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ANNUAL REPORT 2003

4983IMBAnnualReport1-36 12/7/04 10:14 AM

The IMB acknowledges and thanks our supporters and partners

Recommended further reading in conjunction with this Annual Report

• IMBcom Annual Report 2003• SRC for Functional and Applied Genomics Annual Report 2003• ARC for Bioinformatics Annual Report 2003


Creativity, motivation and intellectualfreedom are the vital components

of scientific discovery and technologicalprogress, and underpin the research

philosophy of the Institute for Molecular Bioscience.

Our research mission is to understand the informationcontained in our genes and proteins - the very foundation

of our existence and our health.

By understanding how and why humans and animalsdevelop the way they do, we will be better equipped to

understand the basis of our differences and how and whythings go wrong in disease states like cancer.

In time, our collaborative research will lead to improvedtherapies and diagnostics enhancing our ability to combat

common diseases and genetic disorders.

It will also give rise to new ideas, technologies andknowledge-based industries to improve the health and

quality of life of future generations.

"Far better it is to dare mighty things, to win glorious triumphs even though checkeredby failure, than to rank with those poor spirits who neither enjoy nor suffer much

because they live in the grey twilight that knows neither victory nor defeat." Theodore Roosevelt


01 1. Chair’s Report

02 2. Organisational Chart

03 3. Director’s Report

06 4. IMB Advisory Board

10 5. IMB Year Highlights

15 6. IMB Research

17 Mammalian Genomics and Genetic ProgrammingTim BaileyKevin BurrageSteve BarkerSean GrimmondJennifer HallinanGeoff McLachlanJohn MattickMark Ragan

37 Organogenesis, Tissue Damage and RegenerationDavid HumeStuart KelliePeter KoopmanMelissa LittleGeorge MuscatJoe RothnagelRick SturmBrandon WainwrightMichael WatersCarol Wicking

65 Cell Architecture and DynamicsJohn HancockBen HankamerAlisdair McDowallRob PartonJennifer StowRohan TeasdaleAlpha Yap

85 Chemical and Structural GenomicsPaul AlewoodRob CaponDavid CraikDavid FairlieJeffrey GormanBostjan KobeRichard LewisJenny MartinMark Smythe

113 Issues in Genetic and Cellular Medicine and TechnologiesWayne Hall

117 7. Community Engagement and Awareness

118 8. Australian Collaborative Research

124 9. IMB Graduate Program

128 10. IMB Speakers

132 11. IMB Systems andAdministration

134 12. Glossary of Terms

136 13. Financial Statements

ContentsPAGE PAGE


IMB ANNUAL REPORT 2003 PAGE 01

CHAIR’S REPORTThe Institute for Molecular Bioscience (IMB) is oneof The University of Queensland’s premier researchinstitutes and I am delighted with the manyachievements detailed in this publication.

In May 2003 the IMB, along with CSIRO, tookpossession of the Queensland Bioscience Precinct,situated at the St Lucia Campus. This $105 millionstate-of-the-art facility has placed the IMB – andQueensland scientific research – firmly on the map.

Biological technology in its many forms is one of themajor growth areas for the future. Since itsestablishment in 2000, the IMB has earned areputation as one of our region’s leading researchinstitutes. The IMB is playing an increasinglyimportant role in providing the foundation forQueensland's economic development and definingthe future high technology industrial base of south-east Queensland.

The superb Queensland Bioscience Precinct bringstogether 700 scientists from the IMB and CSIRO –this collaborative research environment is ensuringmajor research advancements in biological, medicaland agricultural sciences.

I would like to thank The Atlantic Philanthropies, theFederal and Queensland governments, CSIRO,

research industry and private partners for their visionand support in helping to bring the QueenslandBioscience Precinct to fruition. Their funding hashelped to create a climate in which investment inbiotechnology is encouraged. We can see thisapproach already paying dividends with theestablishment of a series of spin-off companies thatwill create many new jobs.

The IMB is part of a strategic cluster of researchexcellence at UQ - the Australian Institute forBioengineering and Nanotechnology (AIBN) and theQueensland Brain Institute (QBI) currently underdevelopment are modelled on the successful IMB.

As Chair of the IMB Board, I would like to express my sincere thanks to the members of the IMB Boardand Scientific Advisory Board for the contribution oftheir time, skills and energy to manage and developthe Institute.

Professor John Hay ACVice-ChancellorThe University of Queensland

Professor John Hay AC1.


Organisational Chart

2.

University of Queensland Senate UQ Holdings Pty Ltd

Vice-Chancellor/IMB BoardIMB Board

Senior Deputy Vice-Chancellor

Institute Director IMBcom Pty LtdIMB Scientific Advisory Board

Deputy Director(Research)

Head, Division of Genomics & Computational

Biology

Head, Division of MolecularGenetics &

Development

Head, Division of Molecular Cell Biology

Head, Division of Chemical &

Structural Biology

Office of PublicPolicy & Ethics

GraduateEducation Office

Marketing &Communications

Administration

InformationTechnology

Services

LaboratoryServicesResearch Groups (32 groups as of February 2004)

Deputy Director(Systems & Administation)



DIRECTOR’S REPORT2003 was a milestone year for the IMB. It was theyear that our 480 staff and students, who hadpreviously been housed in six different buildingsacross the University of Queensland were broughttogether under one roof, at the QueenslandBioscience Precinct (QBP).

This outstanding facility, located at the University ofQueensland’s St Lucia site, was officially opened byQueensland Premier Mr Peter Beattie and FederalMinister for Education Dr Brendan Nelson in May 2003.The opening was accompanied by a major scientificsymposium featuring the research of IMB and that of anumber of our scientific advisors from Australia,Japan, Singapore, the United States and Europe.

The state-of-the art laboratories and facilitiesrepresent a significant investment by both the Stateand Federal Governments in the future of bioscienceand biotechnology research in Australia. The onus isnow on IMB researchers to capitalise on thisopportunity to propel Australian research to theforefront by conducting innovative and paradigm-shifting science. To this end we are developing asuite of integrated core programs with the ability tochange the international landscape in molecularbioscience. These programs are (1) MammalianGenomics and Genetic Programming, (2)Organogenesis, Tissue Damage and Regeneration, (3)Cell Architecture and Membrane Dynamics, (4)Chemical and Structural Genomics, and (5) Issues inGenetic and Cellular Medicine and Technologies.

The relocation to our new facilities has allowedfurther growth and development of IMBs intellectualand physical resources with several new researchgroups commencing operations. Professor RobCapon joined IMB to head the new Centre forMolecular Biodiversity, which seeks to developdiscover and develop natural compounds that havebioactivity. Professor Jeff Gorman, an IMB-CSIROjoint appointment, is establishing a joint IMB-CSIROProteomics Laboratory. This key facility will promote

synergies with CSIRO's Divisions of LivestockIndustries and Plant Industry, with whom we sharethe QBP.

We have also substantively increased our strength incell biology by the appointments of Professor JohnHancock, Professor Rob Parton, Professor MikeWaters, and Associate Professor Alpha Yap, all ofwhom had previously had joint appointments withIMB but were located in other departments of the University.

I am also delighted to report that the University ofQueensland has appointed Professor David Weisbrot,Head of the Australian Law Reform Commission inSydney, Professor Nic Nicola, Assistant Director ofthe Walter and Eliza Hall Institute of MedicalResearch in Melbourne, Professor YoshihideHayashazaki, RIKEN Genomic Sciences Center inTokyo, and Professor Gene Myers, University ofCalifornia at Berkeley, as Honorary Professors at theInstitute for Molecular Bioscience. We thank themfor honouring us by accepting this appointment.

In other developments, IMB is the lead partner in theAustralian Research Council's Centre forBioinformatics, headed by Professor Mark Ragan.IMB has also further developed its very importantstrategic research alliance with RIKEN GenomeSciences Center in Tokyo, an alliance that wassymbolically recognised by RIKEN last August whenthe IMB was presented with RIKEN’s first distributedcopy of the Mouse Genome Encyclopedia.

IMB also attracted significant funding from the USNational Institutes of Health (NIH) through majorgrants to Professors John Hancock and Rob Parton,and to Associate Professor Jenny Stow andProfessor David Hume, for their work to understandthe dynamics of the cell surface and the regulation ofimportant biological functions in cancer andinflammation. In addition a consortium of scientistsfrom around Australia, led by Associate ProfessorMelissa Little, was awarded a major NIH grant fortheir project in kidney regeneration.

Professor John Mattick AO3.


DIRECTOR’S REPORT CONTINUED

Our success in the national competitive ARC andNHMRC schemes for funding in 2004 was alsopleasing. We were awarded seven Discovery, twoLinkage and one LIEF grant in the ARC round, with atotal value of approximately five million dollars, andwe were successful in 15 NHMRC project grantapplications, with a total value of nearly six milliondollars. In addition, Professor John Hancock wasawarded an NHMRC Principal Research Fellowshipand Dr Rohan Teasdale was awarded an NHMRC R DWright Career Development Fellowship, as well as aUniversity Research Excellence Award. NHMRCIndustry Fellowships were awarded to Norelle Dalyand Brownyn Battersby.

In my last Director’s Report I bade farewell toProfessor Peter Andrews, who resigned from theIMB as a Co-Director at the end of 2002. The newCEO of IMBcom, Dr Peter Isdale, joined us early in2003 and he and Dr Peter Riddles have workedtirelessly to identify and develop the manycommercial opportunities arising from the Institute’sresearch, assisting with grant applications, providingadvice and guidance to students and facilitatingsmooth relations between stakeholders and the IMB.It has been a pleasure working alongside theIMBcom team over the past year and I look forwardto many productive years to come.

I am delighted to report that Peter Andrews washonoured for his contributions to the development ofa research-based pharmaceutical industry byappointment as an Officer in the Order of Australia(AO) in the Australia Day Honours list. Peter has alsobeen appointed to the new post of Chief Scientist ofQueensland. In addition, the Vice Chancellor andChair of the IMB Board, Professor John Hay, wasappointed as a Companion in the Order of Australia,this nation’s highest honour, for his enormouscontributions to the development of this and otheruniversities, including the development of IMB, forwhich we are truly grateful.

I would like to thank the IMB's senior executiveteam, in particular Professor Brandon Wainwright(Deputy Director Research) who is responsible foroverseeing the research management of the

Institute, and Dr Ian Taylor (Deputy Director Systemsand Infrastructure) who is responsible for themanagement of the Institute’s administration andsupport facilities, and whose experience was criticalin the design of the building and its exceptionalfeatures. Additionally I thank IMB's Division HeadsProfessors Mark Ragan, George Muscat, JohnHancock, Paul Alewood, as well as Professor DavidHume, Director of the ARC Special Research Centrefor Functional and Applied Genomics, and ProfessorWayne Hall, Director of the Institute’s Office of PublicPolicy and Ethics for their invaluable contributions tothe development and running of the Institute. Wealso welcome Dr Lindsay Hood, who will manage theInstitute’s high performance computing andinformation technology systems.

Finally, I would like to thank the Vice ChancellorProfessor John Hay, the Senior Deputy ViceChancellor Professor Paul Greenfield, the Deputy ViceChancellor (Research) Professor David Siddle and ourother senior colleagues at the University ofQueensland for their ongoing support of the Institute.We are also fortunate to have very experienced andcommitted IMB Board and Scientific Advisory Boardmembers, many from interstate and overseas, whogive of their extremely valuable time to providegovernance, advice on strategic development, andcritical review of the performance of the Institute. Myfinal thanks go to the State and Federal governments,without whom the wonderful new facilities we nowoccupy would have remained a dream.

We look forward to demonstrating to the communitythat their investment is well placed and will yieldlarge dividends in terms of our contributions to worldknowledge in biomedical science, and to thedevelopment of knowledge-based industries inQueensland and Australia.

Professor John Mattick AODirectorInstitute for Molecular Bioscience


We look forward todemonstrating to thecommunity that theirinvestment in us is wellplaced and will yieldlarge dividends in termsof our contributions toworld knowledge inbiomedical science, andto the development ofknowledge-basedindustries in Queenslandand Australia.



IMB Advisory Board

4.

Professor John Hay AC (Chair)(Pictured 1)

Professor John Hay has been Vice-Chancellor andPresident of The University of Queensland since 1996.He is a graduate of the University of Western Australiaand Pembroke College, Cambridge where he held aHackett Research Fellowship. He held the Chair ofEnglish and was Head of the Department in theUniversity of Western Australia where he was alsoDeputy Chair of the Academic Board. At MonashUniversity, he was Dean of Arts and Chair of theNational Key Centre for Australian Studies and wasthen appointed Senior Deputy Vice-Chancellor ofMonash University. In 1992 Professor Hay wasappointed Vice-Chancellor and President of DeakinUniversity in Victoria. In 2002 Professor Hay wasappointed to the Higher Education Review ReferenceGroup. Professor Hay was Chair of the Group of Eight,Australia's leading research-intensive universitiesfrom January 2002 to May 2003. He is currently Chairof the Australian Universities Teaching Committee, andUniversitas 21, a consortium of international research-intensive universities.

Professor John Mattick AO (Director)(Pictured 2)

Professor Mattick was responsible for thedevelopment of the IMB with Professor PeterAndrews. In 1988 he was appointed the FoundationProfessor of Molecular Biology and Director of theCentre for Molecular Biology and Biotechnology atthe University of Queensland. The Centre wassubsequently designated a Special Research Centreof the Australian Research Council (1991-1999) andwas re-named the CMCB. He was responsible for thedevelopment of one of the first recombinant DNA-based vaccines, and was the recipient of the 1989Pharmacia-LKB Biotechnology Medal from the

Australian Biochemical Society, and the inaugural(2000) Eppendorf Achievement Award from the LorneGenome Conference. Professor Mattick is a memberof the Australian Health Ethics Committee and theResearch Committee of the NHMRC. He is a foundationmember of the recently established InternationalMolecular Biology Network (Asia-Pacific), was afoundation member of the Board of ANGIS (theAustralian National Genome Information Service) from1991-2000 and is currently a member of the Board ofthe Australian Proteome Analysis Facility.

Mr Paul Fennelly(Pictured 3)

Appointed as Director-General, Department of StateDevelopment and Co-ordinator General of Queenslandin February 2002. Mr Fennelly has recently beenappointed as Director-General of the newly establishedDepartment of State Development and Innovation. TheDepartment is responsible for driving the economicdevelopment of Queensland and the delivery of theGovernment's Smart State Strategy.

The Department's activities involve:• Major Projects & Infrastructure• Investment Attraction• Public Private Partnerships• Industry Development• Innovation• Small Business

From January 2000 to January 2002, Mr Fennelly wasthe State Director of Australian Industry Group,Victoria's largest business organisation, representingapproximately 6,000 companies. Mr Fennelly wasalso the Queensland Director of MTIA / AustralianIndustry Group from 1993 - 1999. Mr Fennelly holdsdegrees in Law and Arts, as well as a GraduateDiploma in Industrial Law.



The IMB is part of a strategic cluster of researchexcellence at UQ - the Australian Institute forBioengineering and Nanotechnology (AIBN) and theQueensland Brain Institute (QBI) currently underdevelopment are modelled on the successful IMB.

Members of the IMB Advisory Board: Professor John Hay AC, Professor John Mattick AO, Mr Paul Fennelly,Mr Scott Flavell, Professor Frank Gannon, Professor Paul Greenfield, Dr Russell Howard, Dr Peter Isdale, Ms Helen Lynch AM, Professor Mick McManus, Mr Ross Rolfe, Sir Sydney Schubert.

1 2 3 4

5 6 7 8

9 10 11 12


Mr Scott Flavell(Pictured 4)

Scott Flavell has been the Director-General of theDepartment of Innovation and Information Economy,Sport and Recreation Queensland since 3 June 2002.Prior to his current position, Scott was the ExecutiveDirector of the Office of Energy. He has worked asan economist and policy advisor in senior positions inthe Commonwealth and Queensland Governments forthe past 18 years, including Queensland Treasury, theDepartment of the Premier and Cabinet, theDepartment of the Prime Minister and Cabinet andthe Department of Finance.

Professor Frank Gannon(Pictured 5)

Since 1994, Frank Gannon has been the ExecutiveDirector of the European Molecular BiologyOrganisation (EMBO), Secretary-General of theEuropean Molecular Biology Council (EMBC), andSenior Scientist at the European Molecular BiologyLaboratory (EMBL) in Heidelberg, Germany. He is alsoSenior Editor of EMBO Reports and Associate Editor ofthe EMBO Journal. He serves on a number of scientificadvisory boards at institutes throughout the world.

Professor Paul Greenfield (Pictured 6)

Professor Greenfield is Senior Deputy Vice-Chancellor of the University of Queensland. Aftergraduating Bachelor of Engineering, first-classhonours in chemical engineering, from the Universityof New South Wales (UNSW), Professor Greenfieldworked in the private sector before completing a PhDat UNSW. He worked at CSIRO before winning athree-year fellowship to the U.S. In 1975, he joinedthe University of Queensland as a lecturer inchemical engineering and a decade later becameHead of Department and then Pro-Vice-Chancellor(Physical Sciences and Engineering) before beingappointed an inaugural Executive Dean in 1997.Currently, he chairs the Scientific AdvisoryCommittee overseeing the $5.2 million Moreton Bayand Brisbane River Wastewater Management Study(since 1994); the Waste Technical Working Group,Basel Convention (since 1995); and the AdvisoryBoard of I.P. Australia (since 1999). He is also aDirector of several University companies including

UniQuest Pty Ltd. In 1995, he won the ChemecaMedal, awarded jointly by the Institution of ChemicalEngineers and the Institute of Engineers Australia foroutstanding contribution to the profession.

Dr Russell Howard(Pictured 7)

Dr. Howard is Maxygen's Chief Executive Officer andone of the company's co-founders (founded in 1997).Originally trained in biochemistry and chemistry, Dr.Howard has spent over 20 years studying infectiousdiseases, primarily malaria. Before joining Maxygen,Dr. Howard served as the President and ScientificDirector of Affymax Research Institute, an instituteemploying combinatorial chemistry and highthroughput target screening to discover drug leads.Prior to joining Affymax, Dr. Howard held variousresearch positions at DNAX Research Institute andthe National Institutes of Health. Dr.Howard receivedhis Ph.D. in biochemistry from Melbourne University,Australia. In addition to numerous patents, Dr.Howard has over 140 publications in peer-reviewedjournals. Today, Maxygen is focused primarily ondevelopment of protein pharmaceutical drugs, withother therapeutics programs in vaccines. Maxygenspun-out its chemicals manufacturing division,Codexis, in 2002 and retains its wholly-ownedAgbiotech subsidiary, Verdia.

Dr Peter Isdale(Pictured 8)

Peter Isdale was appointed Chief Executive Officer ofIMBcom Pty Ltd in March 2003. He spent 15 years asa marine scientist before trading his wetsuit for abusiness suit at the Australian Institute of MarineScience (AIMS), the country's marine nationalscience agency, where he had been a PrincipalResearch Scientist who is the author or co-author ofmore than 30 papers in his special field of research.As the Business Director and Executive at AIMS, Dr Isdale directed the strategic development ofAIMS' business and commercial interests, includinglicensing and company spinouts, and managed theInstitute's legal and intellectual property affairs. DrIsdale has had 17 years of directorship on companyboards, and a record of achievement in the operation


and governance of both private, public and ASX-listed companies in Australia, Asia and the PacificRim. He is a Member of the Australian Institute ofCompany Directors, and currently holds the positionsof non-executive director, Great Barrier ReefResearch Foundation, non-executive chairman ofThe Wetlands and Grasslands Foundation, SeniorFellow, Chaiyong Limthongkul Foundation, Bangkok,Thailand and Adjunct Professor, Department of LandDevelopment and Environmental Planning, School ofArchitecture, Texas A&M University.

Ms Helen Lynch AM(Pictured 9)

Helen Lynch AM is Deputy Chairman of Pacific BrandsLimited, Chairman of the Sydney Symphony Orchestra,and a Non-Executive Director of Southcorp Limited,Westpac Banking Corporation. Helen Lynch's previousdirectorships include Chairman of OPSM Group Limiteduntil 2003, Director of Coles Myer Ltd.1995-2003,Chairman of the Superannuation Funds ManagementCorporation of South Australia 1995-2000. Currentinvolvements include member of Advisory BoardCaliburn Partnership and External Advisor MallesonsStephen Jaques. External Board Member Institute ofMolecular Bio-Science University of Queensland.Helen Lynch had a distinguished career, spanning 35 years, in the Banking and Finance Industry atWestpac Banking Corporation including being amember of the Bank's executive committee. She leftWestpac in 1994 and was appointed a Non-ExecutiveDirector of the Bank in 1997. In 1990 Helen Lynch wasthe Bulletin/Qantas Business Woman of the Year.Helen was made a member of the Order of Australiain 1994 for services to the Banking and FinanceIndustry. In 2003, Helen received the CentenaryMedal in recognition of her service to Australia:Society in Business Leadership.

Professor Mick McManus(Pictured 10)

In 1998, Mick McManus was appointed ExecutiveDean of the Faculty of Biological & ChemicalSciences and prior to this he was Head of theDepartment of Physiology & Pharmacology from 1993to 1997. Mick's initial appointment to the universitywas as Foundation Professor of Pharmacology and

he was President of the Australasian Society ofClinical & Experimental Pharmacologists &Toxicologists from 2000 - 2001. He came to theUniversity from a National Health & MedicalResearch Council Principal Research Fellowshipposition in the Department of Clinical Pharmacologyat Flinders University in Adelaide. He was initiallytrained as a pharmacist at Curtin University ofTechnology and completed his PhD at the Universityof Western Australia in 1978. Mick has held researchpositions at the Royal Postgraduate Medical School,University of London and the National CancerInstitute, National Institutes of Health in Bethesda,Maryland, USA. He continues to have a strongresearch interest in the area of xenobioticmetabolism, especially on the role humansulfotransferases play in this process.

Mr Ross Rolfe(Pictured 11)

Ross Rolfe was appointed the Director-General of theDepartment of State Development and Co-ordinatorGeneral in 1998. In 1996, he was the Director-Generalof the Department of Environment and Heritage,under the previous Labor Government. Mr Rolfe has abackground in issues relating to land management,the energy industry and the environment. Mr Rolfe’sexpertise and knowledge has been utilised by suchcompanies as Chevron Asiatic, PowerlinkQueensland, BHP - Coal Division, industryassociations and a range of development companies.

Sir Sydney Schubert(Pictured 12)

Sydney Schubert has had a career spanning 40 yearswith the Queensland Government, including Co-ordinator General and Director-General between1976 and 1988. He was Executive Chair of DaikyoGroup of Companies, Australia and New Zealand,from 1988 to 2000. Currently he is Chair of the CRC forGreat Barrier Reef World Heritage Area, CRC forTropical Rainforest Ecology and Management andCRC for Torres Strait. He is also Director of theAustralian Tropical Forest Institute and AustralianCanopy Crane.



IMB Year Highlights

5.

The highlights for 2003 were varied from outstandingresearch achievements, relocation to our new homein the Queensland Bioscience Precinct and visitsfrom internationally acclaimed researchers.

FACILITIES

Opening of the Queensland BiosciencePrecinctThe opening of the Queensland Bioscience Precinct(QBP) and subsequent relocation of the IMB into itsnew home was a watershed for the emergence ofQueensland as a regional and international centre foradvanced bioscience research.

Opened by the Federal Minister for Education,Science and Training Dr Brendan Nelson andQueensland Premier Peter Beattie on 21 May 2003,the QBP brings together for the first time under oneroof all aspects of the IMB.

The Precinct offers IMB research and support staff awork environment the equal, if not better, than anyother research facility in the nation.

UQ's equipment sharpening the cutting edgeThe ability of IMB and UQ researchers to solveextremely difficult molecular problems has taken agiant leap forward with the installation of Australia'smost powerful X-ray crystallography instrument.

This new weapon in the research arsenal of IMB andUQ will help in the fight against many humandiseases such as cancer, diabetes and Alzheimer's toname a few.

The high resolution and exquisite sensitivity of thisnew piece of equipment can only be bettered by asynchrotron facility, which at a cost of over $150million and the size of a large football field, iscurrently unavailable to Australian researchers.

New building allows new appointmentsTwo internationally recognised scientists migratednorth to join the IMB and further their researchexploring Australia's biodiversity and setting up aworld class proteomics facility.

Professor Jeff Gorman (Molecular and CellularProteomics) and Professor Rob Capon (Centre forBiodiversity) were attracted by the leading edgefacilities and collaborative opportunities available atIMB and the QBP.

Prior to joining IMB, Jeff Gorman was a seniorprincipal research scientist with CSIRO/TheBiomolecular Research Institute in Victoria. He is onthe editorial boards of several leading journals in thefield of protein and proteomic research.

Rob Capon was formerly a Professor of Chemistry atthe University of Melbourne where he led the Marineand Natural Products Research Group.

(Left) IMB’s Jenny Martin and the new X-Ray Crystallography instrument.(Right) New appointments Jeff Gorman and Rob Capon.



RESEARCH

Anti-obesity gene flexes its muscleA critical target in the war against obesity, whichmay lead to improved treatments, was identified in aworld first by a research team from the IMB.

Obesity has reached epidemic proportions as poordiet and sedentary living have equalled tobacco asthe leading cause of death in the US with Australiaexpected to follow this trend.

George Muscat and his research team showed thatactivation of the gene PPAR-delta in muscle cellsincreases lipid metabolism and the production of HDLor 'good' cholesterol.

The nature of venom reviewed in NatureCancer signal localisedIMB scientists John Hancock and Rob Parton brokenew ground this year with their studies on the rassignalling pathway and provided novel insights as tohow a cell receives information from its environmentand transmits it to the nucleus.

Ras signalling is perturbed in many forms of cancerand essential for the normal functioning ofmammalian cells. The Hancock and Parton team,recent recipients of an NH&MRC Program Grant,demonstrated that ras signalling occurred inlocalised microdomains throughout the plasmamembrane. Differential spatial localisation within thisframework can likely account for the distinct signaloutputs from Ras proteins.

This work has far reaching consequences for ourunderstanding of cell signalling and identified anorganisational structure which had not beensuspected previously. The work required anintegration of powerful cell biology techniquesincluding advanced microscopy and the developmentof a novel statistical treatment of cell signalling.

Medication has helped reduceAustralian suicide rateAccess to antidepressant medication had asignificant impact on suicide deaths in Australia amajor national study found.

Wayne Hall along with researchers from theUniversity of New South Wales and theCommonwealth Department of Health and Ageing,analysed national trends in suicide rates andantidepressant prescribing from 1991 to 2000.

The study found that while overall suicide ratesremained constant over the ten year period studied,there was a decline in the suicide rate for older menand women.

Assigning function to the transcritomeIMB scientists led by David Hume, played a vital rolein the international consortium that provided thefunctional annotation to the mouse transcriptomeproject (FANTOME2).

This resulted in a special issue of the journal Genome Research providing an overview of theFANTOM2 project.

Inflammatory argumentThe treatment of inflammatory disease is a majorunmet clinical need world wide. David Fairlie andcolleagues from the Physiology and PharmacologyDepartment of the University of Queensland haveidentified a potent class of molecules with anti-inflammatory activity.

Using a rational drug design approach the IMB groupsynthesised a molecule targeted at a humancomplement receptor, C5a. This receptor is notnormally associated with pathology such asinflammatory bowel disease (IBD) but Fairlie andcolleagues argued that it may have a role. This wasborne out when potent novel agonist of the C5areceptor significantly reduced inflammation in a ratmodel of IBD.

These findings are an additional demonstration thatchemistry allied to detailed biological knowledge cangenerate novel therapeutic insights applicable inmany areas.

Venom switches functionA collaborative research team headed by PaulAlewood along with scientists from UQ's Biologicaland Chemical Sciences Faculty demonstrated thatspecific conotoxins from the venom of marine conesnails could switch function.

Until recently it was thought that α-conotoxins couldact solely in an antagonistic manner, blocking thenicotinic receptors that play a vital role in humanneuronal transmissions. This discoverydemonstrated that a minor chemical change to an α-conotoxin could open up an as yet unexploredrealm of therapeutic lead development.


AWARDS

Centenary HonourIMB Director John Mattick was awarded aCentenary Medal in 2003. These medals werecreated to recognise Australians who have made asignificant contribution to our society or government.

National honour for QueenslandresearcherAustralia's peak scientific body the AustralianAcademy of Science awarded IMB's Melissa Little theprestigious Gottschalk Medal for medical sciences.

The award recognises Melissa's groundbreakingwork to understand the complex genetic messagescontrolling kidney development and how this may beapplied to prevent or cure chronic renal failure.

New mining technology to help identify genesIMB researcher Rohan Teasdale won a $75,000 UQFoundation Research Excellence Award to continuehis important work using 'database mining' to extractvaluable information about how cells work.

Rohan is essentially digging through the incrediblewealth of information contained in the genomes of mice and humans to understand the role of cell membranes.

IMB researcher tops world list Queensland's reputation as the Smart State wasfurther enforced when an IMB researcher was ratedas one of the world's most cited authors.

The US based Institute for Science Informationidentified Director of IMB's Office of Public Policyand Ethics, Wayne Hall, as one of the foremostexperts in his research field and ranked him in thetop 0.5 percent of publishing authors worldwide overthe last 20 years.

Researcher rewarded with Federation FellowshipThe Federation Fellowship is awarded to leadingAustralian researchers working in fields of nationalbenefit. Valued at over $1.15 million over five years,the Fellowship supports internationally competitiveresearch resulting in economic, environmental andsocial benefits for Australia.

Kevin Burrage, from UQ's Department ofMathematics, School of Information Technology andElectrical Engineering and a Joint Appointment withIMB uses computational biology to provide afoundation for developing improved pharmaceuticalsand genetic treatments for human diseases likeobesity, different types of cancer and Alzheimer'sdisease to name a few.

(From left) Melissa Little; Rohan Teasdale; Wayne Hall; Kevin Burrage (2nd from right) and other Federation Fellows with The Hon. Dr Brendan Nelson Minister for Education (4th from right).



GRANTS

US supports IMB researchTwo IMB research teams were awardedapproximately US$1 million (about A$1.6 million) eachby America's premier science funding body theNational Institutes of Health.

These grants enable the research teams toinvestigate and design new therapies for debilitatinghuman diseases like chronic inflammatory boweldisease, cancer and arthritis and to develop anti-cancer therapeutics.

Jennifer Stow and David Hume are investigating thecellular processes that regulate the secretion of tissuenecrosis factor alpha (TNFα) by macrophages, aprocess vital to fighting bacterial infections. Howeverexcess TNFα is a major cause of tissue damage inchronic inflammatory diseases and cancer.

Meanwhile John Hancock and Rob Parton areinvestigating the molecular switches that controlmany human biochemical and signalling pathwaysand are frequently mutated in human tumours.

Boost for Australia's health research – NHMRC and ARC grant successIMB research performed exceptionally well in theAustralian Research Council (ARC) and NationalHealth and Medical Research Council's (NHMRC)2003 funding rounds.

IMB researchers were successful in three ARCcategories attracting over $5.2 million throughDiscovery, Linkage and Linkage - InfrastructureEquipment and Facilities Project categories.

In addition IMB researchers were awarded over $5.6million for project investigating the molecular basis ofhuman diseases and developing drugs to assist intreating these conditions.

A highlight of the IMB's grant applications was thehigh level of collaboration with other research

organisations boosting the Institute's capacity toundertake globally important research in thebiosciences.

New research centre in bioinformatics Understanding how all the information encoded inthe human genome actually 'comes to life' wasboosted when the Federal Government announcedalmost $4 million funding for the Australian ResearchCouncil Centre for Genome-Phenome Bioinformatics,based at IMB.

Spread over five years the ARC funding will enableresearchers to model and visualise complexmolecular processes in mammalian cells based onthe transformation of genetic information into cellularform and function.

CONFERENCES

ISMB ConferenceIMB was integral in the successful running of theprestigious Intelligent Systems in Molecular Biology(ISMB) conference held in Brisbane in July.

This was the first time the conference had been heldoutside North America and Europe and attractedworld leaders in the fields of computational biologyand bioinformatics.

Hosting this internationally important event cementedthe IMB as a key driver of Australian research at thenexus of traditional biology and information technology.

IMB SymposiumThe first major event held in the IMB's new home,the QBP, was the IMB Symposium.

IMB hosted an exciting convergence of researchspecialists discussing the topic ‘Towards SystemsBiology’.

The Symposium featured international leaders in thefield and showcased groundbreaking researchconducted at the IMB and abroad.


COMMERCIALISATION

CEO boosts Queensland's commercialisationIMBcom, the company set-up by the University of Queensland to commercialise research of the IMB, appointed inJanuary 2003 its new Chief Executive Officer.

Chair of IMBcom's Board of Directors Emeritus Professor Ted Brown AC announced that Dr Peter Isdale was thenew person responsible for the strategic oversight of the practical application of IMB's leading research.

Commercialisation boost for Queensland researchResearch into repairing damaged kidneys and a company developing a remarkable Queensland technology thatbar-codes chemicals were boosted by the Innovation Start Up Scheme grants announced by the Minister forInnovation and Information Economy Mr Paul Lucas in December.

IMBcom, the commercialisation company for the IMB, was instrumental in the success of the application forNephrogenix Pty Ltd and helped Nanomics Biosystems Pty Ltd with the application in the state-wide competitiveselection process.

CEO of IMBcom Dr Peter Isdale said he was delighted with the success of these grants and that IMBcom'stranslation of research in to high value applied and commercial outcomes was reaping rewards for Queensland'sburgeoning biotechnology industries.

Below: IMBcom CEO Peter Isdale


IMB Research

"If you're going to be a biologist and alive at any point in timein human history, you'd choose to be alive right now."Professor Brandon Wainwright, Deputy Director Research.

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Every individual inherits around 3 billion bits ofinformation from each parent. This information isstored in our genome and programs the entirety ofhuman development and all of the components of our body.

The research focus of the Institute for MolecularBioscience is to investigate the basis of human andmammalian growth and development, at the genetic,molecular, cellular and organ levels.

We wish firstly to understand the wonderful processof normal development from a single fertilized cell toan adult, and the various stages and transitions thatoccur from conception to aging.

We also wish to understand what aspects of theprocess go awry in various disease processes,including cancer and other complex diseases thatare the major health burden of our population.

Finally, arising from these insights, we also wish todevelop pharmaceutical and cellular therapies,

technologies and diagnostics to prevent or repairsuch diseases, and to pursue other opportunities forthe practical applications of our understanding ofmammalian genetic programming and moleculararchitectures, which have the capacity to transformand to create new industries both in biology and ininformation technology.

The following pages outline the IMB's researchprojects and achievements in 2003.

The IMB is a highly collaborative environment whereresearchers from different fields combine tocontribute to strategic research programs. This isunderpinned by our highly developed infrastructurein informatics, genomics, chemistry, structuralbiology, cell and developmental biology and genetics.Consequently, IMB researchers may pursue apowerful combination of technical approaches andbiological systems in order to gain insightsmammalian biology.



MAMMALIAN GENOMICS ANDGENETIC PROGRAMMINGFocussing on• Comparative mammalian and vertebrate functional

genomics

• Rnomics

• Computational modelling of genetic and cellularregulatory networks

This program includes the ARC Centre in Bioinformaticsand intersects with the University of QueenslandDepartment of Mathematics and School of InformationTechnology and Electrical Engineering.

Research Group LeadersTim BaileyKevin BurrageSteve BarkerSean GrimmondJennifer HallinanGeoff McLachlanJohn MattickMark Ragan


Tim Bailey

COMPUTATIONAL BIOLOGY,BIOINFORMATICS, STATISTICALMODELING

Research overviewIn 2003 we concentrated on development ofalgorithms for modelling DNA sequences responsiblefor transcriptional regulation. We developed andalgorithm for searching genomic DNA for regionscontaining statistically significant clusters of sitesmatching known transcription binding factor signals.We also continued work on improving motif-discovery algorithms.

CollaboratorsKevin Burrage Department of Mathematics, UQ and IMB

Mark Ragan, IMB

Rohan Teasdale, IMB

Sean Grimmond, IMB

Bill Noble, Department of Genome Sciences andDepartment of Computer Science and Engineering,University of Washington, Seattle, USA

Undergraduate research scholarsDeanne HummelstadBryce Shepherd

Staff and Students

GrantsARC Centre in Genome/Phenome Bioinformatics

ARC discovery grant Membrane Proteins within theMouse Transcriptome – Annotation of theirOrganisation and Subcellular Localisation

PublicationsBailey, T.L., Noble, W. (2003) Searching forstatistically significant regulatory modules.Bioinformatics, 19:1116-1125.



Kevin Burrage

BIOINFORMATICSThis group works on developing simulation andvisualisation methodologies for understanding thebehaviour of genetic regulation. The simulation modelstake into account stochastic effects, while thevisualisation focuses on three-dimensional display.

ProjectStochastic models and simulations for chemicallyreacting systemsIn microscopic systems formed by living cells, thesmall numbers of reactant molecules can result indynamical behaviour that is discrete and stochasticrather than continuous and deterministic. Thisresearch introduces a new class of discretestochastic methods based on Poisson processes thatmore accurately reflect the underlying cellular models.

The stochastic simulation algorithm (SSA) due toGillespie has become a fundamental tool forsimulating individual molecular reactions in themodelling of cellular behaviour and regulation.However, this method can be computationally quitedemanding. We introduce a new class of numericalmethods, called Poisson Runge-Kutta methods, thatgeneralise this approach.

A general formulation and order theory for this classof Poisson Runge-Kutta methods is given, and highorder methods constructed. Attention is given tosuch issues as stiffness and efficient implementation.Numerical simulations illustrate the performance of these new simulations on some important cellular models.

We have investigated bistability and switching issuesin the Genetic Regulatory networks of lambda phageusing these approaches.

