhD student (Josh). One of the aims of the year was to give BABSOC an identity to set it apart from the 200-odd clubs competing for student attention at UNSW. The executive achieved this by creating a new logo for the society that depicts BABS as a tree nourished by the roots of BABSOC (the BABS community), with the branches representing the School’s output via its four research disciplines. The logo was incorporated into T-shirts for the executives to wear during events, as well as mugs and stubby holders reserved for gifts at special occasions. This not only helped make BABSOC identifiable to all its members, but also served as an effective advertisement of its existence and value to the School. BABSOC organised many great events in 2014, including barbeques for students and staff, a Careers Night, a meet-and-greet for prospective Honours students to chat with academics and potential supervisors, the Great Debate, and assisted with the management of the BABS Research Symposium. Feedback from all these activities reconfirmed the successful addressing of the BABSOC mission: encouraging students to undertake Honours, informing career choices, providing platforms for networking between students, academics and professionals, and above all, showing off the excellent research carried out in BABS. Two free barbeques held in the Wilton room were overwhelmingly successful, with well over 100 students and staff attending each event. The BABSOC team was actually overwhelmed, running out of sausages both times and having to dispatch runners to the local supermarket to replenish supplies. The barbeques were a great means to promote awareness of BABSOC and provide an opportunity for students to mingle with staff outside of an academic atmosphere and, in doing so, help develop that sense of community we are so keen to achieve within the School. The annual BABSOC Careers Night was held in September with the theme “Where can Honours take you?”. A panel of recent BABS graduates told stories of how they secured their first job, and demonstrated how a BABS Honours degree could enable many career paths, from research, product development and finance, through to business. The night wrapped up with a pizza networking session, with the speakers being flocked by enthusiastic enquiring attendees. Something new for BABSOC in 2014 was the inaugural Great Debate, towards the end of Semester 2 during one of the regular bi-weekly Friday afternoon research seminar timeslots. The topic was “Use of Experimental Drugs is Ethical in the Case of Ebola”, and the contesting teams were selected from undergraduate BABS student applicants. To ensure the quality of the debate, DebSoc (UNSW Debating Society) kindly agreed to train the speakers and adjudicate on the day. Following a splendid to and fro, the winner was declared to be the ‘Aye’ team. It was a great success for all involved and provided an excellent opportunity for the students to develop 49 | Bachelor of Science student Rhys Keirle cooking up a storm. valuable communication skills and network with academics and researchers. with non-scientists – as well as the very important role of selfies! Finally, after the success of the inaugural event in 2013, the greatly anticipated annual BABS Research Symposium was held at the stunning Randwick Racecourse. The event, which BABSOC assisted to organise and deliver, was a highlight of the BABS year and drew in over 200 people from the BABS community. They could not have been disappointed, as every speaker had worked diligently through practice sessions to ensure that their presentations were free from unnecessary jargon so that they could be readily understood by a broad audience. Head of School Professor Andrew Brown closed the event, commenting on how successful the day had been, and thanking Dr Bridge and the BABSOC executive for their great work in organising such a wonderful event. It was then time for what was possibly another highlight for some delegates, a happy hour at the nearby Doncaster Hotel. The Symposium commenced with eight talented Honours students presenting their research findings. With the high standard of the day already set, the next two sessions for PhD students and postdoctoral researchers built on this, as they continued to share the great work that they and their labs were undertaking. Delegates heard topics from a wide array of research areas, including molecular medicine, environmental microbiology, infectious disease and systems biology. Over 30 posters that had been presented at conferences within the previous year, both locally and internationally, added to the already sensational day. The 2014 Symposium also saw a presentation on science communication by the ABC’s Surfing