School of Chemistry & Molecular Biosciences CHEMISTRY ... CHEM_MBS Project... · BSc Honours Projects 2014 CHEMISTRY, BIOCHEMISTRY & MOLECULAR BIOLOGY and MICROBIOLOGY & PARASITOLOGY

BSc Honours Projects 2014

CHEMISTRY, BIOCHEMISTRY & MOLECULAR BIOLOGY andMICROBIOLOGY & PARASITOLOGY

School of Chemistry & Molecular BiosciencesFaculty of Science

Chemistry&MolecularBiosciencesHonoursProjects2014

CONTENTS

THEHONOURSPROGRAM PageNo.

HONOURSINCHEMISTRY,BIOCHEMISTRY&MOLECULARBIOLOGY,MICROBIOLOGY&PARASITOLOGY2014

SCMBACADEMICSTAFFSCMBContributors SchoolLocation PageNo.

ProfStephenBarker MolecularBiosciencesBuilding 8

ProfPaulBernhardt ChemistryBuilding 9

DrJoanneBlanchfield ChemistryBuilding 10

DrMikaelBoden MolecularBiosciencesBuilding 11

ProfMelissaBrown ChemistryBuilding 12

ProfPaulBurn ChemistryBuilding,COPE 13

A/ProfBernieCarroll MolecularBiosciencesBuilding 14

DrJackClegg ChemistryBuilding 15

ProfJamesDeVoss ChemistryBuilding 16

A/ProfVitoFerro ChemistryBuilding 17

DrJamesFraser MolecularBiosciencesBuilding 18

ProfLawrenceGahan ChemistryBuilding 19

ProfMaryGarson ChemistryBuilding 20

ProfIanGentle ChemistryBuilding 21

ProfElizabethGillam MolecularBiosciencesBuilding 22

A/ProfLisbethGrondahl ChemistryBuilding 23

A/ProfLukeGuddat MolecularBiosciencesBuilding 24

ProfRoyHall MolecularBiosciencesBuilding 25

ProfPhilHugenholtz&DrGeneTyson MolecularBiosciencesBuilding,ACE 26

DrUlrikeKappler MolecularBiosciencesBuilding 27

A/ProfStuartKellie MolecularBiosciencesBuilding 28

ProfAlexanderKhromykh MolecularBiosciencesBuilding 29

ProfBostjanKobe MolecularBiosciencesBuilding 30

DrGwenLawrie ChemistryBuilding 31

DrShih‐Chun(Lawrence)Lo ChemistryBuilding,COPE 32

ProfAlanMark MolecularBiosciencesBuilding 33

A/ProfRossMcGeary ChemistryBuilding 34

DrEvanMoore ChemistryBuilding 35

ProfPeterO’Donoghue MolecularBiosciencesBuilding 36

A/ProfMarkRiley ChemistryBuilding 37

A/ProfJoeRothnagel MolecularBiosciencesBuilding 38

DrSusanRowland MolecularBiosciencesBuilding 39

ProfMarkSchembri MolecularBiosciencesBuilding 40

A/ProfGarySchenk ChemistryBuilding 41

ProfRossSmith MolecularBiosciencesBuilding 42

DrKateStacey MolecularBiosciencesBuilding 43

ProfIstvanToth ChemistryBuilding 44

ProfMarkWalker MolecularBiosciencesBuilding 45

DrJackWang MolecularBiosciencesBuilding 46

A/ProfLeighWard MolecularBiosciencesBuilding 47

DrNickWest MolecularBiosciencesBuilding 48

A/ProfCraigWilliams ChemistryBuilding 49

DrSimonWorrall MolecularBiosciencesBuilding 50

ProfPaulYoung MolecularBiosciencesBuilding 51

Chemistry&MolecularBiosciencesHonoursProjects2014

SCMBACADEMICSTAFFWITHJOINTAPPOINTMENTSJointContributors Organisation/BusinessUnit PageNo.

ProfDebraBernhardt AustralianInstituteforBioengineeringandNanotechnology(AIBN)

DrGrahamLeggatt UniversityofQueensland DiamantinaInstitute(UQDI)

ProfMichaelMonteiro AustralianInstituteforBioengineeringandNanotechnology(AIBN)

ProfMattTrau AustralianInstituteforBioengineeringandNanotechnology(AIBN)

SCMBRESEARCHFELLOWSResearchFellowContributors SchoolLocation PageNo.

DrElizabethKrenske MolecularBiosciencesBuilding 56

DrMeganO’Mara MolecularBiosciencesBuilding 56

DrBenjaminSchulz MolecularBiosciencesBuilding 57

DrAnnetteShewan MolecularBiosciencesBuilding 57

DrPavlaSimerska ChemistryBuilding 58

DrMariuszSkwarczynski ChemistryBuilding 58

DrMakrinaTotsika MolecularBiosciencesBuilding 59

DrGeorgeVamvounis ChemistryBuilding,COPE 59

SCMBAFFILIATESTAFFAffiliateContributors Organisation/BusinessUnit

ProfPaulAlewood InstituteforMolecularBioscience(IMB) 60

ProfRobCapon InstituteforMolecularBioscience(IMB) 60

A/ProfNickDavis‐Poynter SirAlbertSakzewskiVirusResearchCentre/ClinicalMedicalVirologyCentre(SASVRC/CMVC)

DrAnnetteDexter AustralianInstituteforBioengineeringandNanotechnology(AIBN)

A/ProfRalfDietzgen Queensland Alliance for Agriculture and FoodInnovation(QAAFI)

ProfDavidFairlie InstituteforMolecularBioscience(IMB) 62

DrMaryFletcher Queensland Alliance for Agriculture and FoodInnovation (QAAFI)

ProfRobertGGilbert CentreforNutritionandFoodSciences(CNAFS) 63

ProfGlennKing InstituteforMolecularBioscience(IMB) 64

DrKirstenSpann SirAlbert Sakzewski VirusResearchCentre/ClinicalMedicalVirologyCentre(SASVRC/CMVC)

A/ProfRickSturm InstituteforMolecularBioscience(IMB) 65

DrMattSweet InstituteforMolecularBioscience(IMB) 65

A/ProfRohanTeasdale InstituteforMolecularBioscience(IMB) 66

ProfBrandonWainwright InstituteforMolecularBioscience(IMB) 66

ProfAndrewWhittaker AustralianInstituteforBioengineeringandNanotechnology(AIBN)

AFFILIATEDINSTITUTIONS Organisation/BusinessUnit PageNo.

AdvancedWaterManagementCentre(AWMC) 68

AustralianInstituteforBioengineering&Nanotechnology(AIBN)

CentreforAdvancedImaging(CAI) 68

InstituteforMolecularBioscience(IMB) 68

UniversityofQueenslandCentreforClinicalResearch(UQCCR)

UniversityofQueenslandDiamantinaInstitute 68

Chemistry&MolecularBiosciencesHonoursProjects2014

(UQDI)

EXTERNALINSTITUTIONS INCLUDINGSCMBADJUNCTACADEMICSTAFFExternalContributors Organisation/BusinessUnit PageNo.

ProfJohnManners CSIRO 69

ProfMarkMorrison CSIRO 69

ProfJeffGorman QueenslandInstituteofMedicalResearch(QIMR) 69

DrLutzKrause QueenslandInstituteofMedicalResearch(QIMR) 69‐70

A/ProfIanMMackay SirAlbert SakzewskiVirusResearchCentre(SASVRC)

INDUSTRYPROJECTSIndustryContributors Organisation/BusinessUnit PageNo.

HonoursinIndustry 71

ProfJamesDeVoss&DrJoanneBlanchfield IntegriaHealthcare 73

ProfRossBarnard CookMedical 74

SirrometWines 74

Chemistry&MolecularBiosciencesHonoursProjects2014

HONOURS IN CHEMISTRY, BIOCHEMISTRY & MOLECULAR BIOLOGY,

MICROBIOLOGY & PARASITOLOGY 2014

The School of Chemistry&Molecular Biosciences (SCMB) offers the Bachelor of SciencewithHonours,BSc(Hons). It isundertakenonafull‐timebasis.TheProgramcanbecommenced ineitherfirstorsecondsemester.

TheImportanceofanHonoursyearTheBSc(Hons)ProgramprovidestrainingwellbeyondthatprovidedbythebasicBScdegree,particularlyintheareaofresearchmethodsand inproblemsolving.Forthosestudentsseekingemploymentaftertheirdegree,theextratrainingofHonoursequipsthemforawiderrangeofpositions,inindustry,governmentlaboratoriesandelsewhere,thandoesthebasicBScdegree.Honoursgraduatesgenerallyhaveagreaterinvolvement in researchanddevelopment; responsibility levelsarehigherand therearebetter financialrewards.Honoursisalsothekeyprerequisiteforenrolmentinahigherdegree.AnHonoursyeargradedatClassIallowsfordirectenrolmentintoaPhDprogram.OftenaClassIIAperformanceallowsadmissionalso.EntryRequirementsTheHonoursprogramcanbeentered from theBScdegree from thisoranotheruniversity.ForstudentsfromtheUniversityofQueensland,normally8units(#8)ofrelevantthird levelcoursesshouldhavebeencompleted,ataGradePointAverageof4.5orabove.Insomecasescoursesfromotherrelevantdisciplinesmaybe included inthe#8.TheSchoolofChemistryandMolecularBioscienceshassomediscretion intheapplicationoftheentryrules,andmay,ontherecommendationoftheHonoursDirector,allowentryfromstudentswhofallslightlybelowthiscut‐off.Studentswithagoodacademicrecordmayalsobeacceptedwith a BSc qualification from another university. An original or certified copy of your final academictranscriptmustbesubmittedwithyourapplicationform.InternationalstudentsmustsubmitanapplicationformthroughtheInternationalOffice.Visittheirwebsiteonwww.uq.edu.au/international/orcontactanyIDPEducationAustraliaofficeorAustralianDiplomaticMissioninyourcapitalcity.EnrolmentProcedures,FeesandChargesApplytoenrol intheHonoursprogrambycompletingtheformavailablefromtheschoolreceptionoffice68‐302 (ChemistryBuilding)andsubmitting to theofficeof theHonoursAdministrativeAssistant,LouiseNimwegen68‐316.FormscanalsobedownloadedfromtheSchoolwebsitewww.scmb.uq.edu.au.Successfulapplicantswillbesentanofferletterafterallresultsareknown.OnacceptancetheirenrolmentintheprogramwillbeactivatedbytheSchool.HonoursstudentsmustenrolthemselvesviamySI‐netintherelevantcoursesforeachsemester.AnyqueriesrelatedtoenrolmentmaybedirectedtoLouiseNimwegen([emailprotected])orTammieFair([emailprotected]).FulltimedomesticHonoursstudentsstudyasundergraduateCommonwealthsupportedstudentsandarerequired to pay a Student Contribution Amount in both semesters of theirHonours program. It is thestudent’sresponsibilitytoensuretheyeducatethemselvesontheir individualrequirementwithregardtotheir Student Contribution Amount. As a first step you may consult the UQ Fees and Costs websitewww.uq.edu.au/study/index.html?page=947 (further details can be obtained from the Student Centre,Level1 JD StoryBuilding (61). International studentsplease see InternationalOfficewebsite for currentfees:www.uq.edu.au/international/).

Chemistry&MolecularBiosciencesHonoursProjects2014

FinancialSupportUp to sixhoursperweekof teachingdutiesmaybeavailable.AllHonours students (dependingonpastexperience)areeligibletoseekemploymentaspart‐timetutorsforlaboratoryclasseswithintheSchoolofChemistry&MolecularBiosciences.Please indicate your interest toundertake tutoringon theHonoursapplicationform.CommencementDateThecommencementdatesforHonoursstudentswillbeMonday10Februaryor,mid‐year,Monday28July2014.AnumberofintroductoryprogramsforHonoursstudentsarerunearlyinthesemester.Thesecomprise:

SchoolSafetyInduction,whereSchoolproceduresareexplained,particularlysafetyandwastedisposalmethods(mandatory)

TutorTraining

A librarycourse,whereuseofelectronicdatabasesaredescribed.Training isprovidedforreferencingsoftware(eg.EndNote).

ResearchProjectsStudentsareinvitedtodiscusstheprojectslistedinthisbookletwiththestaffmembersconcernedandtosubmit the application form to the SchoolofChemistry&MolecularBiosciences as set out above. TheHonoursProgramDirectorswillmakerecommendationsonassignmentofsupervisors,takingintoaccount:

thestudent’spreferences

theacademicbackgroundofthestudent

thetotalnumberofstudentssupervisedbyeachstaffmember

resourceimplications

plannedextendedabsencesofthestaffmemberfromtheSchool

other factorsthatmayaffectthestaffmember’sabilitytosuperviseeffectivelyaparticularstudent’sresearchproject.

Forstudentsstartinginsemester1,itishighlyrecommendedtosubmityourapplicationbeforetheendofsemester2thepreviousyear(17November2013).Ifyoudothis,youwillbenotifiedofyoursupervisorbymid‐January. Studentswho submit their applications latermay have less chance ofobtaining their firstpreference.Studentscommencingmid‐yearshouldsubmittheirapplicationpriortotheendofsemester1(29June2014)inanticipationofasuccessfulmid‐yearcompletionoftheirBSc.TheBSc(Hons)ProgramThe16unitsofcreditassociatedwith theHonoursprogram isamixtureof researchandcoursework. Itcomprisesfourcomponents:HonoursResearchProjectThisisayear‐longcomponentandculminatesinthesubmissionofaresearchreport.Theresearchprojectiscarriedoutunderthesupervisionofamember(ormembers)oftheacademicstaff.Theresearchtopicisassigned by the supervisor after consultation with the student. This booklet containsmany potentialsupervisorsandresearchprojects.

Chemistry&MolecularBiosciencesHonoursProjects2014

HonoursResearchProposalThe researchproposaloutlines thework that thestudentwillundertakeandwhy theyaredoing it.Thismustbecompletedinthesemesterthattheybeginworkasitisintendedtoprovideanearlyfocusforthestudenton theirprojectwork. Itmay also form thebasisof the student’s introductory research reportchapter.HonoursSeminarsTworesearchsymposiawillbeheldduringtheHonoursyear–oneatthebeginning,andonetowardstheendof the year.Each studentwillgivean assessed research seminar inboth symposia, in the firstoneoutliningtheirproposedproject,inthesecondoneoutliningtheirachievements.Attendance at theweekly School Seminar series is compulsory. Although occasional absencesmay beunavoidable,theymustbeaccompaniedbyanapologysenttotheSeminarcoordinatorandavalidreasonfor your inability to attend. Students are required to maintain a seminar notebook which must besubmittedforscrutiny.SpecialTopicsinBiochemistryandMolecularBiologyorMicrobiologyandParasitologyThis takes the formofacritiqueofa researchpaperusingotherscientific literature forcomparisonandincludesanoralpresentationandawrittenreportofthefindings.Thegoalofthisexerciseistodeveloptheabilityofstudentstoanalysepublishedscientificworkcriticallyandtoanalysethedevelopmentofscientificideas.SpecialTopicsinChemistryEachstudentshallchooseoneofthefollowingmodules.Dependingonenrolments,somemodulesmaynotbeoffered.Moredetails(courseprofiles,timetablingetc.)willfollowlater.

Module1 OrganicChemistryModule2 InorganicChemistryModule3 PhysicalChemistryTheselectionofcourseworkbyhonoursstudentsshouldbediscussedwiththestudent’ssupervisor.ThefinalchoiceissubjecttoapprovalbytheHonoursDirector.CourseworkComponentIn addition to research seminars students participate, on a regular basis, in additional events thatwillprovideadditionalskillsasasuccessfulscientist.Theyincludeeg.acourseonscientificwritingandseminardebriefing sessions.Theseevents servealso as regular contacteventswith the School and improve thecohortexperience.AdministrationoftheHonoursProgramTheMolecularBiosciencesHonoursprogramiscoordinatedbyDrJamesFraser([emailprotected],33654868),ProfessorRoyHall([emailprotected],33654647)andDrGeneTyson ([emailprotected],33653829).TheChemistryHonoursprogramiscoordinatedbyDrJoanneBlanchfield([emailprotected],3365 3622). Enquiries regarding the program should be directed to either staff member in the firstinstance.Administrative assistance is provided by Louise Nimwegen, ([emailprotected], 3365 3509) orTammieFair,Manager,CourseworkAcademicAdministration([emailprotected],33657976).