We have also started to develop a three dimensionalvisualisation framework for simulating cellularmodels, both within a cell and for colony of cells.

CollaboratorsProfessor Perry Bartlett, Queensland Brain Institute,UQ

Dr Santiago Schnell, Centre for MathematicalBiology, University of Oxford, UK

Grants 2004ARC Centre for Genome/Phenome Bioinformatics

ARC Discovery 2004 - 2006

Publications

5 papers have been written in the above areas

The figure depicts a rectangular discretisation of the spaceoccupied by the cell colony. This discretisation is used toefficiently locate nearest neighbours, done by queryingneighbouring volumes as opposed to querying the entire colonyitself. In collaboration with Mr David Woolford.

Tianhai TianFrancis ClarkNick HamiltonDavid Woolford

Staff and Students


Steve Barker

ARTHROPOD EVOLUTIONARYGENETICS

Research OverviewWhile most animals arearthropods, their genomes andevolutionary genetics are poorlyunderstood. Our researchfocuses on the mitochondrialgenomics of ticks and lice, theevolution of resistance toinsecticides in lice andmosquitoes, and thephylogenetic relationships of liceand other insects.

ProjectsMitochondrial genomics Mitochondria have their owngenomes, and in most groups ofanimals the order of genes isremarkably similar.

However, we discovered twoextraordinary exceptions: agroup of hard ticks, and lice andtheir kin. The arrangement of the37 genes in the mitochondrialgenomes of these animals haschanged so many times it isdifficult to reconstruct theevolutionary path of thesemitochondrial genomes.

By studying the mitochondrial genomes that havechanged a lot, we hope to learn why thearrangements of genes in mitochondria evolve so slowly.

Resistance to insecticides The insecticides that people rely on to control pestslike lice and mosquitoes do not always workeffectively because the insect develops resistance tothe chemicals in the insecticide.

Our group studies the epidemiology of resistance andalso seeks to understand the genetic andbiochemical basis behind it.

Evolutionary relationships of lice Human head lice are a severe social problem indeveloped countries yet body lice, which areassociated with diseases like Typhus, are not.

The two are closely related and may even be thesame species. We are studying whether the headand body lice of humans are interbreeding andtherefore conspecific.

We also study the evolution of all lice (orderPhthiraptera) and their relationships to the free-livingPsocoptera.

CollaboratorsDr Michael Whiting, Bringham Young University,Utah, USA

Professor Masahito Fukunaga, Fukuyama University,Hiroshima, Japan

Associate Professor Rick Speare, James CookUniversity, Townsville Australia

2003 Grants Uniseed Pty Ltd Seed funding for Hatchtech Pty Ltd

Biotechnology Innovation Fund to Hachtech Pty LtdA novel strategy for controlling lice of humans

ARC Linkage Grant Resistance to pediculicides inhead lice, Pediculus humanus capitis

ARC Grant Origins of parasitism in the Psocodeainsecta

Fisheries Research & Development Corporation(FRDC) Control of Perkinsus disease in abalone



(Left) This is Pediculus humanus, the head louse of humans; (Right) A cattle tick from Zimbabwe, Amblyomma hebraeum

(0pposite page above) A wildlife tick from Australia, Haemaphysalis bremneri; (0pposite page below) The cristae of the mitochondria of a louse

PostdocsRenfu ShaoAnna MurrellSteven Cameron

PhD studentsNatalie LeoCath Covacin

Honour studentsCassie JansenConor McMenimanCarl Davis (with CSIRO LivestockIndustries, QBP)

Staff and Students

PublicationsMurrell, A., Klompen, J.S.H., Barker, S.C. (2003)Synonymy of Boophilus Curtice, 1891 andRhipicephalus Koch, 1844; Boophilus is a derivedgroup within Rhipicephalus. Systematic Parasitology56:169-172.

Hunter, J. and Barker, S.C. (2003) Susceptibility ofhead lice (Pediculus humanus capitis) topediculicides in Australia. Parasite Research90:476-478.

Barker, S.C., Whiting, M., Johnson, K. Murrell, A.(2003) Phylogeny of the lice (Insecta, Phthiraptera)inferred from small subunit rRNA. Zoologica Scripta32:407-414.

Shao, R., Murrell, A., Dowton, M. Barker, S.C. (2003)Rates of gene rearrangement and nucleotidesubstitution are correlated in the mitochondrialgenomes of insects. Molecular Biology and Evolution20:1612-1619.

Murrell, A., Dobson, S., Yang, X., Lacey, E. Barker,S.C. (2003) A survey of bacterial diversity in ticks,lice and fleas from Australia. Parasitology Research89:326-334.

Robinson, D., Leo, N., Prociv, P., Barker, S.C. (2003)Are head lice, Pediculus humanus var. capitis,potential vectors of Rickettia prowazekii?Parasitology Research 90:209-211.

Shao, R., Barker, S.C. (2003) The Highly RearrangedMitochondrial Genome of the Plague Thrips, Thripsimaginis (Insecta: Thysanoptera): Convergence ofTwo Novel Gene Boundaries and an ExtraordinaryArrangement of rRNA Genes. Molecular Biology andEvolution 20:362-370.

Barker, S.C. (2003) The Australian paralysis tick,Ixodes holocyclus, may be the missing link in thetransmission of Hendra virus from bats to horses tohumans. Medical Hypotheses 60:481-483.

Murrell, A., Campbell, N.J.H., Barker, S.C. (2003) Thevalue of idiosyncratic markers and conserved tRNAsequences from the mitochondrial genomes of hardticks (Acari: Ixodida: Ixodidae) for phylogeneticinference. Systematic Biology 52:296-310.


Sean Grimmond

EXPRESSION GENOMICS

Research OverviewThe central focus of my research is to captureinformation associated with global gene expressionand use it to define the key gene products thatcontrol important biological processes andpathological conditions.

Undertaking this sort of research requires anintegrated pipeline that uses

1) Microarray technology to capture alltranscriptional consequences of a challengeto a biological system (eg chemical,environmental, genetic mutation, growthfactor) gene expression,

2) Bioinformatics for annotating putativefunctions to all active genes,

3) Computational tools to identify genes whoseexpression pattern correlates with thechallenge and

4) High throughput functional genomic assaysfor validating the role of lead genesgenerated by this and other pipelines. Onceestablished this pipeline is a powerful toolfor lead gene discovery in almost anybiological system.

Since the completion of mammalian genome andtranscriptome sequencing projects, the fullcomplement of genes in the mouse and the humanhave been elucidated. The key challenges for mylaboratory are to catalogue putative roles for all geneproducts, exploit genomic tools to fast track thediscovery of lead genes and develop betterunderstanding of the networks that control keyprocesses. Integrating global assays of promoteractivity, globally defined gene expression andphenotypic events attain these insights.

Projects:Annotating the mammalian transcriptome:2003 saw the systematic compilation of functionalannotations to every gene present on the human andmouse microarrays generated in house. Genomic,transcriptomics, proteomic and ontological data have

been collated from public sources (egENSEMBL, Swiss Prot, GenBank),collaborative efforts (eg. FANTOM2) aswell as results of our own initiatives(the secretome. Phosphoregulators,cell cycle related genes etc).

Temporal expression profiling ofkidney development:As part of the “Towards RenalRegeneration” Stem Cell Genome Anatomy Project(NIDDK-NIH) we have undertaken expressionprofiling of murine kidney development. This data hasbeen combined with the annotation described in theprevious project to rapidly identify putative functionalleads that are now being studied further to determinetheir role in metanephric development. Efforts intothe expansion of in situ expression profiling as a toolfor providing high resolution spatial expression datahave also commenced.

Advances in microarray based technology:In addition to gene expression profiling microarraytechnologies can be used to perform other massivelyserial assays. This year has seen is developmethodologies and resources for perform reversetransfection or cell based microarrays as well asgenomic based array technologies for studyingpromoter activity and DNA dosage. Reversetransfection has been used to perform a highthroughput analysis of novel protein-proteininteracting partner define by RIKEN genomesciences. This project has demonstrated that reversetransfection can be used to rapidly assay transienttransfection events and has provided importantinsights into PPI data quality.

CollaborationsNIDDK NIH Stem Cell Genome Anatomy Project:• Melissa Little, IMB

IMB-RIKEN Sub-Cellular Localisation Project: • Rohan Teasdale, IMB• Harukazu Suzuki at Genome Sciences RIKEN, Japan• David Hume, IMB

Grants awardedARC Centre for Genome/Phenome Bioinformatics


Publications and papersAshton, K., Holmgren, K., Lankford, A.R., Matherne,G.P., Grimmond, S., Headrick, J. (2003) Effects of A1adenosine receptor overexpression on normoxic andpost-ischemic gene expression. Cardiovasc. Res.57:715-26.

Ravasi, T., Huber, T., Zavolan, M., Forrest, A.,Gaasterland, T., Grimmond, S., RIKEN GER GroupMembers, Hume, D.A. (2003) Systematiccharacterization of the zinc finger containing proteinsin the mouse transcriptome. Genome Research13:1430-42.

Forrest, A., Ravasi, T., Hume, D., Taylor, D., Huber, T.,RIKEN GER Group Members, Grimmond, S.M. (2003)Protein Phosphoregulators: Protein Kinases andprotein phosphatases of the mouse. GenomeResearch 13:1443-54.

Kanapin, A., Gough, J., Grimmond, S.M. Davis, M.,RIKEN GER Group Members, Teasdale, R.D. (2003) Themammalian proteome. Genome Research 13:335-44.

Gustincich, S., Arakawa, Y., Batalov, S., Beisel, K.W.,Bono, H., Carninci, P., Fletcher, C.F., Grimmond, S.M.,Hirokawa, N., Jarvis, E.D., Jegla, T., Kawasaka, Y.,Miki, H., Raviola, E., Teasdale, R.D., Waki, K., Zimmer,A., Kawai, J., Hayashizaki, Y., Okazaki, Y. (2003)Analysis of the mouse transcriptome for genesinvolved in the function of the nervous system.Genome Research 13:1395-401.

Forrest, A., Taylor, D., RIKEN GER Group Members,Grimmond, S. (2003) Cell cycle regulators of themouse. Genome Research 13:1366-75.

Grimmond, S., Miranda, K., Yuan, Z., Davis, M., Hume,D., Yagi, K., Tominaga, N., Bono, H., Hayshizaki, Y.,Okazaki, Y., RIKEN GER and GSL Members, TeasdaleR.D. (2003) The mammalian secretome: Functionalclassification of the proteins secreted into the extra-cellular environment. Genome Research 13:1350-9.

de Sousa Nunes, R., Rana, A., Kettleborough, R.,Brickman, J., Clements, M., Rodriguez, T.A., Forrest,A., Bullock, S., Martinez Barbera, J.P., Grimmond,S.M., Avner, P., Smith, J.C., Dunwoodie, S.L.,Beddington, R.S.P. (2003) Characterizing EmbryonicGene Expression Using a Non-Redundant Sequence-Based Selection Method. Genome Research 13:2609-20 (Journal cover)


Research officersTina MaguireDonna MahonyNic WaddelBrooke Taylor

Research assistantMilena Gongora

BioinformaticianDarrin Taylor

PhD studentAlistair Forrest

Honours studentRowena Cecil

Staff and Students


Jennifer Hallinan

COMPLEX SYSTEMS NETWORKS

Research overviewThe cell is a complex system of a myriad of differentinteracting molecules. DNA, RNA, proteins andbiochemicals interact to maintain the cell in a robust,dynamic non-equilibrium state.

We are interested in the structure, dynamics andevolution of intracellular interaction networksranging from metabolic networks through protein-protein interaction networks to the intricate networksof genetic regulation, which determine the type andactivity of the cell.

Our research aims to understand how criticalbiological phenomena, such as homeostasis,mutational robustness and flexible gene regulationarise from interactions between the components of acomplex biological system. We use the techniques ofnetwork analysis, already applied in fields as diverseas sociology, economics, physics, computer scienceand mathematics, to pursue this goal.

ProjectsDevelopment and analysis of computational modelsof networksUsing the IMB’s High Performance Computingfacilities, we use a variety of algorithms, developedby our own researchers and those from other groups,to investigate the way interesting emergent

behaviour unfolds in intracellular interactionnetworks. Highlights include the development of anArtificial Genome (AG) model for the study of geneticregulatory networks. The AG model was used toinvestigate the question of how interesting dynamicbehaviour, in the form of fuzzy limit cycles, can arisein asynchronous networks, in which the nodes arenot all updated simultaneously. Asynchronousnetworks are more biologically plausible thansynchronous ones, but generally lack interestingbehaviour. We have evolutionary algorithms to"evolve" more biologically plausible models ofnetwork behaviour.

Network models based on biological dataJennifer Hallinan recently received an Early CareerResearcher grant to support the development of adatabase of the genetic regulatory interactionssurround the important oncogene, p53, mutations inwhich are associated with many cancers. This verylarge database will eventually bring together datacurrently widely scattered throughout the researchand medical literature, as well that generated by themolecular biologists of the IMB. It will provide thebasis for the development of detailed geneticregulatory network models targeted towards anunderstanding of the systems biology of cancer.

Grants awardedUQ Early Career Researcher Grant The structure anddynamics of the p53 genetic regulatory network.

ARC Australian Centre for Genome-PhenomeBioinformatics.



CollaboratorsAssociate Professor Janet Wiles, The Complex andIntelligent Systems Group, School of InformationTechnology and Electrical Engineering, TheUniversity of Queensland.

Dr Ricarda Thier, Department of Physiology andPharmacology, The University of Queensland.

PhD studentBen Skellett

Staff and Students

Publications and papersHallinan, J. (2003). Self-organization leads tohierarchical modularity in an internet community. InPalade, V., Howlett, R. J. & Jain, L. (eds.) Proceedingsof the 7th International Conference on Knowledge-Based Intelligent Information and EngineeringSystems. Lecture Notes in Artificial Intelligence 2773914 - 917.

Hallinan, J. (2003). Gene duplication and hierarchicalmodularity in intracellular interaction networks.BioSystems.

Wiles, J., Hallinan, J. (2003). Evolutionarycomputation and cognitive science. In Fogel, D. B. &Robinson, C. J. (eds.) Computational Intelligence: TheExperts Speak. San Diego: IEEE Press: 179 - 189.

Speaking engagementsIEEE Congress on Evolutionary Computation,

The First Australian Conference on Artificial Life

7th International Conference on Knowledge-BasedIntelligent Information and Engineering Systems.

Department of Pathology, University of New South Wales.


Geoff McLachlan

DATA MINING ANDCOMPUTATIONAL STATISTICS

Research overviewMy research in statistics is in the related fields ofclassification, cluster and discriminant analyses,image analysis, machine learning, neural networks,and pattern recognition, and in the field of statisticalinference. The focus in the latter field has been onthe theory and applications of finite mixture modelsand on estimation via the EM algorithm.

A common theme of my research in these fields hasbeen statistical computation, with particular attentionbeing given to the computational aspects of thestatistical methodology. This computational themeextends to my interests in the field of data mining.

More recently, I have become actively involved in thefield of bioinformatics with the focus on the statisticalanalysis of microarray gene expression data.

Grants (2003)Australian Research Council Unsupervised Learningof Mixture Models in Data Mining Applications

Australian Research Council Classification ofMicroarray Gene-Expression Data

National Health & Medical Research CouncilHierarchical finite mixture modelling of healthoutcomes: a risk-adjusted random effects approach

Innovation Access Program Development of marketdriven computational biology infrastructure foradvanced education and training

CollaboratorsDr Christophe Ambroise, University of Compiegne,France

Dr Kim Anh-Do, MD Anderson Cancer Center,University of Texas, USA

Professor Christine McLaren, University of California,Irvine, USA

Dr Kelvin Yau, University of Hong Kong

Professor Kaye Basford, School of Land and Food,UQ.

Dr Andy Lee, School of Public Health, CurtinUniversity of Technology, Perth, Western Australia

Research officersRichard BeanLiat JonesAbdollah Khodkar

PhD studentsSoong ChangJustin ZhuKatrina Monico

Staff and Students


Prizes/keynote addressesNovember-December, 2003. Invited lecturer at thewinter school jointly sponsored by the universities inthe French-speaking part of Switzerland, Villars-Sur-Ollon, Switzerland. Lectures on Finite Mixture Modelsand The EM Algortihm.

November, 2003. The fourth international conferencefor the Critical Assessment of Microarray DataAnalysis (CAMDA 2003), Durham, North Carolina. Use of microarray data via model-basedclassification in the study and prediction of survivalfrom lung cancer (presentation of finalist paper in theCAMDA 2003 Challenge).

September-October, 2003. Workshop of the Institutefor Mathematics and its Applications on StatisticalMethods for Gene Expression: Microarrays andProteomics, University of Minnesota. Classificationof Microarray Gene-Expression Data.

September, 2003. Opening address at the 5thCongresso Nazionale of the Italian Region of theInternational Biometric Society, Marina di Massa.Some Applications of Mixture Models.

August, 2003. 54th Meeting of the InternationalStatistical Institute, Berlin. Organizer of invited papersession on Mixtures and Applications.

July, 2003. Royal Statistical Society Workshop onThe Statistical Analysis of Gene Expression Data,Wye College Conference Centre, Kent, England.Classification of Tissue Samples on the Basis ofMicroarray Gene-Expression Data.

Publications (2003)Kim, S.-G., Ng, S.K., McLachlan, G.J., and Wang, D.(2003). Segmentation of brain MR images with bias-field correction. In Proceedings of WDIC2003, APRSWorkshop on Digital Image Computing, B.C. Lovelland A. Maeder (Eds.). Brisbane: Australian PatternRecognition Society, pp. 3-8.

Mar, J.C. and McLachlan, G.J. (2003). Model-basedclustering in gene expression microarrays: anapplication to breast cancer data. InternationalJournal of Software Engineering and KnowledgeEngineering 13:579-592.

Mar, J.C. and McLachlan, G.J. (2003). Model-basedclustering in gene expression microarrays: anapplication to breast cancer data. In Conferences inResearch and Practice in Information TechnologyVol. 19, Y.-P. Chen (Ed.). Sydney: The AustralianComputer Society, pp. 139-144.

McLachlan, G.J., Ng, S.K., and Peel, D. (2003). Onclustering by mixture models. In Studies inClassification, Data Analysis, and KnowledgeOrganization: Exploratory Data Analysis in EmpiricalResearch, O. Opitz and M. Schwaiger (Eds.). Berlin:Springer-Verlag, pp. 141-148.

McLachlan, G.J., Peel, D., and Bean, R.W. (2003).Modelling high-dimensional data by mixtures offactor analyzers. Computational Statistics & DataAnalysis 41:379-388.

Ng, S.K. and McLachlan, G.J. (2003). On the choice ofthe number of blocks with the incremental EMalgorithm for the fitting of normal mixtures. Statisticsand Computing 13:45-55.

Ng, S.K.and McLachlan, G.J. (2003). An EM-basedsemiparametric mixture model approach to theregression analysis of competing-risks data.Statistics in Medicine 22:1097-111.

Ng, S.K. and McLachlan, G.J. (2003). On somevariants of the EM algorithm for the fitting of finitemixture models. Austrian Journal of Statistics32:143-161.

Ng, S.K. and McLachlan, G.J. (2003). Robustestimation in Gaussian mixtures using multiresolutionkd-trees. In Proceedings of DICTA 2003, 7thConference of Digital Image Computing: Techniquesand Applications Vol. 1, C. Sun, H. Talbot, S. Ourselin,and T. Adriaansen (Eds.). Sydney: Australian PatternRecognition Society, pp. 145-154.



John Mattick

RNA-BASED GENE REGULATIONIN EUKARYOTIC DEVELOPMENT

Research OverviewOur group takes a genomic and molecular geneticapproach to the role of noncoding RNA in theprogramming of differentiation and development inhumans and other complex organisms.

For a number of years our group has been developingan interest in one of the great mysteries of biology –what, if anything, is the function of the vast amount ofintrons and intergenic sequences in the genomes ofthe higher organisms that do not appear to have any function?

These sequences are usually assumed to beevolutionary debris (“junk DNA”). However many ofthese sequences are expressed as non-protein-codingRNAs, and account for around 98% of all genomicoutput in humans. Therefore either the human genomeis replete with useless transcription, or these RNAs arefulfilling some unexpected function(s).

Perhaps the most fundamental belief in molecularbiology is that genes are generally protein-coding, asan extension of the central dogma and the fundamentalethos of biochemistry. This is essentially correct forprokaryotes, wherein the early experiments thatdefined our understanding of genes and geneexpression were carried out. It has been assumed thatthe same is true in multicellular organisms, despite thefact the proportion of protein-coding sequencesdeclines as a function of complexity and is only a smallminority of the genomic programming of complexorganisms like mammals.

We have advanced the hypothesis that the higherorganisms have in fact evolved an advanced andhighly parallel genetic operating system based ondigital RNA signals derived from the introns ofprotein-coding genes, as well as other genes that donot encode protein at all, which integrate complexsuites of gene activity and control the trajectories ofdifferentiation and development. This hypothesis isconsistent with all of the known data, and if correcthas the capacity to transform our understanding ofthe genetic programming of higher organisms, theirevolution and diversity, with considerable practical

consequences for medicine, agriculture andinformation science, in terms of genetic diagnostics,therapies, advanced genetic selection andengineering, and the design of artificial systemscapable of self-referential assembly.

We are using bioinformatic techniques to identify andmap RNA regulartory networks in a variety of keyorganisms from yeast to mammals, developing newdatabases and microarray chips to examine theexpression of noncoding RNAs in humans and miceduring development and in different disease states,and undertaking genetic and molecular geneticexperiments to test crucial parts of the hypothesis. Weare also using computational modelling to examine theability of such networks to evolve and to program theontogeny of complex organisms and to test the powerof the system and its potential for rational design ofcomplex systems.

CollaboratorsProfessor Yoshihide Hayashazaki, RIKEN GenomeSciences Centre, Yokohama, Japan

Professor Claes Wahlstedt, Karolinska Institute,Stockholm, Sweden

Professor Peter Arctander, University of Copenhagen,Denmark

Dr John Logsdon, University of Iowa, USA

Dr David Haussler, Dr Gill Bejerano, Dr Jim Kent,University of California Santa Cruz, USA

Dr John Doyle, California Institute of Technology,Pasadena, USA

Dr Weisan Chen, Ludwig Institute for CancerResearch, Melbourne

Professor Robert Giegrich (Bielefeld University,Germany)



Research officersDr Michael GagenDr Evgenj GlazovDr Igor Makunin

PhD studentsKhairina Tajul ArifinMichael PheasantCas Simons

Masters studentStuart Stephen

Honours studentMichael Lai

Research assistantsKelin Ru

Visiting scholarsMarcus HinchcliffeKen PangHidayatTrimarsanto

Visiting researcherProfessor Peter Arctander

Staff and Students

PublicationsMattick, J.S. (2003) Challenging the dogma: thehidden layer of non-protein-coding RNAs in complexorganisms. Bioessays 25:930-939.

Mattick, J.S. (2003) Noncoding RNAs: a regulatoryrole? In “Nature Encyclopaedia of the HumanGenome” (D. N. Cooper, ed.), Nature PublishingGroup, Macmillan Publishers Ltd.

Mattick, J.S. (2003) Introns and noncoding RNAs: thehidden layer of eukaryotic complexity. In “NoncodingRNAs: Molecular Biology and Molecular Medicine”(J. Barciszewski and V.A. Erdmann, eds.) LandesBioscience, Georgetown TX.

Croft, L.J., Lercher, M.J., Gagen, M.J., Mattick, J.S. Isprokaryotic complexity limited by accelerated growthin regulatory overhead? Genome Biology PreprintDepository http://genomebiology.com/qc/2003/5/1/p2(2003).

Tajul-Arifin, K., Teasdale, R., Ravasi, T., Hume, D.A.,Mattick, J.S.; RIKEN GER Group; GSL Members.(2003) Identification and analysis of chromodomain-containing proteins encoded in the mousetranscriptome. Genome Res. 13:1416-1429.

Saunders, N.F., Thomas, T., Curmi, P.M., Mattick, J.S.,Kuczek, E., Slade, R., Davis, J., Franzmann, P.D.,Boone, D., Rusterholtz, K., Feldman, R., Gates, C.,Bench, S., Sowers, K., Kadner, K., Aerts, A., Dehal, P.,Detter, C., Glavina, T., Lucas, S., Richardson, P.,Larimer, F., Hauser, L., Land, M., Cavicchioli, R. (2003)Mechanisms of thermal adaptation revealed from thegenomes of the Antarctic Archaea Methanogeniumfrigidum and Methanococcoides burtonii. GenomeRes. 13:1580-1588.

Huang, B., Whitchurch, C.B., Mattick, J.S. (2003) LinksFimX, a multidomain protein connectingenvironmental signals to twitching motility inPseudomonas aeruginosa. J Bacteriol. 185:7068-7076.

Nouwens, A.S., Beatson, S.A., Whitchurch, C.B.,Walsh, B.J., Schweizer, H.P., Mattick, J.S., Cordwell,S,J. (2003) Proteome analysis of extracellularproteins regulated by the las and rhl quorum sensingsystems in Pseudomonas aeruginosa PAO1.Microbiology. 149:1311-1322.

Mattick, J.S. (2003) The human genome and thefuture of medicine. Med J Aust. 179:212-216.


Keynote and invited lectures at nationaland international conferencesMattick, J.S. (2003) Programming of complexorganisms: the hidden layer of noncoding RNA. LorneProtein Conference, Lorne (plenary).

Mattick, J.S. (2003) The autopoietic programming ofcomplex organisms: the hidden layer of noncodingRNA. Bioinformatics 2003, SocBIN – Society forBioinformatics in the Nordic Countries, Helsinki,Finland (plenary).

Mattick, J.S. (2003) Programming of the autopoieticdevelopment of complex organisms: the hidden layerof noncoding RNA. 11th International Conference onIntelligent Systems for Molecular Biology(ISMB’2003), Brisbane (plenary).

Mattick, J.S. (2003) Genetic programming of complexorganisms: the hidden layer of noncoding RNA.International Congress of Genetics (ICG’2003),Melbourne (invited).

Mattick, J.S. (2003) Genetic programming of complexorganisms: the hidden layer of noncoding RNA. IXthInternational Congress on Inborn Errors ofMetabolism (ICIEM’2003), Brisbane (plenary).

Mattick, J.S. (2003) Genomic programming ofcomplex organisms: the hidden layer of noncodingRNA. Okinawa International Symposium: NewHorizons in Molecular Sciences and Systems - AnIntegrated Approach, Nara, Japan (invited).

Mattick, J.S. (2003) The hidden layer of efferenceRNA-mediated regulatory networks: a digital feed-forward system underpinning the evolution anddevelopment of complex organisms. 2003 Congresson Evolutionary Computation (CEC’2003), Canberra(plenary).

Invited talks at other institutionsMattick, J.S. (2003) The hidden layer of eukaryoticcomplexity: introns and noncoding RNAs ineukaryotic evolution and development. EuropeanMolecular Biology Laboratory (EMBL), Heidelberg,Germany.

Mattick, J.S. (2003) The autopoietic programming ofcomplex organisms: the hidden layer of noncodingRNA. Karolinska Institute, Stockholm, Sweden.

Mattick, J.S. (2003) The autopoietic programming ofcomplex organisms: the hidden layer of noncodingRNA. National Cancer Institute, NIH, Bethesda, USA.

Mattick, J.S. (2003) The genomic programming ofcomplex organisms. RIKEN Genome Sciences Center,Yokohama, Japan.

Mattick, J.S. (2003) Genomic programming ofcomplex organisms: the hidden layer of noncodingRNA. Affymetrix Inc., Santa Clara CA, USA.

Mattick, J.S. (2003) Genomic programming ofcomplex organisms: the hidden layer of noncodingRNA. California Institute of Technology, PasadenaCA, USA.

AwardsHonorary Fellowship of the Royal College ofPathologists of Australasia (FRCPA)

Australian Government Centenary Medal, forservices to biotechnology


For a number of years our group has beendeveloping an interest in one of the great mysteriesof biology – what, if anything, is the function of thevast amount of introns and intergenic sequences inthe genomes of the higher organisms that do notappear to have any function?



Mark Ragan

COMPARATIVE ANDCOMPUTATIONAL GENOMICS

Research overviewWe use advanced bioinformatic, computational anddatabase methods to investigate similarities anddifferences among genomes and the proteins theyencode. Our goal is to make quantitative inferencesabout how genomes have come to have their observedcontents of genes, how protein families havediversified, and how cellular function has evolved.

ProjectsAutomated inference of vertical and lateral genetransmission in prokaryotic genomesFor nearly 150 years, biologists believed that allgenetic information was transmitted “vertically” fromparents to offspring. The very few exceptions – as inthe spread of antibiotic resistance among bacterialpopulations – were seen as extraordinary, highlyspecialised phenomena. Within the past few years,this orthodoxy has been turned on its head. Lateralgene transfer – the transmission of geneticinformation across, not within, genealogical lineages– is now suspected to be much more common thanpreviously imagined. The evidence remainssomewhat controversial, but in the case of manybacterial genomes is increasingly convincing. Ifdiverse types of bacteria participate in a commongene pool, the consequences could be immensethroughout environmental science, biotechnology,agriculture and medicine.

We are constructing an automated computer-basedsystem to collect and manage bacterial genomesequences, identify protein families, generate andoptimise multiple sequence alignments, rigorouslyinfer phylogenetic trees, and find all statisticallysupported instances of incongruence among them.Our “phylogenetic pipeline” has already spun-outchallenging projects in algorithmics, computational

modelling, distributed and parallel computation, datahandling and information integration. Althoughdesigned to search for laterally transferred genes,the system will also yield comprehensive libraries ofprotein motifs and other information useful in appliedareas of bioscience, including drug design andmetabolic engineering.

Component and related projects• Hybrid Markov-plus-linkage-based approach for high-

throughput recognition of protein-sequence clusters

• Automated recognition of maximally representativeclusters of protein sequences

• Word-oriented objective function for scoring andranking multiple sequence alignments

• Application of pattern discovery to alignment-freeinference of molecular phylogenetic trees

• Bayesian and maximum likelihood phylogeneticanalyses of protein sequence data under branch-length bias and model violation

• New algorithms to describe and compare protein folds

• Information integration in bioinformatics

• Workflow-enabled pipeline for bioinformatics

• Java interfaces for bioinformatic tools on IBM p690

ARC Centre in BioinformaticsThe Australian Research Council (ARC) Centre inBioinformatics, with headquarters at IMB, started-upunofficially in late 2003 ahead of a formal start in early2004. This Centre coordinates research (for 13investigators across five institutions) in bioinformatics,cellular network modelling, advanced bioinformaticdatabases, 3D visualisation, and high-throughputexperimental validation focused on understanding themammalian cell as a complex system of regulatoryand molecular interaction networks.

Mark Ragan is Centre Director (Director of Research,and Chief Operations Officer) for the ARC Centre inBioinformatics.



Grants AwardedARC Centre in Bioinformatics

ARC Computational infrastructure for high-throughput genome bioinformatics.

Australian Partnership for Advanced ComputingComparison of protein families among completelysequenced genomes.

CollaboratorsRobert Charlebois, University of Ottawa, Canada andNeurogadgets Inc.

Jonathan Keith, Peter Adams and Darren Bryant,Department of Mathematics, University ofQueensland

Isidore Rigoutsos, IBM Thomas J. Watson ResearchCenter, USA

Nicholas Hamilton, Thomas Huber and KevinBurrage, Advanced Computational Modelling Centreand Department of Mathematics, University ofQueensland

Robin Gutell, Jamie Cannone, Usman Roshan, andTandy Warnow, Institute for Cellular and MolecularBiology, University of Texas at Austin, USA

Samuel Thoraval, Université Montpellier, France

Catherine Letondal, Institut Pasteur, Paris, France

Jess Mar, Harvard School of Public Health, Boston, USA

Phoebe Chen, Deakin University, Melbourne

Research officersRobert BeikoNicholas HamiltonJosef Pánek

PhD studentsCheong Xin ChanAlex GarciaMichael Höhl

Research assistantTimothy Harlow

Database administrator/developerJohn Opitz

Postgraduate trainee Adrian Miranda

Volunteer Chikako Ragan

International intern Samuel Thoraval

Administrative assistants Edith HiiLanna Wong

Staff and Students


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Publications and PapersRagan, M.A., Murphy, C.A., Rand, T.G. (2003). AreIchthyosporea animals or fungi? Bayesianphylogenetic analysis of elongation factor 1α ofIchthyophonus irregularis. Molecular Phylogeneticsand Evolution. 29:550-62.

Charlebois, R.L., Beiko, R.G., Ragan, M.A. (2003)Microbial phylogenomics: Branching out. Nature421:217.

Pekkarinen, M., Lom, J., Murphy, C.A., Ragan, M.A.,Dykova, I. (2003) Phylogenetic position andultrastructure of two Dermocystidium species(Ichthyosporea) from the common perch (Percafluviatilis). Acta Protozoologica 42:287-307.

Ragan, M.A. (2003) Bioinformatics: a glimpse of thefuture. BioSilico 1:119-120.

Published AbstractsHöhl, M., Rigoutsos, I., Ragan M.A. Freeingphylogenies from alignments (2003). Program, 11thInternational Conference on Intelligent Systems inMolecular Biology, p. 117.

Garcia, A., J. Cleary, M.A. Ragan & J.-P.P. Chen.SEMA, a semantic literature annotator (2003).Program, 11th International Conference on IntelligentSystems in Molecular Biology, p. 66. [Co-awardee,best Australian student poster.]

Garcia, A., L.J. Garcia, M.A. Ragan & Y.-P.P. Chen.GPIPE, a pipeline module for JEMBOSS (2003).Program, 11th International Conference on IntelligentSystems in Molecular Biology, p. 83.

Beiko, R.G., R.L. Charlebois & M.A. Ragan. Genomephylogenies based on the mean normalized BLASTscore (2003). Program, 11th International Conferenceon Intelligent Systems in Molecular Biology, p. 117.

Harlow, T.J., J.P. Gogarten & M.A. Ragan. A hybridclustering approach to genome-scale recognition ofprotein families (2003). Program, 11th InternationalConference on Intelligent Systems in MolecularBiology, p. 115.

Conference Papers/Lectures24th Lorne Genome Conference, Lorne, Victoria,February 2003

Second IMB Symposium (on the occasion of theopening of IMB), University of Queensland, May 2003

Australian Partnership in Advanced ComputingAPAC03, Gold Coast, October 2003 (Keynote address)

Canadian Institute for Advanced Research, Programin Evolutionary Biology, White Point Beach, NovaScotia, September 2003

Australian Mathematics Society Institute, SummerSymposium in Bioinformatics, ANU, Canberra,December 2003 (Invited plenary)

First Australian Conference on Artificial Life, ANU,Canberra, December 2003 (Invited plenary)

Association of Asian Societies of Bioinformatics,Yokohama, December 2003



ORGANOGENESIS, TISSUE DAMAGEAND REGENERATIONFocussing on• Urogenital development• Inflammation• Cell signalling and cancer• Molecular genetics and molecular biology of aging

This program includes IMB’s participation in theCooperative research Centre for Chronic InflammatoryDiseases; the ARC Centre of Excellence in Stem CellBiology; the Centre for Biotechnology and Development;and the NIH funded project Nephrogenix, an initiativedesigned to develop new therapies for renalregeneration.

Research Group LeadersDavid HumeStuart KelliePeter KoopmanMelissa LittleGeorge MuscatJoe RothnagelRick SturmBrandon WainwrightMichael WatersCarol Wicking


David Hume

MACROPHAGES ANDOSTEOCLASTS

Research overviewThe central issue being addressed in theMacrophage and Osteoclast Biology Research Groupis the mechanism controlling the differentiation ofmacrophages and osteoclasts from their progenitorcells and the regulation of the function of these cellsin health and diseases.

The group is a major node of the CooperativeResearch Centre for Chronic Inflammatory Diseases,which focuses on identifying targets for thedevelopment of drugs to treat diseases such asosteoarthritis, rheumatoid arthritis and chronicobstructive lung disease (emphysema). We also havecollaborations addressing the roles of macrophages inrenal disease, tissue regeneration, malignancy, cysticfibrosis and inflammatory bowel disease.

We are interested in the signalling pathways thatpermit macrophages and osteoclasts to respond to agents such as growth factors (macrophagecolony-stimulating factor, CSF-1; RANK ligand) andmicrobial products such as lipopolysaccharide andmicrobial DNA.

To assess the function of individual gene productswe utilise a combination of transfection analysis andtransgenics using new technologies developed in thegroup, including macrophage and osteoclast-specifictransgenes.

We are developing systems biology approachesbased upon cDNA microarray expression profiling,proteomics, high throughput structural genomics andcomputational network modelling, to try to gain anoverview of how macrophages and osteoclastsfunction and to predict the way that they will respondto external agents including candidate drugs.

ProjectsFunctional Regulation (Matthew Sweet and Kate Stacey)Macrophages express a number of receptors thatregulate cellular function. The CSF-1 receptor allowsfor proliferation and differentiation of macrophagesin response to the growth factor, CSF-1. It is alsoinappropriately expressed in a number of cancersand is likely to contribute to metastasis. We haveused cDNA micro-arrays to identify CSF-1-regulatedgenes in macrophages. Such genes are likely to beinvolved in a diverse range of functions includingdifferentiation, phagocytosis and tumour biology.

During pathogenic challenge, macrophages detectforeign products such as bacterial CpG DNA,lipopolysaccharide and bacterial lipoproteins. Thisactivates the innate immune response and triggersthe development of the acquired immune response.Bacterial CpG DNA in particular is a potent activatorof a Th1-type immune response and has been usedtherapeutically as an adjuvant in anti-cancervaccines and for the treatment of allergies. We arecharacterising CpG DNA responses in macrophagesand the role of CpG DNA during pathogenicchallenge in vivo.