Scientist and Catalyst presenter Ruben Meerman, who wowed the audience after exploding a balloon within a balloon using just a class IIIB laser. He spoke on the importance of trying to make research sound relevant and interesting when communicating | 50 2014 Honours Completions Name Supervisor Project Title Akerman, Anouschka Louise Lutze-Mann/Noel Whitaker The role of human papillomavirus-encoded miRNAs in HPV transformation. Araghi, Hamid Richard Lock/Marc Wilkins/Sibasish Dolai) Targeting insulin-signalling pathway in high-risk B-cell precursor acute lymphoblastic leukaemia Bainbridge, Emily Hazel Mitchell The role of the Campylobacter concisus virulence plasmid in autophagy manipulation. Benaud, Nicole Belinda Ferrari/John Kalaitzis Polar soil aActinobacteria: a potential source of novel antibiotic secondary metabolites. Caruana, Beth Louise Lutze-Mann Targeting site-1 protease as a novel therapeutic for glioblastoma. Chadwick, Justin John Foster Genetic response of Human Adult Dermal Fibroblasts (HDFa) to novel biomaterials for wound healing applications. Chan, William Torsten Thomas/Nicholas Barraud Nitric oxide-mediated regulation of bacterial biofilm dispersal and virulence in plant hosts. Chen, Jieqiong Michael Janitz Molecular analysis of long intervening non-coding RNAs highly expressed in the white matter of the human brain. Davis, Sarah Antony Cooper Novel long non-coding RNAs as Parkinson’s Disease blood biomarkers. Dutton, Rosanna Kevin Morris The identification and characterisation of DNAmethyltransferase 3A associated long non-coding RNAs. Enosi Tuipulotu, Daniel Peter White Recognition sequences and template specificity of viral polymerases. FigueroaCrisostomo, Carah Bill Rawlinson/Maria Craig/Ammir Al-Shabeeb Circulating microRNAs distinguish enterovirus infection in type 1 diabetes patients: potential biomarkers? Gana, Christine Andrew Brown Post-translational regulation of DHCR7, the terminal enzyme of cholesterol synthesis. Gaweda, Yvette Brett Neilan Biotic and abiotic factors influencing toxic cyanobacterial blooms in an urban and residential freshwater environment. Gokoolparsadh, Akira Irina Voineagu Functional role of IMMP2L in human astrocytes and implications for Tourette Syndrome. Hegarty, Narelle Rebecca Lebard The aflatoxin mystery. Holland, Sophie Mike Manefield Organochlorine metabolism in chloroform-respiring cultures. Kastury, Farzana Mike Manefield Ecotoxicology of neutral red for environmental applications. Kotevski, Damian Rob Yang The role of FLD1 in the regulation of yeast GPAT and AGPAT activity. Lee, Sandra Li Zhang The investigation of the biological effects of toxins produced by Campylobacter concisus CON_phi2 prophage. 51 | Name Supervisor Project Title Liew, Heng Brett Neilan/Brendan Burns Shark Bay microbial mats: key to reveal UV adaptation strategies of archaean life. Luk, Alison Mike Manefield Quantification of microbial groups involved in subsurface biogas production. Lun, Jennifer Peter White Epidemiologic surveillance of Norovirus in NSW, 20132014. Marczuk, Jevira Marc Wilkins/Boris Martinac Engineering E.coli MscL for x-ray crystallography. Moreau, Alexandre Torsten Thomas Utilisation of biochar by soil bacteria. Ng, Hong Noel Whitaker Impact of HPV-infection on hu-miR-145 and transcription factor KLF4 expression. Nguyen, Kim Stuart Tangye Impact of a mutation in phosphatidylinositol 3-kinase (PI3K) on B cell development and function. Nicholls, Laura Irina Voineagu Gene expression profiling of Rett syndrome brain tissue. Pontifex, Ashleigh Brendan Burns A day in the life of a stromatolite: innovative metaproteomic analyses of early Earth microbial communities. Poon, James Rob Yang/Daniel Hesselson A new pink1-deficient zebrafish PD model to investigate gene X environment interactions. Ray, Jason Chris Marquis Isolation and characterisation of a lesser chlorinated benzene degrading community Stewart, Shannan Marc Wilkins Construction of a switchable two-hybrid system for detecting PTM-mediated protein-protein interactions. Tam, Hon Belinda Ferrari Partners of candidate division TM7 in soil. Tan, Hao Torsten Thomas/Shaun Neilsen Isolation and characterisation of biochar-utilising bacteria from soil. Tan, Jessica Bettina Rosche/John Kalaitzis The effect of the traditional Chinese medicine Jie Geng on Pseudomonas aeruginosa biofilm development and integrity. Tan, Amanda Vladimir Sytnyk Regulation of synaptic activity in hypothalamic neurons by NEGR1. Wang, Zichen Kevin Morris Investigating the effects of RNA-directed transcriptional gene silencing on BIRC5 (Survivin) Wong, Alan Brendan Burns Depth profiling of microorganisms in Hamelin Pool microbial mats Yao, Pu Irina Voineagu Comparsion of brain and LCL transcriptome