Chemistry&MolecularBiosciencesHonoursProjects2014

SummaryforBSc(Hons)IfyouwishtocommenceBSc(Hons)in2014youshouldaddressanygeneralenquiriestoeitherofthestaffmembersmentionedabove.Even if you already have a firm idea about the supervisor you are likely to nominate as your firstpreference,consultwidelywithmembersoftheacademicstafftofindoutmoreabouttheprojectsbeingoffered and the style of work involved. Remember, your first preferencemay not ultimately be yourallocatedsupervisor,so it is importanttobeawareofalternativeprojects.Beawarethatsomedetailsofprojectsbeingofferedmaychangebetweenthetimewhenthisbookletwasprepared(July2013)andyourcommencementtime.ForstudentscommencinginFebruary,lodgeyourapplicationformwithyourlistofprojectpreferencesat68‐316beforeChristmas. Youdonothave to (and should not)wait for your examination results tobereleased before submitting the form. Preferences should indicate three different supervisors orcombinationsofsupervisorsinthecaseofjointprojects.Pleasenote:theprincipalsupervisormustbe(a)anacademicstaffmemberoftheSchool;(b)aresearchstaffmemberoftheSchoolwhoholdsanexternalcompetitiveresearchfellowship,(c)anaffiliateacademicstaffmemberoftheSchool;(d)anadjunctacademicstaffmemberoftheSchool,or(e)aHeadofSchool‐approvedemployeeofaresearchinstituteorindustry.Forstudentscommencing inJuly, indicateyour likelymid‐yearenrolmenttotheHonoursDirectorduringSemester1,2014.Lodgeyourapplicationbeforeorduringyourmid‐yearexaminations.Pleaseprovideacontactphonenumberandaddressoremailaddress.DrJamesFraser,ProfessorRoyHall,DrGeneTysonMolecularBiosciencesHonoursProgramDirectorsDrJoanneBlanchfieldChemistryHonoursProgramDirectorAugust2013

SCMB ACADEMIC STAFF

PROFESSOR STEPHEN BARKER Phone:0733653303Email:[emailprotected]

Biologyandcontrolofliceandticks,andthepathogensthatliceandtickstransmittohumans

Project1.NewpublichealthstrategiesforLouse‐BorneEpidemicRelapsingFever,whichiscausedbythespirochaetebacteriumBorreliarecurrentis,inEthiopia:iseradicationdesirableand/orfeasible?Borrelia recurrentis, the spirochaete bacterium that causes epidemic‐relapsing‐fever, is transmitted topeople by the body louse, Pediculus humanus. Epidemic‐relapsing‐fever is usually fatal if not treated.Epidemic‐relapsing‐fever isoftenoneofthetop10reasons for admission to hospital in the Horn ofAfrica, particularly Ethiopia. New public healthstrategies are needed for this disease which hasbeen eradicated in all countries, except thecountries in the Horn of Africa, Ethiopia, NorthSudan, South Sudan, Eritrea and Djibouti. But iseradicationdesirableand/orfeasible?

Project2.NewdiagnosticsfortheIxodesticksofAustralasia.The current diagnostic guide to the 24 species ofIxodesticks inAustralasiawasmadehalfacenturyagoand iswoefully inadequate.Anewdiagnosticguide forthe IxodesticksofAustralasia,thatcombinesgeneticandmorphologicaldiagnosticsisfeasibleandneeded.

Project3.Assemblyofthegenomesequenceoftheheadlouse,Pediculuscapitis.In2010,mycolleaguesandIsequenced,assembledandannotatedthenucleargenomeofthebodylouse,Pediculushumanus(Kirknessetal.PNAS107,12168‐12173).Lastyearwesequencedthegenomeofsister‐speciesof thebody louse, thehead lousePediculuscapitis.Thisgenomes is remarkablebecause it issosmall for ametazoan animal (ca. 110megabases) and because the introns are few and short in thisgenome.

Project4.Phylogenyofsoftticks.JointheInternationalTickTreeofLifeProject.Phylogeny(evolutionaryhistory)oftickspredictedfromthenucleotide sequences (mitochondrial and SSU rRNA). Studentswill sequence part of themitochondrialgenomesof1or2interestingticksfromAfricaandthenuseacomputertopredicttheevolutionarytreeof

theticks.

BahirDah,Ethiopia.AfocusofLouse‐borneRelapsingFever

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

–200 0 200

/ mV vs. Ag/AgClE

PROFESSOR PAUL BERNHARDT Phone:0733654266Email:[emailprotected]

Our research efforts are concerned with coordination chemistry of relevance to biology, analytical science andtechnology.StudentsinterestedinanyoftheseareasofresearchshouldcontactProf.Bernhardtforamoredetailedprojectdescription.

(a) NovelligandsthatstabilisecomplexesinunusualoxidationstatesWeareworkingonligandsthatarecapableofstabilisingmetalsinunusuallyhighoxidationstates(Cu(III),Fe(IV)etc.).Understanding how these ligands achieve this stabilisation and avoid decomposition pathways (sacrificial ligandoxidation) is a central goal of thisproject.RelevantPublication1. M.AkbarAli,P.V.Bernhardt,

M.A.H.Brax,J.England,A.J.Farlow,G.R.Hanson,L.L.Yeng,A.H.Mirza,andK.WieghardtInorg.Chem.,2013,52,1650.

(b)CoppercomplexesascatalystsforatomtransferradicalreactionsSince the discovery in 1995 that the simple Cu(I) complex [Cu(bipy)2]

+ (bipy = bipyridyl) is capable of generatingorganicradicalsfromsimplealkylhalideprecursors,similarcomplexeshavebeenusedextensively insocalledatomtransfer radical polymerisation, a major area of polymersynthesis.Themechanismbywhichtheradicalisproducedand theinfluenceofsolventremainscontroversial.Thisprojectwillusespectroscopicandelectrochemicalmethodstounderstandthereactivityofthesesimplebuthighlyreactivecompounds.RelevantPublications1. C.A.Bell,P.V.BernhardtandM.J.Monteiro,J.Am.Chem.Soc.,2011,133,11944.2. T.J.Zerk,P.V.Bernhardt,DaltonTrans.2013,DOI10.1039/C3DT51100F

(b) EnzymeElectrochemistryEnzymeelectrodebiosensorsaredevicesthatcomprisearedoxactiveenzymeintegratedwithelectroniccircuitrytogivereal‐timequantitativeanalysisofchemicalcompoundsinbiologicalfluidsortheenvironment.Thecurrentthatisgenerated by the oxidation or reduction of the substrate provides a quantitative measure of the substrateconcentration (see below). This projectwill involve the electrochemical investigation ofmetalloenzymes currentlyavailablewithininourgroup.

S OHS OHS OHS OHS OHS OHS OHS OHS OHS OH

Au electrode

2 Cyt cOX

2 Cyt cRED

SDHRED

SO32- H2O+

2H+ +

2e-

membrane

bulk solution

SO42-

SDHOX

S OHS OHS OHS OHS OHS OHS OH

inner membranesolution

Scheme 2

RelevantPublications1 P.V.BernhardtChem.Commun.2011,47,1663.2. P.Kalimuthu,S.Leimkuhler,P.V.Bernhardt,Anal.Chem.2012,84,10359.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

EnergyminimisedmodelofHPVdiscontinuousepitopedisplayedonahexaphenylbenzenescaffold.

DR JOANNE BLANCHFIELD Phone:0733653622Email:[emailprotected]

SynthesisofRevolutionarySyntheticVaccineConstructs(projectwithProfessorPaulBurn)

In collaborationwithDr.Graham Leggatt (TRI) and Professor Paul Burnwe are building fully syntheticconstructsthatdisplayantigenicpeptidesorcarbohydratesfromHPV,HIVandStaphylococcusaureus.Fordetails of the project please contact Joanne Blanchfield or PaulBurn.

Thisprojectwouldinvolve:

organicsynthesis

carbohydratesynthesis

solidphasepeptidesynthesis

cell culture and plasma stability assays and aseptictechniques

assaydevelopmentandmoleculecharacterisationincludinguseofHPLC,LC/MS,NMR,GC/MSequipment.

BioavailabilityofNaturalProductsfromHerbalExtracts(projectwithProfessorJamesDeVoss)

Herbal remedies are a major source of medical treatment for much of the world’s population.Unfortunately, little isknownabout the fateof thenaturalproducts in theextractsorwhich, ifany,arebiologicallyactive. Weareofferingaprojectthatusesacellularmodelofthesmall intestine(Caco‐2cellmonolayers)toinvestigatewhichnaturalproductsarelikelytoenterthebloodstreamafteroralintakeofsome popular herbal remedies. We also look closely atwhat changes the compounds undergo duringdigestionandabsorption.

UseofpreparativeandanalyticalHPLCequipment to isolatepotentiallyactivecompounds fromherbalextracts.

UseofNMRandIRspectroscopictechniquesandMStocharacteriseandidentifythecompoundsisolated.

CulturingandmaintaininghumanCaco‐2cellsunderasepticconditions.

Performanceof in vitrobiological assays todeterminepermeability (Caco‐2 cellassay), stability(CC2hom*ogenateassay,plasmastability)assays.

AnalyticalanalysisusingLC/MSandHPLCofthesolutionsresultingfromtheinvitroassays.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

DR MIKAEL BODEN Phone:0733651307Email:[emailprotected]

Usingbioinformaticsandhigh‐throughputdatatoexplainmolecularbiologyBioinformatics isamaindriverofnext–generationmolecularbiology.Smart integrationofdata,producedbyemerginghigh‐throughputtechnologies,enablesustocapture,andunderstandDNA,RNAandproteinsincontext:iftheyinteract,fold,regulate,catalyse,modifyortranslocate(tomentionbutafewfunctions)across multiple species, tissues and developmental time points. My research aims to developbioinformaticsmethods and apply them to further our understanding of a range of open problems ingenomics,molecular and systemsbiology (exemplifiedbelow). Indoing so,we actively collaboratewithstructuralandcellbiologists,proteinengineersandgeneticsresearchers.

GenomicfeaturesunderlyingtripletexpansionassociatedgeneticdefectsExpansion of nucleotide repeats underlies several genetic diseases such as Friedreich ataxia, fragile Xsyndrome and Huntington’s disease. Through genomics and systems biology approaches, leveragingemerging (next‐gen sequencing) data sets, this project will investigate features that determine theprobabilityofarepeattoundergoexpansion.(WithSureshBalasubramanianatMonashUniversity.)

Themeta‐structureofregulatorynetworksThe combination of chromosome conformation with DNase hypersensitivity data has the potential ofrevealinginteractionsamongsttargetgenes,complementinganalysisofDNAbindingofregulatoryfactors.This project will tap the burgeoning ENCODE repository to investigate a “spatialmap” between DNAbindingsitesofspecificco‐regulatoryproteins(inarelevantcelltype).

Buildingphosphorylationmaps:fromstructuretosystem‐widenetworksDataonpost‐translationalmodifications range fromdetailedmolecularbindingevents to low‐resolutionsystem‐scalenetworks.Thisprojectwillstudyhowheterogeneousdatasets(eg.bindingmotifs,structuresandinteractionnetworksrelevanttophosphorylation)withdependencies(eg.betweensimilarkinasesandsimilarsubstrates)canbeintegrated,atdifferentscalesanddealwithscarcityofdata.(WithBostjanKobe.)

UsingstatisticalmachinelearningtoevolvebiocatalystsProteins like the P450 enzymes are highly versatile biological catalysts with potential to improve theefficiencyofmany chemicalprocesses. Thisprojectwillusemachine learning and statistical analyses torevealhowtoredesignproteinstobethermostablebasedonthesequence‐structureexamplesnaturehasrefinedovermillionsofyears(withElizabethGillam).

Allprojects involvesomecomputing, though theextentcanbevariedgreatly.Youareexpected tohavesomeprogrammingskills,ananalyticalabilityandaboveallscientificcuriosity.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

PROFESSOR MELISSA BROWN Phone:0733654622Email:[emailprotected]

MolecularGeneticsandBiologyofBreastCancerBreastcancer isthemostcommoncancer inwomenandresultsfromabnormalexpressionorfunctionofmultiple tumour suppressor genes and oncogenes. Our laboratory is interested in the regulation andfunctionof anumberofbreast cancer‐associated genes including thoseencodingBRCA1,BRCA2, and arangeofmiRNAs.Weuseawidevarietyofmolecularandcellulartechniquestostudyhowtheexpressionof thesegenes is regulatedand toexamine themolecularand cellular consequencesofdisrupting theirfunctioninbreastepithelialcell‐linesandthemammaryglandofmousemodels.

Project1:RegulationoftheBreastCancerSusceptibilityGeneBRCA1ThisprojectwillinvolveidentifyingnovelregulatoryelementscontrollingtheexpressionoftheBRCA1gene.Weareespecially interested in the3’UTRofBRCA1andmiRNAs that target this region.Thisprojectwillinvolveelucidatingthestructure,functionandclinicalrelevanceoffunctionalelementsintheBRCA13’UTR.Theseelementshavethepotentialto formthebasisof improvedpre‐symptomaticdiagnostics forbreastcancer.

Project2:RegulationofMicroRNAGenesinAdvancedBreastCancerTheaimofthisprojectistoidentifyandfunctionallycharacterizemiRNApromotersandtheirdownstreamtargetgenes.Particular interestwillbegiven tomiRNAs thatmaybe susceptible toaberrantepigeneticregulation.ThesemiRNAhavethepotentialtobenovelbiomarkersfortheidentificationandmanagementofpatientsthataresusceptibletoadvancedbreastcancer.

Project3:MolecularandCellularConsequencesofDisruptingBreastCancerGenesTheaimofthisproject istounderstandhowchanges intheregulationorfunctionofbreastcancergenesresultsinthedevelopmentofbreastcancer.Thisprojectwillinvolveexaminingtheeffectofincreasinganddecreasingtheexpressionofnormal,variantandmutantformsofbreastcancergenesontheexpressionofgenes, includingmiRNAs, in breast epithelial cells. Thesemolecules have the potential to be targets ofnoveltherapeuticagentstotreatbreastcancer.Techniques: Bioinformatics, gene cloning andmutagenesis,mammalian cell culture and gene transfer,reporter gene assays, real‐time PCR, Northern blotting, chromatin conformation assays, methylationspecificDNAanalysis,cellcultureassaysincludingcellproliferationanddifferentiation.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

PROFESSOR PAUL BURN UQViceChancellor’sSeniorResearchFellowDirector–CentreforPhotonicsandElectronics(COPE)Website:www.physics.uq.edu.au/cope/Phone:0733653778Email:[emailprotected]

TheresearchmissionoftheCentreforOrganicPhotonicsandElectronics(COPE)istotakenanotechnologyfromthe“benchtothemarket”.COPEcontainsstate‐of‐the‐artsynthesis laboratories,aClass1000cleanroom,devicefabricationfacilities,andasuiteofinstrumentroomsforthecharacterizationofmaterialsandopto‐electronic devices. COPE has Honours research projects in all branches of Chemistry (organic,inorganic,materials,physical,andcomputation)givingafantasticopportunityforyoutodevelopyourowninterests and skills at the cutting edgeof a technological area, e.g., solar cells, flat panel displays andlighting,plasticelectronics,explosivessensors,fuelcells,andsyntheticvaccines.Below isasnapshotofsomeoftheprojectsonofferandIwouldbehappytodiscussthemwithyou.