Genetic Networks underlying MacrophageActivation (Christine Wells and Tim Ravasi)By surveying the transcripts expressed inmacrophages under different activation ordifferentiation contexts, we are able to measure thegenetic network underlying macrophage responses.We use DNA microarray technology, coupled withbioinformatics-based genomic analysis andtraditional genetic mapping strategies to look forthese genetic networks. This approach has allowedus to identify genetic and epigenetic elements thatmodify the activation potential of inflammatorymacrophages. The data generated from these studiesform the “target-identification” side of the CRCpipeline designed to identify and test potentialtherapeutics for chronic inflammatory diseases.

Gene expression in macrophages and osteoclasts(Dmitry Ovchinnikov)The ultimate goal of my research is to establish aversatile and reliable set of modern mouse moleculargenetics tools for the alteration of gene expression inmacrophages and osteoclasts. These tools will allowus to overexpress genes and/or inactivate them, in


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spatially and temporally controllable fashion. This willprovide a novel approach to gene “replacement”,allowing the simultaneous control of both geneinactivation and overexpression.

Osteoclast and bone biology (Ian Cassady)My research interests centre on gene regulation inbone-resorbing osteoclasts and their general role inbone biology and homeostasis. Bone is a dynamicorgan that not only provides structural support for thebody but also acts a sink and source of Ca2+ and P tomaintain serum mineral homeostasis. A precisebalance is required between the synthetic activity ofosteoblasts and the resorptive activity of osteoclasts.Dysregulation of either arm of these activities canresult in bone diseases such as osteoporosis.Osteoclasts have a central role as the effector cellsof bone homeostasis and as such have been thetarget of therapeutic intervention. In spite of theirimportance the biology of osteoclasts remains poorlyunderstood. To address this issue I have establisheda number of projects either directly in this laboratoryor by collaboration with other groups to focus on thefollowing areas:

• Gene regulation during osteoclastogenesis,

• Modulation of gene expression in osteoclasts in vitro or in vivo by transgenesis,

• Comparative promoter analysis of osteoclastmarker genes and the role of PPARs,

• Specific gene expression in osteoclasts withtherapeutic objectives,

• Analysis of the gene expression in bone in responseto mechanical stress,

• Characterization of the functional role of TRAP inosteoclasts and in bone biology,

• Osteoclast and macrophage activity towards novelbone biomaterials.

Studies on macrophage inflammatory proteins (IanRoss)We are analysing the pathogen sensor moleculeNod2 (a susceptibility gene for the chronicinflammatory diseases Crohn's disease, Blausyndrome and psoriasis) to help reveal the way theinflammatory cascades are controlled and how thisfails in chronic inflammation. We are also usingproteomic discovery approaches to reveal proteinswith altered expression or location within themacrophage as a result of stimulation with microbialmolecules such as lipopolysaccharide, peptidoglycanand muramyl dipeptide. This approach is identifyingpotential drug targets, which we are in the processof validating for biological effects.

GrantsNHMRC Project grant Th2-Promoting Stimulus, ES-62

NHMRC Project grant TLR 9 and response to foreignDNA

NHMRC Project grant Osteoclast-specific generegulation

NHMRC Project grant COX-2 regulation of boneturnover and mechanically induced bone formation

UQ Research Development grant Design andprototyping of a novel dynamic mechanicalbioreactor for bone tissue engineering

ARC Discovery grant Discovery of novel macrophageproteins

ARC Linkage grant Development of tyrosine kinaseinhibitors

CRC for Chronic Inflammatory Diseases(supplementary funding)

US National Institutes of Health and AustralianKidney Foundation's Bootle Bequest. NephrogenixConsortium

US National Institutes of Health Cytokine traffickingand secretion in macrophages

Amgen Development grant


Senior research fellowIan Cassady

Senior research officersRoy HimesIan RossKate StaceyMatthew Sweet

Research officersBarbara FletcherDmitry OvchinnikovAllison Pettit (NHMRC, CJ MartinFellow)Liza-Jane Raggatt (NHMRC,Doherty Fellow)Tim RavasiTedjo SasmonoKathy Speed

Administrative officerJulie Osborne

Lab managerGreg Young

Research assistantsJane ClarksonStephen CronauGeoffrey FaulknerGreg KellyJane MooneyVisala RaoElke SeppanenAngela Trieu

Dabatase manager (CRC)Xiang Liu

PhD studentsGuy BarryMyrna ConstantinTamarind HamwoodKatherine Irvine Nicholas MeadowsVera RipollTara Roberts Kate SchroderBrendan TseNicole Walsh

Christine WellsAndy WuRicha Dave

Honours students Ming Chang

Vacation scholarChien-chi Lo

Staff and Students

PublicationsBono, H., Yagi, K., Kasukawa, T., Nikaido, I., Tominaga,N., Miki, R., Mizuno, Y., Tomaru, Y., Goto, H., Nitanda,H., Shimizu, D., Makino, H., Morita, T., Fujiyama, J.,Sakai, T., Shimoji, T., Hume, D.A., Hayashizaki, Y.,Okazaki, Y.. (2003) Systematic Expression Profiling ofthe Mouse Transcriptome Using RIKEN cDNAMicroarrays. Genome Res. 13:1318-23.

Carninci, P., Waki, K., Shiraki, T., Konno, H., Shibata,K., Itoh ,M., Aizawa, K., Arakawa, T., Ishii, Y., Sasaki,D., Bono, H., Kondo, S., Sugahara, Y., Saito, R., Osato,N., Fukuda, S., Sato, K., Watahiki, A., Hirozane-Kishikawa, T., Nakamura, M., Shibata, Y., Yasunishi,A., Kikuchi, N., Yoshiki, A., Kusakabe, M., Gustincich,S., Beisel, K., Pavan, W., Aidinis, V., Nakagawara, A.,Held, W.A., Iwata, H., Kono, T., Nakauchi, H., Lyons, P.,Wells, C., Hume, D.A., Fagiolini, M., Hensch, T.K.,Brinkmeier, M., Camper, S., Hirota, J., Mombaerts, P.,Muramatsu, M., Okazaki, Y., Kawai, J., Hayashizaki, Y..(2003) Targeting a complex transcriptome: theconstruction of the mouse full-length cDNAencyclopedia. Genome Res. 13:1273-89.

Cassady, A.I., Luchin, A., Ostrowski MC, Hume DA.(2003) Regulation of the murine TRACP genepromoter. J Bone Miner Res. 18:1901-4.

Forrest, A.R, Ravasi T, Taylor D, Huber T, Hume DA,Grimmond S. (2003) Phosphoregulators: proteinkinases and protein phosphatases of mouse. GenomeRes. 13:1443-54.

Grimmond, S.M., Miranda, K.C., Yuan, Z., Davis, M.J.,Hume, D.A., Yagi, K., Tominaga, N.,, Bono, H.,Hayashizaki,Y., Okazaki, Y., Teasdale, R.D. (2003) Themouse secretome: functional classification of theproteins secreted into the extracellular environment.Genome Res. 13:1350-9.

Holmes, R., Williamson, C., Peters, J., Denny, P.,Wells, C. (2003) A comprehensive transcript map ofthe mouse gnas imprinted complex. Genome Res.13:1410-5.

Kasukawa, T., Furuno, M., Nikaido, I., Bono, H., Hume,D.A., Bult, C., Hill, D.P., Baldarelli, R., Gough, J.,Kanapin, A., Matsuda, H., Schriml, L.M., Hayashizaki, Y.,Okazaki, Y., Quackenbush, J. (2003) Development andevaluation of an automated annotation pipeline andcDNA annotation system. Genome Res. 13:1542-51.



Numata, K., Kanai, A., Saito, R., Kondo, S., Adachi, J.,Wilming, L.G., Hume, D.A., Hayashizaki, Y., Tomita, M.(2003) Identification of Putative Noncoding RNAsAmong the RIKEN Mouse Full-Length cDNACollection. Genome Res. 13:1301-6.

Okazaki, Y., Hume, D.A. (2003) A guide to theMammalian genome. Genome Res. 13:1267-72

Ravasi, T., Huber, T., Zavolan, M., Forrest, A.,Gaasterland, T., Grimmond, S., Hume, D.A. (2003)Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome.Genome Res. 13:1430-42.

Sasmono, R.T., Oceandy, D., Pollard, J.W., Tong, W.,Pavli, P., Wainwright, B.J., Ostrowski, M.C., Himes,S.R., Hume, D.A. (2003) A macrophage colony-stimulating factor receptor-green fluorescent proteintransgene is expressed throughout the mononuclearphagocyte system of the mouse. Blood 101:1155-63

Stacey, K.J., Young, G.R., Clark, F., Sester, D.P.,Roberts, T.L., Naik, S., Sweet, M.J., Hume, D.A. (2003)The molecular basis for the lack ofimmunostimulatory activity of vertebrate DNA. J Immunol. 170:3614-20.

Sweet, M.J., Hume, D.A. (2003) CSF-1 as a regulatorof macrophage activation and immune responses.Archivum Immunologiae et Therapiae Experimentalis.51:169-77

Tajul-Arifin, K., Teasdale, R., Ravasi, T., Hume, D.A.,Mattick, J.S. (2003) Identification and analysis ofchromodomain-containing proteins encoded in themouse transcriptome. Genome Res. 13:1416-29.

Walsh, N.C., Cahill, M., Carninci, P., Kawai, J.,Okazaki, Y., Hayashizaki, Y., Hume, D.A., Cassady, A.I.(2003) Multiple tissue-specific promoters controlexpression of the murine tartrate-resistant acidphosphatase gene. Gene 307:111-23.

Wells, C.A., Ravasi, T., Faulkner, G.J., Carninci, P.,Okazaki, Y., Hayashizaki, Y., Sweet, M.J., Wainwright,B.J., Hume, D.A. (2003) Genetic control of the innateimmune response. BMC Immunol. 4:5

Wells, C.A., Ravasi, T., Sultana, R., Yagi, K., Carninci,P., Bono, H., Faulkner, G., Okazaki, Y., Quackenbush,J., Hume, D.A., Lyons, P.A. (2003) Continued discoveryof transcriptional units expressed in cells of themouse mononuclear phagocyte lineage. GenomeRes. 13:1360-5.

Zavolan, M., Kondo, S., Schonbach, C., Adachi, J.,Hume, D.A., Hayashizaki, Y., Gaasterland, T. (2003)Impact of alternative initiation, splicing, andtermination on the diversity of the mRNA transcriptsencoded by the mouse transcriptome. Genome Res.13:1290-300.

PatentsCSF-1 Immunomodulation patent has entered PCTPhase Publication Date 10th April (2003)

Key Conference Presentations Hume D.A. Invited speaker: International Society forInterferon and Cytokine Research Annual Meeting,Cairns, Australia, October 2003

Hume, D.A., Sasmono, T., Ravasi, T., Wells, C.A.Himes, S.R. Transcriptional Regulation ofMacrophage Differentiation. Lorne GenomeConference, Lorne, Australia

Hume, D.A. Transcriptional control in macrophages.European Macrophage and Dendritic Cell Society,Leicester, UK


Stuart Kellie

MACROPHAGE SIGNALLING

Research overviewAs part of the CRC for Chronic InflammatoryDiseases, my laboratory collaborates closely withDavid Hume and groups in Monash and Melbourne toidentify and investigate the function of a number ofgenes regulated in macrophages after cytokineactivation. The aim of this work is to identify thosegenes or proteins which are aberrantly expressedduring chronic inflammation, and to show aninvolvement in chronic inflammatory diseases suchas rheumatoid arthritis and chronic obstructivepulmonary disease (COPD). The long-term aim is togenerate inhibitors of these genes for therapeuticuse in chronic inflammation, in collaboration withindustrial CRC partners.

ProjectsGeneration of target validation platforms forfunctional analysis of macrophage genesWe have identified numerous genes whoseexpression is regulated by inflammatory cytokines,however in many cases the function of these genesin macrophages has not been investigated. Toidentify such geens as valid targets for therapy it isimportant to establish their role in macrophagebiology. A number of cellular and molecularapproaches are being established to investigatedgene product function in macrophages: these includethe establishment of inducible macrophage cell lines,siRNA, protein transduction methodology and the useof dominant-negative mutants.

Tyrosine phosphatases in macrophage functionTyrosine phosphorylation is central to many aspectsof cellular responses to extracellular stimuli. Whilstmuch is known about tyrosine kinases and their rolein cell activation, less is known about how proteintyrosine phosphatases (PTPs) act as a biochemicalcounterbalance to the kinases to regulate tyrosinephosphorylation. PTPs are a large gene family andindividual members exhibit substrate selectivity andcontrol specific aspects of intracellular signalling. Inrecent years they have been recognised as bothintiators and regulators of signalling in the immunesystem. A number of PTPs have been shown to beenriched in macrophages, however for the most parttheir function is unknown. We are investigating theexpression and function of several PTPs inmacrophages using a combination gene arraytechnology, PCR, heterologous expression using anumber of systems.

Kinases in macrophage functionCytokines or stress leads to the activation in theMAPK/jun pathway in many cells types which in turnleads to new gene expression. This pathway appearsto be particularly important for macrophage functionand survival. There are still gaps in our knowledgeabout the molecular mechanisms controlling thissignalling pathway. We have been investigating aclass of intracellular signalling molecules termedSTE20-related kinases. These are the mostmembrane-proximal kinases of this pathway, and inmodel systems regulate jun kinase and thus newgene expression. Using mutagenesis and expressionwe are investigating the regulation of activity ofthese molecules. Such studies will give insight intoimportant activation pathways in inflammatory cellssuch as macrophages.

The long-term aim is to generate inhibitors ofthese genes for therapeutic use in chronicinflammation, in collaboration with industrialCRC partners.


Peter Koopman

MOLECULAR GENETICS OFMAMMALIAN DEVELOPMENT

Research OverviewWe are studying the genes that control the formation ofvarious organs during the development of a mammalianembryo. In particular we are striving to understand theevents that regulate the development of the embryo asa male or a female, and the laying down of an intactand functional network of blood vessels.

ProjectsSex Determination and Gonadal DevelopmentDevelopment of two distinct sexes is critical to thesurvival of animal species, and defects in sexualdevelopment in humans are both common anddistressing. My group is studying the molecular andcellular biology of Sry and several other genes inorder to understand their role in male sexdetermination and the defects that can result in sexreversal. We are also searching for other genesdownstream in the sex-determining pathway, usingexpression screening approaches such asmicroarrays. We have recently begun to characterisethe molecular events leading to ovarian developmentin the embryo, an important process about whichlittle is currently known.

Sox Gene Function and EvolutionAs well as providing a point of entry to the sex-determining pathway, the discovery of Sry has led tothe identification of a family of structurally related

genes called Sox genes. The Sox gene familycomprises 20 genes in humans and mice, known tobe active during embryo development in specificsubsets of tissues. We have identified several newmembers of this gene family and are examining theirroles in mouse development. We are also interestedin the phylogeny, evolution, and functionalrelationships between the various Sox genes and thefactors they encode.

Molecular Genetics of Vascular DevelopmentWe discovered a gene, Sox18, that is expressedtransiently in endothelial cells during vascularformation in the embryo and in the adult. Mutations inSox18 disrupt vascular development and/or function.We are currently studying the genetics and biology ofthe role of Sox18 and related genes in vasculardevelopment, and exploring the possibility thatangiogenesis can be modulated by enhancing orsuppressing Sox18 activity.

Development of Male Germ CellsAs members of the ARC Centre for Excellence inBiotechnology and Development, we have begun toexamine the specification and differentiation of themale germ line. This collaborative group aims todissect the complex developmental networksunderlying germ cell differentiation, with the aims ofidentifying genes involved in testicular and childhoodcancers, elucidating mechanisms underlyingidiopathic male infertility, developing newapproaches to transgenic animal production,identification new targets for pest control,reprogramming germ cells for applications inbiotechnology, and formulating innovative strategiesfor enhancing or suppressing fertility.

E14.5 male gonad sections (12um): SFI PECAM; SFI GATA4; GATA4 Sox9; SFI Sox9

Research officersJosephine BowlesDagmar WilhelmMegan WilsonAnnemiek BeverdamShuji TakadaNeville YoungAsanka KarunaratneCate Browne

PhD studentsKelly LofflerFred MartinsonJames SmithMeredith DownesStephen Bradford

Visiting academicCarolyn Dong

Honours studentsSonjia LaytonEugene Huang

Research assistantsAngela JeanesDeon KnightAndrew JacksonKristy James

Staff and Students



PublicationsFowles, L.F., Bennetts, J.S., Berkman, J.L., Williams,E., Koopman, P., Teasdale, R.D. and Wicking, C.(2003) Genomic screen for genes involved inmammalian craniofacial development. Genesis35:73–87.

Koopman, P., Loffler, K.A. (2003) Sex determination:The fishy tale of Dmrt1. Current Biology 13:R177–179.

James, K., Hosking, B., Gardner, J., Muscat, G.E.O.,Koopman, P. (2003) Sox18 is mutated in ragged-likeand opossum mice. Genesis 36:1–6.

Loffler, K.A, Zarkower, D., Koopman, P. (2003) Etiologyof ovarian failure in blepharophimosis-ptosis-epicanthus inversus syndrome: FOXL2 is aconserved, early-acting gene in vertebrate ovariandevelopment. Endocrinology 144:3237–3243.

Schepers, G., Wilson, M., Wilhelm, D., Koopman, P.(2003) SOX8 is expressed during testis differentiationin mice and synergizes with SF1 to activate the Amhpromoter in vitro. J. Biol. Chem. 278:28101–28108.

Koopman, P (2003). Gender benders. Nature 426:241.[News and Views commentary]

Takada, S and Koopman, P (2003). Origin and possibleroles of the Sox8 transcription factor gene duringsexual development. Cytogenetic and GenomeResearch 101:212–218.

Beverdam, A, Wilhelm, D and Koopman, P (2003).Molecular characterization of three gonadal celllines. Cytogenetic and Genome Research101:242–249.

Bowles, J, Teasdale, R, James, K and Koopman, P(2003). Dppa3 is a marker of pluripotency and has ahuman homologue that is expressed in germ celltumours. Cytogenetic and Genome Research101:261–265.

Plenary or keynote speakerKoopman P. (2003) Regulation of endothelialphenotype by the transcription factor SOX18. GordonResearch Conference, Angiogenesis andMicrocirculation, Newport, RI, USA, 11–15 August.

Koopman, P. (2003) Sex determination, Sox genes,and developmental biology in the genome era.Opening Symposium, Institute for MolecularBioscience, University of Queensland, 19 May.

Koopman, P. (2003) Sox8, like Sox9, is expressedduring testis differentiation in mice and synergizeswith SF1 to activate the Amh promoter in vitro. ThirdInternational Symposium on Vertebrate SexDetermination, Kailua-Kona, Hawaii, 24–28 March.

Invited seminarsKoopman, P. (2003) Sex determination in mice: Sry,testes and everything in between. EuropeanMolecular Biology Laboratory, Mouse BiologyProgram, Rome, Italy, 14 July.

Koopman, P. (2003) Sox transcription factors and theregulation of vascular and hair follicle developmentin mice. European Molecular Biology Laboratory,Mouse Biology Program, Rome, Italy, 14 July.

Koopman, P. (2003) Regulation of angiogenesis inmice by SOX transcription factors. Biomedical andBiomolecular School, Griffith University, Brisbane,Queensland, 9 April.

Koopman, P. (2003) Piecing together the moleculargenetic pathway of sex determination and gonadaldevelopment in mammals. Monash Institute ofReproduction and Development, Melbourne, 20November.


Melissa Little

RENAL DISEASE

Research OverviewThe central theme of thislaboratory is the molecular basisof the development of the kidney.

Each of us has a pair of kidneysthat function to excrete wasteproducts in the form of urine. Thekidneys do this by filtering ourentire blood volume around 30times per day through tiny filterscalled nephrons. Yet only around2 litres of fluid is lost from the

body in the form of urine due to the enormous capacityof the kidney to reabsorb water, ions and nutrients.

The kidneys therefore also play an important role inmaintaining fluid balance, blood volume and electrolytebalance. On top of this, they regulate blood pressure,bone density and number of red blood cells via theproduction of specific growth factors.

Loss of renal function is not compatible with life. Hence,chronic renal failure (CRF) is a devastating disease andan expensive one to treat. It is estimated that 60,000Australians between 12 and 74 yrs have CRF. Each year,approx. 4000 Australian adults will be diagnosed withCRF, costing the health system >$30 million.

The most common cause of end stage renal failure(ESRF) is glomerulonephritis. However the currentsteady rise in ESRF rates is primarily due to anincrease in the number of people with Type IIdiabetes. There is a critical need for the developmentof new therapeutic strategies for the treatment ofCRF. A greater understanding of the processesinvolved in normal kidney development will underpinsuch developments and hence unravelling themolecules directing kidney development is the focusof our laboratory.

ProjectsA master gene involved in generating a kidneyThe WT1 gene encodes a nuclear regulatory proteinessential to giving us kidneys. Without it no kidneysdevelop. Mutations in this gene later in life lead to avariety of kidney diseases, including the childhood

kidney cancer, Wilms' tumour. Hence, normal functionof WT1 is critical for both kidney development and theongoing function of the kidney after birth. Our researchhas focussed on how this regulatory protein works tocreate a kidney and keep it functioning by examiningthe genes it regulates, what proteins and nucleic acidsis interacts with and to what end. This research islikely to identify other genes involved in kidneydevelopment and function and a mutation in whichleads to kidney cancer or disease.

Using comparative biochemistry to understandfunctionOne of the genes that we have discovered plays arole in the development of the kidney is Crim1. Thisgene makes a protein that determines the ability of anumber of other growth factors to move around aswell as regulating the cells they can act on. We haveshown that a loss of this gene results in a number ofkidney defects in mice. We have also usedcomparative biology to study the biochemicalfunction of this protein in fish, in which more isknown about the role of the growth factors regulatedby Crim1. And so the fish, an organism with a verysimple excretory system, can tell us more about thekidneys of more complex animals like humans.

Towards new therapies for renal diseaseIt has long been assumed that development of thekidney ceased at birth with no prospect ofregeneration of new functional units after that time.Developments in stem cell biology over the past 5years has brought in to question similar assumptionsin other organs and we now know that the braincontains neural stem cells and that these can indeedchange into many cell types. What about the kidney?Is there a renal stem cell and might it be used to treatrenal disease?

The other milestone in stem cell biology has been theisolation of human embryonal stem cells bringingwith it the prospect of regenerating tissue even ifthere is no persistent stem cell population. Could weregenerate a kidney or repair kidney damage usingembryonal stem cells?

These two long-term questions are being tackled inthis laboratory by systematically cataloguing all thesecreted and cell surface proteins produced duringkidney development using the genomic technique ofexpression profiling using glass microarray chips.Novel growth factors isolated from these screens arethen assessed for their role in kidney development



using organ culture assays. They can then beassayed for their ability to direct embryonal stemcells towards as renal fate. In addition, we haveestablished an embryonal kidney transplantationassay in which we can test the effect of novel growthfactors on the development of the kidney in vivo.Novel cell surface markers are being used to isolateputative renal stem cells or purify renal progenitorsfrom differentiating embryonal stem cells.

Our work on developing new therapies for CRF formspart of a national consortium linking our laboratorywith others within the IMB, University of Queensland,Monash University and the Monash Institute forReproduction and Development. The group isreferred to as the Renal Regeneration Consortiumand our research is supported by the National

Institutes of Health, USA, along with the AustralianKidney Foundation (recently renamed Kidney HealthAustralia, http://www.kidney.org.au). Our renal stemcell work form part of an international consortium ofNIH funded groups referred to as the Stem CellGenome Anatomy Project (http://www.scgap.org).The kidney component of this work is described athttp://kidney.scgap.org.

Grants awarded in 2003NHMRC Project grant: The role of Crim1, a novelTGFB superfamily modulator, in early vertebratepatterning, vascular and renal development

Research officersGemma MartinezFiona RaeParimala VajjhalaLorine WilkinsonKyra Woods

PhD studentsShannon ArmstrongGrant Challen

Administrative officerMiranda Free

Research assistantsSelena BoydKylie GeorgasKevin Gillinder

Honours studentsGenevieve Kinna

Staff and Students

PublicationsVajjhala, P.R., Macmillan, E., Gonda, T., Little, M. (2003) The Wilms' tumour suppressor protein, WT1, undergoesCRM1-independent nucleocytoplasmic shuttling. FEBS Lett. 554:143-8.

Wilkinson, L., Kolle, G., Wen, D., Piper, M., Scott, J., Little, M. (2003) CRIM1 regulates the rate of processing anddelivery of bone morphogenetic proteins to the cell surface. J Biol Chem. 278:34181-8.

Piper, M., Little, M. (2003) Movement through Slits: cellular migration via the Slit family. Bioessays. 25:32-8.

Kolle, G., Jansen, A., Yamada, T., Little, M. (2003) In ovo electroporation of Crim1 in the developing chick spinal cord.Dev Dyn. 226:107-11.

Samuel, T., Douglas-Denton, R., Hoy, W.E., Hughson, M., Little, M.H., Bertram, JF. (2003) Nephron endowment andpotential therapies for nephron deficit. Todays Life Sciences. 15(5), 30-33

Gross I, Morrison DJ, Hyink DP, Georgas K, English MA, Mericskay M, Hosono S, Sassoon D, Wilson PD, Little M,Licht JD. (2003)The receptor tyrosine kinase regulator sprouty1 is a target of the tumor suppressor WT1 andimportant for kidney development. J. Biol Chem 278(42):41420-30


George Muscat

NUCLEAR HORMONE RECEPTORSAND GENE REGULATION

Research overviewMy research interests focus on the molecularregulation of fat metabolism, cholesterol and energyhomeostasis in skeletal muscle by nuclear hormonereceptors (NHRs). Specifically, we aim to understandthe role of skeletal muscle in cardiovascular diseaseand to elucidate the functional role of orphanreceptors in metabolism.

ProjectsObesity is recognised by the World HealthOrganisation as one of the top ten global healthproblems. It is the leading cause of heart disease,cancer and stroke - the top three causes of death inthe USA, and also causes hypertension, highcholesterol and diabetes. Obesity has now reachedepidemic proportions, as poor diet and sedentaryliving have equalled tobacco as the leading cause ofdeath in westernised world. Moreover, obesity leadsto syndrome X, a disorder that includes elevatedlevels of triglycerides and LDL (bad) cholesterol, lowlevels of HDL (good) cholesterol and hypertension.These are cardiovascular risk factors for diseasessuch as atherosclerosis and type II diabetes.

In this context, skeletal muscle is a major massperipheral tissue that accounts for 40% of the totalbody mass and is a primary site of glucose and fatmetabolism. Consequently, it has a significant role inthe blood lipid profile, insulin sensitivity, andcardiovascular health. Skeletal muscle has a majorprotective role by burning fats and sugars, and theproduction of HDL-cholesterol.

Metabolism is regulated by Nuclear Hormonereceptors (NRs) which function as hormone activatedtranscription factors that bind DNA and control geneexpression NRs function as the conduit betweenphysiology and gene expression. Furthermore, thesehormone regulated DNA binding proteins mediate thelink between genome and phenome, by operating atthe nexus of pathways that control cell specifictranscription, signalling, differentiation and metabolism.

Specific projects in our laboratory include:• Genetic programs induced by the oxy-cholesterol

dependent nuclear receptor, LXR, in skeletalmuscle: regulation of cholesterol metabolism

• Understanding the role of Peroxisome Proliferator-Activated Receptors in skeletal muscle energy andlipid homeostasis.

• Structure/Function and mechanistic analysis oforphan nuclear receptor mediated transcription (e.gNur 77, NOR-1, ROR,and Rev-erb)

• Elucidating the metabolic role of the orphan nuclearreceptors in skeletal muscle and cardiovasculardisease.

• Regulation of gene expression and mammaliandifferentiation by tissue specific transcriptionfactors (e.g Sox 18) and chromatin remodelingfactors (e.g protein arginine methyl transferases).

• Understanding the role of Sox18 in fat metabolism

In 2003 we identified a ‘drugable’ gene, PPAR delta,that plays a key role in increasing metabolic rate andreducing cellular energy stores in a major massperipheral tissue. With diet and fat metabolism themost significant factors in controlling weight gain,the identification of PPARdelta opens up newstrategies and targets for the development of fatburning drugs that increase the metabolic rate.

The functional role of the NR4A subgroup of nuclearreceptors remains obscure however the group hasbeen implicated in cell proliferation, differentiation, T-cell apoptosis, chondrosarcomas, neurologicaldisorders, inflammation, and atherogenesis.

Using structure-function analysis we recentlyidentified the first small molecule regulator of thisclass of orphan NRs. The NR4A subgroup isselectively activated by the purine anti-metaboliteand anti-neoplastic/anti-inflammatory compound 6-Mercaptopurine. Analogues of which are used in thetreatment of leukemias, autoimmune disorders andprevention of organ transplant rejection, gout andherpes virus infections.



This suggests that the signalling pathways inhibitingproliferation via inhibition of de novo purine and/ornucleic acid biosynthesis are involved in the regulationof NRA4A activity. Furthermore, we hypothesize thatthe NR4A subgroup mediates the genotoxic stressresponse, and believe this subgroup may function assensors, which respond to genotoxicity.

The NR4A subgroup clearly represents an excitingscientific challenge, and unlocking the molecularmechanisms that mediate NR4A-dependenttranscription provides the platform for theidentification of novel drug targets

Grants awardedNHMRC Understanding the mechanism of actionand pathophysiological function of the NOR-1 andNur77 orphan nuclear receptors.

NHMRC Genetic programs induced by the nuclearhormone receptor, PPARd, in muscle: control of lipidand energy homeostasis.

NHMRC Transcriptional control of blood vesseldevelopment. (With Peter Koopman)

UQ Research & Development Grant PPAR delta inbreast cancer: gene transcription and molecularmechanisms. (With Dr Sarah Roberts-Thompson)

UQ Research & Development Grant Understandingthe pathophysiological role of the orphan nuclearreceptor, Nurr1 in Neurological disease:pharmacogenomic identification of Nurr1 genes.(With Dr Helen Cooper)

CollaboratorsPeter Koopman, IMB

Professor Peter Leedman, Deputy Director, WesternAustralian Institute for Medical Research, Perth

Dr Jonathan Harris, School of Life Sciences,Queensland University of Technology, Brisbane

Research officersUwe DresselBrett HoskingPatrick Lau

Research assistantsMegan MaxwellRachel BurowShayama WjedesaPaul Rhode

PhD studentsSenali Abayratna WansaMary WangTamara AllenJyotsna Pippal

MPhil studentCatherine Jones

Staff and Students



PublicationsDressel, U., Allen, T.L., Pippal, J.B., Rohde, P.R., Lau,P., Muscat, G.E. (2003) The Peroxisome ProliferatorActivated Receptor {beta}/{delta} agonist, GW501516,regulates the expression of genes involved in lipidcatabolism and energy uncoupling in skeletal musclecells. Mol Endocrinol. 17:2477-2493

Figueroa, A., Cuadrado, A., Fan, J., Atasoy, U.,Muscat, G.E., Munoz-Canoves, P., Gorospe, M.,Munoz, A. (2003) Abstract Role of HuR in skeletalmyogenesis through coordinate regulation of muscledifferentiation genes. Mol Cell Biol. 23:4991-5004.

James, K., Hosking, B., Gardner, J., Muscat, G.E.,Koopman, P. (2003) Abstract Sox18 mutations in theragged mouse alleles ragged-like and opossum.Genesis. 36:1-6.

Wansa, K.D., Harris, J.M., Yan, G., Ordentlich, P.,Muscat, G.E. (2003) Abstract The AF-1 domain of theorphan nuclear receptor NOR-1 mediates trans-activation, coactivator recruitment, and activation bythe purine anti-metabolite 6-mercaptopurine. J Biol Chem. 278:24776-90.

Speaking engagementsOct 2003 Induction of Fatty Acid Oxidation and EnergyUncoupling in Skeletal Muscle Cells by PPAR Delta:PPAR Alpha, Delta and Gamma Have Distinct RolesUS Endocrine Society Hot Topics in Endocrinologymeeting: The Role of Nuclear Receptors inCardiovascular Disease

Feb 4-Feb 9, 2003 ‘Hot to Press’ speaker PPARs:Transcriptional Regulators of Metabolism andMetabolic Disease Keystone meeting Keystone,Colorado

Sept 2003. Late-breaking science session. EndocrineSociety of Australia ESA-SRB 2004

Anything Else• Member of the editorial board for Nuclear Receptor.

A journal to be published by Biomed central limited.

• Editorial board member of Journal of BiologicalChemistry. 2003-2008

The team that identified a new target in the battle of the bulge.


Specifically, we aim tounderstand the role ofskeletal muscle incardiovascular disease andto elucidate the functionalrole of orphan receptors inmetabolism.



Joe Rothnagel

MOLECULAR ANALYSIS OFCUTANEOUS SYSTEMS

Research overviewMolecular genetics and molecular cell biology usingthe mammalian epidermis as the model system.

Keratinocytes are the major cell type of the epidermisand have evolved to make terrestrial life possible. Inlaying down their lives, they provide a barrier thatprotects the organism from harmful UV radiation andfrom viral, fungal and bacterial invasions as well aspreventing desiccation. Keratinocytes express aunique subset of proteins depending on their state ofdevelopment, differentiation or proliferation. Thesecharacteristics make the skin a valuable resource forobtaining expression sequences. In addition, theaccessibility of skin makes it the model system ofchoice for testing gene expression constructs thatcould be used in gene therapy applications.

ProjectsA major focus of this laboratory is currently directedtowards the use of tissue specific promoters for usein expression vector constructs. We use keratinpromoters as the model system because they showcell type and differentiation state specific expression.

In addition, they are some of the most efficientmammalian promoters thereby ensuring high levelsof expression. In parallel to the promoter studies weare also investigating the role of post-transcriptionalmechanisms in regulating the final levels of geneproducts. This has led to the development of shortcis-sequences (GeneDimmer & GeneBooster) thatcan be used to turn up or down gene expression.

In addition we have examined alternative splicing ofkey transcripts expressed by keratinocytes usingboth data mining and candatiate gene approaches.This has resulted in the amazing finding that thekinesin light chain gene has the potential to produceover 280,000 alternative forms from the differentialsplicing of exons 13 to 23. We have also analysed thealternatively-spliced exons of the Gli1 oncogene thatresult in 5' leader sequences with differingtranslational capacities. Only the transcript with thehighest translational capacity was associated withbasal cell carcinoma. We have also characterisedthe mouse and human Frizzled-3 genes and identifiedseveral alternatively spliced variants that arepredicted to interact with each other to modulateWnt signalling.

GrantsNHMRC Alternative splicing of GLI1 and its role intumorigenesis

Uniquest Pty Ltd GeneDimmer Development grant



PublicationsEllis T, Smyth I, Riley E, Bowles J, Adolphe C,Rothnagel JA, Wicking C, Wainwright BJ. (2003)Overexpression of Sonic Hedgehog suppressesembryonic hair follicle morphogenesis. Dev Biol.263:203-15.

McCart AE, Mahony D, Rothnagel JA. (2003)Alternatively spliced products of the human kinesinlight chain 1 (KNS2) gene. Traffic. 4:576-80.

Research officersXue qing WangLexie Friend

PhD studentsMonica KesslerJonathan BeesleyAmy McCartWolfgang Hofmeister

Research assistantTom Hadwen

Staff and Students

CollaboratorsBrandon Wainwright, IMB

Ross Smith, Department of Biochemistry andMolecular Biology, UQ

Timothy Rayner, Child Health Research Institute,Adelaide

Pritinder Kaur, Peter MacCallum Cancer Centre,Melbourne

Paul Bowden, University of Wales College ofMedicine, Cardiff, UK

Richard Presland, University of Washington, Seattle,USA


Rick Sturm

MELANOCYTE BIOLOGY ANDPIGMENTATION GENETICS

Research overviewThe pigmentary system is dependent on the productionof the light absorbing biopolymer, melanin and isresponsible for skin, hair and eye colour. Melanocyteswithin human skin are situated on the basal layerbetween the dermis and epidermis and have a numberof dendritic processes that interdigitate with thesurrounding keratinocytes. The characterisation ofproteins responsible for the pigmentation pathway hasprovided the basis to the biochemical understanding ofsome of the mouse coat colour and human albinismconditions. Darker forms of melanin protect the skinfrom solar radiation exposure, however melanocytes arealso the cell-type from which malignant melanoma canoriginate. We are studying the human pigmentationsystem to understand the genetic basis of cellulardifferentiation, tissue-specific gene expression andcellular transformation induced by solar UV light.Primary melanocyte and melanoblast precursor cellshave been cultured from human skin and thepigmentation, growth and differentiation characteristicsof each cell-type are being investigated.

The major goal of our research efforts is to understandthe genetic basis of human pigmentation and toassess the phenotypic association of these physicaltraits with skin UV-sensitivity and skin cancerpromotion. The group has isolated and characterisedseveral human genes that encode enzymes, structuralproteins, signaling molecules and receptors that areinvolved in this process. Functional analysis of thisgene set will ultimately provide a full appreciation ofthis biological system.

ProjectsMC1R polymorphism in skin cancer risk phenotypesPopulation studies have revealed the coding region ofthe human melanocortin-1 receptor (MC1R) gene to beremarkably polymorphic, with over 30 allelic variants sofar identified.

Several of the MC1R variant alleles have beenassociated with the red hair and fair skin (denoted RHC;red hair colour) phenotype, a condition that is caused bythe synthesis of a high level of pheomelanin which canplace individuals at a higher risk of skin cancer.