profilling by RNA-seq and CAGE. Yap, Samantha Marc Wilkins/S ven Delaney Genetic variation in mitochondrial and nuclear DNA of Wollemi pine. Yee, Mon Mike Manefield Manipulating electron flow in methanogenic microbial communities using semiconductive phenazine crystals. | 52 2014 PhD Completions Name Supervisor Title Ballestriero, Francesco Suhelen Egan/ Staffan Kjelleberg Combining microbial functional metagenomics and Caenorhabditis elegans genetics to uncover and characterise novel bioactive compounds. Blaber, Elizabeth Brendan Burns Stem cell-based tissue regeneration in space. Bone, Simon Alison Todd The development of signal amplification detection technology utilising dnazymes. Burdach, Jonathan Merlin Crossley Insights into in vivo transcription factor targeting through studies of the archetypal zinc finger protein KLF3. Castãno Rodriguez, Natalia Hazel Mitchell The role of innate immunity in helicobacter pylorirelated gastric cancer. Chan, Carmen Mark Tanaka Developing new mathematical models of the evolutionary dynamics of viruses. Chan, Rodman John Foster Natural synthetic composites of poly(hydroxybutyrate) poly(ethylene glycol) as potential scaffolds for nerve repair. Chenu, Jeremy Julian Cox A (semi-) quantitative approach towards a better understanding of the ecological dynamics of Campylobacter spp. in a commercial broiler chicken operation. Correa Ospina, Claudia Bill Ballard Evolution of cytoplasmic genetic variation: studying Wolbachia from a mitochondrial perspective. Eltahla, Auda Peter White Non-nucleoside inhibitors of viral RNA polymerases; scaffolds for rational drug design. Flannery, David Malcolm Walter Palaeobiology of the Neoarchean Fortescue Group. Gardiner, Melissa Suhelen Egan Molecular determinants of bacteria colonisation on macroalgal surfaces. Hazrin Chong, Nur Hazlin Mike Manefield Microbial cell attachment, colonisation and degradation of coal. Hui, Janice Scott Rice The genes and factors that drive the conversion of the Pseudomonas aeruginosa Pf4 prophage into the superinfective form. Kapterian, Tamar Robert Yang The characterisation of CDP-Diacylglycerol synthases in lipid droplet dynamics and adipocyte development. Kohli, Gurjeet Brett Neilan/Shauna Murray Diversity and genetics of Australasian dinoflagellates, including Gambierdiscus spp., the causative agent of ciguatera fish poisoning. Lam, Connie Ruiting Lan Effects of vaccine selection pressure on the genetic diversity and evolution of Bordetella pertussis. Linardy, Evelyn Alison Todd The development of nuclease-mediated amplification technology for analyte detection. 53 | Name Supervisor Title Luu, Winnie Andrew Brown The role of signalling and sensing in cellular cholesterol homeostasis. Mohd Omar, Suhaila Rick Cavicchioli Utilising Antarctic metagenomic resources for the identification of hydrolases. Moradi Manesh, Donya Richard Lock Molecular determinants of T-cell acute Iymphoblastic Ieukaemia sensitivity to the pre-prodrug PR-104. Ongley, Sarah Brett Neilan Development of a system for the heterologous expression of cyanobacterial natural products. Sach, Roy Malcolm Walter Containing space warfare in the early decades of the twenty-first century. Stevenson, Julian Andrew Brown Cholesterol-dependent degradation and unsaturated fatty acid-dependent stabilisation of squalene monooxygenase in the control of cholesterol synthesis. Taleb, Imam Mike Manefield Linking the degradation of model saturated and aromatic crude oil components to specific marine microbial taxa during biostimulation and bioaugmentation using RNA-stable isotope probing. Timms, Verlaine Brett Neilan The mycobacteriology of inflammatory bowel disease. Van Dorst, Josie Belinda Ferrari Microbial indicators of diesel fuel toxicity in polar soils Wijenayake, B Nirmani Louise Lutze-Mann Investigation of psychotropic drugs for the treatment of glioblastoma. Winsley, Tristrom Belinda Ferrari An Investigation into the bacterial phylum, candidate division TM7. Woodhouse, Jason Brett Neilan The microbial and metabolic diversity associated with cyanobacteria-dominated consortia. Zerenturk, Eser Andrew Brown The regulation and membrane topology of DHCR24, a key enzyme in cholesterol synthesis. Zhang, Yuxi Robert Yang Molecular analysis of lipid storage and trafficking. Zhang, Lelin Marc Wilkins Discovery and characterisation of novel protein methyltransferases in Saccharomyces cerevisiae. | 54 4 Research Funding Grants awarded in 2014 commencing in 2015 Australian Research Council ARC Discovery Project Ballard JWO & Wade CM. Defining unconscious and artificial selection. 2015-2017: $374,900. Brown MV, Ostrowski ML, Bodrossy L, Beman JM & Fuhrman JA. Mapping and modelling the ocean’s unseen biodiversity. 