Project1:PlasticsolarcellMan‐made global warming is a scientific fact and a key component ofslowing and ultimately halting climate change is the provision of clean(non‐fossil fuel) energy. Ifwe convert a proportion of the 1 kJ of solarenergythatfallsoneachsquaremetreoftheEarth’ssurfacepersecondofevery daylight hour into electricity [photovoltaics (PV)] it will make adramaticeffecton theworld’senergysupply.Wouldyou like touseyourorganic chemistry skills to create new polymers, dendrimers or smallmolecules that can be used in efficient, flexible, and lightweight plastic

solarcellsfabricatedatCOPE?Doyourinterests lie instudyingstructureusingneutronscatteringorwouldyou liketoapplycomputationtodevelopanunderstandingofwhysomematerialsworkwellandsomedonot,leadingtonewdesigncriteria?

Project2:FlatpaneldisplaysandlightingLighting and displays based on organic light‐emitting diodes (OLEDs) have thepotential advantages of cheapmanufacturing, better power consumption, bettercolours, andultimatelybeing flexible. Imagine a TV screen that could rollup intoyourmobile phone! The best emissivematerials are comprised of organometalliccomplexes.Would you like to apply your interest in synthetic inorganic chemistryand/or materials chemistry to develop new emissive complexes and/orpoly(dendrimers) that can be incorporated into real OLEDs at COPE? OLEDs aremadeupofthinlayersoforganicandinorganicmaterialsandwhathappensastheyage is notwell understood.An interest in physical chemistrywould allow you to

makeanimportantcontributiontoourunderstandingofhowOLEDsdegrade.

Project3:SensingexplosivessensorsHow do we detect explosives in real time selectively and sensitively?Currentlythemostsensitivedetectorsforexplosivesarecanines.AtCOPEwe are developing in partnership with industry our own handheldtechnology. The explosive analytes are detected by fluorescencequenching. The project brings together synthetic organic chemists whodesign dendrimers for sensing explosives and spectroscopists tounderstandhowtheanalytesaredetected.Areyouanorganicchemistorphysicalchemistwhowouldliketoworkinaninterdisciplinaryteam?

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

ASSOCIATE PROFESSOR BERNIE CARROLL Phone:0733652131Email:[emailprotected]

RNAinterference(RNAi)andgenesilencinginArabidopsisGenesilencing isahighlyconservedprocess inplantsandanimals,and isof fundamental importance todevelopmentalregulationofgeneexpression,defenceagainstviruses,transposonsilencing,adaptationtoenvironments and genome evolution.We are using Arabidopsis thaliana as amodel for studying themechanismsofgenesilencinginplants.

SystemicmovementofgenesilencingRemarkably,whengenesilencing istriggered incellsofplantsandanimals, itcanspreadthroughouttheorganism.Weareusingaforwardgeneticapproachandmap‐basedgenecloningtofurtherelucidatethemechanismsofsystemicmovementofgenesilencinginArabidopsis.

IntronsplicingregulatesgenesilencinginArabidopsisTheroleof intronshaspuzzledmolecularbiologistssincetheirdiscoveryin1978.Butwerecentlyshowedthat intron splicing protects genes from being silenced in Arabidopsis. Additionally, when wemutateintrons to compromise their splicing, they become potent inducers of gene silencing. Defective intronsplicinghasbeenassociatedwithgeneticdiseasesinbothplantsandhumans.ThisprojectaimstofurtherinvestigatethemechanismofintronsuppressionandintronactivationofgenesilencinginArabidopsis.

GeneticengineeringofinsectresistanceinplantsbasedonRNAiWe are using RNAi to engineer plant resistance to insect pests, and it has the immense potential fordramaticallydecreasing theuseoftoxic insecticides. Incontrasttochemical insecticides,RNAimoleculescanbedesigned to target specific insects, avoiding anydeleteriouseffectsonnon‐target species in theenvironment.

Selectedrecentpublications:Brosnan et al. (2007) Nuclear gene silencing directs reception of long‐distance mRNA silencing inArabidopsis.PNAS104,14741‐14746.Gursansckyetal.(2011)MobilemicroRNAsh*tthetarget.Traffic12,1475‐82.Christieetal.(2011)IntronsplicingsuppressesRNAsilencinginArabidopsis.PlantJournal68,159‐167.

Image:GFPsilencing(redareas)canbeseenspreadingsystemicallythroughouttheplant.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

DR JACK CLEGG Phone:0733654384Email:[emailprotected]

Metallo‐SupramolecularChemistryandMetal‐OrganicFrameworksMetallo‐supramolecularchemistrybridgesthetraditionalfieldsoforganicandinorganicchemistry.Byusingself‐assembly the inherent physical and chemical properties of simple metallic and organic (ligand)componentsarebroughttogethertoformbeautifulcomplexandfunctionalarchitectures.Inparticular,weare interested in the design and synthesis of newmaterials with central cavities that are capable ofselectivelybindingsmallermolecules.Projectsinvolveacombinationofsynthesis,characterisation,bindingstudies,Xraydiffraction,spectroscopy,dataanalysisandinvestigationsintophysicalpropertiesandcanbetailortosuittheparticularinterestsofastudent.Exampleprojectsaregivenbelow.

TrappingGuestMoleculesinMetal‐OrganicFrameworksMetal‐Organic Frameworks are a class of polymeric hybridmaterial formed from organic andmetalliccomponents.Thesematerialshavelargesurfaceareasandhighporosityandarefindingapplicationingassequestration and separation technologies. Accordingly it is possible to trap a large variety of guestmoleculesinsidethem.Inthisprojectyouwillinvestigatethebindingofdifferentsolventmoleculesinsideoneoftheseframeworkstoexploreselectivityandpotentialseparationapplications.

NewMetallo‐SupramolecularArchitecturesCareful consideration of the geometrical properties ofmetals and organic components allows for theconstruction of a variety of discrete “supermolecules” formed from the spontaneous aggregation ofnumerouspredesigned components. These structures,oftenwith central cavities, takenumerous formsfromtwo‐dimensionalarchitecturessuchastriangularandsquarearchitecturestoelaborateandbeautifulthree‐dimensionalspeciessuchastetrahedraandcubes.Changingthesize,shape,propertiesandchargeofthearchitectureallowsfortheselectiveencapsulationofdifferentmaterialsinsidethem.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

PROFESSOR JAMES DE VOSS Phone:0733653825Email:[emailprotected]

My group is concernedwithbiological and synthetic chemistry and inparticularwith the applicationofchemicalprinciplestotheunderstandingofbiologicalprocesses.Mostprojectsareablendofdisciplinesinbio‐organicchemistry:synthesis,structuredetermination,molecularbiology,proteinpurification.Arangeof techniques isemployed, ranging from thebiochemical (e.g.PCR,gelelectrophoresis) to the chemical(e.g.NMR,HPLC,GC/MS).Thefollowingareasillustratetheresearchinmylaboratorybuttheexactprojectwillbedeterminedbythestudent’sinterests.

Project1:CytochromesP450P450scatalyseanamazingvarietyofoxidativetransformations,rangingfromsimplealkeneepoxidationallthewaythroughtooxidativeC‐Cbondcleavage.Theyareofinterestasthey(i)areoftenuniqueenzymesin a biosynthetic pathway and as such represent new targets for chemotherapeutic agents or (ii) areextremelyefficientcatalyststhatofferthepotentialofdevelopingtailoredoxidativecatalystsforsynthetictransformations.WeareinterestedinunderstandingthemechanismofactionofanumberofP450s.OneexampleisCYP61,auniqueP450involvedinsteroidbiosynthesisinfungiandotherpathogenicorganisms.Assuch itrepresentsapotentialtargetfornovelchemotherapeutics.CYP61catalysesanunusualreactionforaP450,namelythedehydrogenationofanalkanetoanalkene.However,essentiallynothingisknownabouttheexactstructureofthesubstrate,thestereochemistryofthereactionoritsmechanism.Projectsin this area will involve the synthesis ofmechanistic probes, the analysis of the products of enzyme‐catalysedreactions,characterisationofenzymemutantsanddesignandsynthesisofinhibitors.

Project2:ConstituentsofMedicinallyUsedHerbsWhilstherbalmedicinesarewidelyusedandhavea longhistoryofsuchuse,theirchemicalconstituentsareoftenpoorlycharacterised.Incollaborationwithalocalcompanywehaveembarkeduponaprogramofphytochemical characterisation of a number of therapeutically prescribed herbs. The results have beensurprisingwithanumberofpreviouslyunknowncompounds isolated fromsupposedlywell‐characterisedspecies.Thisprojectwouldinvolvetheisolation,chromatographicpurificationandstructuredetermination(especiallyemploying1Dand2Dnmr)of thechemicalconstituentsof selectedherbs. Thestructuresofsomerecentlyisolatedcompoundsaregivenbelow.

RelevantRecentPublications1. Slessor,KateE.,Farlow,Anthony J.,Cavaignac, SoniaM., Stok, JeanetteE.,DeVoss, James J.OxygenactivationbyP450(cin):Proteinand

substratemutagenesisArch.Biochem.Biophys.2011,507154‐162. 2. N. J.Matovic, J.M.U.Stuthe,V.L.Challinor,P.V.Bernhardt,R.P.Lehmann,W.Kitchingand J. J.DeVossTheTruthaboutFalseUnicorn

(Chamaelirium luteum):TotalSynthesisof23R,24S‐ChiograsterolBDefines theStructureof theMajorSaponins from thisMedicinalHerbChem.Eur.J.201117,7578‐91.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

ASSOCIATE PROFESSOR VITO FERRO Phone:0733469598Email:[emailprotected]

Myresearchinterestsencompasscarbohydratechemistryandmedicinalchemistry,withafocusonthesynthesisofcompounds toprobeand/or inhibitcarbohydrate‐protein interactions involved indiseaseprocesses. Of particular interest is heparan sulfate (HS) and the development of HS‐mimetics aspotential drugs for cancer and various other diseases. Previous work in this area resulted in thediscovery of PG545, a potent inhibitor of angiogenesis andmetastasis that recently entered Phase Iclinicaltrialsincancerpatients.

1.DevelopmentofafluorometricassayforheparanaseHeparanaseisaglycosidasethatcleavesHSintheextracellularmatrixandfacilitatesmetastasisoftumourcellsandvascularremodellingassociatedwithangiogenesis.PG545isanexampleofaheparanaseinhibitorwithpotentinvivoactivityinmetastaticandangiogenicmodels.Despitetheadvancementtoclinicaltrialsofinhibitors,heparanaseresearchhasbeenlimitedbythelackofasimpleandrobustassayforenzymaticactivity. This project aims to address the situation by the synthesis of novel fluorogenic substrates forheparanase.

2.SynthesisofpharmacologicalchaperonesforlysosomalstoragediseasesLysosomalstoragediseases(LSD)arecausedbymutationsinenzymesthatdegradepolysaccharidessuchasHS,resultingintheaccumulationofundegradedsubstrateinthelysosomesofcells.Somepatientsmaybetreated with enzyme replacement therapy. Unfortunately, the replacement enzyme cannot cross theblood‐brainbarrier and thus cannot treat theneurological symptoms associatedwith severe cases. Theaimsof thisprojectare todevelopsmallmolecules for the treatmentofLSD,whichunlikeenzymes,arecapable of crossing the blood‐brain barrier and thus may offer relief of neurological symptoms. Thecompoundsaredesigned toactas“chaperones” toprotect thedefectiveenzyme fromdegradationandrestoreenzymeactivitytosufficientlevelstoalleviatesymptoms.

3.GlycosylatedliposomesfortargeteddeliveryofsiRNATargeteddeliverytoaspecificcelltypeisdesirabletoimprovetheeffectivenessandspecificityofsiRNAforgene silencing.Theaimof thisproject is togenerate specificallyglycosylated liposomes thatwillenabledeliveryofsiRNAtoparticularcelltypespossessingreceptorsfortheseglycans.

4.Synthesisofinhibitorsofvirus‐cellattachmentManyviruses,includingHSVandHIV,useHSasanentryreceptororco‐receptor.ThisprojectwillfocusonthesynthesisofnovelHSmimeticsthatinhibitvirus‐cellattachmentandpossessvirucidalactivity.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

DR JAMES FRASER Phone:0733654868Email:[emailprotected]

InfectiousDisease:FungalPathogenesis&EvolutionOurresearchgoalsaretoidentifyweaknessesinfungalpathogensthatcanbeexploitedasdrugtargetstocombat life‐threatening systemic infections, and to discover new Cryptococcus neoformans virulencefactorsbyidentifyingmicroevolutionaryeventsthatoccurinitsgenomewhileinfectinghumans.

AntifungaldevelopmentEveryyear,upto1.5millionAIDSpatientsareinfectedbythepathogenicyeastC.neoformans.Up to1millionof thesedie,makingcryptococcosisoneof thetop threekillersofAIDSpatientsworldwide.Thishighmortality rate isdue tothe absence of an adequate array of antifungal agents.We are using awidearrayoftechniquestoidentifynewdrugtargetsinC.neoformansinthehopeofreducing this highmortality rate.We have already identified some excellenttargetsandpotentialtherapeuticagents.Honoursstudentsworkingonthisprojectwillhavetheopportunitytoemployavery large array of experimental techniques, ranging from the creation ofmutants, performing phenotypic screens (including drug susceptibility),analysinggeneregulationusingtranscriptomesequencingand,dependingonthediscoveriesmade,usingamurinemodelofinfectiontotesttheefficacyofnewantifungalcompounds.

Evolutionofapathogen'sgenomeEvenifapatientsurvivesaninfectionbyC.neoformans,theyarelikelytosufferarelapseinfectionthatiseven more deadly within twelve months of treatment. These C. neoformans isolates have usuallyundergone chromosomal rearrangements, which we have shown to correspond with an increase invirulence that enables the relapse infection tooccur. Through collaborators atDukeUniversityMedical

CenterandtheAlbertEinsteinCollegeofMedicine,wehaveacquiredalargecollectionofsuchstrainsfromindividualswhohavesufferedrepeatedroundsof infection. We are investigating these strains to identify undiscoveredvirulence factors and potential vulnerabilities thatwe could employ in thedevelopmentofnoveltherapeuticinterventions.Honoursstudentsworkingonthisprojectwillusenext‐generationsequencingtechnology to sequence whole genomes of clinical strains of interest,characterise chromosomal rearrangements, createmutants and investigatetheeffectsofthesemutationsonvirulence.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

PROFESSOR LAWRENCE GAHAN

Phone:0733653844Email:[emailprotected]

Iron(III)‐Zinc(II)ComplexesasAnaloguesofPhosphom*onoesterases(WithAssociateProfessorGarySchenk)

Wehaveforsometimebeen interested insimplecoordinationcomplexeswhichmimictheactivesitesofmetalloenzymesandwehavepublishedanumberofpapersand reviewson the topic. Whilstwehavemade heterobinuclear mimics of the phosphodi‐ and tri‐esterase enzymes like GpdQ theglycerophosphodiesterasefromEnterobacteraerogenes(GpdQ)wehavebeenlesssuccessfulwithligandswhichmodelmetal ion content (Fe(III)/Zn(II)) thatmimics the active site of the enzyme purple acidphosphatase (PAP). An earlier attempt resulted in the ligand 2‐((2‐hydroxy‐5‐methyl‐3‐((pyridin‐2‐ylmethylamino)methyl) benzyl)(2‐hydroxybenzyl)amino)acetic acid (H3HPBA; see below), where wepreparedanFe(III)/Fe(III)complexwithinterestingmagneticandspectroscopicproperties.Surprisingly,thecomplexwas catalyticallyactive towardsphosphom*onoesters. In thisprojectwewill tailor the ligand tohaveonepronounced zinc(II)binding site and a site specfic for iron(III). Theprojectwill involve ligandsynthesis, structural and spectroscopic studies and an investigation of the kinetics of phosphate esterhydrolysis.