MC1R encodes a seven-transmembrane G-proteincoupled receptor belonging to the melanocortinreceptor family and binds the α-melanocyte stimulatinghormone (α-MSH). Hormonal stimulation of MC1Rexpressed on the cell membrane surface is central tothe tanning response of human melanocytes followingUV irradiation.

Stimulation of the MC1R receptor results in a rise inintracellular cAMP levels to elicit changes inmelanocyte gene expression largely through themicrophthalmia transcription factor (MITF), whichappears to be critical for activation of theeumelanogenic pathway producing the black/browneumelanin pigment. Combined treatment ofmelanocytes with UV and α-MSH also potentiates celldendricity and transfer of pigment to keratinocytes.

Given that pigmentary traits such as fair skin, lack oftanning ability and propensity to freckle have beenidentified as risk factors for both melanoma and non-melanocytic skin cancer (NMSC), it follows that MC1Rvariants that are associated with these pigmentary traitsshould also be found in association with an increasedrisk for these forms of skin cancer.



Several of the studies of the MC1R variants inrelation to the RHC phenotype have suggested theirassociation with the number of freckling sites or sun-induced lentigines. In most cases two MC1Rvariants are required to express the red hair-fair skinphenotype. In particular the R151C, R160W andD294H variants are the most commonly associatedvariants seen in the South East Queenslandpopulation with at least one of these alleles found in93% of those with red hair.

We have examined MC1R variant allele frequenciesin the general population and a collection ofadolescent dizygotic and monozygotic twins todetermine statistical associations of pigmentationphenotypes with increased skin cancer risk. Thisincluded hair and skin color, freckling, mole countand sun exposed skin reflectance. Nine variantswere studied and designated as either strong R (OR =63; 95% CI 32-140) or weak r (OR = 5; 95% CI 3-11) redhair alleles. Penetrance of each MC1R variant allelewas consistent with an allelic model where effectswere multiplicative for red hair but additive for skin reflectance.

Functional testing of MC1R variant allelesTo address the cellular effects of MC1R variantalleles in signal transduction these receptors wereexpressed in permanently transfected HEK293 cells.Measurement of receptor activity via induction of acAMP-responsive Luciferase reporter gene, foundthe R151C and R160W receptors were active in thepresence of α-MSH ligand but at much reducedlevels compared to that seen with the wildtypereceptor. The ability to stimulate phosphorylation ofthe CREB transcription factor was also apparent inall stimulated MC1R variant allele expressing HEK293cell extracts as assessed by immunoblotting. Incontrast human melanoma cell lines showed widevariation in the their ability to undergo cAMP-

mediated CREB-phosphorylation. Culture of humanmelanocytes of known MC1R genotype may providethe best experimental approach to examine thefunctional consequences for each MC1R variantallele. With this objective we have established over300 melanocyte cell strains of defined MC1Rgenotype. These include strains which are MC1Rwildtype consensus, variant heterozygotes, andhomozygotes for strong R alleles R151C and R160W.Ultrastructural analysis demonstrated that onlyconsensus strains contained Stage III-IVmelanosomes in their terminal dendrites whereasR151C and R160W homozygote strains contained onlyimmature Stage I-II melanosomes. Such geneticassociation studies combined with the functionalanalysis of MC1R variant alleles in melanocytic cellsshould provide a link in understanding theassociation between pigmentary phototypes and skincancer risk.

Culture of human melanoblast stem cells from skinMany diseases of pigmented cells, from vitiligo andpiebaldism to melanoma, are caused by aberration inmelanocyte growth or differentiation. Investigationsinto the pathways of melanocyte formation anddifferentiation from precursor melanoblast cultures areessential for the analysis of basic mechanisms in cellcommitment and differentiation, for comparison withpoorly-differentiated cells from melanoma, and for themolecular analysis of the many known geneticdisorders of melanocyte development. Recentlymethods for establishing mouse melanoblasts havebeen published and while there are differences inmouse and human skin we sought to adapt thesetechniques to investigate the human melanocyte stemcell from neonatal foreskin. The ability to growmelanoblasts will provide an invaluable source of cellsto allow the study of the pathway of melanocytedifferentiation and cancer formation.


Oculocutaneous albinism in a PolynesiancommunityWe have initiated a study of an original humanoculocutaneous albinism (OCA) phenotype in aSouth Pacific island community of Polynesiandescent to establish the nature of itsinheritance through extensive pedigreeanalysis and to experimentally determine thegenetic cause. Oculocutaneous albinism type2 (OCA2) is a human autosomal recessivehypopigmentation disorder associated withpathologic mutations of the P-protein. Thefunctional interaction of the OCA2 geneencoding the melanosomal P-protein productwithin the biosynthesis of melanin pigment hasnot yet been defined however, its disruptionresults in a generalised reduction of pigment inthe skin, hair and eyes plus associated visualimpairment. In the last few decades there hasbeen little published about OCA in the SouthPacific Region and no causative molecularmutation has so far been previously reported.In this study, we investigated a form of OCA ina Polynesian population with an observedphenotype characterised by fair skin withgreen or blue eyes. Hair presented with aunique red colouration since birth, with tonesranging across individuals from Yellow-Red toBrown-Red/Auburn. We have geneticallyscreened for mutations in the P-protein andMC1R as their products have previously beenshown to be associated with red hair/ fair skinand OCA2.

Grants awardedQueensland Cancer Fund Role of Beta3integrin induced osteonectin expression inmelanoma metastasis.

NHMRC The role of MC1R polymorphism inskin cancer risk phenotypes.

ARC Parallel genetic and cellular analysis ofmelanogenesis: A new paradigm to studyvariation in pigmentation.

CollaborationsNicholas Hayward, Queensland Institute of Medical Research.

Helen Leonard, Queensland Institute of Medical Research.

Nicholas Martin, Queensland Institute of Medical Research.

Peter Parsons, Queensland Institute of Medical Research.

Jenny Stow, IMB

Dorothy Bennett, Department of Basic MedicalSciences, St. George's Hospital MedicalSchool, London, UK.

Meenhard Herlyn, Wistar Institute,Philadelphia, USA.



Publications and papersLeonard, J.H.,. Marks, L.H., Chen, W.,. Cook, A.L.,Boyle, G.M., Smit, D.J., Brown, D.L., Stow, J.L.,Parsons, P.G., Sturm, R.A. (2003) Screening of humanprimary melanocytes of defined melanocortin-1receptor genotype: pigmentation marker,ultrastructural and UV-survival studies. Pigment CellResearch, 16:198-207

Sturm R.A., Duffy, D.L., Box, N.F., Newton, R.A.,.Shepherd, A.G, Chen, W., Marks, L.H., Leonard, J.H.,Martin, N.G. (2003) Genetic Association and CellularFunction of MC1R Variant Alleles in HumanPigmentation. Proceedings of the 5th InternationalMelanocortin Meeting. Annals of the NY Academyof Science, 994:348-358.

Sturm, R.A. Duffy D.L., Box N.F., Chen W., Smit D.J.,.Brown D.L, Stow J.L., Leonard J.H. Martin. N.G.(2003) The role of melanocortin-1 receptorpolymorphism in skin cancer risk phenotypes.Proceedings of XVIIIth International Pigment CellConference. Pigment Cell Research, 16:266-272

Cook, A.L., Donatien, P.D., Smith, A.G., Murphy, M.,Jones, M.K., Herlyn, M., Bennett, D.C.,, Leonard, J.H.,Sturm, R.A. (2003) Human Melanoblasts in Culture:Expression of BRN2 and Synergistic Regulation byFibroblast Growth Factor-2, Stem Cell Factor andEndothelin-3. Journal of Investigative Dermatology,121:1150-1159.

ConferencesR.A. Sturm “Human pigmentation and melanoma:MC1R genotype, phenotype and populationgenetics”. First Annual Melanoma ResearchCongress, Wyndham Franklin Plaza Hotel,Philadelphia, Pennsylvania, USA, June 16-18, 2003

R.A. Sturm. “Human pigmentation and skin cancer:MC1R genotype, phenotype and population genetics”Mutagenesis and Experimental Pathology Society ofAustralasia, Conference on Prevention, Repair andRegeneration of Environmental Epithelial Damage,The Veterinary Science Conference Centre, TheUniversity of Sydney, November 26-28, 2003.

OtherAssociate Editor of Pigment Cell Research

Associate Editor of Melanoma Research

Research officersRichard Newton

Research assistants:Darren SmitWei Chen

PhD students:Brooke GardinerAnthony CookLuke KirkwoodHelene Johanson

Staff and Students

The major goal of ourresearch efforts is tounderstand the geneticbasis of humanpigmentation and toassess the phenotypicassociation of thesephysical traits with skinUV-sensitivity and skincancer promotion.


Brandon Wainwright

MOLECULAR GENETICS OFHUMAN DISEASES

Research overviewOur research group is focused on elucidatingmolecular pathology of human genetic disease,primarily through the analysis of the single genedisorder, cystic fibrosis and through the discovery ofpatched, the gene responsible for both the inheritedand sporadic forms of basal cell carcinoma of the skin.

ProjectsOur group examines the molecular pathology of twodistinct genetic diseases. Cystic fibrosis (CF) is themost common inherited lethal disorder in caucasianpopulations affecting the lung and digestive system.CF patients have a chronic infection with thebacterial pathogen Pseudomonas aeruginosa.Accordingly we examine the role of the cysticfibrosis gene (and modifier genes) in responding toinflammation and bacterial infection in the lung.

Through cloning the gene mutated in inherited skincancer we identified the tumour suppressor genepatched. Analysis of patient material has indicated arole for this gene and its signalling pathway in manytumour types. Our laboratory applies geneticinformation from patient analysis to further ourunderstanding of the patched pathway. A powerfulapproach to the analysis of human genetic disease isthe use of model systems, such as the mouse.Consequently, many of our studies are directed atunderstanding gene function in murine systems. As aresult of these studies we have a particular interestin the interface between developmental biology andhuman genetics, and in therapeutic strategies suchas gene therapy.

Key projects include:• Structure/function of the patched tumour

suppressor gene

• The cellular origin of basal cell carcinoma andcommon brain tumours.

• Regulation of the inflammatory response by CFTR

• Origin of the cystic fibrsosis inflammatory response

• Novel mouse modifer genes affecting lungdevelopment and inflammation

Research officersChristelle AdolpheElaine CostelloeTammy EllisBrendan McMorran

PhD studentsAzita AhadizadehSusan GilliesWendy IngramKaren McCueJim Palmer

Research assistantsMelissa BourboulasRehan HeatheringtonStephanie MartellEmily RileyLiam Town

Honours studentsJack King-Scott

Staff and Students


IMB ANNUAL REPORT 2003 PAGE 00IMB ANNUAL REPORT 2003 PAGE 59

PublicationsEvans, T.M., Ferguson, C., Wainwright, B.J., Parton,R.G., Wicking, C. (2003) Rab23, a negative regulator ofhedgehog signaling, localizes to the plasma membraneand the endocytic pathway. Traffic. 4:869-84.

Ellis, T., Smyth, I., Riley, E., Bowles, J., Adolphe, C.,Rothnagel, J.A., Wicking, C., Wainwright, B.J. (2003)Overexpression of Sonic Hedgehog suppressesembryonic hair follicle morphogenesis. Dev Biol.263:203-15.

Wells, C.A., Ravasi, T., Faulkner, G.J., Carninci, P.,Okazaki, Y., Hayashizaki, Y., Sweet, M., Wainwright,B.J., Hume, D.A. (2003) Genetic control of the innateimmune response. BMC Immunol. 4:5.

Oceandy, D., McMorran, B., Schreiber, R.,Wainwright, B.J., Kunzelmann, K. (2003) GFP-taggedCFTR transgene is functional in the G551D cysticfibrosis mouse colon. J Membr Biol. 192:159-67.

Our research group isfocused on elucidatingmolecular pathology ofhuman genetic disease,primarily through theanalysis of the singlegene disorder, cysticfibrosis and through the discovery ofpatched, the generesponsible for both theinherited and sporadicforms of basal cellcarcinoma of the skin.

A key signalling molecule c-fos activates transcription 60 minutes after infecting epithelial cells with Pseudomonas aeruginosa

The human cystic fibrosis gene (green) is active in mouse lung andcorrects the cystic fibrosis defect.


Michael Waters

GROWTH HORMONE ANDCYTOKINE SIGNALLING

Research overviewThe final height of an individual is determined by theactions of growth hormone during childhood andadolescence. In the adult, growth hormone is animportant metabolic agent regulating bodycomposition and strength, opposing the actions ofinsulin. In old age, growth hormone status determineslifespan, at least in animal models. We study themeans used by growth hormone to achieve thesechanges, from high resolution protein structures togenetically engineered animals.

The centrepiece of these studies is the action of thegrowth hormone receptor, which determines thedegree of the cell response to growth hormone, andwhich we cloned collaboratively with Genentech.

ProjectsBeing able to modify the functioning of this receptorallows us to control body growth, body compositionand ageing, liver regeneration and certain cancers.Currently, our research has:

(1) Elucidated the signalling mechanism used by thehormone to activate the receptor at a molecularlevel through X-ray crystallography, fluorescenceand bioluminescence resonance energy transfer,site directed mutagenesis and the creation ofreceptors which are active in the absence of

hormone. We propose that the hormone activatesa preformed receptor dimer by rotating itstransmembrane domains, switching on the JAKtyrosine kinases bound to the receptor below thecell membrane, allowing them to initiate thegrowth signal.

(2) Determined the cellular domain of the receptorresponsible for postnatal growth by creatinggenetically engineered mice with deletions andmutations in the internal signalling sequences ofthe receptor.

(3) Determined which genes are regulated by thedifferent signalling domains within the internalsignalling sequence of the receptor, using genemicroarrays.

(4) Defined novel actions of growth hormone,particularly related to exacerbation ofinflammation, through the use of these engineeredmice and the gene microarrays. This may beimportant in autoimmune diseases such asrheumatoid arthritis and systemic lupuserythematosus.

(5) Defined a role for the growth hormone receptorwhich is found in the cell nucleus, and themechanism used to transport it there. Our datasupports a role in cell proliferation, especiallyduring liver regeneration. This is potentiallyimportant in breast and colon cancer.

(6) Created several "superactive" porcine growthhormones for use in increasing food conversionefficiency and lean meat accretion in the pig industry.

(Left) Molecular modelling of GH receptor agonist monoclonal antibody docking to GH receptor; (Centre) Targeting knock-in mutations to thesignalling domain of GH receptor decreases growth proportionate to severity of mutation; (Right) A new model for GH receptor activationbased on relative rotation of receptor subunits.



Grants awardedNHMRC Proliferative role of nuclear GH and cancer.

NHMRC The genetic programs induced by growthhormone

NHMRC A transgenic analysis of the physiologicalroles of signalling domains in the growth hormonereceptor

NHMRC Structure – function studies on the growthhormone receptor

Collaborators International

Prof G Morel, CNRS Lyon, France

Prof R Ross, University of Sheffield, UK

Prof S. Swanson, Chicago, USA

Dr B Hendricks, Utrecht, Netherlands

Prof D Langosch, Munich, Germany

Prof S Frank, Alabama, USA

Prof S Gilmour, University of Auckland, New Zealand

Prof M Parker, St Vincents Medical ResearchInstitute, Sydney

Dr K Eidne, University of Western Australia

Prof D Jans, Monash University, Melbourne

Prof Patrick Tam, Children's Medical ResearchInstitute, Sydney

Research officersDr Richard BrownDr Agnieszka LichanskaDr Hideo Yoshizato

Research assistantsLinda KerrKathryn Fletcher Min RaoLiz Holliday Elizabetta D'Aniello

PhD studentsBecky Conway CampbellRebecca PelekanosYu Wan Jongwei Wooh

Honours studentKate Palethorpe

Staff and Students

PublicationsParsons, S.A., Banks, G.B., Rowland, J.A.,Coschigano, K.T., Kopchick, J.J., Waters, M.J.,Noakes, P.G. (2003) Genetic disruption of the GHreceptor does not influence motoneuron survival inthe developing mouse. Int J Dev Biol 47:41-49.

Haase, H.R., Ivanovski, S., Waters, M.J., Bartold, P.M.(2003) Growth hormone regulates osteogenic markermRNA expression in human periodontal fibroblastsand alveolar bone-derived cells. J Periodontal Res.38:366-74.

Shang, C.A., and Waters, M.J. (2003) ConstitutivelyActive Stat5 can replace the requirement for GH inadipogenesis of F442A. Mol Endocrinol. 17:2494-508.

Raccurt, M., Tam, S.P., Lau, P., Mertani, H., Lambert,A., Garcia-Caballero, T., Li, H., Brown, R.J., McGuckin,

M.A., Morel, G., Waters, M.J. (2003) Suppressor ofcytokine signalling gene expression is elevated inbreast cancer. Brit J Cancer 89:524-32.

Wan, Y., Zheng, Y.Z., Harris, J.M., Brown, R., Waters,M.J. (2003) Epitope map for a GH receptor agonistmonoclonal antibody, MAb 263. MolecularEndocrinology 17:2240-50.

Conferences, invited lecturesPlenary lecture for Asia-Oceania Medal of theSociety for Endocrinology, Royal College ofPhysicians, London

Symposium on role of GH in embryo and fetaldevelopment, Australian Society for MedicalResearch


Carol Wicking

DEVELOPMENTAL GENES AND HUMAN DISEASE

Research overviewDefects arising from abnormal embryonicdevelopment are a major cause of infant mortalityand childhood disability. Many such disorders arecharacterised by anomalies of the limbs andcraniofacial region, supporting the conservation ofmolecular processes governing the development ofthese structures. We are involved in isolation ofnovel genes involved in embryonic development ofthe limb and face, as well as more fullycharacterising the role of these and other knowngenes in embryogenesis and disease.

ProjectsRegulation of the hedgehog pathway by intracellulartrafficking and sterol levelsThe hedgehog signalling pathway is central to thecorrect development of an embryo, as well as beinginvolved in a range of tumour types. The elucidationof the steps involved in the correct functioning of thispathway is likely to shed light on a range of diseaseprocesses. The regulation of this pathway at thecellular level is extremely complex and has beenshown to involve intracellular trafficking events andsterol levels. We are investigating the subcellularlocalisation of members of the hedgehog pathway atboth the light and electron microscopy levels. To datethis analysis has focussed on the receptor molecule

Patched and Rab23, a vesicular transport proteinknown to negatively regulate vertebrate hedgehogsignalling.

Microarray analysis in a mouse model of limbdevelopment We have used microarray technology to investigateexpression differences in the embryonic limb of themouse mutant extra-toes (XtJ) versus the wild-typelimb bud. This mutant involves a deletion of the geneencoding the Gli3 transcription factor which, togetherwith Gli1 and Gli2, is involved in mediating the outputof the hedgehog signalling pathway. As a result ofour microarray analysis we have identified a numberof known developmental genes as well as completelynovel genes which are regulated by Gli3 in thedeveloping limb. Given that Gli3 is a key molecule inpatterning of the embryonic limb bud we believe thatmany of the genes we have identified will encodemolecules which are also important to this process.

Identification of genes involved in craniofacialdevelopmentDefects in facial development are a common featureof human dysmorphology syndromes. Using themouse as a model system, we have adopted agenomics approach based on subtractivehybridisation to enrich for genes expressed inpharyngeal arches, the precursors to the mammalianface. As a result we have isolated a large number ofboth novel and previously identified genes whoseexpression pattern during embryogenesis suggests aspecific role in the development of a range of organsystems. Functional and cell biologicalcharacterisation of a number of these genes iscurrently underway.



CollaboratorsRob Parton, IMBBrandon Wainwright, IMBMarcelo Bento Soares, University of Iowa, USAPete Scambler, Institute of Child Health, London, UK

Joy Richman, University of British Columbia,Vancouver, CanadaAndrew Lidral, University of Iowa, USAS. Peter Klinken, University of Western Australia

Research officersFiona Simpson

Research assistantsNatalie ButterfieldKelly Lammerts van Bueren

PhD studentsTim EvansEdwina McGlinnJenny Bennetts

Summar scholarVicki Metzis

Staff and Students

PublicationsFowles, L.F., Bennetts, J.S., Berkman, J.L., Williams, E.,Koopman, P., Teasdale, R.D., Wicking, C. (2003)Genomic screen for genes involved in mammaliancraniofacial development. genesis 35:73-87.

Ellis, T., Smyth, I., Riley, E., Graham, S., Elliot, K.,Narang, M., Kay, G.F., Wicking, C., Wainwright, B. (2003)A Patched1 conditional null allele in mice. genesis36:158-161.

Ellis, T., Smyth, I., Riley E., Bowles, J., Adolphe, C.,Rothnagel, J.A., Wicking, C., Wainwright, B.J. (2003)Overexpression of Sonic Hedgehog suppressesembryonic hair follicle morphogenesis. Dev. Biol.263:203-215.

Evans, T.M., Ferguson, C., Wainwright, B.J., Parton,R.G., Wicking, C. (2003) Rab23, a negative regulator ofhedgehog signaling, localizes to the plasma membraneand the endocytic pathway. Traffic 4:869-884.

Conferences & SeminarsIdentification and analysis of genes involved inmammalian craniofacial development COMBIO,October 2003, Melbourne, Australia

We are involved in isolation of novel genes involvedin embryonic development of the limb and face, aswell as more fully characterising the role of theseand other known genes in embryogenesis anddisease.


CELL ARCHITECTURE ANDDYNAMICSFocussing on• Visual cell project• Cell architecture and trafficking• Virtual membrane project

This program has received considerable support fromthe NANO major national research facility, the AustralianCancer Research Foundation and NIH, and is a majorinitiative of the IMB with the application of cyro-electronmicroscopy, cell tomography, advanced visualisation andhigh performance computing. It also includes the ARCCentre in Bioinformatics.

Research Group LeadersJohn HancockBen HankamerAlisdair McDowallRob PartonJennifer StowRohan TeasdaleAlpha Yap



John Hancock

SIGNAL TRANSDUCTION

Research overviewOur group studies mammalian intracellular signalling.We are especially interested in the function of Rasproteins. These small GTP binding proteins operate asmolecular switches in signal transduction pathwaysand are present in a mutant, activated state in manyhuman tumours. Understanding the basic biology ofRas has major implications for the development ofnovel anti-cancer therapeutics.

ProjectsRas proteins operate as molecular switches in signaltransduction pathways downstream of tyrosine kinaseand G-protein coupled receptors. This is a fascinatingmodel system because there are three highlyhomologous Ras isoforms that generate different signaloutputs despite sharing a common set of effector andactivator proteins. Our studies strongly suggest theexistence of parallel Ras signalling pathways that arebased on different plasma membrane microdomains. Amajor thrust of our current program is to dissect thecomposition and function of these microdomains.Specific themes include:

• Molecular mapping of the proteins and lipids ofplasma membrane microdomains.

• Electron microscopic visualization and quantitativecharacterization of surface microdomains to build upa high-resolution 2D map of the microdomains of theinner plasma membrane.

• Investigation of the dynamic regulation ofmicrodomain localization of Ras and Ras-interactingproteins in response to physiological stimuli.

• Mechanism of Raf-1 activation, to characterize themultistep Raf-1 activation process spatially within theplane of the plasma membrane.

• Characterization of the mechanism(s) whereby K-rasis transported to the plasma membrane and how Rasproteins engage different endocytic pathways.

CollaboratorsYoav Henis and Yoel Kloog, University of Tel Aviv, Israel

Mark Philips, New York University, USA

Brian Gabrielli, Queenland Institute of MedicalResearch

GrantsNational Institutes of Health Plasma membranemicrodomains and Ras function

Queensland Cancer Fund Switch-like signaling in theRaf/MEK cascade

ARC Investigation of the mitotic function of MEK

NHMRC Plasma membrane structure and function

Research officersSandrine RoySarah PlowmanMichael Hanzal-BayerAngus HardingMichelle Hill

PhD studentsAndrew GoodallChi-Yan Lau

Research assistantsAnnette LaneCornelia MunckeElizabeth Westbury

Research fellowKim Yap-Weber

Staff and Students



PublicationsHansen, M, Prior, I.A., Hughes, P.E., Oertli, B., Chou, F.L.,Willumsen, B.M., Hancock, J.F., Ginsberg, M.H. (2003)C-terminal sequences in R-Ras are involved in integrinregulation and in plasma membrane microdomaindistribution. Biochem Biophys Res Commun.311:829-38.

Harding, A., Hsu, V., Kornfeld, K., Hancock, J.F. (2003)Identification of residues and domains of Raf importantfor function in vivo and in vitro. J Biol Chem.278:45519-27.

Hancock, J.F. (2003) Ras proteins: different signals fromdifferent locations. Nat Rev Mol Cell Biol. 4:373-84.

Wyse, B.D., Prior, I.A., Qian, H., Morrow, I.C., Nixon, S.,Muncke, C., Kurzchalia, T.V., Thomas, W.G., Parton,R.G., Hancock, J.F. (2003) Caveolin interacts with the

angiotensin II type 1 receptor during exocytic transportbut not at the plasma membrane. J Biol Chem.278:23738-46.

Prior, I.A., Parton, R.G., Hancock, J.F. (2003) Observingcell surface signalling domains using electronmicroscopy. Sci STKE 8:PL9.

Harding, A., Giles, N., Burgess, A., Hancock, J.F.,Gabrielli, B.G. (2003) Mechanism of mitosis-specificactivation of MEK1. J Biol Chem. 278:16747-54.

Prior, I.A., Muncke, C., Parton, R.G., Hancock, J.F. (2003)Direct visualisation of Ras proteins in spatially distinctcell surface microdomains. J Cell Biol. 160:165-70.

Understanding the basic biology of Ras has major implications for the development of novelanti-cancer therapeutics.


Ben Hankamer

MEMBRANEPROTEINSTRUCTURES

Research OverviewOur group is focused ondeveloping a broad basedplatform for the structuredetermination of membraneproteins and macromolecularassemblies, based upon singleparticle analysis, electron and X-ray crystallography.

A strong research focus of the group involvesautomation to increase the rate of protein structuredetermination. A selection of proteins involved in arange of important biological processes andbiotechnology applications (eg. Biohydrogen) arealso currently being investigated as part of the IMB'sVisual Cell program.

ProjectsStructural Biology

Single Particle analysisSingle particle analysis (SPA), when coupledwith electron cryo-microscopy, is ideal for thestructure determination of large membraneproteins and macromolecular assemblies. Inessence, SPA is the process of determining 3Dreconstructions of macromolecules from theirconstituent 2D projection images captured byelectron cryo-microscopy.

Images of randomly oriented particles supportedin a thin layer of vitreous ice are aligned andclassified according to their orientation. Theclass averages are then merged to produce 3Dreconstructions.

Electron CrystallographyElectron crystallography requires the use of 2Dcrystals. These are particularly well suited formembrane protein structure determination as the

crystallised proteins are arrayed within a nearnative lipid bilayer.

The 2D crystals are imaged over a range of tiltangles and the processed images merged tofacilitate 3D image reconstruction. Newprocesses of monolayer and bilayercrystallogenesis methods are being developed tofacilitate template mediated crystal production.

Cubic Phase crystallizationThe use of cubic phase lipids for the purpose ofmembrane protein crystallisation is also beingexplored. Cubic phase lipid structures are highlyordered, contorted bilayers, which arecontinuous and organized in 3D space.

Membrane proteins can be inserted into thesecubic phase lipid matrices and induced to formhighly ordered three-dimensional crystals wellsuited for high resolution X-ray crystallographicanalysis. The method can be thought of as a hybridbetween 2D bilayer and 3D crystal production.

Biology and Biotechnology

Bio-HydrogenThe development of a clean, sustainable andeconomically viable energy supply for the futureis one of the most urgent challenges of ourgeneration, given that oil production is estimatedto peak in 5-33 years time.

There is now a concerted international effort toswitch from a fossil fuel to a hydrogen economy.We are exploring the use of a green algal systemthat uses solar energy to split water (H2O) intohydrogen (H2) and oxygen (O2), for large scale H2production. Subsequent combustion of H2 yieldsonly H2O eliminating both net H2O use and theproduction of harmful greenhouse gases,associated with the burning of fossil fuels.

The identification of marine algae capable ofproducing H2 has the added benefit that H2production could be coupled with H2Opurification, as the product of H2 combustion ispure H2O.


GrantsARC Discovery grant High resolution single particleanalysis of biological macromolecules

UQ Research Development grant Structural biologyof macromolecular assemblies as part of the visualcell program

CollaborationsDr Olaf Kruse, Department of Biology, University ofBielefeld, Germany

Professor Bernard Pailthorpe, VisLab and School ofPhysics, The University of Sydney

Dr Paul Young, Department of Microbiology andParasitology, The University of Queensland

Dr Jasmine Banks, Advanced ComputationalModelling Centre, The University of Queensland

Associate Professor Alasdair McDowall, IMB

Dr Geoff Ericksson, Advanced ComputationalModelling Centre, The University of Queensland

(Opposite page) A Chlamydomonas reinhardtii cells (biohydrogen), B Photosystem II structure determined by electron crystallography

(Above) A Single particle images, B 3D Reconstruction of PSPA, C 2D Crystal of photosystem II, D Cubic phase matrix

Research officerJens Rupprecht

Research assistantsRosalba RothnagelMichael Landsberg

Honours studentCameron Votan

Staff and Students

Publications and papersSennoga, C., Heron, A., Seddon, J.M., Templer, R.H.,Hankamer, B. (2003) Membrane-protein crystallizationin cubo: temperature-dependent phase behaviour ofmonoolein-detergent mixtures. Acta Cryst Section DBiological Crystallography 59: 239-246

Conferences Boden Artificial Photosynthesis Conference 2003

Broome Crystallography Conference 2003

Seefeld Electronmicroscopy Conference 2003

Combio 2003



Alasdair McDowall

CRYO-ELECTRON MICROSCOPYOF VITREOUS SECTIONS

Research overviewOur group is studying biological structures by cryo-sectioning vitreous bulk material for cryo-electronmicroscopy (cryo-em). Considered the dream methodof structural cell biologists, it involves vitrifying anative sample of cells or tissue by rapid cooling,cutting into ultra-thin <100nm sections and cryo-emobservation of the perfectly preserved details.

In collaboration with the Centre for Microscopy andMicroanalysis at UQ, Brad Marsh at the IMB andProfessor Jacques Dubochet from the University ofLausanne we are using high pressure freezing andcryosectioning to investigate bulk structure systemsof mammalian cells, bacteria and chloroplastorganelles. We are also using cryo-electronmicroscopy together with thin cryo-preparations toinvestigate plasma membrane protein packingarrangements in collaboration with the Parton groupat the IMB.

Cryo-electron microscopy of vitreous sections(CEMOVIS) demonstrates its full potential whencombined with computerized electron tomography for3-D reconstruction.

Projects3D electron (cryo ET) tomography of cellularorganellesAs seen in figure 1, the detail of this cryo-section ofnative cellular chloroplast ultrastructure is welldefined. Studies are underway to incorporate 3Dtomography of similar structures providing valuablenew insights into the 3D ultrastructure of the lightcapturing machinery of Chlamydomonas reinhardtiiand may yield new information on the functionalinteraction between mitochondria and chloroplasts.

The ultimate vision of the Visual Cell ProjectTechnologies as described here are at the front endof a series of projects to provide a web-basedgraphical user interface (GUI) which in time will linkresearchers to individual “Visible Cell” projects i.e.3D reconstructions of entire cells at ≤5nm resolution.Examples include the pancreatic beta cell (Marshgroup at IMB), C. rheinhardtii (Hankamer group atIMB), and cyanobacteria Lyngbya majuscula(Dubochet group, University of Lausanne).

In the "Visible Cell" environment researchers will beable to manoeuvre within the raw 3D cellularvolumes together with their accompanying 3D modeldata to selectively inspect and visualize organelles,macromolecular assemblies (modelled into thetomograms) and the structures of individual subunitsof these assemblies.

With the installation in 2004 of the MNRF- NANO300keV cryo electron microscope, 3D electrontomogram reconstructions will be built from stacks ofthick (300-400nm) serial sections cut from cells andimaged by dual-axis EM tomography with a targetresolution of ≤5nm. This resolution is sufficientlyhigh to allow us to determine the feasibility andlimitations of trying to resolve macromolecularcomplexes within the 3D cellular data by virtue oftheir structural signatures alone.

CollaboratorsProfessor Jacques Dubochet, University of Lausanne,Switzerland

Dr Mark Blackford, Australian Nuclear Science andTechnology Organisation, ANSTO, , Menai, N.S.W

Dr Minoo Moghaddam and Dr Gerald Both, CSIROMolecular Science, North Ryde, NSW 1670, Australia

2003 GrantsARC Discovery Project High resolution single particleanalysis of biological macromolecules

PublicationsHankamer, B., Rothnagel, R., McDowall, A., Ericksson,G., Clark, F., Banks, J., Pailthorpe, B., Sennoga, C.,Heron, A., Seddon, J., Templer, R., Crout, D. (2003)Systematic approaches for membrane proteinstructure determination. AsCA‚03/Crystal 23, 11-13Aug. Broome, Australia.

(From left) Figure 1, the detail of this cryo-section of native cellular chloroplast ultrastructure is well defined; other captions to go here


Research officerMatthais Floetenmeyer

Laboratory technicianEunice Grinan

Staff and Students

Our group is studyingbiological structures bycryo-sectioning vitreousbulk material for cryo-electronmicroscopy (cryo-em).

Rob Parton

CELL SURFACE IN HEALTH AND DISEASE

Research overviewOur research interests focus on the organisation,dynamics, and functions of the plasma membrane. Inparticular, we are interested in the formation andfunction of caveolae, small pits, which cover thesurface of many mammalian cells, and in a relateddomain termed a ‘lipid raft’. Caveolae have beenimplicated in regulation of cell growth and inmaintaining the balance of lipids in the cell. Inaddition, caveolae and caveolins, the major proteinsof caveolae (see opposite page), have beenimplicated in a number of disease states includingtumour formation, atherosclerosis, and musculardystrophy. We are using a number of systems inorder to understand how caveolae form and their rolein cellular function. In addition, our studies areproviding new insights into the organisation andfunction of lipid raft domains.

ProjectsCaveolin functional studiesTo address the role of caveolae and caveolins incellular function we investigated whether caveolinmutants would act as dominant negative inhibitorymutants making use of our earlier finding that entryof the virus, SV40, occurs via caveolae. Two mutantshad a specific inhibitory effect on SV40 infection.

With John Hancock we showed that one of themutants was a highly potent inhibitor of Ras signallingand this inhibition was specific to the palmitoylatedform of Ras, H-ras, with no effect on the related butnon-palmitoylated isoform, K-ras. Inhibition wasovercome by adding cholesterol to the cells.

These studies suggested that H-ras signallingrequires cholesterol-enriched lipid raft domains andprovided a system and tools to characterise thesedomains. Secondly, our findings suggested a hithertounexpected link between caveolin, cholesterolregulation, and lipid bodies. These two areas areactively being pursued in the laboratory as outlined below.

Characterisation of Ras microdomains; novelmethods and new paradigmsIn order to characterise the domains with which H-rasand K-ras associate, we employed subcellularfractionation and developed new electron microscopic(EM) techniques. The studies generated a newconcept in cell biology; dynamic lipid raft associationregulated by the GTPase state of the Ras protein. Thenovel technique we have developed with the Hancocklaboratory, involves a statistical analysis of the spatialdistribution of proteins on the surface of the plasmamembrane and provides a completely unbiasedquantitative analysis of the distribution of proteins Thishas allowed us to identify and characterise severaldistinct domains. Our future studies are aimed atmapping other proteins with respect to these domainsand understanding the molecular basis ofmicrodomain formation and function.

Caveolin, cholesterol, and lipid bodies; in vitro andin vivo studiesThe other avenue of research developed in responseto our studies of the inhibitory caveolin mutants wasaimed at understanding the molecular basis of theinhibition of H-ras function. We showed that themutant caveolin which associated with lipid bodiesdisrupted lipid regulation, a completely unexpectedfinding which has generated great interest in thefield. These studies have implications forunderstanding the role of lipid bodies in cellularfunction and provide a model system for studyinglipid body biogenesis and function.

We have now extended these studies to examine theeffect of the caveolin mutant at the molecular leveland to examine the role of caveolins in lipid bodyfunction. We have shown that the caveolin mutantinhibits microtubule-dependent lipid body motility andinhibits loss of lipids from lipid bodies. In addition, wehave shown that endogenous caveolins canassociate with lipid bodies and this is regulated byfatty acids (see following page).

This may have physiological importance as we havefound that in regenerating liver, in which lipid bodiesaccumulate to high levels, endogenous caveolinredistributes from plasma membrane caveolae tolipid bodies. Experiments are in progress to examinewhether liver regeneration is affected in caveolin-1null mice.


A major focus of future experiments is to understandthe role of caveolin in lipid regulation and to test thehypothesis that regulated association of caveolinwith lipid bodies and surface caveolae plays a role incholesterol homeostasis. These studies haveimplications for many disease states includingatherosclerosis and Niemann-Pick disease.

Caveolae and caveolin-3 in muscleSome years ago, we discovered a second member ofthe caveolin family (now termed caveolin-3). Weshowed that caveolin-3 localises to the surfacecaveolae of mature muscle but during developmentassociates with the developing Transverse (T)-tubulesystem suggesting a novel role in T-tubule formation.

A major aim of our future studies is to determine therole of caveolin-3 in muscle, particularly in view of aseries of papers from other groups showing thatcaveolin-3 is mutated in some forms of musculardystrophy and other muscle diseases. We generateda series of caveolin-3 mutants corresponding tothose occurring in patients with the muscle diseases;the analysis of these mutant proteins is ongoing. Weshowed that one caveolin-3 point mutant associatedwith muscular dystrophy specifically inhibits H-rassignalling suggesting that like the inhibitory mutantdescribed above it perturbs lipid raft domains.