2015-2017: $532,200. Cavicchioli R, Raftery MJ & Papke RT. How do microbes grow in high salt at very cold temperatures? 2015-2019: $835,200. Crossley M & Mackay JP. The role of DNA methylation in transcription factor activity. 20152017: $428,100 National Health and Medical Research Council NHMRC Project Grant Yang HR. Molecular characterization of SEIPIN function: implications for lipogenesis and adipogenesis. 2015-2018: $737,660. Early Career Fellowship Palmer A. Understanding the mechanisms of drug-drug synergy in combination chemotherapy. 2015-2019: $375,932. Man SM. The role of interferon-regulatory factors in the host defense against bacterial infection. 2015-2018: $334,284. Plus associated NHMRC RG Menzies Fellowship 2015-2018: $40,000. ARC Linkage Project Neilan BA & Van Asten M. Heterologous expression of cyanobacterial compounds of analytical and therapeutic value. 2014-2017: $401,219. ARC Linkage Infrastructure and Equipment Facilities Wilkins MR, Cavicchioli R, Morris KV, Thomas T, Charles IG, Djordjevic SP, Darling A, Petty NK, Paulsen IT, Gillings MR, Holmes EC, James DE, Wade CM & Dinger ME. PacBio long read sequencer for the Ramaciotti Genomics Consortium of NSW. 2015: $630,000. [UNSW Central contribution $160,000.] ARC Future Fellowship Tanaka M. How microbes build their environments through evolutionary feedback. 2015-2018: $808,160. Other National Schemes Autism Cooperative Research Centre Innovation Project Voineagu I. Transcriptome analyses of human ASD brain tissue as a complementary method to aid the identification of ASD susceptibility genes. 2014-2015: $50,000. Ramaciotti Australia Foundation Voineagu I. Functional genomic studies in autism spectrum disorders. 2014-2015: $74,000. International Schemes Hope Funds for Cancer Research (US) Postdoctoral Fellowship Byrne FL. Reversing Warburg metabolism to treat cancer. 2014-2017: $176,962. Thomas T. The dynamics of evolution: How horizontal gene transfer drives the diversification and adaptation of complex, bacterial communities. 2015-2018: $892,402. ARC DECRA Fellowship Hart-Smith GO, Protein network regulation: A systems-level analysis of methylation. 2015-2017: $352,000. 55 | UNSW Internal Schemes Faculty of Science Research Grant Major Research Equipment Infrastructure Initiative (MREII) Galea A. Investigating the interaction of cisplatin and cisplatin analogues with different human genomic DNA targets. 2015: $12,000. Brown AJ & Hoehn KL. Fluorescent screening facility for cellular drug discovery. 2015: $111,947. Brown AJ & Marquis C. HPLC for peptides and proteins. 2015: $145,908. UNSW Goldstar (ARC) Brown AJ. Uncovering new regulatory programs in sterol production. 2015: $40,000. Crossley PM. A new generation of designer DNAbinding factors. 2015: $40,000. Tanaka M. The evolutionary dynamics of hostassociated microbial communities. 2015: $40,000. UNSW Goldstar (NHMRC) Ballard JWO. Can dietary modification that minimises mitochondrial stress reduce cellular and organismal dysfunction caused by mutations in the fly homologue of a gene known to cause familial Parkinsonism? 2015: $40,000. Lan R. Elucidating the role and mechanisms of Bordetella pertussis adaptation to vaccine selection pressure in the 2008-2012 pertussis epidemic in Australia. 2015: $40,000. Ferrari B. Landscape connectivity and microbial community assembly in terrestrial Antarctica. 2015: $10,000. Burns B. Correlating population dynamics and elemental cycling in modern stromatolites. 2015: $10,000. Zhang L. Examination of the impact of polymorphic Campylobacter concisus zonula occludens toxin on the intestinal epithelial barrier. 2015: $12,000. Lutze-Mann L. Site 1 Protease as a chemotheraputic target in cancer. 2015: $8,000. Janitz M. The role of long intervening non-coding RNA 00263 in regulation of oligodendrocyte maturation. 2015: $12,000. Waters P. Sex chromosome dosage compensation – novel insights gained from the genome to proteome. 2015: $14,000. Murray V. The precise location of DNA adducts caused by the anti-tumour drug Cisplatin in the entire human genome. 2015: $14,000. Morris KV. Activating cystic fibrosis conductance regulator expression: the therapeutic potential of RNA directed gene activation. 2015: $40,000. Sytnyk V. Mechanisms of abnormal neuronal differentiation induced by hyperactivation of the Junctional Adhesion Molecule B (JAMB): implications for Down syndrome. 2015: $12,000. Faculty of Science Silverstar (ARC) Faculty of Science Early Career Researcher Grant Wilkins M. Methylation of glutamic acid: a new switch for protein-protein interactions. 2015: $35,000. Erce M. Code of conduct: are all hub proteins governed by an interaction code? 2015: $13,200. Faculty of Science Silverstar (NHMRC) Nil. | 56 Ghai R. The mechanism of lipid trafficking orchestrated by oxysterol binding proteins. 