Boudalis,AK.,Aston,R.E.,Smith,S.J.,Mirams,R.E.,Riley,M.J.,Schenk,G.,Blackman,A.G.,Hanton,L.R.,&Gahan,L.R.Synthesisandcharacterizationofthetetranucleariron(III)complexofanewasymmetricmultidentateligand.Astructuralmodelforpurpleacidphosphatases.DaltonTransactions2007,5132‐5139.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

PROFESSOR MARY GARSON Phone:0733653605Email:[emailprotected]

BioactiveChemicalsfromMarineSpongesandMollusksThe research in my group focuses on the biological chemistry of natural products from marine andterrestrial sources.Onequarterof theworld’sdrugscome fromNature,primarily frommicro‐organismsandfromrainforestplants.Asterrestrialresourcesbecameoverexploited,attentionturnedtothemarineenvironmentasanalternativesourceofnovelbioactivemetabolites.Honoursprojectsareavailablewhichprovide experience of: (i) isolation & structure elucidation of metabolites; (ii) small scale syntheticmanipulationofisolatedmetabolites;(iii)marinechemicalecology;(iv)marinemicrobialchemistry.Fig.(a)LowtemperatureNMRstudyofplakortoperoxideA;(b)TerpenemetabolitesofThuridillasplendens

RecentprojectshaveinvolvedstudiesonPlakinastrellaclathratasp.1andonVerongidspongesthatcontainantimalarialorcytotoxicmetabolites,oncomplexterpenesfromnudibranchsofthegeneraChromodoris2,3andThuridilla,andoncomplexpolyketidesisolatedfromthemarinefungusAcremoniumsp.Frequentlyintheseprojects,submiligramamountsofmetabolitesarestudiedbyNMRat500and900MHz.1Dand2DNOESYdata are combinedwithmolecularmodelling studies and/or 3JCHmeaurements todetermine thestereochemistryofisolatedcompounds.Chemicalecologystudiesexploretheroleofmarinemetabolitesinchemicaldefenseaseitherantifeedants,4orasantifoulingcompounds,andusesimplebenchtopassays.RecentPublications:

1.Yong,K.W.L.,Lambert,L.K.,DeVoss,J.J.,andGARSON,M.J.,‘OxidativeprocessesintheAustralianmarinespongePlakinastrellaclathrata;isolationofplakortolideswithoxidatively‐modifiedsidechains,’J.Nat.Prod.,75,351‐360.2012.

2.Katavic,P.L.,Jumaryatno,P.,Hooper,J.N.A.,Blanchfield,J.T.,andGARSON,M.J.,‘OxygenatedditerpenoidsfromtheAustralianspongesCoscinodermamathewsi,Dysideasp.andthenudibranchChromodorissplendida.’Aust.J.Chem.,65,531‐538.2012.

3.Suciati,Lambert,L.K.,andGARSON,M.J.,‘StructuresandanatomicaldistributionofoxygenatedditerpenesintheAustraliannudibranchChromodorisreticulata.’Aust.J.Chem.,64,757‐765.2011.

4.GARSON,M.J.,‘Marinenaturalproductsasantifeedants,InComprehensiveNaturalProductsChemistryII,Mander,L.,Lui,H.‐W.,Eds.;vol4,Elsevier:Oxford,pp503‐537.2010.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

PROFESSOR IAN GENTLE Phone:0733654800Email:[emailprotected]

Researchinmygroupisfocussedontheself‐assemblyofmaterialsatinterfacesandisdirectedattwomainareas of application: advanced materials for electrodes for batteries and supercapacitors; and thefabrication and characterization of thin‐film structures for organic light‐emitting diodes (OLEDs),photovoltaicsolarcellsandvapoursensors.Weworkcloselywithcollaborators intheCentre forOrganicPhotonicsandElectronics(COPE)andtheARCCentreofExcellenceforFunctionalNanomaterials.Thereareworld‐leading facilities forthisworkavailableatUQandexternal facilitiesthatweuseextensively.Theseinclude X‐ray and neutron reflectometry (facilities such as the Australian Synchrotron, OPAL ResearchReactor and facilities in the UK are normally used for these measurements), X‐ray photoelectronspectroscopy(XPS),atomicforcemicroscopy(AFM),smallangleX‐rayscatteringandX‐raydiffraction.

ConductingPolymerMaterialsforHighEnergyBatteriesAsalternativeenergysourcesare increasinglybeingexploitedaswaysofprovidingsustainable,low‐carbonenergy,theissueofstorage isbecomingevermore important.Forapplicationssuchastheelectricvehiclemarketthereisapressingneedforbatterieswithhigherenergydensity (that is,energyperunitmass) than is currentlyavailable.Coupled to thisneed is theability forbatteriestobeabletoberechargedrapidlyandto

be durable enough to survive up to 1000 charge/dischargecycles.Wehavebeenexploringanumberoftechnologiesthatshowgreatpromiseforincreasingthecapacityanddurabilityofbatteries for this purpose. We realized in recent work theimportanceofconfinementofactivematerialsinamatrixforachievinggoodstabilityofbatteries.Totakethisconcept further,we intend toextendtheconfinementsystem from inorganicmaterialstopolymericmaterials, which are anticipated to facilitate chemical bonding within confinement for even superiordurabilityofbatteries.Thisprojectwillbeasystematicinvestigationofaconductingpolymericcathodesystemproducedbysoft‐templated polymerization in amicellar solution, involving spontaneous encapsulation of active storagematerials inside polymer spheres, characterization of the structure and composition using Ramanspectroscopy, X‐raydiffraction, FTIR spectroscopy, X‐ray photoelectron spectroscopy, thermogravimetricanalysis,porositymeasurementandfinallyelectrochemicalevaluationofthereversibilityofthematerials.Theoutcome is expected tobe anunderstanding of the advantagesof chemicallybonded confinementcomparedtophysicalconfinement.

Thin‐filmorganicoptoelectronicdevicesMostorganic‐basedoptoelectronicdevicessuchasorganicsolarcellsand light‐emittingdiodesarebasedonmultilayersoforganicmaterials.Inpreviousworkwehavediscoveredthatdiffusionbetweenthelayersisacrucialcharacteristicofsuchstructures.Usingneutronreflectometrywecansensitivelyandinrealtimemeasure theextentofdiffusion inmultilayer films. In thisprojectweare interested in the structureofinterfaces and the processes that occur at the interface between the organic layers and the inorganicmaterials of the electrodes (normallymetals ormetal oxides). The aim is to be able to developmoredurableandefficientdevicesthroughunderstandingandcontroloftheseprocesses.

Confinedsulfurinanewcathodematerialfor

lithiumsulfurbatteries

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

PROFESSOR ELIZABETH GILLAM Phone:0733651410Email:[emailprotected]

CytochromeP450enzymes:Nature’smostversatileenzymesCytochromeP450enzymesareoneofthemostfunctionallyversatilegroupsofbiocatalystsknown.Theycarryout diverse roles in all domains of life because they can catalyse an extraordinary range of chemicaltransformationsonanunprecedentedvarietyofsubstrates.Our group is interested in finding out how P450swork andhowtheycanbemadetoworkbetter.ProjectsintheGillamlabinvolvecutting‐edgetechniquesinartificial evolution, protein design and high throughputscreening, as well as fundamental methods of molecularcloning, genotyping, protein chemistry and metaboliteanalysis.

1.ArtificialevolutionofP450sfordrugdevelopmentandbioremediation.We are using artificial (or directed) evolution to engineerenzymesthataremoreefficient,robustandspecializedthannaturally occurring enzymes for application in drugdiscoveryanddevelopmentandcleaninguptheenvironment.Theapproachweareusingalsoallowsustoexplore the essential sequence and structural features that underpin all ~12000 known P450s so as todeterminehowP450swork.

2.AncestralreconstructionofP450s,enzymesevolvedtodealwiththeunknownFive P450s metabolise ~ 95% of all drugs to which humans are exposed as well as innumerableenvironmental chemicals ‐ an extraordinary range of substrates,manyofwhich havenot been presentduringevolution.Wearestudyinghowtheseenzymeshaveevolvedsuchextremesubstratepromiscuitybyreconstructingancestralprecursorsandevolutionarypathways.

3.P450sinbrain:relevancetomentalillnessandneurodegenerativediseases(withProf.PeterDoddandDr.SimonWorrall)P450slocalisedinmitochondriahaverecentlybeenshowntocontributetotheneurotoxicityofsomedrugsand can lead to oxidative damage tomitochondria.Genetic differences between individuals affect theexpressionofP450sinmitochondriaandmaycontributetosusceptibilitytodiseasessuchasAlzheimer’s.

4.P450Nanodiscsforbiosensors(withProf.PaulBernhardt)SinceP450srespondtosuchavarietyofdifferentsubstratestheyarewellsuitedforuseasbiosensorstodetect trace environmental contaminants, drugs and other chemicals. We will formulate P450s intonanodiscs –minute protein‐bounded lipid bilayer discs – to characterise their electrical properties byproteinelectrochemistry.Ourresearchsuitsstudentsinbiochemistry,molecularbiology,chemistry,biotechnology,orbioinformaticswho are interested in discovering how enzymes work, how to engineer them to provide clean greenalternativestochemicalprocesses,andthemolecularbasistothetoxicityofdrugsandotherchemicals.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

ASSOCIATE PROFESSOR LISBETH GRONDAHL Phone:0733653671Email:[emailprotected]

TheprimaryresearchareaoftheGrondahlGroupisbiomaterialsdesignandevaluation.AllprojectsbuildsonInterfacialScienceandMaterialsChemistryfundamentals.Collaborationswithotherchemists,engineersandbiologistsatUQenable the tailoringofprojects to specific interestsof students.Theprojects listedbelowareexamplesofwhatcouldconstituteanhonoursprojectintheGrondahlGroup.

ProteinAdsorptiontoWell‐DefinedSurfacesManybiomaterialspossesssuitablebulkproperties;however,theirsurfacepropertiesarenot ideal. Thematerialsurfacecharacteristicsinfluencethefinaltype,orientationandconformationofadsorbedproteinsand hence the subsequent cell‐surface interactions. Biomaterials with non‐ideal surface propertiesthereforefrequentlyfailtoperformappropriatelyinvivoleadingtoanextensiveprolongedinflammation,fibrous capsule formation and implant rejection. Investigating the protein adsorption to surfaces withcontrolledsurface featureswilladvance theknowledgeneeded todesign futuregenerationbiomaterialswith optimal properties. This study involves surface modification of biomaterials as well as proteinadsorptionstudies.

HAPnano‐compositesHydroxyapatite (HAP) isthemainmineralphaseofboneandteeth. Invivothebiomineralisationprocessoccurs in the presence of biological macromolecules where the ion concentrations are too low forspontaneousnucleationandgrowthofcrystalstooccur.Inaddition,themorphologyoftheHAPcrystal isaffectedbythepresenceofthesebiomacromolecules. InordertoproduceHAPnanoparticlessuitableforcompositebonebiomaterials a betterunderstandingofhow to control size and shape is required. Thisstudywill investigate thenucleation and growthofHAP in thepresenceofmacromolecules. It involvescollaborationwithDrKevinJack(CMM).

TailoredmatricesfortemporaldeliveryofdrugsinbonerepairNon‐unionanddelayedunion fracturesareunable tohealbythemselvesand therapeuticoptionswouldtherefore greatly benefit from delivery of bone‐growth inducing factors. Successful delivery of factorsrequiresthedevelopmentofdrugdeliverysystemsoptimisedforthesemolecules.Biodegradablegelscanbe used to encapsulate these bone‐inducing factors. Specifically, one project will investigatefunctionalisation of alginatewith amino acids for tailoring the gelmatrix and another project involvesinvestigationofusing LbLassemblies to control thedrug release rate.Thedrugdelivery systemswillbecharacterised using a combination ofmicroscopic techniques (optical, fluorescence, and cryo‐EM) andspectroscopictechniques (Fluorescence,FTIR)andtheirstability inasimulatedbodyenvironmentwillbeassessed. In addition, drug encapsulation efficiency and the drug release rate from the systemwill beoptimised.ThisstudyinvolvescollaborationwithDrGwenLawrie.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

ASSOCIATE PROFESSOR LUKE GUDDAT Phone:0733653549Email:[emailprotected]

Branched‐ChainAminoAcidBiosynthesis:Atargetfordrugdiscovery

Acetohydroxyacidsynthase(AHAS)andketolacidreductoisomerase(KARI)arethefirsttwoenzymesinthebranchedchainaminoacidbiosynthesispathway. There isnowa largebodyofevidence tosupportthehypothesis that the inhibitionof thispathway canbeused todiscovernew antibacterial and antifungalagents. Thegoal inthisproject istodiscoveranddevelopnew inhibitorsofAHASorKARIusingstate‐of‐the‐artrationaldrugdesigntechniquesandX‐raycrystallography.Wehavebeen successful inusingX‐ray crystallography todetermine the three‐dimensional structureofAHAS (yellow crystals because of the presence of FAD) and KARI.We have also shown how a potentinhibitorofAHASbinds to theenzymewithnanomolaraffinity,making itanexcellent startingpoint fordrugdiscovery.WehaveprojectsforhonoursstudentsthatcouldinvolveX‐raycrystallography,chemicalsynthesis,enzymeassay, small molecule screening, fragment screening, computer modelling, antibacterial or antifungaltesting,andproteinexpressionandpurification(oranycombinationoftheabove). Thework iscurrentlyfundedbyanNHMRCprojectgrant.

OCH2CH3

S NH C

NCl

OCH3

chlorimuron ethyl (CE)

S NH C

NCH3

monosulfuronester (MSFE)

O O CH3

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

PROFESSOR ROY HALL Phone:0733654647Email:[emailprotected]

AreasofResearch:

Studiesonthemolecularbiologyandpathogenesisofmosquito‐borneflavivirusesthatcausediseasessuchasJapaneseencephalitis(JEV),WestNilevirus(WNV)andMurrayValleyencephalitisvirus(MVEV).

StudiesontheimmuneresponsetoJEV,MVEVandWNVandthedesignandevaluationofnovelvaccinestotheseviruses.

DevelopmentofnovelmolecularandserologicaldiagnosticassaysforJEVandWNV.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

PROFESSOR PHIL HUGENHOLTZ DR GENE TYSON Phone:0733653822 Phone:0733653829Email:[emailprotected] Email:[emailprotected]TheAustralianCentreforEcogenomics isaresearchcentrewithintheSchoolofChemistryandMolecularBiosciencesfocusingonculture‐independent investigationofmicrobialcommunitiesinenvironmentalandclinicalhabitats.Thisapproachiscrucialtounderstandingthemicrobialworldasmostmicroorganismsarenot culturable in the laboratory. Key molecular and imaging techniques are now available for highthroughputandhighresolutionanalysisofmicroorganismsintheirnativesettingsincludingmetagenomics,metatranscriptomics, fluorescence in situ hybridization (FISH) and flow sorting. We are looking formotivatedhonoursstudentstojoinourranksonanumberofexcitingandcutting‐edgeprojects.

Environmentalprojects:Microorganismsdriveallthemajorbiogeochemicalprocessesonearth.Only in the last fewyearshas themolecularecological toolkitbecomeavailable to fully illuminate the microbial underpinnings of theseprocesses. Wehaveongoingprojectsavailable to study themicrobialcommunity structure and dynamics of the following environments;alkalinesegmentsoftermitehindgutstoidentifypopulationsofinterestforcellulosicbiofuelpretreatment, thesugarcane rootmicrobiome forsustainable agriculture, coal seam methane formation waters tounderstand methane generation, and thawing permafrost soils toidentifykeypopulationsinvolvedincyclingofcarbon.

Clinicalprojects:Perhapsnotsurprisinglymostclinicalresearchfocusesonrecognised pathogens. There is an increasing realisation,however,thatmostpathogensdonotactinisolationwiththeir host and that infections have ‘polymicrobial’phenotypes. In fact it has been shown that somemicrobial species will compete with pathogens forresourcesandprovideabeneficialeffecttothehost.Wehave a number of ongoing projects that will apply 16S rRNA gene pyrosequencing‐based (pyrotag)communityprofilingandpopulation‐specificFISH imagingtoanumberofclinicalsamples. These includelung,skinandgut.