These results provide new insights into the effect ofcaveolins on raft signalling and the molecular defectswhich may contribute to the disease phenotype. Wehave also established collaborations with KathrynNorth (Sydney) to identify dystrophy patients withabnormal levels of caveolin-3 and caveolin-3interacting proteins.

Caveolins in zebrafishStudies of caveolin knockout mice have providednew insights into the role of caveolins. However, theexact role of caveolae is still far from clear. We areusing zebrafish as an in vivo system to examinecaveolae function.

The well-characterised developmental pathways inthe zebrafish, the ease of knockout of proteinexpression, and the amenability to microscopiccharacterisation provide tremendous advantages forthese experiments.

We have characterised caveolae distribution byelectron microscopy and we have cloned andcharacterised caveolins from zebrafish. The proteinsare well conserved; for example those amino acids inhuman caveolin-3 which are mutated in muscledisease patients are conserved in the zebrafish.

We have localised caveolin-1 and caveolin-3 andhave ablated the expression of both successfully.This is providing new insights into caveolin function.For example, we have shown a role for caveolin-3 inmyoblast fusion and myotube differentiation and havemimicked this by expression of a dystrophy-associated mutant protein. Future experiments willaim to elucidate the precise role of caveolae inmuscle and non-muscle cells in the zebrafish.

Caveolae BiogenesisFinally we are interested in how a caveola isgenerated. How can such a uniformly shapedstructure be formed (see following page) and what isthe role of caveolin in this process?

We have shown that lymphocytes lack caveolae butthat expression of a single protein, caveolin, in thesecells caused caveolae biogenesis. This represents aunique system in cell biology allowing us to dissectthe information in the caveolin molecule whichcauses the formation of both the characteristicmorphology of the caveolae as well as their uniquemolecular composition.

We are currently using caveolin-null fibroblasts,which totally lack caveolae, to address the moleculardeterminants involved in caveolae formation. We arealso using cryoEM and electron tomography toexamine caveolae structure at high resolution.

Staining for caveolin-1, the major protein of caveolae, in afibroblast. The dark staining indicates the caveolin-1 protein. The insets show caveolae by electron microscopy.

Grants awardedNHMRC Program Grant The role of membranemicrodomains in cellular function

National Institutes of Health Plasma membranemicrodomains and Ras function

CollaboratorsProf. Jean Gruenberg, University of Geneva,Switzerland

Dr. Gisou van der Goot, University of Geneva,Switzerland

Dr. Elina Ikonen, National Public Health Institute,Helsinki, Finland

Dr. Marino Zerial, Max Planck Institute, Dresden,Germany

Dr. Jitu Mayor, National Centre for BiologicalSciences, Bangalore, India

Dr. Carlos Enrich and Dr. Albert Pol, University ofBarcelona, Spain

Prof. Monte Westerfield, University of Oregon, USA

Prof. Richard Pagano, Mayo Clinic, USA

Prof. Michel Desjardins, University of Montreal,Canada

Dr. Teymuras Kurzchalia, Max Planck Institute ,Dresden, Germany

Prof. Kathryn North, Institute for NeuromuscularResearch, Sydney

Dr. Wendy Jessup, Department of Medical Sciences,The University of New South Wales, Sydney

Prof. John Hancock, IMB

Prof. David James; Garvan Institute for MedicalResearch, Sydney

Associate Professor Alpha Yap; UQ, IMB;

Dr. Carol Wicking, IMB;

Dr. Rohan Teasdale, IMB

Prof. Brian Key; School of Biomedical Sciences, UQ

Caveolae and caveolins, the major proteins ofcaveolae, have been implicated in a number ofdisease states including tumour formation,atherosclerosis, and muscular dystrophy. We areusing a number of systems in order to understandhow caveolae form and their role in cellular function.

(Left) Caveolin (green staining) associated with lipid bodies; (Right) Caveolae in a human fibroblast as seen by electron microscopy. The dense staining is due to labelling of the interior of the caveolae by a marker attached to cholera toxin.


Research officersMatthias FloetenmeyerMargaret Lindsay Sally Martin

PhD studentsMatthew KirkhamIsabel MorrowSusan Nixon

Research assistantsCharles FergusonRobert LuetterforstAyanthi RichardsAnnika Stark

Visiting scientistsAki FujitsuManuel Fernandez Rojo

Staff and Students

PublicationsParton, R.G. (2003). Caveolae--from ultrastructure tomolecular mechanisms. Nat Rev Mol Cell Biol. 4:162-7.

Parton, R.G., Richards, A.A. (2003). Lipid rafts andcaveolae as portals for endocytosis: New insights andcommon mechanisms. Traffic. 4:724-738.

Prior, I.A., Parton, R.G., Hancock, J.F. (2003). Observingcell surface signaling domains using electronmicroscopy. Sci STKE. 2003:PL9

Emery, G., Parton, R.G., Rojo, M., Gruenberg, J. (2003).The trans-membrane protein p25 forms highlyspecialised domains that regulate membranecomposition and dynamics. J Cell Sci. 116:4821-32.

Evans, T.M., Ferguson, C., Wainwright, B.J., Parton,R.G., Wicking, C. (2003). Rab23, a Negative Regulator ofHedgehog Signalling, Localises to the PlasmaMembrane and the Endocytic Pathway. Traffic.4:869-884.

Lahtinen, U., Honsho, M., Parton, R.G., Simons, K.,Verkade, P. (2003). Involvement of caveolin-2 incaveolar biogenesis in MDCK cells. FEBS Lett. 538:85-8.

Mayran, N., Parton, R.G., Gruenberg, J. (2003).Annexin II regulates multivesicular endosomebiogenesis in the degradation pathway of animalcells. EMBO J. 22:3242-53.

Paterson, A.D., Parton, R.G., Ferguson, C., Stow, J.L.,.Yap, A.S. (2003). Characterization of E-cadherinendocytosis in isolated MCF-7 and chinese hamsterovary cells: the initial fate of unbound E-cadherin. J Biol Chem. 278:21050-7.

Prior, I.A., Muncke, C., Parton, R.G., Hancock, J.F. (2003).Direct visualization of Ras proteins in spatially distinctcell surface microdomains. J Cell Biol. 160:165-70.

Wyse, B.D.,. Prior, I.A., Qian, H., Morrow, I.C., Nixon, S.,Muncke, C., Kurzchalia, T.V., Thomas, W.G., Parton,R.G., Hancock, J.F. (2003). Caveolin interacts with theangiotensin II type 1 receptor during exocytic transportbut not at the plasma membrane. J Biol Chem.278:23738-46.

ConferencesParton, R.G. (2003) Meeting of the Juan Marchfoundation; ‘Membranes, Trafficking and Signallingduring Animal Development’ Madrid, Spain. Invited speaker

Parton, R.G. (2003) Euresco Conference on‘Microdomains, lipid rafts and caveolae’. Tomar,Portugal. Invited speaker

Parton, R.G. (2003) XIX International Congress ofBiochemistry & Molecular Biology, Toronto, Canada.Chairman and invited speaker (postponed due to SARS outbreak)

Parton, R.G. (2003) FASEB summer researchconference, ‘Glucose transporter biology’, Snowmass,Colorado. Invited speaker

Parton, R.G. (2003) 10th Congress of the Federation ofAsian and Oceanic Biochemists and MolecularBiologists, Bangalore, India. Invited speaker

Parton, R.G. (2003) Combio Melbourne. Sessionchairman and member of international organisingcommittee

Parton, R.G. (2003) The Third Hunter Cellular BiologyMeeting, Pokolbin NSW. Invited Speaker

Jennifer Stow

PROTEIN TRAFFICKING INHUMAN DISEASE

Research OverviewProtein trafficking is the process by whicheach of the many proteins made by cellsare transported to different intracellulardestinations or to the cell surface forsecretion (release). The protein traffickingmachinery of each cell is highly complexinvolving many gene products.Deciphering how individual proteins aretrafficked is important for understandingtheir cellular function, regulation and rolein disease. Our lab is studying thetrafficking of key proteins in epithelial cellsand in macrophages with a long term viewto converting proteomic and genomicinformation into dynamic visual andfunctional maps of these pathways withincells. Generating this information for theepithelial cells and macrophages beingstudied in our lab is vital to developingnew therapeutic approaches for use incancer and immunological disease.

ProjectsCadherin trafficking in epithelial cellsE-cadherin is a key cell adhesion protein, incomplex with catenins, other regulatorymolecules and receptors on the lateralsurface of epithelial cells, it performsessential roles in cell polarity and cell-cellcontact. E-cadherin is also a powerfultumour suppressor and its loss ordysfunction is an early event in manymetastatic tumours. Our studies involvecharacterizing the endocytic and exocyticpathways for E-cadherin trafficking in

normal epithelial cells and in breast cancer cells. Ourexperimental approaches include mutagenesis andexpression of proteins, in vitro vesicle assays, immuno-electron microscopy and fluorescence microscopy infixed and live cells. Current projects include:

• define roles for specific trafficking machineryproteins in the transport of E-cadherin, including,sorting signals, adaptors and vesicle coats, actin-modifying proteins, GTPases and SNAREs.

• the assembly and role of the cadherin-catenincomplex and cell surface receptors in traffickingand alternative functions of E-cadherin.

• the role of endocytosis in regulating cell adhesionduring cell growth and differentiation and in cancer.

Together our findings provide a context forunderstanding how and when adhesion complexesbecome functional and how cell adhesion andpolarity can be regulated during the development andmaintenance of epithelia and in tumorigenesis.

Cytokine secretion in inflammatory macrophagesMacrophages perform essential functions in innateand acquired immunity. During inflammatoryresponses macrophages secrete proinflammatorycytokines, one of the most powerful of which istumour necrosis factor alpha (TNF). Excess TNF is akey cause of tissue damage and a major clinicalproblem in chronic inflammation diseases such asinflammatory bowel disease and rheumatoid arthritis.Little is currently understood about howmacrophages traffic or secrete proinflammatorycytokines. Our group has developed gene and proteinscreens and single cell assays to identify strategiccomponents of the trafficking machinery in cytokinesecretory pathways. Proteomic analysis of vesicles,morphological and molecular analysis of specificproteins are used in fixed and live cells tocharacterize the pathways and regulators of cytokinesecretion. Our studies to date have defined some ofthe important features of these pathways, such asthe identification of SNARE complexes for vesicledocking and fusion. Some of the proteins we haveidentified are being investigated as potential drugtargets for the development of new anti-TNFtherapies in inflammatory diseases. Macrophagesand other cells at sites of inflammation in variousinflammatory and autoimmune disease models arebeing studied to determine how traffickingcontributes to immune responses. Ultimately ourstudies will more fully define how cytokines aretrafficked and secreted by macrophages and howspecific trafficking proteins contribute to otherimmune functions such as antigen presentation, cellrecruitment and cell and pathogen killing.


Vesicle budding on Golgi membranesProteins destined for secretion from, or delivery to,the cell surface are packaged into vesicular carriersat the trans-Golgi network. Many molecules arerequired to assemble and generate or bud vesiclesfor the transport of specific cargo - an essential andabundant process for cell viability. We have a long-standing interest in determining how membranebudding occurs. The nature of vesicle carriers, theirbudding, transport and fusion and the roles of Gproteins, and their regulatory molecules are beingstudied by high resolution fluorescence imaging inlive cells. Joint work with collaborators is aimed atalso defining the roles of actin and actin bindingproteins (with Gunning laboratory) and moleculartethers (with Gleeson laboratory) in vesicle budding.Outcomes from these studies will contribute to ourunderstanding of normal cellular function and of celldysfunction in cancer and other diseases.

Grants awardedNHMRC Trafficking of E-cadherin in epithelial cells.

National Institutes of Health, USA CytokineTrafficking and Secretion in Macrophages.

CollaboratorsRohan Teasdale (IMB)

Rick Sturm (IMB)

Alpha Yap (IMB)

David Hume (IMB)

Peter Gunning, The Children’s Hospital at Westmead,Sydney

Paul Gleeson, The University of Melbourne

David James, Garvan Institute of Medical Research,Sydney

Sharad Kumar, Hanson Centre for Cancer Research,Adelaide

Michael Caplan, Yale University School of Medicine,New Haven, Connecticut, USA

Research officerFiona Wylie Rachael Murray

Research assistantsDarren Brown Tatiana Khromykh

Juliana Venturato, Seetha Karunaratne

Postgraduate studentsWang BoDavid BryantShannon Joseph

Jason Kay, Chris Le.John Lock, Daniele Sangermani,

Honours student Stephanie Wood

Staff and Students

PublicationsMiranda, K.C., Joseph, S.R., Yap, A.S., Teasdale, R.D.,Stow, J.L. (2003). Contextual binding of p120ctn to E-cadherin at the basolateral plasma membrane inpolarised epithelia. J Biol Chem. 278:43480-8.

Sturm, R.A., Duffy, D.L., Box, N.F., Chen, W., Smit, D.J.,Brown, D.L., Stow, J.L., Leonard, J.H., Martin, N.G.(2003). The role of melanocortin-1 receptorpolymorphism in skin cancer risk phenotypes.Pigment Cell Res. 16:266-72.

Leonard, J.H., Marks, L.H., Chen, W., Cook, A.L.,Boyle, G.M., Smit, D.J., Brown, D.L., Stow, J.L.,Parsons, P.G., Sturm, R.A. (2003). Screening of humanprimary melanocytes of defined melanocortin-1receptor genotype: pigmentation marker,ultrastructural and UV-survival studies. Pigment CellRes. 16:198-207.

Paterson, A.D., Parton, R.G., Ferguson, C., Stow, J.L.,Yap, A.S. (2003). Characterisation of E-cadherinendocytosis in isolated MCF-7 and Chinese hamsterovary cells: the initial fate of unbound E-cadherin. J Biol Chem. 278:21050-7

Wylie, F.G., Lock, J.G., Jamriska, L., Khromykh, T.,Brown, D.L., Stow, J.L. (2003). GAIP participates inbudding of membrane carriers at the trans-Golginetwork. Traffic. 4:175-89.

Pagan, J.K., Wylie, F.G., Joseph, S., Widberg, C.,Bryant, N.J., James, D.E., Stow, J.L. (2003). The t-SNARE syntaxin 4 is regulated during macrophageactivation to function in membrane traffic andcytokine secretion. Current Biol. 13:156-60.

Rohan Teasdale

COMPUTATIONAL CELL BIOLOGY

Research overviewThe application of computational biology techniquesto cell biology is opening up new areas of scientificexploration. Our group is developing new techniquesto predict the function of novel proteins based ontheir sequence.

Possessing the combination of cellular andbioinformatic skills allows our group more intuitiveinsights into the application of computational biologywithin cellular biology.

Our major research focus is to utilise bioinformaticsor "database mining" to identify novel proteins orgenes, which are then characterised by our group orthrough active collaborations.

Our work includes identification of novel proteinsimplicated in membrane trafficking and theidentification of the signals that proteins utilise forlocalisation to different regions of the cell.

This research has had a major impact onunderstanding the signals responsible for targetingmembrane proteins to various subcellular regionswithin the cell. This is based on our experimentalcharacterisation and exploitation of localisationsignals to develop computational approachescapable of accurately predicting the membraneorganisation and localisation of novel proteins.

We have also applied a range of cellular anddevelopmental techniques to characterise novelproteins localised to distinct regions of the cellincluding the Golgi, polarised cell surfacemembranes, nucleus, endosomes and proteinssecreted into the extracellular environment.

As a result, we recently defined the proteincomposition of the human retromer complex andshowed it was associated with mammalianendosomes.

Our projects combine bioinformatics techniques withtraditional experimental approaches such asmolecular cloning, expression in mammalian cells,immunolocalisation and microscopy.

ProjectsBioinformatic discovery of new genes, proteins and pathwaysA major advance in the biological sciences over thelast decade is the sequencing of genomes fromdifferent organisms. The challenge today for medicalscientists is to utilise this mass of information toexpand their knowledge of the biological processesthey are currently researching. Traditional cellbiology combined with a strong understanding ofbiological sciences allows for a more intuitive"mining" of this wealth of information for novelsequences using various bioinformatic approaches.These "on silica" observations have catalysednumerous new avenues of scientific exploration forresearchers in our group and with collaborators.


The Golgi Apparatus: Computational discovery andfunctional genomics of novel Golgi proteinsThe Golgi is an organelle central to the biosyntheticpathway of eukaryotic cells. It plays a principal rolein the post-translational modification of newlysynthesised proteins and in the sorting, packagingand distribution of these proteins to variousdestinations. It is estimated that at least 1000 proteinsmake up the protein complement of the Golgi, ofwhich less than 200 are currently characterised.

Efficient screens that identify novel Golgi proteinswould clearly enhance our present understanding ofthe biological role of the Golgi. Based on aexhaustive computational interrogation of thegenomes of various organisms for predictable novelGolgi resident proteins combined with theexperimentally validation of their localisation weintend to define the full protein complement of theGolgi. We have successfully applied this strategy topredict greater than 300 putative Golgi residents, ofwhich, we have already experimentally validatedeight novel Golgi proteins. In addition, we willcommence the development of a functional genomicsapproach focused on defining the function of novelGolgi resident proteins. This will include grouping thenovel Golgi proteins based on computational definedfeatures; localisation to sub regions of the Golgi, co-expression during cellular and developmental stagesand mapping protein-protein interaction networks.

Annotation of the membrane organisation andsubcellular localisation of proteins associated withthe mammalian secretory pathway.A major issue in cell biology today is how distinctintracellular regions of the cell maintain their uniquecomposition of proteins. The signals that direct agiven protein's movement through the intracellularorganelles, and thereby determine its eventuallocation in the cell, are contained in its amino acidsequence. Many of these sorting signals have beenexperimentally defined and are able to be predictedutilising computational approaches. I am currentlyannotating the predicted localisation of membraneand peripheral membrane proteins which accumulatein the various intracellular organelles (namely theendoplasmic reticulum, Golgi apparatus, endosomesand plasma membrane). This has been performed onthe protein open-reading frames from the 60,000 full-length mouse cDNA generated by RIKEN. We arecurrently expanding this project to additional protein databases.

Characterisation of novel proteins involved inendosomal membrane trafficking: - The RetromerComplexThe endosomal/lysosomal system of mammalian cellsis a highly dynamic trafficking pathway that includesmembrane transport from both the late Golgi and theplasma membrane. The primary function ofendosomes is the sorting and segregation ofreceptors and ligands, a process that is necessaryfor many cellular operations. The molecular details ofprotein trafficking and biogenesis of the numeroussubcompartments of the mammalianendosomal/lysosomal system are poorly defined. Onestrategy to identify proteins that function in thetrafficking of proteins from endosomes to the TGN isto characterise human homologues of proteins thathave been experimentally implicated in endosomalfunction in other organisms predominantly yeast. Theaim of this project is to gain insight into thebiochemistry and membrane sorting functions ofmammalian VPS protein homologues, primarily theperipheral membrane proteins Vps26p, Vps29p,Vps30p and Vps35p. The principal objective of thisproposal is to determine if these mammalian VPSproteins function in an analogous manner to that inyeast. In particular, we aim to determine theintracellular compartments that these peripheralmembrane proteins associate with, to determine ifthese proteins function in membrane transport fromthe mammalian endosomal system to the TGN.

Intracellular Localisation signals.How do distinct intracellular regions of the cellmaintain their unique composition of proteins andlipids? For these organelles to maintain their functionintegrity, specific resident proteins must be retainedwhile non-residents proteins allowed passagethrough them. Individual proteins must have "signals"that are responsible for their intracellularlocalisation. We are currently in the process ofidentifying such signals on several different proteins.In addition, we are identifying novel proteins thatcontain these localisation signals within the humangenome. These novel proteins are then tested forlocalisation to particular organelles and thenfunctionally characterised.

Towards renal regenerationStem cell-based therapy, utilising either adult orembryonic stem cells, is an unproven approach to thetreatment of kidney disease. Our group is a member ofa consortium formed to perform the basic researchrequired to define the potential of renal regeneration.Our role in the consortium is to provide the expertise incell biology and computational analysis to novel genesof interest identified throughout this research effort.

Reverse Transfection MicroarraysOne of the greatest challenges in the post-genomesequencing era is to develop strategies to rapidlyassign biological roles to each member of the genecomplement. Recently, a microarray based,massively parallel, transfection strategy has beendescribed. Unlike expression profiling, thistechnology provides the opportunity to directly assaybiological endpoints rather than transcriptionalconsequences. We have established this technologywithin the IMB and are currently developing a rangeof novel applications of this technology.

Grants awarded in 2003University of Queensland Foundation ResearchExcellence Awards.

NHMRC Career Development Award RD WrightBiomedical Development Award

NHMRC Project Grant Sorting nexins and their role inendosomal trafficking.

ARC Discovery Project Grant Membrane proteins

within the mouse transcriptome-annotation of their

organisation and subcellular localisation.

CollaborationsSean Grimmond IMB

Melissa Little IMB

Jenny Stow IMB

Mike Waters IMB

Tim Bailey IMB

Malcolm McConville, Department of Biochemistryand Molecular Biology, University of Melbourne

Paul Gleeson, Department of Biochemistry andMolecular Biology, University of Melbourn

Research officerDonna MahonyZheng Yuan

Masters studentMelissa DavisTheingi Tun

PhD studentKevin MirandaMarkus KerrRajith Aturaliya

Research assistantRobert LuetterforstElizabeth O’BrienMelvena TeasdaleShane Zhang

Visiting scholarKelly Hanson

Staff and Students


Publications and papers -2003Bowles, J., Teasdale, R.D., James, K., Koopman, P.(2003) Dppa3 is a marker of pluripotency and has ahuman homologue that is expressed in germ celltumours. Cytogenet Genome Res. 101:261-5.

Yuan, Z., Davis, M.J., Zhang, F., Teasdale, R.D., (2003)Computational differentiation of Nterminal signalpeptides and transmembrane domains. BiochemBiophys Res Commun. 312:1278-83.

Miranda, K.C., Joseph, S.R., Yap, A.S., Teasdale, R.D.,Stow, J.L. (2003) Contextual binding of p120 ctn to E-cadherin at the basolateral plasma membrane inpolarised epithelia. J. Biol. Chem. 278:43480-43488.

Grimmond, S, Miranda, K, Yuan, Z, Davis, MJ, Hume,DA, Yagi, K., Tominaga, N., Bono, H, Hayashizaki, Y.,Okazaki, Y. , RIKEN GER Group Members, Teasdale,R.D. (2003) The mouse secretome. Functionalclassification of the proteins secreted into theextracellular environment. Genome Res. 13:1350-9.

Gustincich S., Arakawa, Y., Batalov, S., Beisel, K.W.,Bono, H., Carninci, P., Fletcher, C.F., Grimmond, S.,Hirokawa, N., Jarvis, E.D., Jegla, T., Kawasaka, Y.,Miki, H., Raviola, E., Teasdale, R.D., Waki, K., Zimmer,A., Kawai, J., Hayashizaki, Y., Okazaki, Y. (2003)Analysis of the mouse transcriptome for genesinvolved in the function of the nervous system.Genome Res. 13:1395-40.

Kanapin, A., Batalov,S., Davis, M.J., Gough, J.,Grimmond, S.G., Kawaji, H., Magrane, M., Matsuda,H., Schönbach, C., Teasdale, R.D., RIKEN GER GroupMembers, Yuan, Z. (2003) Mouse proteome analysis.Genome Res. 13:1335-44.

Tajul-Arifin, K., Teasdale, R.D., Ravasi, T., Hume, D.,RIKEN GER Group Members, Mattick, J.S. (2003)Identification and Analysis of Chromodomain-containing Proteins Encoded in the MouseTranscriptome. Genome Res. 13:1416-29.

Fowles, L.F., Bennetts, J.S., Berkman, J.L., Williams,E., Koopman, P., Teasdale, R.D., Wicking, C. (2003)Genomic screen for genes involved in mammaliancraniofacial development. Genesis 35:73-87.

van Vilet, C., Thomas, E.C., Merino-Trigo, A., Teasdale,R.D., Gleeson, P.A. (2003) Intracellular Sorting andTransport of Proteins. Prog. Biophys. Mol. Biol.83:1-45.

The application of computational biologytechniques to cell biology is opening up new areasof scientific exploration. Our group is developingnew techniques to predict the function of novelproteins based on their sequence.

Alpha Yap

CADHERIN SIGNALING ANDMORPHOGENESIS

Research overviewMy group studies the role of cadherin cell adhesionmolecules in morphogenesis and tumor development.E-cadherin is a key mediator of cell-cell recognition: itparticipates in tissue patterning and its dysfunctioncontributes to tumor progression and invasion. Weseek to understand the cellular basis of cadherinrecognition, and how this controls cell movement andorganization. Our current work builds on two recentdiscoveries made by my lab:

1. We found that E-cadherin, the principal cadherinmolecule found in epithelial tissues, functions as anadhesion-activated cell signalling receptor. Inparticular, upon adhesion E-cadherin activatessignalling via the small GTPase, Rac, and the lipidkinase PI3-kinase.

2. An important potential target of this signallingreceptor is the Arp2/3 complex, a protein machinethat nucleates assembly of actin filaments. We werethe first to discover that E-cadherin interacts withthe Arp2/3 complex to mark sites for actin assemblywithin cells. We are now exploring the generalhypothesis that cadherin-activated signallingcontrols the subcellular localization and activity ofArp2/3 to modulate cell shape changes and motilityin response to productive cell-cell recognition.

ProjectsMembers of my group are studying

1. The molecular mechanism responsible for recruitingArp2/3 to E-cadherin

2. The molecular regulators of Arp2/3 activity atcadherin contacts (including WASP/WAVE proteins,cortactin and ena/VASP family proteins)

3. The molecular basis of cadherin-activated Rac andPI3-kinase signalling.

4. The morphogenetic consequences of cadherin-activated cell signalling and cooperativity with theactin cytoskeleton.

GrantsNHMRC Dora Lush Scholarship to MadhaviMaddugoda

CollaboratorsSean Grimmond IMB

Brian Key Department of Anatomy and DevlopmentalBiology, UQ

Robert Parton IMB

Jennifer Stow IMB

Alan Fanning University of North Carolina, Chapel Hill, USA

Frank Gertler Massacheusetts Institute of Technology,Boston USA

Aki Kusumi Nagoya University, Japan

Denise Montell Johns Hopkins University, Baltimore USA

Al Reynolds Vanderbilt University, Nashville, USA

David Sacks Harvard Medical School, Boston, USA

Lila Solnica-Krezel Vanderbilt University, Nashville, USA

Taodami Takenawa Tokyo University, Japan

Scott Weed University of Colorado Health ScienceCenter, USA

Any prizes, keynote addresses or otherhonours in 2003

PublicationsPeifer, M., Yap, A.S. (2003) Traffic control: p120-catenin acts as a gatekeeper to control the fate ofclassical cadherins in mammalian cells. J Cell Biol.Nov 10;163(3):437-40.

Miranda, K.C., Joseph, S.R., Yap, A.S., Teasdale, R.D.,Stow, J.L. (2003) Contextual binding of p120ctn to E-cadherin at the basolateral plasma membrane inpolarized epithelia. J Biol Chem. Oct 31;278(44):43480-8.

Goodwin, M., Kovacs, E.M., Thoreson, M.A.,Reynolds, A.B., Yap, A.S. (2003) Minimal mutation ofthe cytoplasmic tail inhibits the ability of E-cadherin

to activate Rac but not phosphatidylinositol 3-kinase:direct evidence of a role for cadherin-activated Racsignaling in adhesion and contact formation. J BiolChem. Jun 6;278(23):20533-9.

Paterson, A.D., Parton, R.G., Ferguson, C., Stow, J.L.,Yap, A.S. (2003) Characterization of E-cadherinendocytosis in isolated MCF-7 and chinese hamsterovary cells: the initial fate of unbound E-cadherin. J Biol Chem. Jun 6;278(23):21050-7.

Kraemer, A., Yap, A.S. (2003) Coupling adhesion toactin bundles in the inner ear. Novel functions fornovel cadherins. EMBO Rep. Mar;4(3):244-5.

Yap, A.S., Kovacs, E.M. (2003) Direct cadherin-activated cell signaling: a view from the plasmamembrane. J Cell Biol. Jan 6;160(1):11-6.

Research officersAstrid KraemerJian-Hong PangAnnette Shewan

PhD studentsRadiya AliMarita GoodwinFalak HelwaniAilsa McCormack

Andrew PatersonJeanie Scott

Research assistantsMerali BoyleMatthew CramptonMadhavi MaddugodaTeresa MunchowSuzie Verma

Honours studentsSamantha Stehbens

Undergraduate studentsAmanda HammondStephen White

Staff and Students



CHEMICAL AND STRUCTURALGENOMICSFocussing on• Membrane protein structures• Soluble protein and nucleic acid structures• New drugs and therapies

This program has the most advanced equipment forstructural biology in Australia, with projects exploringQueensland’s biodiversity for potential therapeuticagents. It has been responsible for a number of IMBspinout companies based on new platform technologiesfor drug discovery as well as developing novel drugs forhuman disease.

Research Group LeadersPaul AlewoodRob CaponDavid CraikDavid FairlieJeffrey GormanBostjan KobeRichard LewisJenny MartinMark Smythe

Paul Alewood

BIOACTIVE MOLECULES,CHEMICAL PROTEIN SYNTHESISAND PROTEOMICS

Research overviewThe research interests of our group include thediscovery and total synthesis of toxins from Australia’svenomous creatures, the chemical synthesis ofproteins and bioactive peptides, development of newsynthetic and analytical methods, and proteomics.Special emphasis is placed on determining thestructure-function relationships of natural anddesigned molecules.

ProjectsToxinsVenom peptides make interesting pharmacologicaltools due to their action on ion channels and receptors.Conotoxins are small cysteine-rich peptides isolatedfrom the venom of predatory marine snails. We havedeveloped new synthetic approaches that employselenium chemistry to access fully cyclic analogueswith improved physical and biological properties.These analogues nicely mimic the original nativestructure and maintain high potency.

Significant progress has been made on the Australianparalysis tick with new bioactive molecules isolatedand currently being sequenced.

Studies of the venoms from various species ofAustralian scorpions have now commenced as well asthe glands of the freshwater stone fish (bull rout).

Milk proteomicsGlycosylation is a post-translational modification,which introduces great diversity into the proteomeallowing numerous distinct molecular species to begenerated from a single gene product. We haveidentified numerous different glycoforms of the majormilk protein, k-casein. Using 2D electrophoresis andMALDI -ToF MS, differences in phosphorylation andglycosylation were identified. By analysing theglycopeptides generated from individual species wehave been able to assign molecular identities to 30 ofthese in terms of genetic variant, number and locationof phosphorylation sites, and the number of tri- andtetra-saccharides attached.

New generation antibiotics The replication of DNA in eubacteria involves manyproteins organised into a complex multifunctionalmachine termed the replisome. A central enzymeinvolved in replication is the multi subunit DNApolymerase (pol III). The processivity of thepolymerase is conferred by the β subunit of pol III,which forms a clamp around the DNA. The subunit βis in turn loaded onto the DNA by a clamp loadercomplex comprised of single δ and δ' subunits andthree or four τ/γ subunits. The δ subunit of the clamploader and the polymerase a, bind the β subunit atthe same site or overlapping site.

In a collaborative program with Livestock Industries,CSIRO, an initial lead pentapeptide has now delivereda suite of novel peptidomimetic lead compounds withnanomolar potency that inhibit (in vitro) interaction ofthe α:δ and α:β proteins. Their capacity to enter cellsis now under investigation.

Protein chemical synthesisThe current research project represents a novelapproach using total chemical synthesis to study theenzyme action of the HIV-1 PR, an aspartyl proteaseessential for the replication of AIDS virus. Theredesign of the catalytic apparatus will allow theinvestigation of molecular aspects of its action. Thesynthetic polypeptide chain will be folded andcharacterised for the correct folded structure by NMR,and assayed for enzymatic activity. It can be expectedthat significant new insights into the molecular basis ofthe properties of the HIV-1 PR will be obtained.

CollaboratorsProfessor Steve Kent, Institute for BiophysicalDynamics, University of Chicago, USA

Prof Ian Smith, Baker Heart Research Institute,Melbourne

Professor Ed Nice, Ludwig Institute for CancerResearch, Melbourne

Professor Carolyn Geczy, School of Medical Sciences,University of New South Wales, Sydney

Professor Phil Kuchel, The University of Sydney

Dr Jamie Vanderberg, Garvan Institute of MedicalResearch, Sydney

Grants awarded in 2003ARC Grant Tuning the catalytic apparatus of HIV-1 Protease

NHMRC Development Grant Development of a newclass of antibiotics


PublicationsAlewood, D., Birinyi-Strachan, L.C., Pallaghy, P.K.,Norton, R.S., Nicholson, G.M., Alewood, P.F. 2003Synthesis and characterization of delta-atracotoxin-Ar1a, the lethal neurotoxin from venom of the Sydneyfunnel-web spider (Atrax robustus). Biochemistry42:12933-40.

Torres, A.M., Bansal, P.S., Sunde, M., Clarke, C.E.,Bursill, J.A., Smith, D.J., Bauskin, A., Breit, S.N.,Campbell, T.J., Alewood, P.F., Kuchel, P.W., Vandenberg,J.I. (2003) Structure of the HERG K+ channel S5Pextracellular linker: role of an amphipathic alpha-helixin C-type inactivation. J Biol Chem. 278:42136-48.

Sharpe, I.A., Palant, E., Schroeder, C.I., Kaye, D.M.,Adams, D.J., Alewood, P.F., Lewis, R.J. (2003) Inhibitionof the norepinephrine transporter by the venom peptidechi-MrIA. Site of action, Na+ dependence, andstructure-activity relationship. J Biol Chem.278:40317-23.

Sharpe, I.A., Thomas, L., Loughnan, M., Motin, L.,Palant, E., Croker, D.E., Alewood, D., Chen, S., Graham,R.M., Alewood, P.F. Adams, D.J., Lewis, R.J. (2003)Allosteric alpha 1-adrenoreceptor antagonism by theconopeptide rho-TIA. J Biol Chem. 278:34451-7.

Hogg, R.C., Hopping, G., Alewood, P.F., Adams, D.J.,Bertrand, D. Alpha-conotoxins PnIA and [A10L]PnIAstabilize different states of the alpha7-L247T nicotinicacetylcholine receptor. (2003) J Biol Chem. 278:26908-14.

Torres, A.M., Bansal, P., Alewood, P.F., Bursill, J.A.,Kuchel, P.W., Vandenberg, J.I. (2003) Solution structureof CnErg1 (Ergtoxin), a HERG specific scorpion toxin.FEBS Lett. 539:138-42.

Blanchfield, J.T., Dutton, J.L., Hogg, R.C., Gallagher,O.P., Craik, D.J., Jones, A., Adams, D.J., Lewis, R.J.,Alewood, P.F., Toth, I. (2003) Synthesis, structureelucidation, in vitro biological activity, toxicity, andCaco-2 cell permeability of lipophilic analogues ofalpha-conotoxin MII. J Med Chem. 46:1266-72.

Hodgson, W.C., Eriksson, C.O., Alewood, P.F., Fry, B.G.(2003) Comparison of the in vitro neuromuscularactivity of venom from three Australian snakes(Hoplocephalus stephensi, Austrelaps superbus andNotechis scutatus): efficacy of tiger snake antivenom.Clin Exp Pharmacol Physiol. 30:127-32.

Nicke, A., Loughnan, M.L., Millard, E.L., Alewood, P.F.,Adams, D.J., Daly, N.L., Craik, D.J., Lewis, R.J. (2003)Isolation, structure, and activity of GID, a novel alpha4/7-conotoxin with an extended N-terminal sequence.J Biol Chem. 278:3137-44.

Research officersParamjit BansalPeter CassidyJohn HollandChristopher Armishaw

PhD studentsGene HoppingJean JinLita ImperialRyan O’DonnellNatalie Steen

Research assistantsAaron Poth

Visiting scholarsAndreas BrustMaria Wahlstrom

Vacation scholarsStuart FritzJennifer Smith

Staff and Students

(Left) Three dimensional NMR ribbon structures of cyclic analogues of a-conotoxin ImI overlayed with the native toxin. (Right) Two dimensional gels of milk from individual cows showing the genetic contribution of k-casein heterogeneity.

Rob Capon

CENTRE FOR MOLECULARBIODIVERSITY

Research overviewAustralia is uniquely positioned as the onlyscientifically advanced country endowed with megabiodiversity.

Australian tropical, sub-tropical and temperatemarine and terrestrial ecosystems span an enormousgeographic area and are home to an extraordinaryarray of unique and indigenous life forms, rangingthrough plants and animals, to invertebrates andmicrobes. These organisms produce molecules thatenhance survival through such mechanisms aschemical defence, offence and communication.

Specialist toxins deter predators and paralyse prey,while trail, sex and alarm pheromones influencebehaviour between individuals of the same anddifferent species. Novel bioactive metabolites canprotect against viral, microbial and parasiticinfection, resist biofouling, and selectively modulatelarval development.

Evolutionary pressures have refined natural chemicaldiversity to the point where exquisite biologicalpotency and selectivity makes them attractive drugcandidates, or leads that inspire the development ofnew drugs.

In 2003 my research team relocated from theUniversity of Melbourne to the University ofQueensland, to establish the Centre for MolecularBiodiversity (CMB) within the IMB. The CMB willaccelerate the effective exploration of Australianbiodiversity, as a means to discover new andimproved drugs, with application in the areas ofhuman and animal health, and crop protection.