2015: $13,200. Grants current in 2014 (awarded prior to 2014) Australian Research Council ARC Discovery Project Cavicchioli R, Lauro F, Guilhaus M, Raftery MJ, Rintoul SR & Riddle MJ. Microbial genomics of the southern ocean: monitoring environmental health. 2010-2014: $950,000. Cavicchioli R. What do microorganisms do season by season, year after year in the frigid Antarctic wilderness? 2013-2016: $240,000. Dawes IW. How do cells regulate redox environment at the subcellular level? 2010-2014: $420,000. Manefield MJ, Deppenmeier U & Juhasz A. Synthetic phenazines for enhanced biogas production from renewable and non-renewable resources. 2014-2016: $330,000. Murray, SA & John, U. Can lateral gene transfer lead to ecological innovation in eukaryotes? The role of saxitoxin in the diversification of Alexandrium. 2012-2014: $230,000. Neilan BA. Australia’s freshwater ecosystems: how microbial diversity and functionality influence harmful cyanobacterial blooms. 2013-2015: $349,000. Thomas T. To eat or not to eat? How symbiotic bacteria manipulate the phagocytic behaviour of their eukaryotic host. 2013-2015: $349,000. Walter MR (APF), Neilan BA, George SC, Summons RE & Schopf JW. Oxygenating the Earth: Using innovative techniques to resolve the timing of the origin of oxygen-producing photosynthesis in cyanobacteria. 2010-2014: $715,000. White, PA. Maintaining fidelity in viral Ribonucleic acid (RNA) polymerases. 2012-2014: $215,000. Wilkins MR. Does phosphorylation regulate the methylation of proteins? 2013-2015: $315,000. Yang, HR. Characterisation of novel gene products that regulate phospholipid metabolism and lipid droplet formation in the yeast saccharomyces cerevisiae. 2012-2014: $310,000. Yang HR & Dawes IW. The role of Fld1p protein in lipid droplet formation and growth in the yeast Saccharomyces cerevisiae. 2013-2015: 285,000. ARC Linkage Project Manefield, MJ, Gooding, JJ & Lam, D. Partner organisations: Coffey Environments Australia Pty Ltd, Dow Chemical (Australia) Limited, Orica Australia Pty Ltd. In situ bioremediation solutions for Australia’s organochlorine contaminated aquifers. 2011-2015: $773,000. Manefield MJ, Marquis CP, Lee MJ, Adrian L & Stening R. Partner organisation: Orica Australia Pty Ltd. Development of an anaerobic bioprocess for hexachlorobenzene destruction. 2013-2015: $164,780. Neilan BA. Partner organisation: Diagnostic Technology P/L. Discovery of bioactive natural substances from uncultured bacteria and their production using photosynthetic reactor technology. 2011-2014: $1,058.000. Neilan BA, Burford MA, Jex AR, Orr PT & Azevedo SM. Partner organisations: South East Queensland Water, Federal University of Rio De Janeiro. Adaptive ecotyping of the toxic cyanobacterium Cylindrospermopsis raciborskii to predict its invasive capacity. 2013-2016: $612,756. Thomas T, Munroe PR & Joseph SD. Partner organisation: Renewed Carbon Pty Ltd. Development of the next generation of organomineral fertilisers utilising domestic and commercial waste products. 2012-2015: 340,000. ARC Linkage Infrastructure and Equipment Facilities Manefield MJ, Paulsen IT, Neilan BA, Gillings MR, Conibeer GJ, Ralph PJ, Anderson IC, Lauro F, Seymour JR, Singh BK, Mazard SL, Uddin A, Bissett AP, Richardson AE, Barrett LG & White RG. Partner organisations: Macquarie University, University of Western Sydney, University of Technology, Sydney, Commonwealth Scientific and Industrial Research Organisation. A time of flight secondary ion mass spectrometer facility for elemental and isotopic imaging of ultra-fine features. 2014: $1,000,000. Wilkins MR, Cavicchioli R, Neilan BA, Scott RJ, Foster PS, Dickson PW, Paulsen IT, Packer NH, Gillings MR, Charles IG, Harry EJ, Djordjevic SP & Whitchurch CB. Expanding the genomic frontier from species to strains and individuals to populations. 2014: $475,000. 57 | ARC Future Fellowship Egan S. Chemical warfare in the marine environment: the role of surface-associated bacteria and their antibiotics. 2013-2017: $753,690. Manefield MJ. Harnessing microbial respiration for pollutant degradation and natural gas production. 2011-2015: $808,000. Morris KV. Is ‘junk DNA’ involved in gene editing in human cells. 2013-2017: $821,640. ARC DECRA Fellowship Lauro, F. The role of deep-sea microorganisms in nutrient cycling in the Southern Ocean. 20122014: $375,000. Voineagu I. Genomic diversity in the human brain: the functional role of expandable DNA repeats. 2014-2016: $315.220. National Health and Medical Research Council Yang HR. The role of seipin in adipocyte development and lipid droplet formation. 20122014: $363,510. Yang HR & Brown AJ. Identification and characterization of novel proteins in endosomal cholesterol transport. 