Reference:Hugenholtz,P.andG.W.Tyson.2008.Microbiology:metagenomics.Nature455(7212):481‐483.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

DR ULRIKE KAPPLER Phone:0733652978Email:[emailprotected]

My research is centredonhowbacteria from variousecologicalniches transform inorganic andorganicsulfurcompounds,anareaofresearchthathasreceiveda lotofattention inrecentyearsasmanysulfurcompoundsaretoxic,malodorousandseveralareknowntoinfluenceclimateprocesses.

Many of the bacterial species involved in these processes are also of industrial interest for use inbioreactors that remove sulfur compoundse.g. from fluegasorotherwastestreamsandasa sourceofenzymescatalysingnovelreactions.Bacteriaoxidizingorganicand inorganicsulfurcompounds insoilsarealso crucial formaking sulfur available for plant growth and thus are important in agriculture and soilmanagement.

I am also interested in elucidating the roleofmetalloenzymes in bacterial pathogenesis.Molybdenum–containingenzymescansupportanaerobicgrowthofbacteriawhich is important for survival inbiofilmsandinanaerobicnichesofthehumanbody.

Theworkcarriedout inmygroup isverydiverseandincludesbacterialphysiology,generegulation,somegenomicbiology,proteomicsaswellasproteinpurificationandcharacterizationbyavarietyoftechniquesincludingdifferent typesofspectroscopy.Projectscanbe tailored toyourareaof interest inasmuchaspossible.

Projectsofferedin2013/2014

RegulationofgeneexpressionRegulationofbacterialsulfiteoxidation–anovelroleforextracytoplasmicfunction(ECF)sigmafactors

Enzymes&theirroleinbacterialphysiologyDo metalloenzymes support virulence of human pathogens? Case study: Haemophilus influenzaeMolybdenumenzymes

FriendorFoe?–MetabolicinteractionsbetweenStreptococcuspneumoniaeandHaemophilusinfluenzae

Environmentalmicrobiology&applications

Somelikeitalkaline–Canweusealikaliphilicsulfuroxidizerstotreatsulfurpollution?

Co‐supervisionwithProf.GordonSoutham:“Thegrowthofgoldnuggets”–bacterialdegradationof

thiosulfategoldcomplexes

Ifyoufindthesetopicsinteresting,butwouldliketoworkonotheraspectsoftheprojects,pleasecontact

me–thislistisnotcomprehensiveandadditionalprojectsareavailable.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

ASSOCIATE PROFESSOR STUART KELLIE Phone:0733654613Email:[emailprotected]

SignallingMoleculesinMacrophagesandTumourCellsInterests inmy lab are focussed on themolecules that regulate signalling inmacrophages and otherphagocytes,and in tumourcells. Inphagocytessuchasmacrophages,acuteandchronicstimuli induceanumberof intracellular signallinggenes tobeexpressed.Thesegenes includemolecules thatpotentiateactivation,butalsoincludemoleculessuchastyrosinephosphatasesthatcaninhibitcellactivation.Mylabis interested in the interplay between the positive and negative regulators of cell activation in bothmacrophagesandintumourcells.

Projectscurrentlyavailableinmylabinclude:

Project1:TheRoleoftheTyrosinePhosphataseDEP‐1inMacrophageMotilityandActivationWe have recently shown that the tyrosine phosphatase DEP‐1 is upregulated in macrophages uponstimulationwithinflammatoryfactors.Furthermorethisproteinregulatesmacrophagemembraneactivity,motilityandchemotaxis.Thisprojectwillinvestigatethemolecularmechanismsunderlyingthis.

Project2:TheRegulationoftheTyrosinePhosphataseDEP‐1byNoncodingRNAinTumourCellsandMacrophagesWehaverecentlyidentifiedseveralnoncodingRNAmoleculesassociatedwiththeDEP‐1geneinmammarycells. Thisprojectwill investigatewhether thesencRNA can regulate theDEP‐1gene in these cells. ThepresenceofncRNA inmacrophagesand theirpotential role in regulationof theDEP‐1genewillalsobeinvestigated.

Project3:FunctionalAnalysisofMacrophageGenesInducedbyRespiratorySyncytialVirusThefurin‐likefamilyofpeptidasesareupregulatedbyvirusesinmacrophagesandothercells.Thisprojectwillinvestigatetheroleofmembersofthefurin‐likefamilyintheinfectiousspreadofRespiratorySyncytialVirus.

Project4:StructuralandFunctionalStudiesofMacrophageSignallingMolecules(withBKobeandJMartinandMSweet).TheKobeandMartinlaboratorieshavesolvedthestructureofanumberofmacrophageproteins.Thisprojectwillusethestructuralknowledgegained to investigatethefunctionoftheseproteinsinmacrophageactivation.

Project 5: The Use of Yeast Cells Expressing Mammalian Signalling Molecules as BiologicalScreensforPotentialTherapeuticTargets(withJamesFraser).WhensignallingmoleculessuchastyrosinekinasesareinduciblyexpressedinyeastsuchasSaccharomycespombe, they result in inhibitionofgrowthof thecells.Thisprojectwill involvecloning several signallingmoleculesintoyeast,assessingtheeffectonproliferation,andestablishingthesecellsasbiologicalscreensforinhibitors.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

PROFESSOR ALEXANDER KHROMYKH Phone:0733467219Email:[emailprotected]

RNAvirology laboratorystudymolecularmechanismsofvirusRNAreplicationandvirus‐host interactionswiththemainfocusontheWestNilevirus(WNV)andmorerecentlyonChikungunyavirus.WNVbelongsto Flaviviruses, a group of highly pathogenic positive strand RNA viruses causing major outbreaks ofpotentially fatal diseases and affectingmore than 50million people each year. Chikungunya virus is amemberofAlphavirusesandhasrecentlycausedlargeoutbreaksofdevastatingarthritisdiseaseinReunionIslandandAsiancountries.Weareaimingatabetterunderstandingofhowthesevirusesreplicate inthehostandcausedisease,whichwillhelpinthedevelopmentofantiviraldrugs.Inaddition,wedevelopandevaluatevaccinecandidatestopreventinfectionandoutbreaks.Thefollowingprojectsareavailable:

1. Role of Small Subgenomic RNA in Flavivrus Pathogenicity. We recently identified a smallsubgenomicRNAproducedfromthe3’untranslatedregionoftheviralRNAincellsinfectedwithavarietyofflaviviruses.ThissubgenomicflavivirusRNA(sfRNA)istheproductofincompletedegradationofgenomicRNAbycellularribonucleasesandisrequiredforviralresponse.WewillelucidatethefunctionofsfRNAinthevirallifecycleandidentifyicellularandviralinteractionpartnersofsfRNA.

2.VirulenceDeterminants andHost Innate Immune Response toWestNileViruses.We haveshownpreviouslythatWNVisabletoevadeinnateimmuneresponsewithmorevirulentstrainabletodoitmoreefficiently.Thereareanumberofprojectsavailableincollaborationwithleadingoverseasgroups(MDiamond,USA;MGale,USA;andSAkira,Japan)aswellaslocalvirologists(RoyHall,SCMB)whichwillfocuson themechanisms by which pathogenic (New York 99) and non‐pathogenic (Kunjin) strains ofWNVinteract with the host innate immune response and how these interactions determine outcome ofinfection.

3. KUN Virus DNA‐Based Vaccine against Pathogenic Flaviviruses. We recently published thedevelopmentofahighlyeffectiveDNAvaccineagainstWNVwhichinvolvestheproductionofsingleroundinfectiousparticlesandhasbeenshowntoinducehighantibodylevelsinmiceandhorses.Theprojectwillcontinue incollaborationwithDr.RoyHallatSCMBandDr.AndreasSuhrbierattheQIMRtoextendthetechnology to development of vaccines against other medically important flaviviruses, dengue andJapaneseEncephalitis.

4.TheroleofmiRNAsinFlavivirus‐MosquitoHostInteractions.IncollaborationwithSAsgari(SBMS)wehaveidentifiedafirstmiRNAproducedbyWNVandhaveshownthatittargetsatranscriptionfactorinmosquitocellsthatisessentialforvirusreplication.ThisprojectisaimedatfurtherinvestigationsoftheroleofWNV‐induced/produced cellular and viralmicroRNAs (miRNA) in determining the outcome of virusinfectioninmosquitovector.

5. Innate immune response to Chikungunya virus. This project is a collaboration with AndreasSuhrbier(QIMR)andisfocusedonunderstandinghowtheinnateimmuneresponsetothisinfectionrelatestovirus‐induceddisease.UsingmousemodelofthediseasedevelopedatQIMRthestudieswillemployawiderangeofmousestrainsdeficientinexpressionofvariousfactorsinvolvedininnateimmuneresponseandcelllinesderivedfromthemtoidentifyhostfactorsinvolvedinresponsetoChikungunyavirusinfectionandinthedevelopmentofvirus‐inducedarthritis.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

PROFESSOR BOSTJAN KOBE Phone:0733652132Email:[emailprotected]

StructuralBiologyofInfectionandImmunityOur lab focusesonunderstanding importantbiologicalprocesses including infectionand immunityatthemolecularandstructural levels.Weareusingan integratedapproachcombiningdeterminationof three‐dimensionalstructures(withemphasisonX‐raycrystallography)withcomputationaltechniques,methodsforquantitativeevaluationofmolecularinteractions,proteinchemistryandmolecularbiology.

Projectsinclude:

StructuralStudiesofProteinsInvolvedinMammalianandPlantInnateImmunePathwaysTheaimofthisprojectistousestructuralbiologytounderstandthemoleculareventsoccurringin(i)Toll‐like receptor signallingpathways,with implications for infectiousand inflammatorydisease,and cancer;and (ii) innate immune pathways in plants (plant disease resistance),with the long‐term goal tomakeplants resistant to a variety of pathogens. The projects involve protein expression, purification,crystallization, structure determination, interaction studies and functional studies using site‐directedmutantproteins.

StructuralStudiesofProteinsInvolvedinBacterialPathogenesisTheaimofthisprojectistousestructuralbiologytounderstandtheprocessesofbacterialpathogenesisbydifferentbacterialpathogens.Theprojectsinvolveproteinexpression,purification,crystallization,structuredetermination,interactionstudiesandfunctionalstudiesusingsite‐directedmutantproteins.

UnderstandingtheMechanismandSpecificityofNucleo‐CytoplasmicTransportTheaimofthisprojectistounderstandthemechanismoftransportofproteinsintothenucleus,includingthespecificityandregulation,withthe long‐termgoalofmanipulatingthisessentialprocess.Theprojectsinvolveproteinexpression,purification,crystallization,structuredetermination,andinteractionstudies,aswellasbioinformatics/computationalaspects.

LinearMotifsinSignalTransductionLinear sequence motifs are recognized in many signalling processes, including protein kinases, MHCmolecules involved in the immune response, and nuclear transport factors. This computational projectfocusesondevelopingbioinformatictoolsthat integratesstructural informationwithsequenceandotheravailabledata.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

DR GWEN LAWRIE Phone:0733657848Email:[emailprotected]

Projectsareavailableinthefieldofchemicaleducationinmygroupandfocusesonhowstudentsconstructand apply their understanding of chemistry concepts. Situated at the interface between the fields ofchemistryandeducationalpsychology,currentprojects involveresearch intotheprocessesofknowledgeconstruction,complexreasoningandhigher‐orderthinkingskills.Educationalresearchmethodologieswillbeappliedtocollectandanalysequantitativeandqualitativedata(theseprojectsfollowsameprocessesasbenchchemistryprojects!).

1.Theroleofstudent‐generatedvisualrepresentationsintheacquisitionofchemicalliteracy.Visualrepresentationsofchemicalconceptsandprocessesareusedwidelyinlearningandteachingchemistry.Passiveengagementwiththeseimagesby students supports the construction of incomplete mental models.Recent evidence indicates that student‐generated visual representationsmay introduce a more effective way for students to construct theirunderstanding of chemical concepts, structures and acquire associatedterminology. In this project, student conceptual understanding,perceptions and language will be evaluated and data will be collectedthroughinterviewsandartifactsofstudentwork(qualitativedata).

2. The investigation of formative feedback and activities that introduce cognitive conflict toaddress strongly heldmisconceptions in chemistry. (In collaborationwithDr TonyWright,SchoolofEducation)Studentstypicallyconstructtheirmentalmodelsofchemicalconceptsbasedontheirpriorknowledgeand experiences that have developed across the primary, secondary and tertiary science learningcontexts.Thereareanumberofwell‐characterisedchemistrymisconceptionsreportedintheliteraturethatarestronglyheldovertimedespiteencounterswithsituationswhichchallengetheseconceptions.Inthisproject,theroleofandformofformativefeedbackdelivery,incombinationwithonlineactivitiesthatchallengeconceptions,willbeexploredtoinvestigatethefactorsthatinfluenceconceptualchange.Datawillbecollectedthroughbothstimulated‐responseinterviewsandstudentself‐explanationswhiletheycompleteonlineinterventions.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

DR SHIH-CHUN (LAWRENCE) LO Phone:0733657657Email:[emailprotected]

OrganicmaterialsandNanotechnology

Wearefocusingondevelopingnewclassesofnanomaterialsmainlyforenergyrelatedapplications,suchasphoton‐inducedwatersplitting(forH2generation),solarcells,andorganic lightemittingdiode(OLEDs)aswell as bio‐applications. Honours studentswill learn how to design, synthesise and characterise thesefrontierfunctionalmaterials.

Project1:Cleanhydrogenfuelgeneration

Theuseofhydrogengasasarenewableandcleanfuelhasbeenoneofthemostexcitingresearchfields,inparticular,directhydrogencreationfromwaterdrivenbysunlight.Developingefficientandlong‐lastingwater‐splittingphotosensitisersand catalystshasbeen the key challenge for the technology. Theproject is tosynthesise and characterise new water‐splitting photosensitizers for effectivelightabsorptionandcatalystsforefficientwaterdecomposition.

Project2:Advancedmaterialsforopto‐electronics(e.g.,OLEDs,solarcells,andphotodiodes)Theprojectistodevelopnewelectro‐activematerialsforOLEDs,solar cells,andphotodiodes forournextgeneration flat‐paneldisplays(e.g.,mobilephones,tablets,monitordisplaysandTVsfor the superior display‐quality and superb energy saving),renewableenergygenerationandhigh‐sensitivedetectors.Theproject will involve organic/organometallic and physicalchemistry, and students will learn how to fabricate and

characterisethesedevicesbycloselyworkingwithdevicephysicists.

Project3:BiomaterialsforimagingandtreatmentPhotodynamic therapy (PDT) has been developed toprovide non‐invasive (comparedwith conventionalsurgery)and less sideeffects (compared to chemotherapy) for cancer treatment.PDT canbeaccuratelytargeted, and repeatedly administeredwithout the total‐dose limitationsrelatedwith radiotherapyand result inlittle or no scarring after healing. TofacilitatetheadvantagesofPDT,wearedeveloping novel bio‐compatiblephotodynamic therapy agents fordeeper tissue treatment with lessphotodamage with effective two‐photonabsorptionactivities.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

PROFESSOR ALAN MARK Phone:0733654180Email:[emailprotected]Website:http://scmb.uq.edu.au/staff/alan-mark

Thegroupusescomputersimulationtechniquestomodelthedynamicbehaviourofbiomolecularsystemssuch as proteins, carbohydrates, nucleic acids and lipids. In addition to software and force fielddevelopment we use simulations to understand how protein and peptides assemble into functionalcomplexesandinteractwithpotentialdrugmoleculesorbiologicalmembranes.Welookforstudentswitha background in structural biology, physical chemistry, physics, pharmacology or computational scienceinterestedinworkingattheinterfacebetweendifferentdisciplines.