ProjectsOur research focus on the detection, isolation,identification and evaluation of novel naturallyoccurring bioactive metabolites, primarily frommarine and microbial sources. This research requiresthe extensive use of chromatographic andspectroscopic technologies, and chemical synthesis,and draws on the collaborative expertise of manycolleagues in biology, biochemistry andpharmacology. Our efforts have uncovered many rareand unique bioactive molecules, presenting excitingtechnical and intellectual challenges. Thesecompounds span a wide range of molecular structureclasses including the nematocidal agentsthiocyanatin A (1) and marcfortine A (2), theantibiotics rugulotrosin A (3) and aspergillicin A (4) ,and the acetylcholine mimetic esmodil (5). Researchinto many other bioactive molecules remains work inprogress and/or commercial-in-confidence.

CollaborationsNovartis Animal Health Australasia

Microbial Screening Technologies

PharmaMar

University of Melbourne, School of Botany

Grants AwardedARC Linkage Grant Anticancer Agents fromAustralian Marine Biodiversity


Conferences and Invited Lectures19th Royal Australian Chemical Institute OrganicConference (Lorne)

CSIRO: Biopharmaceuticals, Concept to Clinic(Melbourne)

Queensland Government: Ideas@Powerhouse(Brisbane)

Queensland Government: Science Meets Parliament(Brisbane)

AusBiotech: Biodiscovery (Brisbane)

Queensland Department of Primary Industries:Microbes: Biodiversity, biodiscovery & biotechnology(Caloundra)

World Federation of Culture Collections (Melbourne)

Asia Pacific Biochemical Engineering Conference(Brisbane)

OtherPrinciple scientific consultant for ChemoType Pty Ltd,providing expert advice and guidance to industry(Nufarm), and the legal profession (patent defence,chemical regulations, forensic evidence).

Publications (2003)Capon, R.J., Skene, C., Stewart, M., Ford, J., O'Hair,R.A.J., Williams, L., Lacey, E., Gill, J.H., Heiland, K.,Friedel, T. (2003) Aspergillicins A-E: five noveldepsipeptides from the marine-derived fungusAspergillus carneus. Org. & Biomol. Chem. 1:1856-1862.

Research officersMike Stewart Nick Trotter

Visiting student Torsten Peterle

Research assistantBen Mooney

PhD students Ben ClarkLeith FremlinRanjala RatnayakeMichelle McNallyEd Liu

Staff and Students


David Craik

NMR SPECTROSCOPY

Research overviewOur group uses NMR spectroscopy to determine thestructures of proteins that are important in drugdesign programs and in agriculture. By elucidatingthe structures of biologically active proteins we areable to identify regions crucial for activity and canuse this information to design new drugs. We have aparticular interest in the discovery and structuralcharacterisation of novel protein topologies.

Research ProjectsIn 2003 we solved the structures of novel proteinsfrom bacteria, plants and animals. They haveapplications ranging from the development of newantibiotics, to anti-HIV therapy, to the development ofnew approaches to crop protection. A unifying themeis that we focus on proteins that have the novelfeature of a cyclic backbone. Circular proteins wereunknown until recently and represent an exciting newfield of discovery.

Bioengineering of circular proteins:The unique structures and functions of circularproteins makes them exciting prospects in drugdesign and agriculture. Circular proteins have noends, making them exceptionally stable and resistantto enzyme digestion. Our group uses new approaches

in chemistry, biochemistry and molecular biology tolearn more about naturally occurring circularproteins. We also design and construct syntheticcircular proteins with enhanced stability.

Discovery of new circular proteins:The largest family of circular proteins is thecyclotides, discovered by our group over the last fewyears. Their exceptional stability is due to the unusualfeatures of a cyclic backbone and a cystine knotstructure. This year we continued our program ofdiscovery and structure elucidation of cyclotides.With collaborators at the National Cancer Institute,USA, we recently published the structure of thelargest known cyclotide, palicourein, a potent anti-HIV molecule derived from a South Americantree. We also reported a series of papers defining theknotted topology and pharmaceutical applications of cyclotides.

Venom proteins:Our group is actively involved in determining structuresof disulfide rich proteins from animal venoms usingNMR spectroscopy. Conotoxins continue to be ofinterest for their role as leads in drug design programs.Early this year we reported the structure of a newconotoxin, GID that has an unusual flexible “tail” at itsamino-terminus. Mutagenesis studies are underway toelucidate the role of this tail. Our program on thedevelopment of improved conotoxin drug leads usingcyclisation technology has led to several moleculeswith improved stability that are the subject of a patent application.

(From left) Schematic representations of the cyclic cystine knot topology of the cyclotide family of proteins discovered by our group.

a) Topology of the backbone and disulfide bonds; b) The unique embedded ring of the structure; c) Artistic impression of the cyclic cystineknot motif.


GrantsARC Discovery Project grant Discovery of novelcircular proteins. David Craik and Marilyn Anderson(La Trobe University)

ARC-CSIRO linkage grant Development of novelpesticides. Michelle Colgrave

ARC Linkage Grant Applying the CCK framework toangiogenic-based therapeutics

Biotechnology Innovation Fund grant Kalthera PtyLtd. Proof of concept programs for applications ofcyclotides in agriculture

Biotechnology Innovation Fund grant Cyclagen PtyLtd. Proof of concept programs for applications ofcyclotides in drug design

NHMRC Development of novel drugs for multiplesclerosis. David Craik and Claude Bernard (La TrobeUniversity).

NHMRC Industry Fellowship Norelle Daly

2003 AMRAD Postdoctoral Award Justine Hill

HighlightsFilling the pod:With the move to the new QBP building we installedtwo new high field NMR spectrometers in the NMRfacility (affectionately known as the pod). These are tobe used in a variety of drug discovery projects.

Structures in the news:Our structure of the potent antimicrobial proteinmicrocin J25 created much interest because of itsunusual feature of a protein chain “threading the eyeof a needle” whereby the C-terminal tail of themolecule penetrates though a novel ring structure at

the N-terminus. The work was published in theJournal of the American Chemical Society (125, 12464,2003) and was the subject of a commentary article byjournalists in Chemical and Engineering News. It wasalso selected by the American Chemical Society asone of six highlighted achievements in structuralbiochemistry for the year 2003.

Major lectures:Plenary lecture at the 18th American PeptideSymposium in Boston The study of cyclotides

Invited public lecture at Nanyang University inSingapore.

Reversing Nature:In an exciting new application of chemical biologywe showed that an enzyme such as trypsin, whichnormally cleaves peptide bonds, can be made toreverse its usual role and actually synthesise peptidebonds when presented with a suitable substrate. Inthis case a synthetic peptide corresponding to alinear derivative of a naturally occurring circularpeptide from sunflower seeds was incubated withtrypsin and was quantitatively cyclised. This novelfinding paves the way for applications of enzymes inthe cyclisation of proteins.

Saving cotton:With our collaborator Associate Professor MarilynAnderson we have shown that cyclotide moleculesare potent “natural” insecticides that retard growthof Helicoverpa insect species, which are major pestsin the cotton and corn industries around the world.Commercialisation of this discovery is underway.

Research officersRichard ClarkMichelle ColgraveNorelle DalyJustine HillAmanda NourseJohan RosengrenHorst SchirraManuela Trabi

PhD students Daniel BarryMichael Korsinczky

Erica LovelaceEmma MillardJason MulvennaManuel PlanMaria QuimoAngela SalimLillian SandøIvana SaskaShane Simonsen

Honours student:Louise Dempster

Research assistants:Rekha BharathiFiona Foley

Visiting researchers: Bin ChenUlf GoranssonMarco RetzlaffSeetharama Satyanarayanajois

Visiting scholarUta Kuepper

Staff and Students

Published papers in 2003Lay, F.T., Schirra, H.J., Scanlon, M.J., Anderson, M.A.,Craik, D.J. (2003) The three-dimensional solutionstructure of NaD1, a new floral defensin fromNicotiana alata and its application to a homologymodel of the crop defense protein alfAFP. Journal ofMolecular Biology 325:175-188.

Craik, D.J., Clark, R.J. (2003) NMR and Drug Discovery.Burger’s Medicinal Chemistry and Drug Discovery (Ed:D J Abraham) 6th Edition, Chapter 11, Wiley.

Nicke, A.C., Loughnan, M., Millard, E.L., Alewood, P.F.,Adams, D.J., Daly, N.L., Craik, D.J., Lewis, R.J. (2003)Isolation, structure and functional characterization ofa-GID, a novel 4/7 a-conotoxin with an extended N-terminal sequence. Journal of Biological Chemistry278:3137-3144.

Daly, N.L., Clark, R.J., Craik, D.J. (2003) Disulfidefolding pathways of cystine knot proteins: tying theknot within the circular backbone of the cyclotides.Journal of Biological Chemistry 278:6314-6322.

Rosengren, K.J., Daly, N.L., Plan, M.R., Waine, C.,Craik, D.J. (2003) Twists, knots and rings in proteins:structural definition of the cyclotide framework.Journal of Biological Chemistry 278:8606-8616. [Cover feature]

Craik, DJ., Daly, N.L., Saska, I., Trabi, M., Rosengren,K.J. (2003) Structures of naturally-occurring circularproteins from bacteria. J Bacteriology 185:4011-4021.

Craik, D.J., Anderson, M.A., Daly, N.L. (2003) Circularproteins tied in knots. Today’s Life Sciences 15:28-32.

Blanchfield, J.T., Dutton, J.L., Hogg, R., Gallagher,O.P., Craik, D.J., Adams, D.J., Lewis, R.J., Alewood,P.F., Toth, I. (2003) The synthesis, structure

elucidation, in vitro biological activity, toxicity andCaco-2 cell permeability of lipophilic analogues of α-conotoxin MII. J. Med. Chem. 46:1266-1272.

Barry, D.G., Daly, N.L., Clark, R. J., Sandø, L., Craik,D.J. (2003) Linearisation of a naturally occurringcircular protein maintains structure but eliminateshemolytic activity. Biochemistry 42:6688-6695.

Marx, U.C, Korsinczky, M.L.J., Schirra, H.J., Jones, A.,Condie, B., Otvos, L., Craik, D.J. (2003) Enzymaticcyclisation of the potent Bowman-Birk proteaseinhibitor SFTI-1: Solution structure of linear precursorpeptide. Journal of Biological Chemistry 278:21782-21789. [Cover feature]

Janssen, B.J.C., Schirra, H.J., Lay, F.T., Anderson,M.A., Craik, D.J. (2003) The structure of PhD1, anovel plant defensin with five disulfide bonds.Biochemistry 42:8214-8222.

Meutermans, W.D.F., Bourne, G.T., Golding, S.W.,Horton, D.A., Camitelli, M.R., Craik, D.J., Scanlon,M.J., Smythe, M.L. (2003) Difficultmacrocyclisations: New strategies for synthesisingcyclic tetrapeptides. Organic Letters 5:2711-2714.

Rosengren, K.J., Clark, R.J., Daly, N.L., Goransson, U.,Jones, A., Craik, D. J. (2003) Microcin J25 has aThreaded Sidechain-to-Backbone Ring Structure andNot a Head-to-Tail Cyclized Backbone. J. Amer.Chem. Society 125:12464-12474.

Goransson, U., Craik, D.J. (2003) Disulfide mappingof the cyclotide kalata B1: chemical proof of thecyclic cystine knot. J Biol Chemistry 278:48188-48196.

Jones, C.E., Daly, N.L., Cobine, P.A., Craik, D.J.,Dameron, C.T. (2003) Structure and metal bindingstudies of the second copper binding domain of theMenkes ATPase. J Structural Biology 143:209-218.


(Opposite page - from left) Solution structure of palicourein, the largest cyclotide yet discovered, along with the South American plant,Palicourea condensata, from which it is derived; Cover from the Journal of Biological Chemistry from the issue in which we described theconcepts of “twist, knots and rings” in proteins with reference to the cyclotide family of circular proteins; Structure of the novel conotoxinGID determined by PhD student Emma Millard, Installation of our new high field NMR spectrometers in the NMR “pod” in the QBP complex;The unique structure of the antibacterial peptide microcin J25. It represents a rare example of a threaded protein structure;

(Above) Cover page from the Journal of Biological Chemistry from the issue in which we described the use of an enzyme to reverse itsnormal action and cyclise a small peptide, that itself is a potent inhibitor of the enzyme.

David Fairlie

CHEMISTRY AND HUMANTHERAPEUTICS

Research overviewChemistry underpins all aspects of the molecularbiosciences. Interactions between proteins and eithersmall molecules, proteins, DNA or RNA determine theoutcomes of all biological processes. Patterns areemerging in such molecular recognition and, byunderstanding the consequences of such interactions,we can expect to develop design strategies forcreating generic classes of small molecules that mimicor interfere with biomolecular interactions. We aim touse rational chemical intervention to mimic proteins(Figure 1a,b), inhibit enzymes (Figure 1c), or antagonizereceptors (Figure 1d) that are pivotal in normal humanphysiology, aberrant in disease, or crucial mediators ofinfection. We also use small molecules to betterunderstand the roles of pivotal proteins in life, ageing,and death.

Research OverviewOur group is principally interested in chemical designand synthesis in order to study chemical reactivity,chemical structure, molecular interactions, and themolecular basis for biological processes, diseasedevelopment, and drug action. Some group membersalso study enzymes and receptors on cell surfaces inorder to design new, potent and selective, enzymeinhibitors or receptor antagonists for development intoorally active drugs to treat inflammatory andneurodegenerative diseases, cancers, andviral/parasitic infections. Thus our research interests,while heavily centered on chemistry, extend to amolecular understanding of aspects of biochemistry,pharmacology, immunology, inflammation, virology,parasitology, cancer biology, and neurobiology.

Project AreasFundamental Chemical StudiesMembers of the group are engaged in a wide range offundamental chemical studies towards the discoveryand development of new synthetic methodologies andreagents, investigation of molecular recognition,

identification of the influences of constraints onmolecular structure, understanding steric andelectronic roles in chemistry and catalysis, and use ofchemical templates in building nano-structures. Thework is heavily based on organic synthesis, 2D-NMRspectroscopy, and uses a suite of other spectroscopictechniques for chemical analysis, purification and forassessing potential applications.

Drug Design, Discovery and DevelopmentIn addition to synthetic chemistry, researchers studymacromolecule-ligand interactions using computermodelling, determine NMR and crystallographicstructures, and conduct biochemical andpharmacological assays. As a result of our basic andstrategic research, we have been able to developgeneric approaches to the discovery ofprotease/lipase/transferase inhibitors, G protein-coupled receptor antagonists, and transcriptionalregulators. We have created multiple classes of smallorally active organic molecules and demonstrated theirpotent (IC50 < 1-100 nM) antitumour activity (Figure 2a),antiparasitic activity (malaria, giardia, schistosomalproteases), antiinflammatory activity (blocking humanTNF-a, IL-1b, IL-6, complement receptors, PAR,phospholipases (Figure 2b), antiviral activity (lowresistance inhibitors of HIV, Dengue and West Nile viralproteins), and anti-Alzheimer’s activity (against betasecretase). Such non-peptidic compounds are invarious stages of pharmacological, pre-clinical orclinical development.

Molecular RecognitionOur group uses computers to identify patterns inbiomolecular recognition. We are attempting tounderstand the origin and reasons for such patterns,and are developing generic strategies for rationallycreating small molecules that mimic or interfere withsuch interactions. We have recently completedcomputer modelling analyses of all known structures ofprotease-bound ligands, GPCR-bindingproteins/peptides, and receptor-bound transcriptionfactors. We have established the frequency with whichsuch classes of receptors recognize their ligands inbeta strand, turn, and helix shapes respectively. Wehave also created a database consisting of millions ofsorted small organic molecules for use in silico inmatching to pharmacophores or receptors duringligand- or receptor- based drug design.

Protein Surface MimicsWe are designing and synthesizing new classes ofsmall organic molecules that mimic bioactivesecondary (strand, sheet, helix, turns, combinations)and tertiary (multi-loop, multi-helix, multi-sheetbundles) structural surfaces of proteins. Multi-helixand multi-sheet molecules also led in some cases tosupramolecular nanostructures resembling thoseformed by amyloidogenic proteins associated withneurodegenerative diseases. We use 2D NMRspectroscopy to determine structures for selectedchemical mimics which are then compared withprotein structures. Successful structural mimicry has translated into functional mimicry, and we arenow attempting to discover how universal ourgeneric approaches are for mimicking bioactiveprotein surfaces.

Other highlights were denaturation-resistant alphahelical mimics (Figure 2c), template-assemblednanofibres (Figure 2d), and macromolecules thatmimic protein structures.

CollaborationsDuring the past 5 years our group has published in 5branches of chemistry (organic, medicinal, biological,inorganic, theoretical) and 7 branches of biology(biochemistry, pharmacology, virology, immunology,parasitology, cancer biology, neurobiology)necessitating a wide range of Queensland,Australian, and International collaborators.

Grants NHMRC Project Grant Convertase Inhibitors As ANew Class Of Anti-Inflammatory Drugs

NHMRC Project Grant Design & Development OfSmall Molecules To Regulate Protease ActivatedReceptor-2

NHMRC Project Grant Agonists and Antagonists ofthe Human Complement C3a Receptor

NHMRC Project Grant Design & Evaluation ofInhibitors of Phospholipases A2 as Anti-inflammatoryDrugs

NHMRC Development Grant Developing Anti-Inflammatory Drugs Based on Inhibition of a HumanEnzyme

ARC Discovery Grant Macrocyclic Peptidomimetics

ARC Discovery Grant Metal Clips For Folding ShortPeptides Into Helices

ARC Seed Grant The Australian Protease Network

2nd Hans Werthén Scholarship Pia Kahnberg

NHMRC CJ Martin Fellowship Michael Kelso

ARC Australian Professorial Fellowship Fairlie


Figure 1: Cytokine structure (Fig1a) for which a loop (red) has been mimicked (Fig1b) by a small molecule (yellow); Structure of a beta strandinhibitor bound in the active site of caspase 3 (Fig1c); NMR structure for several cyclic and acrylic agonists and antagonist of a GPCR (Fig1d).

Fig1a Fig1b Fig1c Fig1d

Publications 2003Glenn, M.P., Kelso, M.J., Tyndall, J.D.A., Fairlie, D.P.(2003) Conformationally Homogeneous CyclicTetrapeptides : Useful Three Dimensional Scaffolds.J. Am. Chem. Soc. 125:640-641.

Kelso, M.J., Hoang, H.N., Oliver, W.N., Sokolenko,N.,March, D.R., Appleton, T.G., Fairlie, D.P. (2003) ACyclic Metallopeptide That Induces Alpha Helicity InShort Peptide Fragments of Thermolysin. AngewChem. Int. Edit. 42:421-424.

Reid, R.C., Abbenante, G., Taylor, S.M., Fairlie, D.P.(2003) A Convergent Solution Phase Synthesis of theMacrocycle, Ac-Phe-[Orn-Pro-D-Cha-Trp-Arg], aPotent New Anti-Inflammatory Drug. J. Org. Chem.68:4464-4471.

Hansford, K.A., Reid, R.C., Clark, C.I., Tyndall, J.D.A.,Whitehouse, M.W., Guthrie, T., McGeary, R.P.,Schafer, K., Martin, J.L., Fairlie D.P. (2003) D-TyrosineAs A Chiral Precursor To Potent Inhibitors Of HumanNon-Pancreatic Secretory Phospholipase A2 (IIa)With Anti-Inflammatory Activity. ChemBioChem.4:181-185.

Lucke, A.J., Tyndall, J.D.A., Singh, Y., Fairlie, D.P.(2003) Designing supramolecular structures frommodels of cyclic peptide scaffolds with heterocyclicconstraints, J. Molecular Graphics and Modelling21:341-355.

Woodruff, T.M., Arumugam, T.V., Shiels, I.A., Reid,R.C., Fairlie, D.P., Taylor, S.M. .(2003) A Potent HumanC5a Receptor Antagonist Protects Against DiseasePathology in a Rat Model of Inflammatory BowelDisease. J. Immunol. 171:5514-5520.

Warrener, R., Beamish, H., Burgess, A., Waterhouse,N.J., Giles, N., Fairlie, D.P., Gabrielli, B. (2003) Tumourcell specific cytotoxicity by targeting cell cyclecheckpoints. FASEB J. 17:1550-1552.

Arumgam, T.V., Arnold, N., Proctor, L.M., Newman,M., Reid, R.C., Hansford, K.A., Fairlie, D.P., Shiels, I.A.,Taylor, S.M. (2003) Comparative protection against ratintestinal reperfusion injury by a new inhibitor ofsPLA2, COX-1 and COX-2 selective inhibitors, and anLTC4 receptor antagonist. Br. J. Pharmacol. 140:71-80.

Arumugum, T.V., Shiels, I.A., Strachan, A.J.,Abbenante, G., Fairlie, D.P., Taylor, S.M. (2003) A SmallMolecule Antagonist of C5a Receptors ProtectsKidneys From Ischaemia-Reperfusion Injury in Rats,Kidney International, 63:134-142.

Williamson, A.L., Brindley, P.J., Abbenante, G., Datu,B.J.D., Prociv, P., Berry, C., Girdwood, K., Pritchard, D.I.,Fairlie, D.P., Hotez, P.J., Zhan, B., Loukas, A. (2003)Hookworm Aspartic Protease, Na-APR-2, CleavesHuman Hemoglobin and Serum Proteins in a Host-Specific Fashion, J. Infect. Diseases, 187:484-494.

Senior research staffBob ReidJohn AbbenanteYogendra SinghMartin Stoermer

Postdoctoral research staff Joel TyndallKarl HansfordPhilip SharpeAndrew LuckePia KahnbergBernhard Pfeiffer

Research assistants Huy HoangBernadine FlanniganRenee BeyerTom Guthrie

PhD studentsNick ShepherdHuy Hoang

Len PattendenGavin Bryant

Masters studentAarti Kishore

Honours studentsTessa NallJacky Suen

UROP studentsSarah SmithPaul JaunceyCarol Burnton

Sabbatical visitorDr. Wendy Loughlin

Staff and Students

Stoermer, M.J., Butler, D.N., Warrener, R.N.,Weerasuria, K.D.V., Fairlie, D.P. (2003) Cycloadditionsof Isobenzofuran to a Constrained Template BearingNeighboring Dienophiles. Chem. Eur. J., 9:2068-2071.

Kelso, M.J., Fairlie, D.P. Current Approaches ToPeptidomimetics in Molecular PathomechanismsAnd New Trends In Drug Research, Chapter 44, pp.579-598 (Eds Toth I & Keri G) Taylor & Francis Londonand New York 2003.

Beyer, R.L., Kelso, M.J., Hoang, H.N., Appleton, T.G.,Fairlie, D.P. (2003) “Helix-Inducing Metal Clips inShort peptides” in Biomolecular Chemistry, Proc.First Int. Symp. Biomolecular Chemistry, December 2-5, Awaji, Japan, Chapter 3, pp. 146-149 (Ed. Y. Baba),Maruzen Co. Ltd Tokyo, 2003.

Hoang, H.N., Bryant, G.K., Kelso, M.J., Beyer, R.L.,Appleton, T.G., Fairlie, D.P. (2003) Short Peptide AlphaHelices Induced by Multiple Metal Clips J. Inorg.Biochem. 96:146.

Cusack, R.M., Grondahl, L., Fairlie, D.P., Hanson, G.R.,Gahan, L.R. (2003) Studies of the interaction ofpotassium(I), calcium(II), magnesium(II), andcopper(II) with cyclosporin A. J. Inorg. Biochem.97:191-198.

Conferences Among 11 international, 2 national, and 1 localconference presentations were:

“Template-Assembled Peptide Helices, Loops, Sheetsand Nanofibres”. Fairlie DP, Singh Y, Sharpe P,Stoermer MJ ; American Chemical Society, OrganicDivision, Mar 24, 2003 (New Orleans, USA).

“Proteinases and Inhibitor Design”, Fairlie DP2nd International Industry Conference on ProteaseInhibitors, IBC, Sept. 3-4, 2003 (Zurich).

“Protease Ligand Conformation and InhibitorDesign”, Fairlie DP 57th Harden Conference,Proteinase, Structure and Function, Royal Societiesfor Biochemistry and Chemistry, Sept. 9-13, 2003(Oxford).

“Mimicking Protein Structure in Short Peptides”,Fairlie DP Australian Peptide Symposium, Oct 2-6,2003 (Daydream Is, Qld)

“Towards Small Molecule Mimics Of BioactiveProtein Surfaces” New Zealand Chemical Society,Nov 30-Dec4, 2003 (Nelson, NZ)

“Helix-Inducing Metal Clips In Short Peptides”,Fairlie, D. P. First International Symposium onBiomolecular Chemistry (ISBC 2003), Japan ChemicalSociety, Dec 2-5 2003 (Awaji Is, Japan).

“Towards Mimics Of Protein Surfaces” Fairlie, D. P.Symposium on Biomolecular Chemistry KyushuUniversity, Dec 6, 2003 (Fukuoka, Japan).

Other Developments2003-, Co-Editor of Current Medicinal Chemistry

Started International and National protease researchnetworks (www.protease.net, www.protease.net.au)to facilitate interdisciplinary research interactions inthe field of proteases, their inhibitors and receptors.The networks involve over 100 international researchgroups and 90 Australian research groups.

Figure 2: Structures of potent and selective inhibitors of human histone deacetylases (Fig2a) and human secretory phosopholipase A2 GroupIIa (Fig 2b) that are orally active and respectively exhibit anticancer and anti-inflammatory activity; NMR-derived structures of an alphahelix mimetic in water (Fig 2c). The molecule is conformationally stable to 600C, 8M Guanidine.HCl and trypsin digest; Nanofibrescomprising twisted beta sheet peptides formed from template-assembled bundles of alpha helical peptides (scale 200nm) (Fig 2d).


Fig2a Fig2b Fig2c Fig2d

Jeffrey Gorman

MOLECULAR ANDCELLULARPROTEOMICS

Research overviewResearch carried out by this newgroup will exploit the platform ofcontemporary protein chemistryand proteomics.

This platform is broadly applicableto defining the chemical featuresof purified proteins, interactionsbetween proteins at the molecularand cellular levels and the

dynamics of the protein repertoires of cells in responseto disease states and other stimuli.

Research topics of particular interest involve theinteractions of viral proteins in assembled virusparticles interactions between intracellular proteinsand viral proteins during morphogenesis (virus particleformation) and interactions of viral proteins with cellmembrane receptors during infection of cells.

Our research will be underpinned by our massspectrometry expertise for the analysis of proteins andcomplemented by our excellent mass spectrometryinfrastructure.

In addition to academic interest, our work has thepotential to produce important leads for developmentof therapeutic agents to treat viral infections and otherimportant medical conditions.

This group integrates the proteomics activities ofCSIRO Livestock Industries through the establishmentof a joint laboratory, as well as accommodating theproteomics needs of the SRCFAG.

ProjectsInteractions and structures of proteins in assembledvirus particles.

Viruses consist of nucleic acid genomes packagedwithin protein-containing coats. Coat proteins functionto ensure efficient attachment to target host cells andtransmission of the viral genomes into these cells inwhich the viruses replicate. Proteins also contribute tostructural integrity of the viral particles and the viralgenome as well as functioning in viral replication.

The process of assembly (morphogenesis) of the virus

particles, stabilities of the assembled particles andfunctional activities of the viral proteins are governedby protein-protein interactions.

This project aims to develop and apply methods tobetter understand the interactions between viralproteins during morphogenesis and in the assembledparticles.

Interactions of viral proteins with host cell proteinsduring infection and assembly.

There is a growing appreciation that viral proteins caninteract in a variety of ways with cellular proteinsduring the viral replicative cycle. The interaction ofviral attachment proteins with host cell receptors toinitiate infection is well known, but there is growingevidence of interaction at other steps in the cycle,such as during RNA synthesis, viral assembly, andantagonism of host cell defenses.

Frequently, these interactions are essential for efficientviral replication and can have a major impact onpathogenesis. Relatively little is known about this area,in part because it has not been amenable toinvestigation by traditional biochemical approaches.

However, application of improved techniques of massspectrometry and proteomic-related techniques haveenabled the analysis of proteins present in low quantityor in complex mixtures, and provide new impetus forexamining the effect of viral infection on the hostproteome and possible physical interaction betweenviral and cellular proteins.

Regulation of signal-activated transcription factors bypost-translational modifications and protein-proteininteractions.

Transcription factors with a general basic helix-loop-helix/Per Arnt-Sim (bHLH/PAS) domain architecture actwithin the cell nucleus to coordinate transcription ofspecific genes. Heterodimerisation with the arylhydrocarbon receptor nuclear translocator (Arnt) isessential to form DNA binding complexes. Otherproteins are recruited to form the active transcriptioncomplexes. Ligand binding or other cellular signals canmodulate nuclear translocation of the transcriptionfactors and their ability to form active complexes.

In collaboration with Dr Murray Whitelaw's group fromthe University of Adelaide, we have demonstrated thatthe transcriptional potency of hypoxia-inducible factor(HIF)-transcriptional complexes is inhibited byhydroxylation of a specific asparagine residue of HIF.Oxygen activates this post-translational modificationand it also serves as the substrate for the hydroxylase(Factor that Inhibits HIF, or FIH) which hydroxylates the

regulatory asparagine of HIF. This normoxichydroxylation inhibits the recruitment of thetranscriptional co-activator p300/CBP to the DNA-bound complex, thereby repressing transcription. Thepurpose of this regulation is to prevent transcription ofgenes whose products are only required to respond tolow cellular oxygen levels.

Other uncharacterised proteins are also recruited tothe transcription complexes to influence thetranscriptional activity of HIF. One of our current aimsis to identify these unknown proteins and to determinetheir functional roles in the hypoxic regulation oftranscription.

We have recently commenced work on a comparabletranscription factor, the Dioxin (or Aryl Hydrocarbon)Receptor. This factor also appears to be regulated bypost-translational modifications and our aim in thisproject is to define the modifications involved and themechanisms by which they invoke control.

CollaboratorsProf John Bateman, Murdoch Childrens ResearchInstitute, Melbourne

Professor John Hancock, IMB

Professor Rob Parton, IMB

Professor Paul Young, Department of Microbiology,University of Queensland

Dr Murray Whitelaw, School of Molecular andBiomedical Science, University of Adelaide

Dr Peter Collins, National Institutes of Health,Bethesda, Maryland, USA

Professor Mark Peeples, Columbus Children'sResearch Institute and The Ohio State University, USA

GrantsARC Linkage Infrastructure and Facilities Grant (LIEF)Time of Flight Mass Spectrometry and Robots

NHMRC Project Identification and functions ofposttranslational modifications in the Dioxin/Arnttranscription factor. With Murray Whitelaw

AntiCancer Council of South Australia Role of theHypoxia Inducible Factor in Tumourigenesis. WithMurray Whitelaw and Daniel Peet.

Queensland Cancer Fund Proteomics approaches tothe early detection of prostate cancer. With R.Gardiner, J. Clements, T. Walsh, J. Bartley, and T. Pettitt

OtherMember of the editorial boards of the journalsMolecular and Cellular Poteomics and Protein andPepteide Letters

Research officersGary Shooter

Professional officerAlun Jones

Research assistantsNgari TeakleTristan Wallis

PhD students Hong Soon Chin Keyur Dave

Staff and Students


PublicationsLando, D., Gorman, J.J., Whitelaw, M.L., Peet, D.J.(2003) Oxygen-Dependent Regulation of Hypoxia-Inducible Factors by Prolyl and AsparaginylHydroxylation. European Journal Biochemistry,270:781-790.

Campanale, N., Nickel, C., Daubenberger, C.A., Whelan,D.A., Gorman, J.J., Klonis N., Becker, K., Tilley, L. (2003)Identification and Characterization of Heme-InteractingProteins in the Malaria Parasite, Plasmodiumfalciparum. J. Biol. Chem. 278:27354-27361.

Macdonald, W.A., Purcell, A.W., Mifsud, N., Ely, L.K.,Williams, D.S., Gorman, J.J., Clements, C.S., Kjer-Nielsen, L., Koelle, D.M., Borrow, S.R., Tait, B.D.,Holdsworth, R., Brooks, A.G., Lovrecz, G.O., Lu, L.,Rossjohn, J., McCluskey, J.A. (2003) Naturally selectedDimorphism Within the HLA-B44 Supertype AltersClass I Structure, Peptide Repertoire and T CellRecognition. J. Exp. Med. 198:679-691.

Bostjan Kobe

STRUCTURAL BIOLOGY OFPROTEIN – PROTEININTERACTIONS

Research overviewOur research focus on protein structure and function,with the emphasis on understanding the structuralbasis of interactions formed by thesemacromolecules. The primary technique used in thelaboratory is X-ray crystallography, combined with aplethora of other molecular biology, biophysical andcomputational techniques. Our research vision is toapply structural biology in functional annotation ofproteins (functional genomics).

ProjectsSpecificity of signal transduction pathways. The specificity of signal transduction pathways stemsfrom specific recognition and regulatory properties ofproteins involved in these pathways. We are studyinga number of signaling molecules including proteinkinases, the phosphopeptide-binding FHA domains, anovel class of G-proteins, and proteins involved inplant development and disease resistance. In parallel,we are developing bioinformatic tools for functionalannotation of novel signalling molecules. To this end,we have developed the computational tool Predikinthat can predict the substrates for Ser/Thr kinasesbased on their sequence alnoe, providing a powerfultool for genome-wide analysis of signaling pathwaysand identification of new therapeutic targets.

Regulation of nuclear import. Nuclear proteins are synthesised in the cytoplasm andare imported into the nucleus through the nuclear porecomplexes. Such transport is directed by specialsignals, the most common termed the nuclearlocalisation sequences (NLSs). Importin-alpha is thenuclear import receptor that recognises these NLSs.The ongoing crystallographic, biophysical andmutagenesis studies are aimed at shedding light onboth regulation and NLS recognition by importin-alpha,as well as using this protein as a structural frameworkfor engineering new binding specificities useful fordiagnostic and biotechnology purposes.

Structural genomics of macrophage proteins. Structural genomics is a large-scale effort to

determine 3D structures of all representativeproteins, as 3D structural information is one of themost effective ways to infer protein function. Ourstrategy is to use gene expression information fromcDNA microarrays for target selection, and thereforeselectively determine the structures of medicallyrelevant proteins via a high-throughput approach. The structures are used to infer biochemical andcellular function and will serve as templates forstructure-based drug design. Macrophage proteins areof central importance in a wide range ofimmunopathology, including infectious andinflammatory disease, cardiovascular disease and cancer.

Grants awardedARC Discovery Structure and function of novelmacrophage proteins using high throughputcrystallography

CollaboratorsDavid Hume, Institute for Molecular Bioscience,University of Queensland

Jenny Martin, Institute for Molecular Bioscience,University of Queensland

Thomas Huber, Department of Mathematics,University of Queensland

Paul Young, Department of Microbiology andParasitology, University of Queensland

Stuart Kellie, Department of Microbiology andParasitology, University of Queensland

Jimmy Botella, Department of Botany, University ofQueensland

Bernie Carrol, Department of Biochemistry andMolecular Biology, University of Queensland

David Fairlie, Institute for Molecular Bioscience,University of Queensland

Don McManus, Queensland Institute of MedicalResearch, Brisbane

Bruce Kemp, St. Vincent’s Institute of MedicalResearch, Melbourne

David Jans, Department of Biochemistry andMolecular Biology, Monash University, Melbourne

David Jones, Research School of BiologicalSciences, Australian National University, Canberra

Jeff Ellis, CSIRO Plant Industry, Canberra


Peter Anderson, Flinders University of SouthAustralia, Adelaide

Andrey Kajava, Centre de Recherches de BiochimieMacromoléculaire, CNRS, France

Roman Jerala, National Institute of Chemistry,Ljubljana, Slovenia

Matthias Koehler, Franz-Volhard-Klinik, Berlin,Germany

Murray Stewart, Medical Research CouncilLaboratory of Molecular Biology, Cambridge, UK.

Marcos Roberto de M. Fontes, Departamento deFísica e Biofísica, Instituto de Biociências - UNESP,Botucatu, Brazil,

Barbara Valent, Department of Plant Pathology,Kansas State University, Kansas, USA

Robert F. Standaert, Department of Chemistry,University of Illinois at Chicago, USA

Staff and Students

Publications and papers in 2003Brinkworth, R.I., Breinl, R.A., Kobe, B. (2003)Structural basis and prediction of substratespecificity in protein serine/threonine kinases. Proc.Natl. Acad. Sci. USA 100:74-79.

Wooh, J.W., Kidd, R.D., Martin, J.L., Kobe, B. (2003)Comparison of three commercial sparse matrixcrystallisation screens. Acta Cryst. D59:769-772.

Smyth, D.R., Mrozkiewicz, M.K., McGrath, W.J.,Listwan, P., Kobe, B. (2003) Crystal structures offusion proteins with large affinity tags. Protein Sci.12:1313-1322.

Fontes, M.R., Teh, T., Jans, D.A., Brinkworth, R.I.,Kobe, B. (2003) Structural basis for the specificity ofbipartite nuclear localisation sequence binding byimportin-alpha. J. Biol. Chem. 278: 27981-27987.

Kobe, B. (2003) Great expectations: Structural biologyamidst world politics. Australian Biochemist 34:24-27.

Fontes, M.R., Teh, T., Toth, G., John, A., Pavo, I., Jans,D.A., Kobe, B. (2003) The role of flanking sequencesand phosphorylation in the recognition of SV40 largeT-antigen nuclear localisation sequence by importin-alpha. Biochem. J. 375:339-349.

Kobe, B. (2003) Protein regulation, protein-protein

interactions and structural genomics. Acta Chim.Slov. 50:547-562.

ConferencesKobe, B., Breinl, R.A., Brinkworth R.I. (2003)Identification of substrates of protein kinases. – 28thAnnual Conference on Protein Structure andFunction, Lorne, Victoria, Australia, 9-13 February.

Kobe B. (2003) The role of protein structure infunctional annotation of proteins. – Australian Frontiersof Science, Canberra, Australia, 31 July - 1 August.