2013-2015: $521,976. Yang HR. The role of phosphatidic acid in lipid storage and obesity. 2014-2016: $479,838. NHMRC Senior Research Fellowship Yang HR. Lipid storage and trafficking in human diseases. 2014-2018: $664,515. NHMRC Training (Postdoctoral) Fellowship Kaakoush N. Australian Based Biomedical Category. 2011-2014: $290,032. Other National Schemes Bioplatforms Australia/CRIS Bioplatforms Australia Research Infrastructure Scheme Emerging Biomolecular Platforms and Informatics Project (shared grant): NHMRC Project Grant Brown AJ. Characterising an important control point in cholesterol synthesis beyond HMG-CoA reductase. 2014-2016: $464,916. School of Biotechnology & Biomolecular Sciences Systems Biology Initiative Component. Wilkins M. 2013-2015: $300,000. Ramaciotti Centre for Gene Function Analysis Component. Wilkins M & Speirs HJ. 20132015: $287,000. Collins AM. Immunoglobulin germline genes, BCR repertoire development and disease susceptibility. An investigation of haplotypic variation between individuals. 2012-2014: $502,215. Crossley M. Transcriptional control of megakaryopoiesis. 2012-2014: $651,010. Crossley M. Transcriptional regulation of globin genes. 2012-2014: $636,325. Foster LJR. Development of an ocular adhesive film with local drug delivery to prevent infection and inflammation in corneal wounds. 2014-2016: $358,447. Lan R, Sintchenko V, Tanaka M & Octavia S. Molecular epidemiology and high resolution surveillance of Salmonella enterica serovar Typhimurium in Australia. 2013-2015: $563,052. Voineagu I. (New Investigator Grant). The role of the neuronal splicing factor A2BP1 in autism spectrum disorders. 2014-2016: $383,447. | 58 Brain Foundation/Research Gifts Program Janitz M. Identifying the transcriptional cause of multiple system atrophy. 2013-2014: $34,000. Brain and Behaviour Foundation/NARSAD Young Investigator Grant Voineagu I. Brain transcriptome sequencing and non-coding RNA characterisation in autism spectrum disorders. 2013: $29,029. Department of Sustainability, Environment, Water, Population and Communities/Australian Antarctic Division Cavicchioli R, Abdool AA, DeMaere MZ, Wilkins D, Willias TJ & Yau S. Monitoring ecosystem stability in model marine-derived Antarctic lake systems. 2012-2014: $97,875. EIF Super Science Project/Bioplatforms Australia Wilkins MR & Systems Biology Initiative. Foundation datasets and technology in the major -omics facilities of NSW. 2010-2014: $2.0M. Gordon and Betty Moore Foundation Thomas T, Kjelleberg S & Steinberg P. Molecular mechanism of bacteria-sponge symbiosis: Have bacteria acquired eukaryotic-like proteins to control their interactions with a host? 2013-2015: $1,292,000. NSW Department of Trade and Investment/ NSW Research Attraction and Acceleration Program - Collaborative Research Infrastructure Scheme Emerging Biomolecular Platforms and Informatics Project (shared grant): Ramaciotti Centre for Gene Function Analysis Component. Wilkins, M. 2013-2015: $100,000. School of Biotechnology & Biomolecular Sciences Systems Biology Initiative Component. Wilkins M. 2013-2015: $102,000. University of New South Wales/CRIS Central Contribution. Wilkins M. 2013-2015: $75,000. International Schemes UNSW/Go8 German Joint Research Cooperation Scheme UNSW Goldstar (ARC) Ballard WJO. Differentiating unconscious and artificial selection. 2014: $40,000. Brown AJ. Uncovering new programs of regulation in sterol synthesis. 2014: $40,000. Morris KV. Is it possible to parasitise human immunodeficiency virus and drive it towards a symbiotic state in human cells? 2014: $40,000. UNSW Goldstar (NHMRC) Kaakoush NO & Mitchell HM. Does faecal transplantation lead to improved outcomes for patients with ulcerative colitis by modulating their intestinal microbiota. 2014: $40,000. Kaakoush NO, Lemberg DA & Mitchell HM. Investigation of the interplay between host genetics, immune response and the intestinal microbiota in children newly diagnosed with Crohn’s disease and ulcerative colitis. 2014: $40,000. Leshchynska I & Sytnyk V. Molecular mechanisms of neurotransmission abnormalities induced by disruptions of the functions of the neural cell adhesion molecule in bipolar disorder and schizophrenia. 2014: $40,000. Pearson R & Crossley M. The insulin-sensitising factor adipolin: a new target for metabolic health. 2014: $40,000. Faculty of Science Silver Star (ARC) Neilan BA & Muenchhoff J. The regulation and role of toxin production in cyanobacteria. 20132014: $18,750. Foster LJR. What gives Chitosan its antimicrobial properties? - Relating Polymer Chain Conformation to Bactericidal Activity. 2014: $30,000. UNSW Internal Schemes Morris KV. Do non-coding ribonucleic acids function as cellular sensors to the outside environment in human cells? 