Projectsinclude:TheactivationofcytokinereceptorsCell surface receptors suchas thegrowthhormone receptorandthe epidermal growth factor receptor play critical roles in cellregulation.Moleculardynamicssimulationtechniqueswillbeusedtocharacterizetheconformationalchangeswithintheextracellularand transmembranedomains that accompany thebindingof thecytokine (growthhormone,erythropoietin,prolactinorepidermalgrowth factor) to its receptor thereby shedding light on themechanismofactionof cytokine receptors ingeneral. (Dr.DavidPoger)Anti‐microbialpeptidesAntimicrobial peptides (AMP) are small cationic peptides that act asmodulators of the innate immuneresponseand/ordirectanti‐infectionagents.AMPshaveattractedmuchinterestastheyhavethepotentialtoformanewclassofantibioticagentcapableofcombatingbacterialresistancetocurrentdrugs.CytolyticAMPsactbydirectlydisruptingthecellandhaveremainedeffectiveformillionsofyears.However,tobedeveloped into effective therapeutics themolecular properties that give rise to cell specificitymust beunderstood in detail. Using computer‐modelling techniques you will study the peptides in differentenvironments inorderto identify factorsthatmay further improvediscriminationbetweenbacterialandmammaliancelllines.(Dr.DavidPoger)

The group also works on a variety of otherproblems that could be undertaken as honoursprojects. These include the development of novelmethodology for computational drug design,simulating peptide folding and assembly; thenucleation and growth of amyloid fibrils; themechanismofactionofthemultidrugtransportersand the mechanism of action of glycopeptideantibiotics.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

ASSOCIATE PROFESSOR ROSS McGEARY Phone:0733653955Email:[emailprotected]

My research interests lie in the areas ofbiological/medicinal chemistry and syntheticmethodology. I hold a jointappointmentwithUQ’sSchoolofPharmacy.Severalprojectsareavailablewhicharesuitable forHonoursstudents,and these students will gain experience in synthetic organic chemistry, inhibitor design, structure elucidation,instrumentaltechniquesandbioassays,ifappropriate.Iencouragestudentstocontactmetodiscusstheseprojects.New projects are available from time to time, and additional information can be found at my website:www.scmb.uq.edu.au/academicstaff/mcgeary/index.html

DesigningNewReactionsWe have been exploring the synthetic utility of 2‐mercaptobenzothiazole 1, and we have recently developed asimple and mild method for the conversion of epoxides intoalkenes2,with retentionofstereochemistry.Previousmethodsfor achieving this transformation employed harsh reactionconditionsthatwere incompatiblewithmanyfunctionalgroups.Wearecurrentlyexaminingthescopeandlimitationsofthisnewreactionandweareinvestigatingrelatedreactionstoconvert�‐halo ketones to alkynes 3, to prepare vinyl sulfones forcycloaddition reactions 4, and to develop mild and efficientchemistryformalonate‐typeesterpreparations5.

TheRolesofSubstituentsandNewCatalystsintheClaisenRearrangementTherearrangementofallylvinylethers8togive�,�‐unsaturatedcarbonylderivatives9(theClaisenrearrangement)hasproventobeageneralandreliablewaytointroducecontiguouschiralcentresintocarbonframeworks.Assuch,theClaisen rearrangementhasbeenwidelyused in thesynthesisofcomplexnaturalproducts.Studieshaveshownthat the rate of the Claisen rearrangement can be greatly enhanced byelectron‐withdrawing substituents, such as a nitrile group at the allyliccarbon adjacent to the oxygen atom in 8. This promises to significantlyextend the scopeof this reaction.Recentwork fromour labhas revealednew methodology for performing the Claisen rearrangement, eitherthermallyorwithLewisacidcatalysts.ThisprojectwillexaminetheClaisenrearrangement of allyl vinyl ethers 8, derived from allylic alcohol orcyanohydrins.Aromaticsubstrateswillalsobeexamined.

MedicinalChemistry(1):DesignandSynthesisofInhibitorsofPurpleAcidPhosphatases(IncollaborationwithA/ProfLukeGuddatandA/ProfGarySchenk)Purpleacidphosphatase(PAP) isabinuclearmetalloenzymethatoccurs inanimals,plants,fungiandsomebacteria.The enzyme contains either an FeIII‐FeII, FeIII‐ZnII or FeIII‐MnII binuclear centre in the active site.While all of thebiologicalrolesofthePAPshaveyettobeelucidated,itisclearthat,inmammals,theyplayanimportantroleinboneresorption(osteoporosis).Inhibitionofthehumanenzymeisthereforeapromisingpossiblestrategyforthetreatmentof this disease. The crystal structures of a number of variants of this enzyme have been determined and someprogresshasbeenmadeondiscoveringthelikelymodeofactionoftheseinhibitors.Anopportunitynowexiststousethisknowledgetodesign inhibitorsandbetterunderstandthemechanismofactionoftheenzyme.Thisprojectwillinvolveorganicsynthesis,enzymeassays,computermodellinganddrugdesign.

MedicinalChemistry(2):DesignandSynthesisofInhibitorsofMetallo‐�eta‐lactamases(IncollaborationwithA/ProfGarySchenk)For details of this interdisciplinary project targeting drug resistance, see the description listed under AssociateProfessorGarySchenk.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

DR EVAN MOORE Phone:0733653862Email:[emailprotected]

OurresearchfocusesonexploitingtheuniquepropertiesoftheLanthanideseries.Thesemetalsareusedinhigh‐end technological applications, including high strengthmagnets (Nd), contrast agents formedicalimaging (Gd),and as catalytic converters for carexhaust (Ce) toname a few.Current researchprojectsrelatetothedevelopmentoforganicLn(III)complexesforapplicationsinseveralareas

1.LuminescentImagingLn(III)cationshavewellknownluminescenceproperties.Theiremissionbandsareverysharp,asaresultofthe 4f orbitals involved.Moreover, their emission ismuch longerlived (μsec to msec) when compared to organic chromophores(nsec), allowing for improved sensitivity using time gatingtechniques. In particular, we are interested in developingcomplexesof Yb(III) andNd(III),which have emission in theNearInfra‐Red (NIR) region.Thesewavelengthsallow for the improveddepth penetration of light through biological tissues, forapplicationsinNIRimaging.

2.PhotodynamicTherapyDuetotheirhighatomicmassandparamagnetism,Ln(III)cationsexertastronginfluenceontheefficiencyof intersystemcrossing(eg.excitedsinglettotripletstateconversion)fororganicmoleculesbyenhancing

spin‐orbit coupling. The long‐lived excited triplet state of organicmoleculescanactasaphotosensitiserfortripletgroundstate(3Σg)molecularoxygen,leadingtoformationofexcitedstate(1Δg)singletoxygen. This highly reactivemolecule causes significant oxidativestress and damage to cellular structures, forming the basis ofphotodynamic therapy (PDT).We are exploring the use of Ln(III)complexation as a way of influencing the properties of existingorganicphotosensitisersused forPDT,anddevelopingnew Ln(III)basedcompoundswithenhancedefficacy.

3.LanthanideFrameworksCoordination Polymers (CP’s) (or Metal Organic Frameworks –MOF’s) are crystalline materials built from repeating units of(typically) rigidorganic ligands interconnectedbymetal cations toform 1‐, 2‐, or 3‐D structures. Our research involves theconstruction of CP/MOF's utilising Ln(III) metal cations incombinationwithorganicligandssuchasaromaticN‐oxides.Weareinterested in the structural,magnetic, and luminescentpropertiesof thesematerials, together with their applications in importantindustrialprocessessuchasgassorption,separationandstorage.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

PROFESSOR PETER O’DONOGHUE Phone:0733652584Email:[emailprotected]Websites:www.scmb.uq.edu.au/pod/parasite.org.au/introduction/index.html

My research concentrates on protozoan organisms of Australia, especially those implicated in zoonoticdisease, symbiotic relationships, and contaminationofwater supplies.Honoursprojects are tailored forindividual students on the basis of their interests, anticipated career, project novelty and ‘do’‐ability.Students work on topical problems in medical, veterinary or wildlife parasitology using a range ofconventionalandcontemporarytechnologies.

SymbiogenesisinHerbivoresHerbivorousanimalsrelyonendosymbioticmicro‐organismstoaidintheirfermentativedigestion.Studiesin Australia have revealed novel ciliates and flagellates in ruminants, marsupials and insects. Manyprotozoahavealsoharboureduniquesymbioticbacteria.Thisprojectaimstoidentifythesehypersymbioticpartnersbyultrastructuralandmolecularstudies.

CoccidiosisinMammalsLittle isknownabout thecoccidianparasitesofAustraliananimals.Nativeanimalswouldbeexpected tohaveendemicparasitespecies(duetotheirlonggeographicisolation)whileintroducedanimalswouldhavecosmopolitan/exoticspecies.Thisprojectwilltestco‐evolutionarytheories.

HaematozoainWildlifeAustraliananimalsare infectedbya rangeofvector‐borneprotozoa, including trypanosomes (mammalsand reptiles), haemogregarines (reptiles), haemosporidia (mammals, birds) and piroplasms (mammals).Studies with wildlife and museum collections aim to identify these haemoprotozoa, determine theirpathogenicpotentialandinferphylogeneticrelationships.

TestateAmoebaeofAustraliaLittle information is available on the taxa of freshwater amoebae occurring in Australia despite theircontribution towaterqualitybyconsumingbacteriaandalgae.Thisprojectwillcollect testateamoebae(thosewithexternalshells)fromlocalwatersuppliesandidentifythembylightandelectronmicroscopy.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

ASSOCIATE PROFESSOR MARK RILEY Phone:0733653932Email:[emailprotected]

ThestudyoftheantiferromagnetCuB2O4

Crystalsofcoppermeta‐borate(CuB2O4)containsplanarCuIIO4speciesseparatedbyBO4tetrahedra.Itisan

antiferromagneticmaterialbelowTN=20Kandshowsanumberofremarkableproperties.Theseincludeaclaimed ability control of the crystal chirality by amagnetic field [1], the control of themagnetizationdirectionbyanelectricfieldandtheobservationofa“GiantOpticalMagneto‐electricEffect”[2].Thislattereffect results in the crystalhaving the intriguingability to transmit light inonedirection,butnot in theoppositedirection.Theproject can containeither /bothexperimental (spectroscopyand synthesis)andtheoreticalaspectsofmaterialscienceandcanbetailoredtoastudent’sparticularinterest.

TheopticalpropertiesofTanzaniteTanzaniteisaveryraregemstonethatoccursonlyina small area on the slopes ofMt Kilimanjaro. It isbased on the mineral silicate Zoisite but theblue/purple colour is thought to be due to traceamountsofV3+ ionsreplacingsomeoftheAl3+ ions[3].Oneoftheintriguingpropertiesofthegemstoneis that it has a different colourwhen viewed fromdifferentdirectionsunderpolarised light. It isalsoclaimedthatthecoloursbecomesbrighterafterahightemperature heat treatment, but the cause of this is unknown. The student would measure lowtemperaturesinglecrystalpolarisedabsorptionspectrainthevisibleandnear‐IRspectralrangeforthefirsttimeandtheaimoftheprojectistointerprettheseunusualopticalpropertiesintermofthegeometryoftheVIIIO6centres.

LuminescenceandMCDofEgyptianBlueEgyptianBlue(CaCuSi4O10)isapigmentthatwasfirstsynthesizedsome3500yearsago.The pigment is ideal for non‐invasiveinvestigation of archaeological artefacts asitshowsanintenseemissionintheinfra‐red[4].The room temperatured‐demission isvery unusual for a copper (II) compound.The project will aim to understand thereason for this very efficient emissionthroughtimeresolvedfluorescenceandlowtemperaturemagneticcirculardichroism(MCD)spectroscopicstudies.[1]Saitoetal,Phys.Rev.Lett.,2008,101,117402;[2]Saitoetal,NatureMat.,2009,8,634;[3]G.H.Faye,E.H.Nickel,Can.Mineral.1971,812;[4]G.Accorsi,etal.,Chem.Commun.,2009,3392.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

ASSOCIATE PROFESSOR JOE ROTHNAGEL Phone:0733654629Email:[emailprotected]

MolecularGenetics,CellBiologyandBioinformaticsGeneexpressionintheskinOur research is focused on the molecular mechanisms that regulate skin and hair development andepidermaldifferentiation inordertoprovidethebasicknowledgeneededfor improvingthetreatmentofinheritedandacquiredskindisorderssuchaseczema,psoriasis,cancerandwounds.Importantly,theskinservesasanimportantmodelforotherepitheliasuchasthegut,oralcavity,breastandprostatesolessonslearned in these projects are broadly applicable to other tissues.We are looking for studentswith aninterest inmolecularbiology,bioinformatics andgenetics to investigate these areas andhelpusdelivernewwaysoftreatingskinandhairdisorders.

Projectsinclude:

• Post‐transcriptionalregulationofskingenes• TheroleofGli1oncogeneSNPsinthepredispositiontoskincancers• Proteomicanalysisofhumanskin

• Characterisationofsequencevariantson1q21associatedwithhairphenotype

Youdon’thaveenoughgenesbuddy!Afteradecadeof intensivestudy,thecompletesequenceofthehumanandothermammaliangenomeshas been determined. Amazingly, the estimate of the number protein‐coding genes in human is nowthoughttobe lessthan22,000.Yetmostcellsexpressamuchhighernumberofdistinctproteinspecies.While someof thisdiscrepancy canbe accounted forby alternative transcription start sites, alternativesplicing,mRNAeditingandpost‐translationalmodifications,weproposethatourproteomeisalsoderivedfromthetranslationofsmallopenreadingframes(sORFs)presentinavarietyoftranscriptsincludingthe5'untranslated regions (5'UTRs), 3’UTRs ofmany eukaryoticmRNAs and on non‐mRNA transcripts. Thesesmallpeptides (sPEPs)mayformthebasisofahithertounknownregulatorynetwork.Theseprojectswillinvolveamixofbioinformatics,cellbiology,andproteomics.

Projectsinclude:

• IdentificationandcharacterisationofsmallproteinsencodedbysORFs(withRossSmith&AmandaNouwens)

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

DR SUSAN ROWLAND Phone:0733654615Email:[emailprotected]

Gettingthemessage–usingthemediatocommunicatescienceandthecareersofscientistsIamateaching‐focusedacademic–assuchmyresearch interestsrevolvearoundteachingand learning.Iamparticularly interested in theuseofprintand radio/podcastmedia tohelpcommunicate thesciencemessage.

FreeEnergyRadioFreeEnergyRadioisanongoingprojectwheremystudentsandIinterviewscientistsandsciencegraduatesabout their careers. There are several importantquestions to answerhere.What are thequalities thatmakeascientist?Whatfactors influencesciencecareerchoices?Howmuchreal informationdostudentsactuallyhaveaboutsciencecareers?Whatarethestudentresponsestointerviewswithscientists?Canwedefine(andchange)students’conceptionsofacareerinscience?StudentsworkingonthisprojectwillspendtimeintheJACRadiostudiotalkingwithscientistsandsciencestudents.Theywillanalysetheseinterviewsandthestudents’responsestothem.Thereisanopportunitytolearnhowtoruntheproductionsoftwareandeditaudiointerviews.

UQSURJSURJ@UQisUQ’snewScienceUndergraduateResearchJournal;thefirsteditioncameoutin2012andthesecond and third editions will appear in 2013 and 2014. The journal has a website:(https://shire.science.uq.edu.au/surj/)andFacebooksite(facebook.com/SURJ.UQ).

Iam theeditorof this journal,whichaims tohelp studentsdevelop their senseofprofessionalismasascientist, while also increasing their ability to write in the popular science genre. This is particularlyimportant, because the ability towrite for specific genres is amajor area ofweakness in new sciencegraduates. There are several questionswe can answer here aswell,most ofwhich revolve around thedevelopmentof studentwriting skills and students’ self‐authorship as scienceprofessionals and sciencecommunicators.YouwillhavetheopportunitytobeinvolvedintheproductionofUQSURJfromthepointofstudentsubmission,througheditingandcopyproduction,and finallyproduction inhard‐copyasaUQpublication.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

PROFESSOR MARK SCHEMBRI Phone:0733653306Email:[emailprotected]

The common research theme inmy laboratory is the study of surface proteins thatmediate adhesion,aggregationandbiofilm formationbybacterialpathogens.Adhesion is theprimarymechanismbywhichbacteria colonize host tissue surfaces and initiate disease.My research deals primarilywith pathogenicEscherichiacolithatcause intestinalandextra‐intestinal infections.Amajorfocus isuropathogenicE.coliwherewe study the roleofadhesinsandothersurfacecomponents in thedevelopmentofbiofilmsandcolonisation of the urinary tract. Biofilms are microbial communities characterized by cells that areirreversiblyattachedtoasubstratumorinterfaceortoeachother.Biofilmsareofimmensesignificanceinmedical,industrialandenvironmentalsettingsandthisareaofstudyhasenormousscopeandimportanceinthefieldofbacterialpathogenesis.MylaboratoryalsoinvestigatesmechanismsofadhesionandbiofilmformationbyotherpathogensincludingAcinetobacterbaumannii,KlebsiellapneumoniaeandEnterobacterspecies.