Kobe, B., Breinl, R.A., Brinkworth, R.I. (2003) Usingstructural information in functional genomics:Identification of substrates of protein kinases. –AsCA'03/Crystal-23, Broome, Western Australia, 10-13 August.

Fontes, M.R., Teh, T., Toth, G., John, A., Pavo, I., Jans,D.A., Kobe, B. (2003) The elusive role ofphosphorylation in nuclear import. – ComBio2003,Melbourne, Victoria, Australia, 29 September - 2October.

Kobe, B., Brinkworth, R.I. (2003) Prediction of proteinserine/ threonine kinase substrates. – 2ndGarvanSignalling Symposium, Sydney, NSW, Australia, 17-18November.

Research officersRoss BrinkworthJerry JosephPawel ListwanSarah Kruger

Research assistantsMareike Kurz

Huang-Teck LeeTrazel Teh

PhD studenta Robert SerekSundy (Ni Yen) YangJames Clark

MPhil students Thorsten KampmannCarmel Walsh

Honours studentsMarek MrozkiewiczSarah ChilcottDmitri Mouradov

(From left) Crystal structure of the nuclear import receptor importin-alpha; Binding of a substrate to protein kinase A.

Richard Lewis

MOLECULAR PHARMACOLOGYResearch overviewMy group’s research focuses is on the discovery andcharacterisation of conotoxins acting at ionchannels, receptors and transporters, especiallythose found in pain pathways (see figure Lewis3.jpg).

Currently we are investigating conotoxins thatselectively target the nicotinic acetylcholine andNMDA receptors, the voltage sensitive calcium andsodium channels, the noradrenaline transporter andthe α1-adrenoceptor. Complimentary interactionsbetween conotoxins and their receptor are beingestablished to better understand where and howthey act. Research on characterising the toxinsinvolved in ciguatera is also undertaken in thelaboratory.

The aim of this research is to develop research toolsand potential therapeutics for poorly treateddiseases, such as chronic pain. This researchinvolves assay-guided isolation of venom peptides,peptide synthesis, tissue pharmacology, radioligandbinding and electrophysiological studies, as well asreceptor mutagenesis, modelling and docking.

ProjectsWe are currently investigating conotoxins thatselectively target:

1. The nicotinic acetylcholine receptor, a non-selectivecation channel stimulated by acetylcholine andnicotine, is selectively inhibited by α-conotoxins. Wehave discovered several new α-conotoxins usingreceptors expressed in oocytes to guide crudevenom fractionation. Several had unusual structureand subtype selectivity. Homology modelling anddocking studies are allowing us to understand at themolecular level how these selectivity differencesarise;

2. The NMDA receptor, an important non-selectivecation channel in the brain, is inhibited byconantokins. Using specific analogues ofconantokin-G, we have recently found that specific

subtypes of the NMDA receptor are lost inAlzheimer’s disease. Currently we are trying toestablish their identity to better understand howAlzheimer’s disease develops;

3. The voltage sensitive N-type calcium, a neuronalcalcium channel found in pathways involved in thetransmission of painful stimuli, is inhibited by ω-conotoxins. We have recently identified a novelvariant of this channel using ω-CVID. The nature androle of this variant is now being investigated tounderstand its role in chronic pain;(figure Lewis1.jpg)

4. The voltage sensitive sodium channels, particularlythose found in neurons that are inhibited by µ-conotoxins, are also under investigation. We haveestablished that µ-conotoxins selectively targetpersistent forms of the TTX-sensitive sodiumchannel. The nature and role of these sodiumchannels is currently under investigation.

5. The noradrenaline transporter (NET) is the primaryroute of noradrenaline removal from synapses. Wehave identified χ-conotoxins as the first peptideinhibitor of NET, which is effective in the treatment ofneuropathic pain and depression. We are presentlyestablishing the complimentary interactions betweenχ-conotoxins and NET to understand where and howthey act at the molecular level.

6. We are also developing an understanding of whereand how the ρ-conopeptides act on the α1-adrenoceptor, and important target for treatingcardiovascular disorders and benign prostatichyperplasia.

7. Finally, we are characterising the novel substratespecific proteases found in cone snail venom thathave homology to pathogenesis related proteins and are up regulated in stress and diseases such as cancer.

GrantsNHMRC grant Selectivity and Mode of Action of Rho-Conopeptide TIA: A Novel Inhibitor of Alpha1-Adrenoceptors

ARC Glycerotoxin, a unique tool to investigate thedynamic interactions between N-type Ca2+ channelsand the exo-endocytic machinery (with FredricMeunier, Physiology and Pharmacology, UQ).


Research officersDenise AdamsMarion LoughnanLeonard MotinAnnette NickeTina SchroederIain Sharpe

PhD studentsTrudy BondSebastien DutertreJenny Eckberg

Fredrik HellqvistLotten RagnarssonDimitra TemelcosVicky TsaiTaka Yasuda

Research assistants:Trudy Bond Linda Thomas

Honours studentNadeeka Dissanayaka

Visiting researcherPatricia Hung

Visiting studentsJessica LarssonPia LarrsonEmma LarzeniusSofie SingbrantAngela Starke

Staff and Students

CollaboratorsProfessor Jean-Paul Vernoux, University of Caen,France

Professor Heinz Bönisch, University of Bonn, Germany

Professor Robert Graham, Victor Chang CardiacResearch Institute, Sydney

Professor MacDonald Christie, Pain ManagementResearch Institute, University of Sydney

Professor Gustaaf Hallegraeff, Department of Botany,University of Tasmania

Professor David Adams, School of BiomedicalSciences, UQ

Dr Lesley Lluka, School of Biomedical Sciences, UQ

Professor Paul Alewood, IMB

Professor David Craik. IMB

Professor Robert Capon, IMB

PublicationsLewis RJ and Garcia ML (2003) Therapeutic potentialof venom peptides. Nature Reviews Drug Discovery2:790-802.

Nicke A., Loughnan M.L., Millard E.L., Alewood P.F.,Adams D.J., Daly N.L., Craik D.J. and Lewis R.J.(2003) Isolation, structure and activity of GID, a novel4/7α-conotoxin with an extended N-terminalsequence. J. Biol. Chem. 278:3137-3144.

Adams D.J., Smith A.B., Schroeder C.I., Yasuda T. andLewis R.J. (2003) ω-Conotoxin CVID inhibits apharmacologically distinct voltage-sensitive calciumchannel associated with transmitter release frompreganglionic nerve terminals. J. Biol. Chem. 278:4057-4062.

Blanchfield J.T., Dutton J.L., Hogg R.C., GallagherO.P., Craik D.J., Jones A., Adams D.J., Lewis R.J.,Alewood P.F., Toth, I. (2003) Synthesis, structureelucidation, in vitro biological activity, toxicity andCaco-2 cell permeability of lipophilic analogues of α-conotoxin MII. J. Med. Chem. 46:1266-1272.

Milne, T.J., Abbenante, G., Tyndall, J.D., Halliday, J.,Lewis, R.J. (2003) Isolation and characterization of acone snail protease with homology to CRISP proteinsof the pathogenesis-related protein superfamily. J Biol Chem. 278:31105-31110.

Sharpe, I.A., Thomas, L., Loughnan, M., Motin, L.,Palant, E., Croker, D.E., Alewood, D., Chen, S.,Graham, R.M., Alewood, P.F., Adams, D.J., Lewis, R.J.(2003) Allosteric α1-adrenoceptor antagonism by theconopeptide ρ-TIA. J Biol Chem. 278:34451-34457.

Bryan-Lluka, L.J., Bonisch, H., Lewis, R.J. (2003) χ-Conopeptide MrIA partially overlaps thedesipramine and cocaine binding sites on the humannorepinephrine transporter. J Biol Chem. 278:40324-40329.

Sharpe, I.A., Palant, E., Schroeder, C.I., Kaye, D.M.,Adams, D.J., Alewood, P.F., Lewis, R.J. (2003)Inhibition of the norepinephrine transporter by thevenom peptide χ-MrIA: site of action, Na+

dependence, and structure-activity relationship. J Biol Chem. 278:40317-40323.

Nicke, A., Samochocki, M., Loughnan, M.L., Bansal,P.S., Maelicke, A., Lewis, R.J. (2003) α-Conotoxins EpIand AuIB switch subtype selectivity and activity innative versus recombinant nicotinic acetylcholinereceptors. FEBS Lett. 554:219-223.

Pottier, I., Hamilton, B., Jones, A., Lewis, R.J.,Vernoux, J-P. (2003) Identification of slow and fast-acting toxins in a highly ciguatoxic barracuda(Sphyraena barracuda) by HPLC/MS andradiolabelled ligand binding. Toxicon 42:663-672.

Lewis, R.J. (2003) Detection of ciguatoxins. In:Manual on Harmful Marine Microalgae (Hallegraeffet al. Eds). pp. 253-263. UNESCO Monographs onOceanographic Methodology, UNESCO.

Marshal, J.A., Nichols, P.D., Hamilton, B., Lewis, R.J.,Hallegraeff, G.M. (2003) Ichthyotoxicity of Chattonellamarina (Raphidophyceae) to damselfish(Acanthochromis polycanthus): the synergistic role ofreactive oxygen species and free fatty acids. HarmfulAlgae 2:273-281.

The aim of this research is to develop research toolsand potential therapeutics for poorly treateddiseases, such as chronic pain.


Jenny Martin

PROTEIN STRUCTURE ANDPROTEIN INTERACTIONS

Research overviewWe are interested in understanding the role ofproteins in disease and developing novel inhibitors tomodify the functions of disease-causing proteins. Weuse protein crystallography as the major biophysicalapproach to investigate protein structure andfunction, protein interactions, and as the foundationfor inhibitor design.

Our goal is to develop, with other researchers at UQ,the best lab-based protein crystallography facility inAustralia and to link these to high throughputapproaches for protein structure determination.Together these facilities will be used to examineproteins of prime importance to human health and willthereby underpin the development of new medicines.

ProjectsStructural Genomics of Mouse Macrophage ProteinsIn 2003, as part of a collaboration with Bostjan Kobeand David Hume, we solved the first structure of aprotein from this high throughput program. Thestructure determination required access to the ALSsynchrotron in Berkeley, USA. We also establishedprocedures for 96-well plate trials for most steps inthe process from PCR to crystallisation.

Dsb Proteins are critical for protein folding inbacteria. We solved the structure of DsbG, a disulfide bondisomerase, and showed that it had an unusuallyunstable disulfide bond at the active site. This

appears to be unique amongst this class of proteins.Structure determination required access to the APSsynchrotron at Argonne in the USA.

PNMT is the adrenaline synthesising enzyme. In this collaboration with Joel Tyndall (IMB), GaryGrunewald (Kansas University) and Michael McLeish(University of Michigan) we aim to develop potent,selective and CNS-active inhibitors of PNMT withwhich to investigate the role of CNS adrenaline. Thestructure of PNMT, solved recently using in-house X-ray equipment, allows structure-based design ofthese inhibitors. We are currently investigating thestructures of several PNMT:inhibitor complexes.

Sulfotransferases The structure of the carcinogen-converting enzyme,SULT1A1, was solved in collaboration with MickMcManus (BACS, UQ) using in-house X-rayequipment and was published early in 2003 in Journalof Biological Chemistry. The structure showed that,unexpectedly, two substrate molecules could beaccommodated at the active site simultaneously. Weare currently investigating how other substrates bindto this protein.

SNARE proteins involved in insulin-regulatedglucose transport. In this collaboration with David James (Garvan) wehave produced recombinant forms of all the SNAREproteins involved in the GLUT4 process as well as theregulatory SM protein Munc18c. We are currentlyinvestigating protein-protein interactions using therecombinant proteins.



Grants awarded for 2003• ARC Discovery Project Investigating the structure,

function and inhibition of the adrenaline-synthesizing enzyme PNMT

• ARC Linkage Project Structural studies oncarbohydrate modifying enzymes

• ARC Linkage Infrastructure and Equipment FundingQueensland high throughput structural biologyscreening facility

Collaborations (not including thosewithin IMB)Gary Grunewald, Kansas University, USA

Michael McLeish, University of Michigan, USA

Linda Thöny-Meyer, ETH Zurich, Switzerland

Mick McManus, School of Molecular and MicrobialSciences, University of Queensland

Paul Young, School of Molecular and MicrobialSciences, University of Queensland

Judy Halliday, Alchemia Pty Ltd

David James, Garvan Institute for Medical Research,Sydney

Research officersAnna AagaardNathan Cowieson Niranjali GamageChristine GeeBegona HerasShu-Hong Hu

Research AssistantsKirra McConnellCasey Pfluger Maria Somodevilla-Torres

PhD studentsMelissa Edeling Cath Latham

Masters StudentsAditya Angadi Frank Lin

Exchange StudentDanny Loveday

Honours studentsElizabeth Westbury

Undergraduate Students Vivian Chan Natalie Saez Rosemary Harrison

Staff and Students

Publications and papers in 2003Heras, B., Edeling, M.A., Byriel, K.A., Jones, A., Raina,S., Martin, J.L. (2003) Dehydration converts DsbGcrystal diffraction from low to high resolution.Structure 11:139-145

Gamage, N.U., Duggleby, R.G., Barnett, A.C.,Tresillian, M., Latham, C.F., Liyou, N.E., McManus,M.E., Martin, J.L. (2003) Structure of a humancarcinogen converting enzyme, SULT1A1: structuraland kinetic implications of substrate inhibition. J BiolChem 278:7655-7662

Hansford, K.A., Reid, R.C., Clark, C.I., Tyndall, J.D.A.,Whitehouse, M.W., Guthrie, T., McGeary, R.P.,Schafer, K., Martin, J.L., Fairlie, D.P. (2003) D-Tyrosineas a chiral precursor to potent inhibitors of humannon-pancreatic secretory phospholipase A2 (IIA) withanti-inflammatory activity. ChemBioChem. 4:181-185

Wooh, J.W., Kidd, R.D., Martin, J.L., Kobe, B. (2003)Comparison of three commercial sparse-matrixcrystallization screens. Acta Crystallogr D BiolCrystallogr 59:769-772

Hu, S.-H., Gee, C.L., Latham, C.F., Rowlinson, S., Rova,U., Jones, A., Halliday, J.A., Bryant, N.J., James, D.E.,Martin, J.L. (2003) Recombinant expression ofMunc18c in a baculovirus system and interactionwith syntaxin4. Prot Expr Purif 31:305-310.


Conferences East Coast Protein Meeting, Coffs Harbour,June 2003 Nathan Cowieson, A. Aagaard, C.Wells, T. Ravasi, C. Gee, T. Huber, .P Listwan, D.Hume, B. Kobe, J.L. Martin. "Structural genomicsof mouse macrophage proteins"

Christine Gee, M.J. McLeish, G.L. Grunewald,J.L. Martin. "Structural studies on PNMT, theadrenaline-synthesizing enzyme"

Melissa Edeling, Begona Heras, Linda Thony-Meyer, Jennifer L. Martin. "The BroadSubstrate Specificity of the Thioredoxin Fold isadapted in CcmG to achieve a very specificfunction" (awarded prize for best studentpresentation)

Combined AsCA and SCANZ meeting, Broome,August 2003 Anna Aagaard, P. Listwan, N.Cowieson, T. Huber, C. Wells, T. Ravasi, B.Kobe, D.A. Hume, J.L. Martin ."Structuralstudies of latexin, a novel carboxypeptidaseinhibitor"

COMBIO 2003, Melbourne October 2003A. Aagaard, P. Listwan, N. Cowieson, T. Huber,C. Wells, T. Ravasi, D.A. Hume, B. Kobe and J.L.Martin. "The crystal structure of latexin - aprotease inhibitor upregulated in stimulatedmacrophages"

Christine Gee, M.J. McLeish, C.L. Grunewald,J.L. Martin. "Structural studies on PNMT, theadrenaline synthesising enzyme: improvingcrystallisation methods and diffractionresolution"

Begona Heras, M. Edeling, S. Raina, J.L. Martin"Crystal structure of oxidized and reducedDsbG"

ASCEPT, Sydney December 2003-12-03 J.L. Martin "Focus on Queensland - the IMBand DDD"

Achievements in 2003• Together with Bostjan Kobe and David Hume

we succeeded in solving what we believe tobe the first "high throughput" crystal structure,that of latexin a novel mammaliancarboxypeptidease inhibitor (see picture onprevious page).

• Installation of the first (and only) highbrightness FR-E X-ray facility in Australia (seepicture on previous page).

• Currently establishing with Bostjan Kobe andDavid Hume a high throughput facility forprotein expression screening (pictures in nextyear's annual report).


Our goal is to develop,with other researchersat UQ, the best lab-based proteincrystallography facilityin Australia and to linkthese to highthroughput approachesfor protein structuredetermination.



Mark Smythe

COMBINATORIALCHEMISTRY ANDMOLECULAR DESIGN

Research OverviewOur research focuses on advancing drugdesign and synthetic organic chemistry todiscover novel biologically activemolecules against numerous targets andtherapeutic indications.

Projects Research undertaken can be summarisedinto the broad thematic areas outlinedbelow:

Development of new molecular designtools• Using advances in information science to

facilitate rapid database searching toidentify topological patterns in largedatabases of molecules

• Using experimentally derived structuraldata of molecules to determine theimportant physicochemical features ofbinding and function. To use thesefeatures as descriptors to design andsynthesise biologically relevant arrays ofmolecules.

Synthetic Chemistry• Develop new linkers and associated

chemistries to rapidly prepare arrays ofmolecules

• To develop new synthetic strategies torapidly access privileged substructures.

Biology• To explore the advantages of combining structural

based drug discovery with phage display for thedevelopment of topologically focussed arrays ofrigid peptide molecules. Use these arrays ofmolecules to discover biologically active leads anddrugs in a target-based discovery approach.

• Express proteins and develop assays to assist drugdiscovery.

Drug Discovery• Use fragment based drug discovery approaches to

identify small molecular fragments that bind toprotein surfaces. Fragment based discoveryinvolves the design and synthesis of libraries ofmolecules comprising a disulfide that are sitespecifically captured on a target protein containinga free cysteine and identified in a massspectroscopy based assay. Fragments that bind tothe protein surface are joined together in acombinatorial fashion and screened using moreconventional assays.

• Use existing chemistry and design infrastructure todevelop potent molecules to modulate the functionof cytokines and GPCR’s, and to block virus andbacterial infection.

CollaboratorsProfessor Garland Marshall. Washington University,St Louis, USA

Professor Mike Waters, IMB

Dr Kritaya Kongsuwan Livestock Industries, CSIRO

Dr Gene Wijffels, Livestock Industries, CSIRO

Dr Peter Adams, Department of Mathematics UQ

Dr Darryn Bryant, Department of Mathematics UQ



Research officersGreg BourneAndreas RuhmannSteve Love

PhD studentsAndrew McDevitt Doug Horton Stephen Long Gerald Hartig

Research assistantsJustin CoughlanJill TurnerNgari TeakleJonathon NielsonCarolyn JacobsWarren Oliver

Staff and Students

PublicationsMeutermans, W.D.F., Bourne, G.T., Golding, S.W.,Horton, D.A., Campitelli, M.R., Craik, D., Scanlon, M.,Smythe, M.L. (2003) Difficult macrocyclizations: Newstrategies for synthesizing highly strained cyclictetrapeptides Org Lett. 5: 2711-2714

Horton, D.A., Bourne, G.T., Smythe, M.L. (2003) The combinatorial synthesis of bicyclic privilegedstructures or privileged substructures Chem Rev.103: 893-930

Our research focuses onadvancing drug design andsynthetic organic chemistry todiscover novel biologically activemolecules against numeroustargets and therapeuticindications.



ISSUES IN GENETIC AND CELLULARMEDICINE AND TECHNOLOGIESThis research program focuses on public understanding,issues and implications of the new genetics and celltechnologies for the prevention and treatment ofcomplex diseases. It explores ethical issues andproblems raised by the genetic modification of plants,animals and humans.

It incorporates the IMB Office of Public Policy and Ethics.

Research Group LeaderWayne Hall


Wayne Hall

OFFICE OF PUBLIC POLICY ANDETHICS

Research overviewThe Office of Public Policy and Ethics undertakesresearch and analysis on ethical and public policyissues raised by advances in the molecularbiosciences and their applications. By detailedanalyses of important public policy and ethicalissues, the Office aims to enhance public discussionand encourage participation in decisions aboutdevelopments in biotechnology.

ProjectsThe Office’s major current areas of research includethe policy implications of the genetics of addictionand mental disorders. The Office has followed theAustralian debate surrounding research on humanembryonic stem cells and cloning and is investigatingthe social and policy implications of research on thegenetics of melanoma and colorectal cancer. We arecollaborating with the Queensland Cancer Fund andUQ's School of Population Health to examine publicperceptions of genetic science and molecularbiotechnology in the context of cancer preventionand management.

Our work in the addictions field also encompassesthe ethical issues raised by neuroscience researchon addiction. We have investigated the ethicalimplications of developing a cocaine vaccine and weare studying the contribution of illicit drug use to theglobal burden of disease, as well as the policy

implications of genetic research on tobacco use,nicotine dependence and the development of anicotine vaccine.

Finally, we are also tackling the ethical and policyimplications of research into the genetics ofdepression and we have collaborated in anevaluation of the impact of antidepressantprescribing on suicide mortality in Australia between1991-2000.

OPPE has developed a seminar program foracademics in the fields of biotechnology, ethics andpublic policy. Commencing in May 2003 the seminarshave attracted leading thinkers in the fields ofphilosophy, education, psychology, genetics,sociology, genetic counselling, and social science.By bringing together these key researchers we arebuilding an academic concentration in biotechnologyethics and public policy.

In addition we have developed a series of fact sheetson topical biotechnology issues ranging fromembryonic stem cells to genetically modified food.These can be accessed on the OPPE websitewww.uq.edu.au/oppe/.

Grants/fundingAustralian Institute of Criminology / CriminologyResearch Council

Queensland Cancer Fund

School of Population Health, University ofQueensland

beyondblue: the national depression initiative

UQ New Staff Research Start-up Fund

Visiting professorsJohn MorganDavid Weisbrot

Adjunct senior research fellowsSusan TreloarKim Summers

Visiting research fellowMartin Wilkinson

PhD studentsLucy CarterJennifer FlemingDavid TurnbullKatie Wilson

Masters studentAngela Wallace

Research assistantsMarla GwynneKatherine Morley

Specialist librarianSarah Yeates

Undergraduate researchopportunities program studentCerys Jones

URSS studentsMoya Anne McCaskillCindy Rinehart

Staff and Students



CollaboratorsProfessor Alan Lopez, Associate Professor ChrisDoran, Professor Neville Owen and ProfessorAndrew Wilson, School of Population Health, TheUniversity of Queensland

Dr Louisa Degenhardt, National Drug and AlcoholResearch Centre, University of New South Wales

Dr Rick Harwood, National Institute on Drug Abuse, USA

Dr Jeff Dunn and Dr Joanne Aitken, QueenslandCancer Fund

Dr Susan Treloar, Ms Kellie Chenoweth and Dr SandyTaylor, School of Social Work and Applied HumanSciences, The University of Queensland

Publications Hall, W., Carter, L., Morley, K.I. (2003) Addiction,ethics and scientific freedom. Addiction 98:873-4.

Hall, W., Carter, L., Morley, K.I. (2003) Addiction,neuroscience and ethics. Addiction 98:867-70.

Lynskey, M., Day, C., Hall, W.D. (2003) Alcohol andother drug use disorders among older-aged people.Drug and Alcohol Review 22:125-133.

Hall, W.D., Mant, A., Mitchell, P.B., Rendle, V., Hickie,I., McManus, P. (2003) Association betweenantidepressant prescribing and suicide in Australia,1991-2000: trend analysis. BMJ 326:1008-1012.

Hall, W.D., Pacula, R. Cannabis use and dependence:public health and public policy: Cambridge UniversityPress; (2003).

Day, C., Topp, L., Rouen, D., Darke, S., Hall, W., Dolan,K. (2003) Decreased heroin availability in Sydney inearly 2001. Addiction 98:93-5.

Carter, L. (2003) The ethics of xenotransplantation. In:Healey J, editor. Organ transplantation. Rozelle,N.S.W: Spinney Press.

Degenhardt, L., Hall W.D., Lynskey M. (2003)Exploring the association between cannabis use anddepression. Addiction 98:1493-1504.

Darke, S., Hall, W.D. (2003) Heroin overdose:research and evidence-based intervention. Journalof Urban Health: Bulletin of the New York Academyof Medicine 80:189-200.

Morley, K.I., Hall, W.D. (2003) Is there a geneticsusceptibility to engage in criminal acts? Trends &Issues in Crime and Criminal Justice;263(September).

Fry, C.L., Hall, W.D. (2003) Key issues in determiningthe ethics of research subject payment: the specialcase of drug abuse epidemiology. AustralasianEpidemiologist 10:41-47.

Hall, W., Degenhardt, L. (2003) Medical marijuanainitiatives:are they justified? How successful are theylikely to be? CNS Drugs 17:689-97.

Degenhardt, L., Hall, W. D. (2003) Patterns of co-morbidity between alcohol use and other substanceuse in the Australian population. Drug and AlcoholReview 22:7-13.

Maher, L., Dixon, D., Hall, W.D., Lynskey, M. (2003)Property crime and income generation by heroinusers. Australian and New Zealand Journal ofCriminology 35:187-202.

Dolan, K.A., Shearer, J., MacDonald, M., Mattick, R.P.,Hall, W., Wodak, A.D. (2003) A randomisedcontrolled trial of methadone maintenance treatmentversus wait list control in an Australian prisonsystem. Drug and Alcohol Dependence 72:59-65.

Morley, K.I., Carter, L. & Hall, W. (2003) Regulation ofembryonic stem cell research and therapeuticcloning: the Australian debate. Plaintiff 55:20-23.

Taylor, D.R., Hall, W.D. (2003) Respiratory healtheffects of cannabis: Position Statement of TheThoracic Society of Australia and New Zealand.Internal Medicine Journal 33:310-313.

Hall, W.D., Mant, A., Mitchell, P., Rendle, V., Hickie, I.,McManus, P. (2003) Responses to our critics. BMJOnline 326.

Degenhardt, L., Hall, W., Lynskey, M. (2003) Testinghypotheses about the relationship between cannabisuse and psychosis. Drug and Alcohol Dependence71:37-48.


Research presentationsCarter, L. (2003) Consequentialist Objections toTransgenesis: GM Foods, Xenotransplantation andGerm Line Gene Therapy. Issues in AnimalTransgenesis: A Symposium. Sydney, NSW.

Carter, L. (2003) Ethics of Somatic and Germ LineGene Therapy. Australian Gene Therapy SocietyMeeting. Brisbane, Queensland.

Fleming, J. (2003) End of Life Session[Chair/Facilitator] The Australian Institute of HealthLaw and Ethics 8th Annual Conference - “The RiskSociety: Challenges in Health Law and Ethics. Hobart,Tasmania.

Fleming, J. (2003) Questions of Balance: MulticentreClinical Trials involving participants with impairedcapacity. Australian Ethics of Research Congress.Canberra, ACT.

Fleming, J. (2003) Great Debate: Swimming in a Seaof Change - Regulation is Killing Innovation[Convenor]. Hosted by Australian Institute of HealthLaw and Ethics and the Australasian ResearchManagement Society. Brisbane, Queensland.

Fleming, J., Lyons, A. (2003) Balancing risks andbenefits: Legal and ethical dimensions in conductingclinical trials involving patients with impairedcapacity. 28th International Congress on Law andMental Health, Sydney, NSW.

Hall, W. (2003) Addiction: What if it’s genetic?[Panelist]. CSIRO-World Genetics CongressSymposium. Melbourne, Victoria.

Hall, W. (2003) Assessing health outcomes: the viewfrom the Drug Utilisation Subcommittee of thePharmaceutical Benefits Advisory Committee. HealthOutcomes Conference. Canberra, ACT.

Hall, W. (2003), Biotechnology, genetics and tobaccocontrol: an ethical and policy analysis of somescenarios. Stanford Centre for Bioethics. StanfordUniversity Medical School, Palo Alto, California.

Hall, W. (2003) Biotechnology, genetics and tobaccocontrol. Centre for Addiction and Mental Health,Toronto, Ontario.

Hall, W. (2003), Ethical issues in neuroscience andgenetic research on addiction. Canadian Institutes ofHealth Research, Jackson’s Point, Ontario, Canada.

Hall, W. (2003) Ethical issues in neuroscience andgenetic research on addiction. Centre for AppliedBioethics, University of British Columbia, Vancouver,Canada.

Hall, W. (2003), Ethical and social implications ofcocaine and nicotine vaccines. Center for HealthCare Evaluation, Veterans’ Affairs Hospital, MenloPark, California.

Hall, W. (2003) Genetics of depression: ethical andpolicy implications. Mental Health and Law Congress.Sydney, NSW.

Hall, W. (2003) Great Debate: Swimming in a Sea ofChange - Regulation is Killing Innovation [Panelist].Hosted by Australian Institute of Health Law andEthics and the Australasian Research ManagementSociety. Brisbane, Queensland.

Hall, W., Carter, L., Morley, K. (2003) Genetics ofdepression: ethical and policy implications. Paperpresented at 28th International Congress on Law andMental Health, Sydney, NSW.

Hocking, B., Campion, V., Fleming, J.. (2003) Mindgames? Crime gene? Clueless in Hollywood? 28thInternational Congress on Law and Mental Health,Sydney NSW.


7.Community Engagement and Awareness

'Attack of the Clones’: Patent Law and Stem Cell Research Dr Matthew Rimmer,Faculty of Law, Australian National University

Patently Justified? Gene Patents, Ethics and Public Policy Prof Wayne Hall, Director, Office of Public Policy and Ethics, IMB

A Bigger Voice? Engaging Citizens with Life Science Questions Dr Tom Shakespeare,Director of Outreach, PEALS Research Institute, UK

Biotechnology, genetics and tobacco control: an ethical and Prof Wayne Hall, policy analysis of some feasible scenarios Director, Office of Public Policy and

Ethics, IMB

Better People Through Better Technology A/Prof Carl Elliott,Center for Bioethics, University of Minnesota

What are the Key Messages in Genetics and how can we Dr Kristine Barlow-Stewart,Broadcast them? Director, Centre for Genetics Education,

NSW Genetics Service

The Popular Press and Genetics Policies: The Nature and A/Prof Timothy Caufield,Impact of "Genohype" Canada Research Chair in Health Law

and Policy, University of Alberta, Canada

Genetic Risk Information – Can it motivate behaviour change? Prof Theresa Marteau,Professor of Health Psychology andPDirector of the Psychology and Genetics Research Group, King's College, London

IMB OFFICE OF PUBLIC POLICY AND ETHICS – OPPEThe OPPE Lecture program is aimed at those with an interest in bioscience, ethics and public policy. The programran throughout 2003 with a series of eight lectures attended by a diverse audience – academics from myriaddisciplines, representatives of government departments, lawyers, policy makers, students, teachers and membersof the general public.



8.AustralianCollaborative Research

Further underlining the Institute's commitment toresearch excellence, IMB Group Leaders are corepartners and participate in several CooperativeResearch Centres (CRC) , a major National ResearchFacility, Australian Research Council (ARC) Centresof Excellence (COE) , an ARC Special ResearchCentre, and a new ARC Centre.

These programs are integral to building Australia'snational and international research capabilities.

They aim to create the scale and focus necessary tomaintain and develop Australia's world-class standingin priority areas through highly innovative researchthat addresses challenging and significant problems.

CRCs and COEs make vital contributions toAustralia's research landscape and produceoutcomes with economic, social and cultural benefitto the country.

Involvement in these ventures reflects very highly onthe participating researchers, indicating the high valueof their work in both scientific and commercial terms.

ARC SPECIAL RESEARCH CENTREFOR FUNCTIONAL AND APPLIEDGENOMICSThe ARC Special Research Centre for Functional and Applied Genomics provides and develops thelatest technologies to enable internationallycompetitive research in the field of genomics. The SRC comprises an integrated network of coretechnologies including computational biology,structural biology, proteomics, animal transgenicsservice, as well as a microarray facility.

The relocation of the IMB to the QueenslandBioscience Precinct brought together groupspreviously dispersed through several buildings on theSt Lucia campus and provided opportunities for therecruitment of new research groups addingsignificant depth to the SRC.

A particular highlight was the recruitment of JeffGorman to head a joint CSIRO /IMB proteomics unit.Jeff successfully applied for funding from the ARC fora ToF-ToF mass spectrometer, which will massivelyenhance the throughput and sophistication ofproteomic tools available to researchers.

In terms of scientific outcomes, SRC affiliatesprovided the largest foreign group in the internationalconsortium that provided functional annotation to the



mouse transcriptome project (FANTOM2) andsubsequent analyses that made a major contributionto a special issue of Genome Research providing anoverview of the FANTOM2 project. The closecollaboration with Japanese colleagues at the RIKENGenome Sciences Centre will continue with ourstrong involvement in FANTOM3 in 2004.

The new resources and common location provide apowerful foundation for the SRC to fulfil its aim ofproviding all of the links in the pipeline from genediscovery to functional assignment and application.The future will see the coordinated application ofthese resources to provide meaningful description ofbiological systems such as mammalian cells, fromthe structure, location and function of individualproteins to the control networks that allow thesystem to respond to its environment in development,differentiation and disease.

AUSTRALIAN PHENOMICSFACILITYThis major national research facility based at theAustralian National University enables Australian andinternational researchers to define the mammalianphenome: how the estimated 40,000 genes in thegenome sequence of humans and other mammalsregulate the phenotype or behaviour of cells, tissuesand the body.

The completion of human and mouse genomesequences catalysed an international race toharness more efficient methods of disrupting genefunction in the mammalian genome so as toilluminate phenotypic consequence and practical usefor human and animal health, industry andenvironmental conservation.

The Australian Phenomics Facility (APF) builds uponand provides wide access to a new technologypioneered in Australia allowing high throughputanalysis of all mammalian genes for their phenotypiceffects by inducing mutations in mice, looking for

specific changes to traits of medical importance andthen isolating the genes responsible.

It includes researchers from John Curtin School ofMedical Research, The Australian NationalUniversity, Monash Institute of Reproduction andDevelopment, Monash University, Dairy CRC, GarvanInstitute, IMB, University of Queensland

The facility keeps Australia at the cutting edge ofinternational efforts to advance human and animalhealth by defining the phenome. The APF is aleading facility of its kind, and in high demandnationally and internationally, generatinginternational recognition, key intellectual property,new skills, and represents a prime opportunity tobuild new industries.

COOPERATIVE RESEARCHCENTRE FOR THE DISCOVERY OFGENES FOR COMMON HUMANDISEASESThe basal cell carcinoma research conducted byBrandon Wainwright and Carol Wicking contributesto the Cooperative Research Centre for the Discoveryof Genes for Common Human Diseases' (GeneCRC)research portfolio to unravel the genetic causesbehind many common human diseases.

Many of the diseases affecting humans have bothgenetic and environmental components. In somecases the genetic component is distinct enough toallow identification of the responsible genes bygenomic experimental techniques. These discoverieshave important applications as diagnostics andpossible development as therapeutics.

In addition to its research focus the GeneCRC has astrong education and ethics program committed toengaging the Australian community in an informeddebate on the applications of human genetictechnology, to which the IMB's Office of PublicPolicy and Ethics makes contributions.


COOPERATIVE RESEARCHCENTRE FOR CHRONICINFLAMMATORY DISEASESThe Cooperative Research Centre for ChronicInflammatory Diseases (CRCCID) focuses on twodiseases that together contribute to a massivecommunity burden, rheumatoid arthritis and chronicobstructive pulmonary disease.

The research activities of the CRC are focused ondeveloping innovative therapies for these chronicinflammatory diseases through understanding theirbasic biology.

In 2004 the disease focus of the CRC will expand toinclude osteoarthritis as a result of a successfulgrant for supplementary funding. This will enabledevelopment of new methods to treat debilitatingjoint disease and generate synthetic tissues to repairinjured joints.

The Queensland node headed by David Hume makesup approximately 40% of the CRC activity with afocus on therapeutic target gene identification andvalidation.

The CRC seeks to identify genes that are regulated ininflammatory disease processes, and determinewhich of those genes is absolutely required fordisease progression. From here, we will developways of screening for potential therapies thatinterfere with the function of the targeted gene.

NANOThe Nanonstructural Analysis Network Organisationis an Australian Major National Research Facility andthe peak facility for nanometric analysis of thestructure and chemistry of materials in both physicaland biological systems.

Spread across five different universities in four states,NANO operates and maintains state-of-the-art facilitiesfor the characterisation and manipulation of matter atthe atomic and molecular scale.

With a primary focus on microscopy andmicroanalysis, this network organisation will createcollaborations to explore and define the structure-function relationships which enable innovation innanotechnology and biotechnology. NANO will developand support a commercial-arm so as to provide avehicle for the rapid commercialisation of results.

ARC CENTRE OF EXCELLENCE INBIOTECHNOLOGY ANDDEVELOPMENTSolving human fertility disorders, fighting testicularcancer and controlling feral pests are the maintargets of the Centre of Excellence in Biotechnologyand Development (CBD).

Composed of researchers from the University ofNewcastle and IMB, the team is focussing ondecoding the complex genetic messages that drivethe production of male germ cells (cells that formsperm cells) to broadly apply the research to people,pets and pests, as well as other targets.

The incidence of testicular cancer has doubled in thelast 30 years while the rates of other cancers (egovarian, uterine and cervical) have remainedconstant. It is therefore imperative scientists find outmore about the complex genetic processes involvedin this cancer, as well as identifying anyenvironmental factors that may be implicated in itsoccurrence.

IMB's Peter Koopman is searching for new genesinvolved in the development of male germ cells andestablishing the function of these genes.