2014: $30,000. Major Research Equipment Infrastructure Initiative (MREII) Brown AJ & Yang HR. Microscale Thermophoresis Monolith NT.115. 2014: $152,000. Faculty of Science Silver Star (NHMRC) Nil Cavicchioli R, Charles IG, Dickson PW, Djordjevic SP, Foster PS, Gillings, MR, Harry EJ, Neilan BA, Packer NH, Paulsen IT, Scott RJ, Whitchurch CB & Wilkins M. Expanding the Genomic Frontier – From Species to Strains and Individuals to Populations. 2014: $180,000. 59 | Faculty of Science Research Grant Burns BP. A day in the life of a stromatolite: innovative metaproteomic analyses of early Earth microbial communities. 2014: $12,000. Ferrari BC. Culture independent and dependent approaches to characterise microbial diversity in Mitchell Peninsula, Antarctica: A biodiversity “hot spot”. 2014: $12,000. Galea AM. Investigating the interaction of cisplatin and cisplatin analogues with different human genomic DNA targets. 2014: $10,000. Janitz M. Investigating the role of hemoglobin genes overexpression in a-synuclein aggregation. 2014: $10,500. Lutze-Mann L. Targeting SCAP as a novel cancer chemotherapeutic. 2014: $8,000. Murray V. The precise location of DNA adducts caused by the anti-tumour drug Cisplatin in the entire human genome. 2014: $10,000. Waters PD. Long non-coding RNAs: shaping the evolution of mammalian transcriptomes and dosage compensation. 2014: $12,000. Whitaker NJ. Exosome medicated cell signalling in Human Papillomavirus (HPV) associated cancer. 2014: $12,000. Zhang L. Characterisation of the biological activities of zonula occludens toxin produced by Campylobacter concisus. 2014: $12,000. Faculty of Science Early Career Researcher Grant Erce M. Cracking the post-translational modification code of the yeast Npl3 protein. 2014: $ 9,635. Hart-Smith G. No project title. 2014: $9,635 Octavia S. Adaptation of Salmonella to different hosts and environments: a genomic and transcriptomic illumination. 2014: $9,635. | 60 SJTU-UNSW Collaborative Research and Development Fund Brown AJ, Du X, Li B, Zhang D & Yang HR. Lipid metabolism and its implications in plant and human development. 2013-2014: $14,500. Burns B, Deng Z, He Y, Li Z, Neilan BA, Xu P, Zhang Z & Manefield M. Establishing a conjoint SJTU-UNSW research initiative on water and wastewater microbiology. 2013-2014: $13,500. Gonzalez P, Huang D, Munroe PR, Nielsen S, Yang H, Ye J, Zhang L, Zhang R & Thomas T. Improving food production: Evaluation of biochar for stimulating the microbial nitrogen cycle in agricultural soil Improving food production: Evaluation of biochar for stimulating the microbial nitrogen cycle in agricultural soil. 2013-2014: $11,000. 2014 Publications Aandahl RZ, Stadler T, Sisson SA & Tanaka MM, 2014, ‘Exact vs. approximate computation: reconciling different estimates of Mycobacterium tuberculosis epidemiological parameters’, Genetics, 196(4): 1227-1230. Aislabie JM, Novis PM & Ferrari BC, 2014, ‘Microbiology of eutrophic (ornithogenic and hydrocarboncontaminated) soil’, in Cowan DA (ed), Antarctic Terrestrial Microbiology, Springer, Heidelberg, ch. 6: 91-113. Alvin A, Miller KI & Neilan BA, 2014, ‘Exploring the potential of endophytes from medicinal plants as sources of antimycobacterial compounds’, Microbiological Research, 169: 483-495. Andrisic L, Collinson EJ, Tehlivets O, Perak E, Zarkovic T, Dawes IW, Zarkovic N & Gasparovic AC, 2014, ‘Transcriptional and antioxidative responses to endogenous polyunsaturated fatty acid accumulation in yeast’, Molecular and Cellular Biochemistry, 399(1-2): 27-37. Ballester B, Medina-Rivera A, Schmidt D, GonzàlezPorta M, Carlucci M, Chen X, Chessman K, Faure AJ, Funnell APW, Goncalves A, Kutter C, Lukk M, Menon S, McLaren WM, Stefflova K, Watt S, Weirauch MT, Crossley M, Marioni JC, Odom DT, Flicek P & Wilson MD, 2014, ‘Multi-species, multitranscription factor binding highlights conserved control of tissue-specific biological pathways’, eLife, 3:e02626. Ballestriero F, Daim M, Penesyan A, Nappi J, Schleheck D, Bazzicalupo P, Di Schiavi E & Egan S, 2014, ‘Antinematode activity of violacein and the role of the insulin/IGF-1 pathway in controlling violacein sensitivity in Caenorhabditis elegans’, PLoS ONE, 9(10): e109201. Barnes RJ, Bandi RR, Chua F, Low JH, Aung T, Barraud N, Fane AG, Kjelleberg S & Rice SA, 2014, ‘The roles of Pseudomonas aeruginosa extracellular polysaccharides in biofouling of reverse osmosis membranes and nitric oxide induced dispersal’, Journal of Membrane Science, 466: 161-172. Barraud N, Kelso M, Rice S & Kjelleberg S, 2014, ‘Nitric oxide: a key mediator of biofilm dispersal with applications in infectious diseases’, Current Pharmaceutical Design, 21(1): 31-42. Barraud