Project1:E.coliistheprimarycauseofurinarytractinfection(UTI)inthedevelopedworld.ItisestimatedthatoneinfourwomenandoneintwentymenwilldevelopaUTIintheirlifetime.TheaimofthisprojectistostudythemolecularcharacteristicsofrecentlyemergedmultidrugresistanturopathogenicE.colistrains.Theprojectwillemploy forefrontmoleculartechniques includinggenomesequenceanalysis,proteomics,mutagenesisandcloningtocharacterisemultidrugresistantstrainsanddissecttheirvirulencecapacity.

Project2:AutotransporterproteinsrepresentamajorgroupofGram‐negativebacterialsecretedproteinsthat contribute to uropathogenic E. coli mediated UTI. Autotransporter proteins possess a range ofvirulence properties such as adherence, aggregation, invasion and biofilm formation. We recentlycharacterised a novel translocation and assembly module that promotes efficient secretion ofautotransporter proteins across the outer membrane and published this in collaboration with otherresearch groups in Nature Structural & Molecular Biology. Recent genome sequencing of severaluropathogenicE. coli strainshasalso identifiedanumberofpreviouslyuncharacterisedautotransporterproteins andwe are currently trying to understand their contribution to virulence. This study aims tocharacterisesomeof thesegenesand theirproducts,study theirmodeof translocationacross theoutermembraneandevaluatetheirroleinadhesion,colonizationandbiofilmformation.

Project3:ColonizationofthebladderbyuropathogenicE.coliresultsintheformationofintracellularcellaggregatesencased inapolysaccharide‐richmatrix(ie.abiofilm).Thesestructuresenablethebacteriatocausechronic,persistentinfections.Biofilmformationonmedicalimplantssuchascathetersisalsoamajorsource of recurrent infection and resistance to antibiotics. This projectwill examine the role of severalputativevirulencefactors(includinguncharacterisedfimbrialadhesins)fromuropathogenicE.colithatareassociatedwithbiofilmformation.

Project4:Klebsiellaarefrequentcausesofnosocomialinfections;itisestimatedthattheyaccountfor8%of all hospital acquired infections in thewesternworld.Next to E. coli infection, Klebsiella is themostcommoncauseofGram‐negativesepticemiawithafatalityrateof25‐50%. Inthemajorityofbacteremiccases,thefocusof infection istheurinarytract.Thisprojectwill identifyandcharacterizenovelvirulencefactorsfromKlebsiellapneumoniae.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

ASSOCIATE PROFESSOR GARY SCHENK Phone:0733654144Email:[emailprotected]

Various Honours projects are available that focus on the study of metal‐ion containing biocatalysts(enzymes) and their application in drug design/development and bioremediation. Below the enzymesystemsand relevant referencesare listed. Theprojectsarepartofa large collaborativenetwork thatincludesseveralmembersofSCMB(Schenk,McGeary,Guddat,Gahan),andarefundedbygrantsfromtheAustralianResearchCouncil(ARC)andtheNationalHealth&MedicalResearchCouncil(NHMRC).

Metallo‐β‐lactamases(MBLs)–atargettofightantibioticresistanceTheseenzymesrequireZn2+fortheirfunctionanddegradeandthusinactivatemanyofthecommonlyusedβ‐lactam‐basedantibiotics(e.g.penicillin).Theyhaveemergedandevolvedrapidlyoverthelastcoupleofdecadesandhenceposeamajorproblemforglobalhealthcaresincetheyareamajorcauseforthespreadofantibiotic‐resistantpathogens. Inthisproject thestudent(s)will investigatethepropertiesofrecentlyidentifiedmembers of this class of enzymes and will design and synthesise potential inhibitors in anattempttocombatantibioticresistance.

Pesticide‐degradingmetallohydrolases–bioremediatorsofthefutureOrganophosphate‐basedpesticideshaverevolutionisedagriculturesinceWorldWarII.Unfortunately,themajorityofthesecompoundsarerathertoxictohumanhealthandtheiraccumulationintheenvironmentandgradual release intogroundwater leads tohundredsof thousandsofpoisoning cases (largely fatal)aroundtheglobe.Somesoil‐dwellingbacteriahaverecentlyevolvedenzymesthatcanbreakdowntheseorganophosphates into far less or non‐toxicmolecules – these bacteria use pesticides as a source forphosphate for theirmetabolism.Hence, these enzymes have great potential as bioremediators. In thisproject students will investigate how these bioremediators work and how they can be optimised forapplicationsintheenvironment(bioremediation).

Purpleacidphosphatases(PAPs)–anewcureforosteoporosis?A“side‐effect”ofourincreasinglifeexpectancyisthatmoreandmorepeoplesufferfromthebonediseaseosteoporosis.Osteoporosisiscausedbyincreasedresorptionofbone,aprocessthatisdirectlycorrelatedwith theexpressionof theenzymePAPbyosteoclasts (bone‐resorbingcells). Hence,PAPhasbecomeamajortarget inthedesignanddevelopmentofnewdrugsagainstosteoporosis. Inthisproject,studentswill design potential PAP inhibitors, assess their efficiency and investigate their interaction with theenzyme.References:[1]MitićN.,SmithS.J.,NevesA.,GuddatL.W.,GahanL.R.&SchenkG.CatalyticMechanismsofBinuclear

Metallohydrolases,Chem.Rev.2006,106:3338‐3363.

[2]SchenkG.,MitićN.,GahanL.R.,OllisD.L.,McGearyR.P.&GuddatL.W.Binuclearmetallohydrolases:complex

mechanisticstrategiesforasimplechemicalreaction,Acc.Chem.Res.2012,DOI:10.1021/ar300067g.

[3]SchenkG.,MitićN.,HansonG.R.&CombaP.PurpleAcidPhosphatase:AJourneyintotheFunctionandMechanismofaColourfulEnzyme,Coord.Chem.Rev.2012,DOI:10.1016/j.ccr.2012.03.020.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

PROFESSOR ROSS SMITH Phone:0733654627Email:[emailprotected]

BiochemistryandMolecularCellBiologyofhnRNPs

Muchofourresearchcentresonpost‐transcriptionalregulationofgeneexpression.Oneofourmajor interests is inthe cellbiologyofRNA trafficking. ManymRNAmolecules are targeted todiscrete locations in cells aspartof amechanism for localising theproteins theyencode. This isespecially evident inoocytesandembryoswhereRNAlocalisationplaysamajorroleintheestablishmentofcellularasymmetryandorganismaldevelopment,butitisalsoimportantinmaturesomaticcells,includingmanybraincells.Ourprincipalfocusisonthemolecularandcellbiologyoftheheterogeneousnuclearribonucleoprotein(hnRNP)A/Bfamilyofproteinmolecules.Wehave identified twohighlyabundant, largelynuclearproteins,hnRNPsA2andA3,whichbindRNAsbearingaspecialtransportsequence(a"zipcode"calledA2RE)intheir3'UTR.Theyaremembersofa*groupofmulti‐taskingproteins,thehnRNPs,thatareessentialfortheformationandtraffickingofmRNAmoleculesintransport particles (“granules”). But there ismore to it than that! In the nucleus they participate in such diverseprocessesasRNApackaging,telomeremaintenance,alternativemRNAsplicing,andRNAexport.Theseproteinsaretruly multi‐functional and they play major roles in alternative splicing of pre‐mRNA, and the formation andmaintenanceoftelomeres,twofunctionsthatarecloselylinkedtocancer.

RNATrafficking,Memory,andMentalRetardation(withJoeRothnagel)SomemRNAsinneuronsarepackagedintogranules,whicharethentransportedalongmicrotubuleswithindendritestodendriticspines.WhentheyarebeingtransportedthesemRNAsaretranslationallysuppressed:onreachingtheirdestination they are activated, translating the protein they encode localized within the dendrites.Many of theproteins that are transported in this fashion are components of the post‐synaptic density and are thought to beinvolved inmemory formation in thehippocampus.One componentcommon tomanygranules isaprotein calledFragileXmentalretardationprotein(FMRP),whichregulatestheothermRNAsthatarepresentintraffickinggranulesandpossesssmallelementsthatmarkthemfordendritictrafficking.PhosphorylationofFMRPresultsinactivationoftranslationofthemRNAsencodingaCaMKII,Arc,NG,PKMz,MAP2,MAP1BandFMRP’sownmRNA.Theseproteinsbecomecomponentsofthepostsynapticdensityinresponsetosynapticactivation.The oncogenic protein, fyn, a tyrosine kinase, activates FMRP,A2 and other postsynaptic proteins, including TOG(Tumour over‐expressed gene). Of particular significance, the phosphorylation of FMRP activates ARC RNA andtherebymediatestheendocytosisofAMPAreceptors,whichareneededformemoryformation.KnockingoutTOGinmiceresultsinbehaviouralchangesthatmimicautisminhumans.TheprincipalaiminthisprojectistoimproveourunderstandingofthemolecularmechanismofmRNAtraffickingandthepartitplaysinmentalretardation,Alzheimer’sDisease,andothermentalconditions.

TelomeresandCancer(withJoeRothnagel)Telomeresare involved in thecarcinogenic transformationofcells.They formstructures inwhich repetitivedsDNAandssDNA isusedtocaptheendsofchromosomes,enablingcellstoundergorepeateddivisionwithout lossoftheremaining,non‐repetitive,genomicDNA.Tumourcellsaredistinguished fromsomaticcellsbyhavingcomparativelylongtelomeresthataremaintainedprimarilybytheenzymetelomeraseor,insome(ALT)celltypes,byrecombinationpathways.ProfessorElizabethBlackburn(fromTasmania)shareda2009Nobelforherdiscoveryoftelomerase.hnRNPsassociatewithtelomericssDNAandtelomere‐associatedproteins.Theymayregulatetelomerelengthandcellproliferation, thereby playing a critical role in the growth ofmany cancers.We, and others, have demonstratedinteractionsbetweenasubfamilyoftheseproteins,theA/BhnRNPs,repeattelomericssDNA,andtheRNAsubunitoftelomerase(hTR).The overarching hypothesis in this project is that the A/B hnRNP protein family has a major role in telomeremaintenanceandhence incarcinogenesis.Wewish todescribe,at themolecular level, themechanism thatallowstumourcellstomaintaintelomerelengthandavoidenteringsenescence,andtherolesplayedbythehnRNPsinthisprocess.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

DR KATE STACEY Phone:0733462072Email:[emailprotected]

RecognitionofCytosolicDNAasaDangerSignal

TheDNAofeukaryoticcells iscontainedwithinamembrane‐boundnucleus,andtheappearanceofDNAwithinthecytosolindicatesadangertothecell.CytosolicDNAcanresultfromviralandbacterialinfectionsortheactivityofendogenousretroviruseswithinthehumangenome.ResponsestocytosolicDNA includeproduction of the anti‐viral protein interferon‐�, and cell death.We identified AIM2 as a receptor forcytoplasmicDNA eliciting celldeath.AIM2 initiates formation of an “inflammasome”which is aproteincomplexleadingtoactivationoftheproteasecaspase‐1andlyticcelldeath.WehaverecentlyshownthatAIM2 recognition of DNA also recruits and activates caspase‐8, which leads to the death of cells byapoptosis.AlthoughtheAIM2pathwayisonlyfoundinmammals,wefindthatchickenandinsectcellscanalso die after introduction of DNA into the cytosol. Consequently we propose that defences againstinvadingDNAareessential fordefendingagainst infectionsandguarding thegenomeofallmulticellularorganisms.

Futurestudieswillfocuson:‐1)CharacterisationoftheroleofDNAdetectionincombattingviralinfections2)DefinitionofpathwaysofrecognitionofforeignDNAinnon‐mammals3)CharacterisationoftheinflammasomecomplexinducedbyAIM2,andnoveldeath‐domaininteractions

involvedinrecruitmentofprocaspase‐84)InvestigationoftheroleofAIM2(absentinmelanoma2)asatumoursuppressor

InflammasomeDeficiencyinAutoimmuneDiseaseThehumanautoimmunediseaselupusinvolvesformationofantibodiesagainstselfmoleculesandtheirdepositionasimmunecomplexesintissues.InflammasomesleadnotonlytocelldeathbutalsotoreleaseoftheinflammatorycytokineIL‐1b.Althoughmostresearchershaveassumedthatinflammasomepathwayswillbeelevatedinautoimmunity,wefindtheopposite;inamousemodeloflupusthereisprofounddeficiencyofthreedifferenttypesofinflammasomestructures.Weproposethisleadstoanalteredresponsetocommensalorganismsandpoorclearanceofpathogens,andpromotesautoimmunity.Projectswillinclude:

1)Establishingthemolecularbasisforinflammasomedeficiencyinthemouse2)InvestigatingwhetherhumanlupuspatientshaveinflammasomedeficiencyRelevantPublication:Roberts,T.L.,Idris,A.,Dunn,J.A.,Kelly,G.M.,Burnton,C.M.,Hodgson,S.,Hardy,L.L.,Garceau,V.,Sweet,M.J.,Ross,I.L.,Hume,D.A.,Stacey,K.J.(2009)HIN‐200proteinsregulatecaspaseactivationinresponsetoforeigncytoplasmicDNA.Science323:1057‐1060.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

PROFESSOR ISTVAN TOTH Phone:0733469892Email:[emailprotected]Website:http://staff.scmb.uq.edu.au/staff/istvan‐toth

OraldeliveryfornextgenerationvaccinesVaccination is one of themost effective public health strategies ever undertaken.Instead ofwhole killed pathogens, next generation vaccines use pathogen‐derivedpeptides, allowing fine control when tailoring the vaccine. This project aims toemployanovel carrier systemusing lipoaminoacids (LAA) tovaccines that canbedelivered orally. Preliminary experiments with a limited number of LAA havedemonstrated theirability to form vesicles aloneor in thepresenceof cholesterol(unpublishedobservations)thatcanactasoralantigens.Itisanticipatedthatvesiclesize,stability,drug loading,permeability, lipophilicity,antigenicity, invivobehaviour,etc.willdependonthe LAA composition of the liposomes. Project aims: to extend the existing liposomal technology bydeveloping novel vesicular drugdelivery systems inwhich vaccine, adjuvant, and particulate carrier arecontainedinasinglemolecularentity.

ANovelSystemforPeptideDeliveryDrugswithpoororalabsorptionprofilescanbedeliveredinastableformwhenconjugatedtoacarrier.Ourlipoaminoacid (LAA)or lipopeptide (LP)based carrier systemshavebeenused to improve the systemicbioavailability of anti‐inflammatory alkaloids, analgesics, GABA, antimicrobials, and several anti‐canceragents.ThisprojectaimstoapplytheexistingcarriersystemtothedeliveryofLHRH,a10aminoacidlongpeptidehormone.Projectaims:1)thechemicalsynthesisofLAA librariesandaseriesofdeliverysystem‐LHRH conjugateswithdifferent linkages,2) in vitrobiological stability studies,3)uptake studies, and4)biologicalactivityassessment.