CENTRE OF EXCELLENCE: THENATIONAL STEM CELL CENTREThe National Stem Cell Centre (NSCC) is a majorAustralian collaborative initiative uniting many of thecountry’s leading academic researchers with thebiotechnology industry to develop innovativetherapeutic products to treat a range of seriousinjuries and debilitating diseases.

The Centre will build on Australia’s existing expertisein stem cell and related platform technologies to laythe foundations for delivering stem cell therapies.

IMB's Melissa Little, Head of the NSCC's ScientificManagement Advisory Committee, is particularlyinterested in renal disease and understanding thedevelopmental processes involved in normal anddiseased kidneys. Using stem cell technologies thiswill lead to new treatments of kidney diesease andpossibly renal regeneration.


ARC CENTRE IN GENOME/PHENOME BIOINFORMATICSHeaded by Mark Ragan, the Centre for Genome-Phenome Bioinformatics is investigating how all theinformation encoded in the human genome actually'comes to life'.

The primary focus is to understand thetransformation of genomic information into cellularform and function, enabling researchers to modeland visualise complex molecular processes inmammalian cells.

Understanding the progression from genome tophenome is pivotal to understanding what makeshumans function at the cellular level, andunderstanding human health and our susceptibility to disease.

The COE will also develop new computer softwareand experimental techniques broadly applicable tobiotechnology all the while building a critical mass ofbioinformatics researchers providing humanexpertise and intellectual property vital to Australia'sinternationally competitive research in advancedbioscience and biotechnology.


Involvement in these ventures reflects very highlyon the participating researchers, indicating the highvalue of their work in both scientific andcommercial terms.


The AGRF isrecognised as a trulynational facilitythrough theestablishment ofsuccessful andcomplementarynodes at theUniversity ofQueensland, theWalter and Eliza HallInstitute and now atthe Waite in SouthAustralia.



AUSTRALIAN GENOMERESEARCH FACILITYThe past twelve months have witnessed furtherconsolidation of the Australian Genome ResearchFacility as the premier national genomics researchfacility.

Financially, the status of the organisation as a MajorNational Research Facility (MNRF) has been renewedby the Federal Government with a $14 million awardthrough the MNRF Program over the next five years(2002-2006) to upgrade its equipment and expand intonew services such as Single Nucleotide Polymorphism(SNP) genotyping.

This has been leveraged with grants from theVictorian State Government, the South AustralianGovernment and Adelaide University to enhance theoutputs of the MNRF in each respective state.Recognition of AGRF support for the development ofbiotechnology in Australia was clearly evident whenAGRF hosted the signing of the Three State Alliancebetween the Premiers of Queensland, NSW and Victoria.

A clear example of the evolution of AGRF has beenthe revision of the organisational structure from ageographic to a functional focus. This has not onlyprovided a more effective point of contact for users,but has significantly improved our financialmanagement of existing and new activities.

The AGRF is particularly proud to have beenassociated with the successful completion of the firstgenome to be sequenced in Australia, that ofLeptospira borgpeterseni with Professor Ben Adlerand colleagues from Monash University fundedthrough the NHMRC Program in Medical Genomics.

Another exciting achievement for the year was ourco-authorship in the prestigious journal, Science, ofthe results of a study aimed at finding genesassociated with the debilitating mental illness,schizophrenia. The well designed and implementedfine mapping study of a segment of chromosome 1was finally able to prove conclusively that there areno schizophrenia genes in this region. This study hasopened up a number of opportunities forcollaboration with other international scientistswithin the consortium. In addition to this landmarkstudy, our clients have published genetic studies thathave located gene regions relevant to hypertensionand bipolar disorder.

Despite growing international competition, the AGRFhas continued to be able to provide a high qualityservice at competitive prices. The recent introductionof new equipment has significantly enhanced thesequencing and genotyping services and throughproductivity gains has allowed the savings to bepassed through to AGRF users. Several newinitiatives important to the future growth of AGRFwere brought to fruition, including successfulimplementation of the SNP analysis service, whichwas launched at the International Congress ofGenetics in July, 2003.

Plans were also completed for co-localisation of anew AGRF node with the Plant Functional GenomicsCentre in Adelaide. This will significantly enhanceAGRF’s ability to play a vital role in enhancing theuptake and utilisation of genomic technologies in theagricultural arena.

The AGRF is recognised as a truly national facilitythrough the establishment of successful andcomplementary nodes at the University ofQueensland, the Walter and Eliza Hall Institute andnow at the Waite in South Australia.


9.IMB Graduate Program

The IMB Graduate program, established in 2000, cameto fruition in 2003, when the first PhD students fullyenrolled through the IMB graduated alongside anumber of their IMB colleagues, enrolled throughother University departments. Additionally, the totalnumber of enrolments in the Graduate ResearchHigher Degree programs of the IMB swelled to 80students throughout 2003. The Program is now widelyrecognized in Australia and around the world and isattracting high quality students.

The year saw a number of changes, with the GraduateProgram's inaugural Graduate Administrative Officer,Ann Day, moving onto other challenges at theUniversity of Newcastle and Dr Amanda Carozzi takingover this role. She is now the very busy adminstratorand mentor for the diverse student cohort at the IMB.

In 2003, increased numbers of undergraduate studentsgained valuable laboratory experience at the IMBthrough several new initiatives. The GraduateProgram instigated the IMB Undergraduate ResearchScholarship Scheme in which third year studentsworked eight hours per week on a mini researchproject in an IMB research lab. The students wereactively involved in all aspects of the researchlaboratory to which they were assigned. Of the 14students that participated in this scheme, six intend toundertake their Honours year at the IMB, a verypositive outcome.

The IMB also became more actively involved in the"Introduction to Research" scheme. This course, run byUQ's School of Molecular and Microbial Sciences,involves third year students undertaking a mini-projectin a research laboratory as part of their BSc program.In yet another positive outcome, over a dozen students

undertook their projects at IMB, with more than halfintending to undertake Honours with an IMB GroupLeader in 2004.

Both schemes not only proved beneficial in recruitingtop quality students to the IMB but also fulfilled ourmandate to make bioscience more widely accessibleand gave talented undergraduates an earlyintroduction to research.

The Graduate Program continued to run workshopsdesigned to assist our students in their overall careerdevelopment through the year. These includedIMBcom’s “Introduction to Bio-Business” workshopfor first year students, covering issues such asintellectual property, patenting and commercialization.This was supplemented by a second workshopcatering for the unique needs of research students inthe fields of bioinformatics and computational biology.

IMBcom also conducted a three day Bio-Entrepreneurism Retreat for third year PhD students,covering topics such as technology transfer, businessplanning, legal issues and communication (includingpeople management, negotiation skills and dealingwith the media). Wayne Hall and the Office of PublicPolicy and Ethics (OPPE) team ran a workshop for thefirst year students, discussing the topic of genepatenting. Particular attention was given to theimplications of Genetic Technologies Ltd patent onnon-coding DNA sequences prompting opendiscussion on the issues associated with the purposeand conditions of patents, IP and the ramifications foraffordability of public health and medical research.



Melissa Little conducted an information sessionabout applying for NHMRC Postdoctoral Fellowships,with a focus on the more popular fellowships such asthe CJ Martin. This was greatly appreciated bystudents in the latter phases of their PhDs. It isintended that this information session become aregular feature of the IMB Graduate Program.

Another highlight for 2003 was the appointment of ourGraduate Coordinator, Jenny Stow, to the GraduateStudies Committee of the University’s Academic Board,the committee responsible for the formulation ofUniversity policy on issues concerning Graduatestudents. A recent decision of direct relevance to IMBstudents was the amendment to thesis format allowinginclusion of bound manuscripts as part of a thesis.

Relocation of the IMB into the QueenslandBioscience Precinct saw, for the first time, all of thestaff and students housed in the same building. Thisproximity prompted a resurgence of the IMB studentassociation, SIMBA, which had effectively gone intohibernation during the busy months leading up to the

relocation. Elections for a new Executive were heldin the second half of the year and new PresidentFred Martinson eagerly embraced the challenge of re-establishing a cohesive and active student body inthe IMB. The results have been impressive withseveral popular social events and the new monthlynewsletter, SIMBAlize.

The IMB Graduate Program has grown to become anactive and important part of the ongoing researchand training at the IMB. It is extremely gratifying tosee our graduates progress on to top research andscience postings around the world. Examplesinclude:

• Asanka Kararatne - Molecular Neurobiology, SalkInstitute for Biological Studies, San Diego, USA

• Nicole Walsh - Rheumatology Division, HarvardMedical School, Boston, USA

• Melissa Edeling - Cambridge Institute for MedicalResearch, UK

IMB GRADUATE FAST FACTSScholarships awarded to IMB for studies commencing 2004:

11 Australian Postgraduate Award/University ofQueensland Postgraduate Research Scholarships (of which 9 were accepted)

8 IMB Scholarships

2 National Health and Medical Research Council Dora Lush Scholarships

2 International Postgraduate Research Scholarships (one with additional stipend scholarship)

2 University of Queensland Graduate SchoolScholarships

1 Australian Rotary Health Research Fund Scholarship


Honours Students

Student SupervisorKatie Baldwin Paul Alewood and Ian GentleMing-Kang Chang David Hume and Stuart KellieLouise Dempster David CraikElizabeth Holliday Mike WatersEugene Huang Peter KoopmanJack King-Scott Brandon WainwrightGenevieve Kinna Melissa LittleSheryl Maher Mike WatersStephanie Martell Brandon WainwrightTessa Nall David FairlieAshley Rossiter Melissa LittleSamantha Stehbens Alpha YapElizabeth Westbury Jennifer Martin

New Research Higher Degree students for 2003

Student SupervisorShannon Armstrong Melissa LittleRajith Aturaliya Rohan TeasdaleStephen Bradford Peter KoopmanDavid Bryant Jennifer StowCheong Xin Chan Mark RaganHong Soon Chin Jeff GormanMyrna Constantin David HumeMelissa Davis Rohan TeasdaleJennifer Fleming Wayne HallAl Forrest Sean GrimmondLeith Fremlin Rob CaponFalak Helwani Alpha YapJason Kay Jennifer StowFrank Lin Jennifer MartinRebecca Pelekanas Mike WatersDaniel Sangermani Jennifer StowCas Simons John MattickStuart Stephen John MattickBrendan Tse David HumeTheingi Tun Rohan TeasdaleOng Wei Wooh Mike WatersAndy Wu Ian CassadyBen Clark Rob Capon University of Melbourne to IMBEmma Millard David Craik SBMS to IMBRanjala Ratnayake Rob Capon University of Melbourne to IMBNatalie Steen Paul Alewood NRAV to IMB



PhD Completions 2003

1. Adolphe Christelle, Examination of the in vivo effect or excess sonic in cuan and descre hedgehog. Brandon Wainwright

2. Christopher Armishaw, The Chemical Synthesis of Proteins. Paul Alewood

3. Julie Dutton Studies of novel disulphide-bonded cyclic peptides. David Craik

4. Melissa Edeling, Protein Folding: Structure-function studies on CycY, a reducing disulphideoxidoreductase. Jennifer Martin

5. Juliet French, Characterisation of G3BP and its implicated role in cancer. John Mattick

6. Brett Hamilton, Development of Detection Methodologies for Ciguatoxins. Richard Lewis

7. Kelly Loffler, Molecular Genetics of Sex Determination in Mice. Peter Koopman

8. Asanka Karunaratne, Molecular Genetics of Cell-Type Specification in Vertebrate Central NervousSystem. Peter Koopman

9. Wendy Ingram, Discovery of novel downstream target genes regulated by the Hedgehog Pathway. Brandon Wainwright

10. Gabriel Kolle, Functional studies of a novel gene, S52 in the development of the central nervoussystem. Melissa Little

11. Fiona McCarthy, Bovine Enterovirus: Molecular characterisation and evaluation as a vaccine vector.John Mattick

12. Michael Piper, Functional analysis of slit2, a human homolog of the Drosphila slit gene, in CNS andkidney development. Melissa Little

13. Ayanthi Richards, Endocytosis and retrograde transport of Simian Virus 40 (SV40) and cholera toxin– a comparative study. Rob Parton

14. Johan Rosengren, Twists, knots and rings -topological features of antimicrobial peptides. David Craik

15. Tedjo Sasmono, Regulation of the C-FMS gene in macrophages and transgenic mice. David Hume

Annette Schewan Molecular dissection of protein trafficking in eukaryotic cells. David James

Christina Schroeder Probing calcium channel selectivity of peptide toxins. Richard Lewis/David Adams

16. Annalese Semmler, Biogenesis and function of Type 4 Fimbriae in Pseudomonas Aeruginosa.John Mattick

17. David Sester, Mechanism of action of bacterial DNA on macrophage activation. David Hume

18. Manuela Trabi, Circular, disulfide rich peptides – sources, properties structures. David Craik

19. Nicole Walsh, The Function and Regulation of Tartrate-Resistant Acid Phosphatase (TRAP). David Hume


10.IMB Speakers

Speakers

Dr David Manallack

Professor Gottfried Otting

Professor Ralph Bradshaw

Professor Nobutaka Hirokawa

Professor Mike Ostrowski

Professor Nigel Laing

Professor Kevin Burrage

Professor Alok Mitra

Professor Bill Denny

Associate Professor Roger Daly

Dr Pritinder Kaur

Professor Chris Goodnow

Seminar Topic

Application of Quasi2 for drug discovery:an extended pharmacophore generationand database searching program

Structural biology, NMR, andparamagnetically labelled proteins

N-Terminal Processing: Role ofAminopeptidases and Transferases

The Kinesin Superfamily Motor Proteins,KIFs and Intracellular Transport:Structures, Dynamics, Functions andDiseases

The microphthalmia transcription factor:coordinating signaling and transcriptionduring osteoclast differentiation

Gene and protein defects in muscledisease

Stochastic multiscale modelling of geneticregulatory networks

Membrane protein channels andmacromolecular complexes at themembrane interface studied by electroncryo-microscopy - what can structure tellus about function

Drugs that target tumour hypoxia: thepromise and the challenge

Adaptor and scaffolding proteins inreceptor tyrosine kinase signalling

Identification of a functional subset ofdermal cells capable of regulatingepithelial tissue regeneration

Elucidating cellular and molecularpathways for human health by genome-wide mutagenesis in mice

Position

Head of Applied DesignDe Novo Pharmaceuticals, Cambridge, UK

Research School of ChemistryAustralian National University, Canberra

Department of Physiology and BiophysicsUniversity of California, at Irvine, USA

Department of Cell Biology and AnatomyUniversity of Tokyo, Japan

Department of Molecular GeneticsOhio State University, USA

Centre for Neuromuscular andNeurological DisordersAustralian Neuromuscular ResearchInstitute, Western Australia

Department of MathematicsThe University of Queensland

School of Biological SciencesThe University of Auckland, NZ

Auckland Cancer Society Research CentreThe University of Auckland, NZ

Cancer Research ProgramGarvan Institute of Medical Research,Sydney

Stem Cell LaboratoryPeter MacCallum Cancer Institute,Melbourne

Medical Genome CentreJohn Curtin School of Medical Research,Canberra

IMB FRIDAY SEMINAR SERIES 2003The IMB’s seminar series presented national and international speakers at the leading edge of the molecularbiosciences.

A highlight of the 2003 seminar calendar was a talk from Nobel Laureate Sydney Brenner who spoke about the roleand goals of computational biology.



Speakers

Dr Charlie Bond

Dr Archa Fox

Professor Ross Coppel

Professor Simon Easteal

Professor Halina Rubinsztein-Dunlop

Associate Professor Vic Nurcombe

Dr Ian Atkinson

Mr Adam Lowe

Professor Edward Baker

Professor Chris Abell

Dr Helen Cooper

Dr Tim Bailey

Professor Kathryn North

Dr Steve Gerondakis

Dr Matthew Rimmer

Seminar Topic

Structural Studies of Holliday JunctionResolution in the Archaea: the resolvingenzymes Hjc and Hje.

New insights into nuclear organisationrevealed by proteomic analysis of humannucleoli

Data, data everywhere, nor any chance to think

Complexity in diversity on the road toinformation-based medicine

Catch, move and twist using opticaltweezers

So long and thanks for all the fish; theanswer is 42 ES cells. Reflections on UQDevelopmental Biology, stem cellengineering, and the use of chopsticks forembryonic manipulation

Molecular self-assembly insupramolecular systems

Combining content and technology ingenomic research

Targeting TB through structural genomics

Explorations in chemical and biologicalnanotechnology

Diverse roles of netrin receptors in central nervous system development

Seaching for statistically significantregulatory modules

The evolution of the _-actinins and theirrole in human skeletal muscle muscleperformance

Mitogen-induced cell growth: B and Tcells adopt different strategies in theexploitation of Rel/NF-kB

Myriad Genetics: patent law & genetictesting

Position

Division of Biological Chemistry andMolecular Microbiology, School of LifeSciencesWellcome Trust Biocentre, University ofDundee, Scotland

Division of Gene Regulation andExpression, School of Life SciencesWellcome Trust Biocentre, University ofDundee

Department of MicrobiologyMonash University, Melbourne

Centre for Bioinformation Science andJohn Curtin School of Medical Research,Canberra

Department of Physics/Centre forBiophotonics and Laser ScienceThe University of Queensland

Department of Anatomy andDevelopmental BiologyThe University of Queensland

Information Technology and ResourcesJames Cook University, Townsville,Australia

Genomic Applications Research andDevelopmentApplied Biosystems Pty Ltd

School of Biological SciencesThe University of Auckland, NZ

Department of ChemistryUniversity of Cambridge ChemicalLaboratory, UK

Neural Migration Laboratory, School ofBiomedical SciencesThe University of Queensland

Advanced Computational Modelling CenterThe University of Queensland

Neurogenetics Research UnitChildren’s Hospital at Westmead ClinicalSchool, Sydney

Immunology DivisionThe Walter and Eliza Hall Institute ofMedical Research, Melbourne

Faculty of LawThe Australian National University,Canberra


Speakers

Dr Tom Garrett

Professor David Vaux

Dr Sigrid Lehnert

Professor Geoff McLachlan

Dr Peter Currie

Professor Michael Johnson

Professor David Weisbrot

Dr Richard Bruskiewich

Dr Patrick Aloy

Dr Martin Frith

Dr Nick Brown

Ms Anneliese Appleton

Dr Christine Vogel

Dr Arnold Falick

Professor Roger Tsien

Seminar Topic

Structure and signalling in the epidermalgrowth factor receptor family

Apoptosis - biology to die for

Transcriptional profiling of bovine muscle

Classification of microarray gene-expression data

Specification, morphogenesis anddifferentiation of skeletal muscle cellswithin the zebrafish embryo

Structural studies of spectrin - anubiquitous protein

Essentially yours: the protection of humangenetic information in Australia

My genome is sequenced! So...what next?

The third dimension for proteininteractions and complexes

Deciphering the Regulation of HumanGenes: Motif Clusters in DNA and RNA

Genetic dissection of the integrin-cytoskeletal link in Drosophila

Accelrys Information Seminar

Domain duplication and recombination inthe evolution of the protein repertoire

Protein identification with a MALDITandem Time-of-Flight mass spectrometer

Breeding molecules to spy on cells

Position

Structural BiologyWalter and Eliza Hall Institute of MedicalResearch, Melbourne

Molecular Genetics of CancerWalter and Eliza Hall Institute of MedicalResearch, Melbourne

Livestock Applications of BiotechnologyProgramCSIRO Livestock Industries, Brisbane

Department of Mathematics and Institutefor Molecular BioscienceThe University of Queensland

Victor Chang Cardiac Research InstituteSydney

Centre for Pharmaceutical BiotechnologyUniversity of Illinois at Chicago, USA

President, Australian Law ReformCommission, Sydney

BioinformaticsInternational Rice Research Institute, LosBaños, Phillipines

BiocomputingEuropean Molecular Biology Laboratory– Heidelberg, Germany

Bioinformatics ProgramBoston University, USA

Wellcome/Cancer Research UK GurdonInstitute and Department of AnatomyUniversity of Cambridge , UK

Accelrys Inc.

MRC Laboratory of Molecular BiologyCambridge, UK

Mass Spectrometry LaboratoryHoward Hughes Medical InstituteUniversity of California at Berkeley, USA

Howard Hughes Medical Institute &Department of PharmacologyUniversity of California at San Diego, USA



Speakers

Dr Andrew Perkins

Professor Walter Birchmeier

Dr Margaret Frame

Dr Matthew Cooper

Dr Scott Weinberger

Professor Peter Roepstorff

Dr Paul Trainor

Dr Anneliese Appleton

Dr Inke Nathke

Dr David Sacks

Dr Irina Mineyev

Dr Al Reynolds

Dr David Hansen

Seminar Topic

Making blood and kidneys: transcriptionalprogramming and ES cell differentiation

b-catenin and Wnt signaling: implicationsfor developmental programming and cancer

New insights into the regulation and action of Src kinases

Drugs, bugs and biotech

Proteinchip arrays: advances in SELDItechnologies for the discovery inidentification and characterisation ofbiomarkers of clinical interest

Current strategies in expressionproteomics and modification specificproteomics

Neural crest cells: patterning anddevelopment of a stem cell populationduring craniofacial development andevolution

Accelrys information seminar

Recent advances in understanding thefundamental biology of the tumorsuppressor, APC

IQGAP1 - a fundamental regulator ofca2+/calmodulin signalling andcytoskeletal architecture

Caliper microfluidics technologies for drugdiscovery and genomics

P120-catenin: a core regulator of cadherinfunction and potential tumour suppressor

Providing integrated access to genomic data

Position

Monash University, Melbourne

Max-Delbrück Center for MolecularMedicine, Berlin, Germany

Beatson Cancer Center, Glasgow, Scotland

Chief Scientific OfficerAkubio Ltd, UK

Director, Research ProteomicsCiphergen Biosystems Inc.

Department of Biochemistry andMolecular BiologyUniversity of Southern Denmark

Stowers Institute for Medical Research,Kansas, USA

Accelrys Inc.

School of Life SciencesUniversity of Dundee, Scotland

Pathology, Brigham & Women's HospitalHarvard Medical School, Boston, USA

Caliper Technologies California, USA

Department of Cancer BiologyVanderbilt University, Tennessee, USA

SRS Software DevelopmentLION Bioscience Ltd, UK

The IMB’s seminar seriespresented national andinternational speakers at theleading edge of the molecularbiosciences.


IMB Systems andAdministration

11.

Construction of the Queensland Bioscience Precinct(QBP) building was completed in early 2003 andfollowed by several weeks of systems testing andbuilding cleaning prior to occupation by CSIRO and IMB.

Relocation of the IMB into the new facility began inlate March and took four weeks to relocate allscientists and support staff. Delicate items ofequipment such as the X-ray crystallography and theNMR machines remained behind until themanufacturer’s specialists were available to assist in relocation.

The titanic effort of Infrastructure Manager ChrisBarnett, the newly appointed Floor Managers, SafetyOfficer Charles Nelson, the Information Technologyteam and the Workshop and Sterilisation staffensured the move was executed as smoothly aspossible. I also congratulate all support andinfrastructure staff for their performance during 2003, which kept disruptions to IMB’s research to a minimum.

IMB researchers were again successful in attractingfunds to purchase significant items of equipmentfacilitating IMB's leading-edge research. The IMBtook delivery of:

• Two new 600MHz Nuclear Magnetic Resonance(NMR) machines extending IMB's ability tosolve the three dimensional structures ofbiological molecules. The new magnets enableIMB to determine highly complex structureswith greater confidence than ever before.

• Australia's most powerful X-Ray Crystallographymachine. The high resolution and exquisitesensitivity of the new machinery can only bebettered by a synchrotron, currently unavailablein Australia. These facilities enable thedetermination of high resolution structures of themost difficult proteins.

• P690 supercomputer equipped withDiscoveryLink software as part of the IBM'sShared University Research program. Thisalliance provides an unparalleled level ofexcellence in an integrated research programcombining the Institute's world-classbioinformatics expertise and IBM's state-of-the-art IT infrastructure for life sciences, aswell as providing access to IBM's ownresearch resources.

(Left) IMB Deputy Director (Systems and Administration) Ian Taylor; (Centre) Dr Steve Tay



Administration and finance Teresa BuckleyJodie CampbellRobyn CraikBarb ClydeMileta DugglebyBarbara FeenstraAngela GardnerJenny GrederJohn Spooner

Animal HouseAnne HardacreDavid McNeillyElena PiottoAnita Swallow

Central Sterilising FacilityRobyn BairdWendy CampbellSherrell McCarthyKarleen MarshMichael TetleyDawn Walsh

Graduate program Amanda CarozziPatricia McCauley

IT services Matthew BryantBrett CravaliatCalvin EvansOndrej HlinkaLindsay HoodIreneusz PorebskiMaria MaddisonNelson MarquesPeter van der HeideCalvin WangKim Welch

Laboratory ManagementChris BarnettJill BradleyKarl ByrielJoanne KellyColin MacQueenCharles NelsonDarren PaulLance RathboneStephen TayGreg Young

Marketing and Communications Russell GriggsTania HudspithAndrea Sackson

WorkshopHenk FaberWayne KirbyJeremy KroesGreg McHughDavid Scarce

Queensland Bioscience Precinct staffRebecca BrooksAlan GilliganEfstratios ManolisBarry PittNathan SteenstraMaria TrubshawRonda Turk

• A Sun fileserver greatly expanding IMB'scapacity to provide storage space for staff and students

• Over $1 million high pressure liquidchromatography equipment to accelerate theeffective exploration of Australian biodiversityas a means to discover new and improveddrugs, with application in the areas of humanand animal health, and crop protection.

The new IMB facilities are designed to meet thelegislative regulations and government guidelines andstandards, including those required by the Office ofthe Gene Technology Regulator, as well as theWorkplace Health and Safety Act of Queensland. TheIMB has implemented procedures to assistresearchers in meeting these legal obligations.Comments received following an EnvironmentalManagement Systems audit conducted late in 2003

confirm the IMB's systems are “functional more sothan any other University area”.

Occupation of the new building resulted in increaseddemands on IMB support services due to therelocation of three research groups from other UQdepartments, as well as the commencement of twonew research groups. Consequently the sterilisation,workshop and animal house facilities have employednew staff to cope with the increased demand forservices. A new central store facility has been setup to meet the day to day needs of all researchers inthe Precinct.

Finally, the IMB was saddened by the sudden deathof Level 7 Floor Manager, Dr Steve Tay in November.Steve joined the IMB as we took up residence in thenew building and in his short time with the Institutehe played a vital role in establishing the chemistrylaboratories on Level 7. He will be sorely missed.

Research Support


Glossary of terms

12.

Some readers may be unfamiliar with some of thescientific terms used in this Annual Report. Pleasecheck below for a short explanation to some of themore common terms. More information aboutcurrent issues in biotechnology can be downloadedfrom the Office of Public Policy and Ethics pages inthe IMB website.

Alzheimer’s disease A disease associated with thebreakdown of nervous tissue in the brain, giving riseto a dementia in the patient.

Amino Acid Amino acids are the building blocks ofproteins. The sixty-four codons of the genetic codeallow the use of twenty different amino acids (theprimary amino acids) in the synthesis of proteins.

Apoptosis The normal process of programmed celldeath. Disruptions to this process often lead tocancers.

ARC Australian Research Council. The ARC plays akey role in the Australian Government’s investment inthe future prosperity and well-being of the Australiancommunity. The ARC’s mission is to advanceAustralia’s capacity to undertake quality researchthat brings economic, social and cultural benefit tothe Australian community.

Bioinformatics The collection, organisation andanalysis of large amounts of biological data usingnetworks of computers and databases

Cancer Any malignant, cellular tumour. Cancers canbe divided into two types carcinoma and sarcoma.

Carcinoma A malignant new growth made up ofepithelial cells tending to infiltrate surroundingtissues and to give rise to metastases.

Chromosome A package of wound-up DNA in thenucleus of a cell. Humans have 23 pairs ofchromosomes.

Combinatorial chemistry A technique forsystematically assembling molecular building blocksin many combinations to create thousands of diversecompounds.

Computational biology The study of living systemsusing computation.

Cryo EM Cryo electron microscopy – an electronmicroscopy technique in which the sample is frozenrather than stained.

Cystic fibrosis A genetic disease with symptoms thatusually appear shortly after birth. They includebreathing difficulties and respiratory infections dueto accumulation of sticky mucous problems withdigestion and excessive loss of salt in sweat.

Diabetes A disorder characterised by excessiveurine production. Commonly used when referring todiabetes mellitus (Type 1) a metabolic disorder inwhich there is inability to oxidise carbohydrates dueto a disturbance of the normal insulin mechanism,producing hyperglycemia, glycosuria, polyuria. Alsorefers to non-insulin dependant diabetes (NIDD) anasymptomatic form of diabetes mellitus with onsetafter 40 years of age. Often brought on by a lifestyleof sedentary living with high intake of lipids in diet.

DNA Deoxyribonucleic acid - the chemical chainthat carries the genetic instructions for making aliving organism.

EM Electron microscope – a microscope that uses abeam of highly energetic electrons to examineobjects on a very fine scale.

Functional Genomics The use of genetic technologyto determine the function of newly discovered genesby determining their role in model organisms.



Gene Considered the basic unit of hereditary, a geneis a region of DNA encodes all the information tomake a protein.

Gene Expression The actual production of the proteinencoded by a gene.

Genome All DNA contained in an organism or cell.

Genomics The study of genes and their function.

Genotype Is the hereditary genetic constitute of an organism.

Inflammatory disease A disease characterized by inflammation. Examples studied at IMB includerheumatoid arthritis, chronic obstructive pulmonary disease.

National Institutes of Health (NIH) A largebiomedical research organization that is part of theU.S. Public Health Service. NIH includes variousinstitutes, centers and divisions including NationalInstitute of Diabetes and Digestive and KidneyDiseases (NIDDK) which funds several groups in the IMB.

Nuclear Magnetic Resonance (NMR) A spectroscopictechnique that analyses the disruptions to a highmagnetic field to elucidate chemical structure andmolecular dynamics of a sample.

NHMRC National Health and Medical ResearchCouncil. A national organisation responsible for,among other things, fostering medical research andtraining and public health research and trainingthroughout Australia.

Peptide Two or more amino acids joined by a peptide bond.

Pharmacogenomics The study of the interaction of anindividual's genetic makeup and response to a drug.

Phenome The physical characteristics of anorganism.

Protein A large molecule composed of one or morechains of amino acids in a specific order; the order isdetermined by the base sequence of nucleotides inthe gene that codes for the protein. Proteins arerequired for the structure, function, and regulation ofthe body's cells, tissues, and organs; and eachprotein has unique functions. Examples arehormones, enzymes, and antibodies.

Proteomics The study of structure and function of allthe proteins expressed in a cell.

Recombinant DNA Any new combinations of genesor gene parts spliced together to form a single DNA molecule.

RNA A chemical similar to a single strand of DNA.RNA delivers DNA's message to the site of proteinsynthesis.

Sarcoma A malignant tumour made up of asubstance like the embryonic connective tissue.

Transgenic An organism that has a transferred gene(transgene) incorporated into the chromosomes of allits cells.

X-ray Crystallography A technique of determining amolecule's three-dimensional structure by analysingthe x-ray diffraction patterns of crystals made up ofthe molecule in question.


13.Financial Statement – Statement of Operating Income and ExpenditureYear Ended 31 December 2003

INCOME:

2000 2001 2002 2003

Note

University of Queensland (Operating Grant) 1 2,942,718 6,664,365 6,023,929 8,122,858University of Queensland Research Grants 200,990 100,000 269,358 277,337State Government 5,500,000 2,500,000 6,000,000 8,500,000SRC Grant (Australian Research Council) 1,631,153 1,039,320 1,148,975 1,005,151Australian Research Council 2 1,131,271 1,668,000 1,599,576 3,218,103Cancer Council South Australia 30,500Clive and Vera Ramaciotti Foundation 43,545 9,545 0CRC for Discovery of Genes for Common Human Diseases 220,958 232,415 122,469 48,946CRC for Chronic Inflammatory Diseases 943,401 968,800Department of Primary Industries 98,040 0Diabetes Australia Research Trust 33,409 35,791 37,700 0Department of Industry Science and Technology 166,400 0 0 0Human Frontiers Science Program 127,242 0 0 146,291Glaxo Welcome Australia 670,000 62,000 0 0Government Employees Medical Research Fund 45,000 0 0 0Juvenile Diabetes Foundation International 299,626 267,704 77,084 0Mayne Bequest Foundation 60,000 0 0 0The Merck Genome Research Institute 261,559 0 0 0National Institute of Health (US) 1,391,005 1,049,548National Health and Medical Research Council 2 2,938,586 5,359,112 4,306,397 6,761,404National Heart Foundation 45,000 0 50,000 42,735Novartis 641,790Post Graduate Scholarships 28,209 15,882 38,214 73,467QIMR 53,908 60,575Queensland Cancer Fund 230,072 116,447 92,750 72,590Sylvia and Charles Viertel Charitable Foundation 165,000 165,000 165,000 0Wellcome Trust 28,011 23,829 0 204,763Commercial Income 1,371,664 2,589,861 2,127,649 1,517,449Cross-Institutional contributions to LIEF 0 0 0 122,500University of Newcastle (re ARC Centre) 0 0 0 127,727QBP recoveries 0 0 0 331,594Shared Grants 0 0 0 105,845Conference Income 0 0 0 55,275Miscellaneous Income 415,591 272,136 19,593 392,822

TOTAL INCOME: 18,556,004 21,121,405 24,565,049 33,878,069

Funds brought forward from previous year 3 1,009,031 3,843,597 3,594,479 7,545,101

TOTAL FUNDS AVAILABLE: 19,565,034 24,965,002 28,159,528 41,423,169

EXPENDITURE:

Salaries-Research 6,549,841 7,809,255 9,066,745 12,238,779Administration 1,090,220 1,117,375 1,342,520 1,365,120Infrastructure 541,043 813,527 1,012,400 1,735,158

Research Services 2,635,745 6,034,723 4,865,433 6,938,972Education Programs 4 317,726 378,436 500,939 484,360Administration 5 937,703 550,574 452,021 519,046Infrastructure 6 357,436 928,651 786,809 1,568,251Capital Equipment 7 2,307,116 3,132,769 1,840,664 8,649,700IMBcom 984,608 605,214 746,896 1,176,785

TOTAL EXPENDITURE: 15,721,437 21,370,523 20,614,427 34,676,171

Funds carried forward: 8 3,843,597 3,594,479 7,545,101 6,746,999



Explanatory Notes to Statement of Income and ExpenditureYear Ended 31 December 2003

1. In-kind Contributions

Figure does not include the following salaries for joint appointments paid by other departments:

School PercentageS. Barker Molecular & Microbial Sci. 80D. Hume Molecular & Microbial Sci. 20J. Martin Molecular & Microbial Sci. 10S. Kelly Molecular & Microbial Sci. 80P. Koopman Biomedical Sciences 10J.Rothnagel Molecular & Microbial Sci. 80B.Wainwright Molecular & Microbial Sci. 20M.Waters Biomedical Sciences 20A.Yap Biomedical Sciences 20B.Kobe Molecular & Microbial Sci. 80J. Stow Molecular & Microbial Sci. 20A. McDowall Microscopy & Microanalysis 80W. Hall Social Behaviourial Sci. 20G. McLachlan Mathematics 80J. Hallinan ITEE 20T. Bailey ACMC 80

2. Fellowship/Projects from Government Agencies

Australian Research CouncilProjects 2,707,459 Fellowships 510,644

3,218,103

National Health and Medical Research CouncilProjects 5,936,844Fellowships 824,559

6,761,404

3. Funds brought Forward from 2002

University of Queensland Operating Grant 4,047,449University of Queensland Research Grants 69,686Post Graduate Scholarships 4,371State Government 346,758SRC Grant 373,794Fellowships (as approved by funding bodies) 91,919Project Grants (as approved by funding bodies) 2,611,123

7,545,101

4. Education ProgramsPostgraduate scholarships 328,357Postgraduate recruitment & training 29,471Public Policy & Ethics 126,532

Total Education Services 484,360


Explanatory Notes to Statement of Income and ExpenditureYear Ended 31 December 2003

5. AdministrationAnnual Report 20,698Marketing 48,102Personnel Recruitment and Training 126,680Visiting Scientists/Seminars 21,687Fees 61,071Entertaining 6,875Equip Lease 0Photocopying 35,486Postage and Freight 6,021Printing & stationery 75,179Telephone 61,008Travel Expenses 12,247Sundries 5,409Cost Recovery 38,581

Total Administration 519,046

6. InfrastructureBuilding Maintenance 66,192Rental -Demountables/Storage 17,092Safety Equipment 67,730Laundry 1,953Minor Equipment & Furniture 32,378Equipment Maintenance 173,956Animals 72,950Computer Services 824,462Glass washing and replacement 40,854Reticulated gases, RO water & dry ice 89,807Sundries 69,746Relocation Costs 84,060Stores 27,072

Total Infrastructure 1,568,251

7. Capital EquipmentScientific Equipment 8,600,104Minor Equipment 49,596

Total Capital Equipment 8,649,700

8. Funds carried forward to 2004University of Queensland Operating Grant 1,645,629University of Queensland Research Grants 26,038Post Graduate Scholarships 3,734State Government 125,166SRC Grant 374,734Fellowships (as approved by funding bodies) 149,096Overseas Grants funded mid year 1,709,903Contract Research 1,270,789Project Grants (as approved by funding bodies) 1,441,911

6,746,999

# Of this, $0.5m is the carry forward on IMB core accounts, $1.0m relates to outstanding 2003 commitments.


IMB Institute for Molecular BioscienceUniversity of QueenslandSt Lucia Queensland 4072Australia

Telephone: +61 7 3346 2100Facsimile: 61 7 3346 2101Email: [email protected]: www.imb.uq.edu.au


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