N, Moscosco JA, Ghigo JM & Filloux A, 2014, ‘Methods for studying biofilm dispersal in Pseudomonas aeruginosa’, in Filloux A & Ramos J-L (eds), Methods in Molecular Biology, vol. 1149, ch. 49: 643-651. Bart MJ, Harris SR, Advani A, Arakawa Y, Bottero D, Bouchez V, Cassiday PK, Chiang C-S, Dalby T, Fry NK, Gaillard ME, van Gent M, Guiso N, Hallander HO, Harvill ET, He Q, van der Heide HGJ, Heuvelman K, Hozbor DF, Kamachi K, Karataev GI, Lan R, Luty ska A, Maharjan RP, Mertsola J, Miyamura T, Octavia S, Preston A, Quail MA, Sintchenko V, Stefanelli P, Tondella ML, Tsang RSW, Xu Y, Yao S-M, Zhang S, Parkhill J & Mooi FR, 2014, ‘Global population structure and evolution of Bordetella pertussis and their relationship with vaccination’, mBio, 5(2): e01074-14. Basha J, Iwasenko JM, Robertson P, Craig ME & Rawlinson WD, 2014, ‘Congenital cytomegalovirus infection is associated with high maternal socio-economic status and corresponding low maternal cytomegalovirus seropositivity’, Journal of Paediatrics and Child Health, 50(5): 368-372. Beard MR, Ffrench R, Gowans EJ, Helbig KJ, Eyre NM, Douglas MMW, Grebely J, Ahlenstiel G, Locarnini S, George J, Shackel NA, White PA, Thompson AJ & Drummer HE, 2014, ‘A summary of the 20th International Symposium on Hepatitis C Virus and Related Viruses’, Gastroenterology, 147(1): e1-e4. Beckmann S & Manefield M, 2014, ‘Acetoclastic methane formation from Eucalyptus detritus in pristine hydrocarbonrich river sediments by Methanosarcinales’, FEMS Microbiology Ecology, 90(3): 587-598. Bernardo BC, Gao X-M, Tham YK, Kiriazis H, Winbanks CE, Ooi JYY, Boey EJH, Obad S, Kauppinen S, Gregorevic P, Du X-J, Lin RCY & McMullen JR, 2014, ‘Silencing of miR-34a attenuates cardiac dysfunction in a setting of moderate, but not severe, hypertrophic cardiomyopathy’, PLoS ONE, 9(2): e90337. 61 | Bernardo BC, Nguyen SS, Winbanks CE, Gao X-M, Boey EJH, Tham YK, Kiriazis H, Ooi JYY, Porrello ER, Igoor S, Thomas CJ, Gregorevic P, Lin RCY, Du X-J & McMullen JR, 2014, ‘Therapeutic silencing of miR-652 restores heart function and attenuates adverse remodeling in a setting of established pathological hypertrophy’, The FASEB Journal, 28(12): 5097-5110. Bissett A, Abell GCJ, Brown M, Thrall PH, Bodrossy L, Smith MC, Baker GH & Richardsson AE, 2014, ‘Landuse and management practices affect soil ammonia oxidiser community structure, activity and connectedness’, Soil Biology and Biochemistry, 78: 138-148. Blaber EA, Dvorochkin N, Torres ML, Yousuf R, Burns BP, Globus RK & Almeida EAC, 2014, ‘Mechanical unloading of bone in microgravity reduces mesenchymal and hematopoietic stem cell-mediated tissue regeneration’, Stem Cell Research, 13(2): 181-201. Bone SM, Hasick NJ, Lima NE, Erskine SM, Mokany E & Todd AV, 2014, ‘DNA-only Cascade: a universal tool for signal amplification, enhancing the detection of target analytes’, Analytical Chemistry, 86(18): 9106-9113. Bone SM & Todd AV, 2014, ‘MNAzymes provide a universal mechanism for triggering DNAzyme synthesis cascades’, Chemical Communications, 50(87): 13243-13246. Brown MV, Ostrowski M, Grzymski JJ & Lauro FM, 2014, ‘A trait based perspective on the biogeography of common and abundant marine bacterioplankton clades’, Marine Genomics, 15: 17-28. | 62 Burford MA, Davis TW, Orr PT, Sinha R, Willis A & Neilan BA, 2014, ‘Nutrient-related changes in the toxicity of field blooms of the cyanobacterium, Cylindrospermopsis raciborskii’, FEMS Microbiology Ecology, 89(1): 135-148. Burgos-Portugal JA, Mitchell HM, Castaño-Rodríguez N & Kaakoush NO, 2014, ‘The role of autophagy in the intracellular survival of Campylobacter concisus’, FEBS Open Bio, 4: 301-309. Byrne FL, Poon IKH, Modesitt SC, Tomsig JL, Chow JDY, Healy ME, Baker WD, Atkins KA, Lancaster JM, Marchion DC, Moley KH, Ravichandran KS, Slack-Davis JK & Hoehn KL, 2014, ‘Metabolic vulnerabilities in endometrial cancer’, Cancer Research, 74(20): 5832-5845. Cannon MJ, Griffiths PD, Aston V & Rawlinson WD, 2014, ‘Universal newborn screening for congenital CMV infection: what is the evidence of potential benefit?’, Reviews in Medical Virology, 24(5): 291-307. Carter A, Lai YW, Pang CNI, Campbell LT, Truong M, Chen S & Wilkins M, 2014, ‘Understanding synergy between iron chelators and antifungals using gene co-expression networks’, MYCOSES, 57: 107. Castaño-Rodriguez N, Kaakoush NO & Mitchell HM, 2014, ‘Pattern-recognition receptors and gastric cancer’, Frontiers in Immunology, 5:336. Castaño-Rodriguez N, Kaakoush NO, Goh K-L, Fock KM & Mitchell HM, 2014, ‘The NODlike receptor signalling pathway in helicobacter pylori infection and related gastric cancer: a case-control study and gene expression analyses’, PLoS ONE, 9(6): e98899. 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