GeneDeliverySystemsGenedeliverytechnologyislimitedbypoorabsorption/uptake,tissuetargeting,genereleaseafteruptake,andrapidenzymaticbreakdown.Thisprojectwilladdressthesemajorissuesthroughanovelstrategyinvolvingionpairformationoflipophilicdendrimerconstructswithanantisenseoligonucleotidesequence(ODN).Anestablishedanimalmodelofchorroidalneovascularisation(CNV)willbeusedtotestthenewdendrimer/ODN1complexes.Projectaims:1)Producenewdendrimer‐oligonucleotide(ODN1)complexes.2)Testthebiologicalstabilityandpermeabilityofthesedendrimercomplexes.3)DeterminetheoptimalratioofthedeliverysystemandtheantisenseDNAusingisothermalmicro‐calorimetry.4)Testtheuptakeandbiologicalactivityofdendrimercomplexesinretinalcells,andselectthemosteffectivecomplexforinvivostudies.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

PROFESSOR MARK WALKER Phone:0733461623Email:[emailprotected]

My lab focuses on themechanism bywhich the group A streptococcus (Streptococcus pyogenes;GAS)causes invasive disease andGAS vaccine development. S. pyogenes is the etiologic agent of numeroussuppurative diseases, ranging frommild skin infections such as pharyngitis, scarlet fever, impetigo andcellulitis, to severe invasive diseases such as septicemia, streptococcal toxic shock syndrome andnecrotizing fasciitis. GAS is placed within the "top 10" infectious disease causes of human deathsworldwide.IndigenousAustralianssufferthehighestratesofafflictionwithGASdiseasesintheWorld.Ofthe over 100M serotypes, theM1T1 clone that emerged in themid‐1980s and disseminated globally,causesmost deaths andmorbidity.Our research projects are undertaken on a collaborative basiswithcolleaguesat theUniversityofQueensland,QIMR,UTS,GriffithU.,U.Adelaide,NotreDameU.,GermanNationalCentreforBiotechnology,U.Cambridge,U.CincinattiandUCSD.

Researchprojects:(1) Role of bacteriophage inGAS evolution: Recent genomic and pathogenesis studies have implicatedbacteriophage determinants as important contributors to GAS virulence. In this project, we will usegenomics to characterize the steps involved inGASevolution and investigate the contributionofphagevirulencedeterminantstothediseaseprocess.(2)ThemechanismofGASinvasivediseaseinitiationandtheroleofhumanplasminogenasaGASvirulencedeterminant: Recent investigations have highlighted the hijacking of human protease plasmin by GAS,whichcontributestodisseminationandinvasivedisease.ThisprojectwillcontinueoureffortstoelucidatethemechanismbywhichGAScauseinvasiveinfections.(3)The interactionofGASwithhumanepithelial cellsand innate immunity:Wehavebegun the taskofdetailed charcterisation of the interaction of GAS with the host epithelial surface and innate immunedefensemechanisms.Thisprojectwillexaminetheroleofhostandpathogen factors inthecolonization,establishmentandclearanceofGASinthehumanhost.(4)GASantigenidentificationandvaccinedevelopment:AsafeandefficaciouscommercialGASvaccinehasyet to be developed. In this project, we are characterizing new surface proteins and examining theirpotentialasGASvaccinecandidates.Groupresearchstaff(involvedinhonoursstudentsupport):NHMRCoverseastrainingFellows:JasonCole,MarkDavies,AndrewHollands;PostdoctoralFellows:TimBarnett,AmandaCork,ChristineGillen,CherylOng.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

DR JACK WANG

Phone:0733469490Email:[emailprotected]

ResearchintoScienceEducationIamaTeaching‐focusedacademic inMicrobiology,andmyresearchrevolvesaround innovativeteachingand learning strategies in Science Education. This type of research is not associated with extensivelaboratorywork,andthereforewillnotprepareyouforacareerasalaboratoryscientist.Itinsteadreliesupon interactingwith largenetworksofpeople–namely thestudents,academics,andadministrators inHigherEducation–toextracttrendsandpatterns intheir ideasregardingteachingand learning. Youwillgainexperienceindesigningandanalysingsurveys,conductingfocusgroupinterviews,preparingvideoandmultimediacontent,interpretingbothquantitativeandqualitativedata,andcommunicatingwithadiverserangeofstakeholdersinScienceEducation.Theseprojectsmaybeusefulforyouifyouareinterestedincareersineducationaldevelopmentandlearningdesigninbothpublicandprivatesectors:

1.Mappingactive‐learningstrategiesacrosslargeundergraduatescienceclassesTeachingandlearningsciencewithinthelargeundergraduateclassroomcanbedauntingforstudentsandacademicsalike.Complexscientificconceptsareconveyedtohundredsofstudentsatthesametime,anditcanbedifficulttoengagethecohort’sinterestandattentionthroughoutthesemester.Thisprojectwillaim to produce a set of case‐study‐driven guidelines for instructors teaching into large undergraduatesciencecourses. Itwillbuild fromexistingbest‐practiceguidelines foreffectiveactive‐learningstrategies,and continue to document and evaluate examples of engaging in‐class activities used in large sciencecourses acrossQueensland universities. Youwill attend a variety of large science classes, collate andinterpretteachingevaluationscores,andsurveyandinterviewlargenumbersofstudentsandacademicsinordertodetermineandevaluatetheeffectivenessofactive‐learningwithineacheducationalcontext.

2.MeasuringtheimpactofauthenticresearchexperiencesthroughoutScienceEducationInordertobetterpreparestudentsforacareerinscientificresearch,authenticresearchexperienceshavebeen increasinglyembeddedacrossall levelsofundergraduate scienceprograms. Thisprojectaims toevaluatethecumulative impactoftheseexperiencesonstudents interested inscientificresearchcareers.The projectmethodology will involve surveying and interviewing students at different stages of theirresearchtraining,andattempttocorrelatetheirconfidenceandcompetenceinkeyresearchskillstotheirprevious experiences in authentic research. Using this data, we will aim to establish which types ofexposuretoauthenticresearchbestpreparestudentsforfutureresearchtraininginthesciences,aswellashowresearchhigherdegreestudentscanbebettersupportedintheirstudies.Keyreferences:Wang, J.T.H.etal., (2013). Howmuch is toomuchassessment? Insight intoAssessment‐driven studentlearning gains in large‐scale undergraduatemicrobiology courses. Journal ofMicrobiology and BiologyEducation,14(1):12‐24.(http://jmbe.asm.org/index.php/jmbe/article/view/449)Wang,J.T.H.etal.,(2012).Immersingundergraduatestudentsintheresearchexperience.BiochemistryandMolecularBiologyEducation40(1):37‐45(http://onlinelibrary.wiley.com/doi/10.1002/bmb.20572/abstract)

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

ASSOCIATE PROFESSOR LEIGH WARD Phone:0733654633Email:[emailprotected]

MedicalandMetabolicBiochemistryHonoursprojectswhichareavailableintheaboveareasareasfollows:

NutritionalBiochemistry–Omega3fattyacidsandcardioprotectionThisproject is inassociationwithProfLindsayBrownUniversityofSouthernQueensland.ThisprojectwillrequirethestudenttoworkperiodicallyatUSQ,Toowoomba.Our recent studies have characterised the cardiovascular changes in high fat, high carbohydrate diet‐induced obesity in rats, showing that these changes can be prevented or reversed by dietaryinterventions such as olive leaf extract and omega‐3 fatty acid (α‐linolenic acid)‐rich chia seedsupplementation.Thisprojectwillextendthesestudiestodeterminethepossiblebeneficialcardiovascularresponses following addition of omega‐3 fatty acids from other sources including deep sea algae(docosahexaenoic acid (DHA)‐rich), fish oil (eicosapentaenoic acid (EPA)‐rich) and flax seed (alternatesourceofα‐linolenicacid)tothisdiet,togetherwithfatredistribution.SeePoudyalHetal.(2012)Chronichigh‐carbohydrate,high‐fatfeedinginratsinducesreversiblemetabolic,cardiovascular,andliverchanges.AmJPhysiolEndocrinolMetab.302:E1472‐1482.

Medical technology – Development of bioelectrical impedance technology for the early detection of

lymphoedemaBioelectrical impedance analysis is a non‐invasive technique for the measurement of the electricalpropertiesofthetissuesandthewholebodythatmayberelatedtoitscomposition.Oneapplicationistheassessmentoffluidaccumulationintissuesthatoccursinbreastcancer‐relatedlymphoedema.Thisprojectwillcontinuedevelopmentofanimpedanceprobeforthedetectionandquantificationoflymphoedema.ItwillaimtovalidatethisnoveltechnologyagainstotherassessmenttoolssuchasMRI,pQCTandDXA.See Ward LC, et al. (2008) Bioelectrical impedance analysis for early detection of lymphoedema. InLymphedemaDiagnosisandTherapyEdsH.WeisslederandCSchuchhardt,Chap15.p502‐517,ViavitalVerlagGmbhPubl.,Essen.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

DR NICK WEST Phone:0733654093Email:[emailprotected]

TuberculosisMycobacterium tuberculosis is the single most important bacterial pathogen of humans, killingapproximately4,000peopleeachday.DespiteaconcertedinternationalefforttoreducetheglobalhealthburdenofTB,morepeoplethaneverbefore,withapprox.1in3,areinfectedwithM.tuberculosis.TBisahighly contagious, disease transmitted by inhalation of aerosol droplets generated from an infectedindividual.TBwasdeclaredaworldhealthemergencyin1993andremainssotoday.

“ThespreadofdrugresistantTBthreatenstodestabilisetheglobal initiativesofTBcontrol.Moreeffectiveanti‐TBdrugsareurgentlyneeded”

Ourresearchiscenteredonthebacteriumandthemechanismsitemploystocausedisease.Overthepastfewyearswehavebeendefining thegenetic repertoire requiredby thebacterium tocolonise thehost,spreadaroundthebodyandtopersist inastateof latency.Wehavecompiledavaluable listofessentialgenesutilizedfortheseprocessesfromwhichwecannowbegintoidentifypotentialnewdrugtargets.

Twoprojectswillbeofferedinthelaboratoryin2013:

1. Essential gene regulation in mycobacteria. Our genetic screening identified a series oftranscriptional regulatorsessential to survivalof thebacterium in vivo. In thisprojectyouwill clone,expressandpurify twonovel regulators.Mutantsof thesegeneswillbeproduced inMycobacteriumsmegm*tis,andavirulentfastgrowingmycobacteria.Inordertodefinetheroleoftheseregulatorstheinfluenceofthesemutationswillbeassessedbytranscriptomicanalysis.TheDNAbindingsiteswillbedeterminedandapreliminaryinhibitorydrugscreenconducted.Skills and Techniques:Variousmicrobiological techniques, PCR andmolecular analysis.Gene cloningand proteomics. DNA binding assays and small molecule inhibition, macrophage cell culture andmycobacterialinfectionmayalsobeperformed.

2. Characterisation of proteins essential for survival in the host.We have identified a series ofbacterialfactorswhicharedispensableforgrowth in laboratorymediabutwhichare in‐dispensable inthehost.Thisprojectwilldefinetheroleofthreeoftheseessentialvirulencedeterminantsbymodernmolecularandproteomicapproaches.Additionallytheseproteinswillbetrialedasvaccinecandidates,establishingtheirImmunogenicityandprotectiveefficacy.SkillsandTechniques:Variousmicrobiologicaltechniques.Genecloningandsitedirectedmutagenesis.Proteinand/orDNAvaccinations. Immunologicalassays includingELIspotandELISA.Macrophage cellcultureandmycobacterialinfection.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

ASSOCIATE PROFESSOR CRAIG WILLIAMS Phone:0733653530Email:[emailprotected]

Naturalproducttotalsynthesis,isolationandassociatedmedicinalchemistry.

DrugDesignandDevelopment

Greenchemistry

Anti‐cancer, neurodegenerative disease and insect active limonoids: [in collaboration with Dr PaulSavage(CSIRO),Prof.PeterDodd(SCMB.UQ)andA/Prof.GimmeWalter(SBS,UQ)].Recentlyweachievedthe total syntheses of a number of the limonoid familymembers, such as, Khayasin 1 and Cipadonoid B 2. Thesynthesisedlimonoids1and2arecloselyrelatedtoGedunin3,anotherlimonoidfamilymember,whichdisplaysanti‐cancerandneurodegenerativediseaseactivityinHeatShockprotein90(Hsp90)models.Wewould now like to investigate the totalsynthesis of gedunin 3,which has yet to bereported,andexplorethegedunin3structureagainstHsp90usingstateoftheartmedicinalchemistrytechniques.

CubaneChemistry:ABenzeneRingDrugIsostere?[incollaborationwithDrPaulSavage(CSIRO)andProf.JamesDeVoss(SCMB,UQ)].Cubane4,whenviewedfromthecorners(i.e.5)canbeconsideredroughlythesamesizeasabenzenering(i.e.6).Thisisequallytruewhenyoutake intoconsiderationthe�cloudsofbenzene,thatis,cubane4 isabout thesame"thickness".Therefore the1,2‐1,3‐and1,4‐substitutedcubanesaresimilar toortho‐,meta‐,andpara‐substitutedbenzenesrespectively.Furthermore,thecubanestructure isactually very stable– cubane ring‐opening is thermallydisallowedbyorbital symmetry.With this inmind theprojectwould involve replacing thephenyl ring ina currentdrugmoleculeandcomparingbioloicalassaydata.Itwouldalsobeexpectedthatcubane4hascompletely different P450metabolism profiles,whichwill be explored in collaborationwithProf.JamesDeVoss.

Discovery and Development of Novel Analgesics [in collaboration with Prof.Maree Smith from theCentre for Integrated Preclinical Drug Development (CIPDD)/TetraQ)]: The prevalence of painful diabeticneuropathy(PDN)is7%withinayearofdiagnosisofdiabetesand50%by25yrsofdiabetes.Themedicinescurrentlyused to treat PDN are not effective in less than 50% of patients. Hence,we propose to develop new, effectivemedicinesforthealleviationofPDNbyinvestigatingthebiology(Smithlab)ofunusualheterocycles(Williamslab)thatdelivertheneurotransmittermoleculeNO(nitricoxide).

Green Chemistry [in collaborationwith Prof. Ian Gentle (SCMB,UQ)].Organic reactionsarekey tonewmolecules thatare inever‐increasingdemandfor applications in thepharmaceutical,materialsand agrichemical sectors.Thisdemand,however,placesgrowingpressureonsyntheticchemiststolimitoreveneradicateenvironmentallyunfriendlychemicalwasteproduction.Steps towardssuchmeasuresarenowcommonlytermed"GreenChemistry".Projectslookingatdeveloping new solvents and new surfactants are available. Applying physicaltechniques [e.g. small angle scattering (SAXS), neutron scattering (SANS) anddynamic lightscattering(DLS)]tounderstandmacromolecularmechanisms isanimportantpartofthework.

A/Prof.Williams(ARCFutureFellow)hehasheldpastandpresentmultimilliondollarindustryresearchcontractsinadditiontoARCandNHMRCgrants.Furtherprojectsareavailableonrequest.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

DR SIMON WORRALL Phone:0733654626Email:[emailprotected]

MechanismsofDrug‐InducedTissueInjuryLiver,muscle,heartandbraininjuryhavelongbeenassociatedwiththeabuseandclinicaluseofdrugs.My research interests focus on ethanol, perhaps themost commonly abused drug. Ethanol is widelytoleratedbut inducestissue injury inasmallnumberof individuals.Thepotentialresearchprojects listedbelowwillinvestigateimmunologicalandgeneticphenomenaassociatedwithalcohol‐inducedtissueinjury.

Thepotentialprojectsavailableare:1. Studieson theaetiologyofethanol‐ induced tissue injury to liver, skeletal and cardiacmuscle, and

brain?2. Isproteinmodificationbyethanolmetabolitesinvolvedintheaetiologyof:

a. Alcoholicliverdisease?b. Alcoholicskeletalandcardiacmyopathy?c. Alcoholicbraininjury(withPeterDodd)?

3. Novelproteinmodificationsinducedbyethanolmetabolism(withCraigWilliams,chemistry)4. DiscoveryofmolecularmarkersfortheseverityofAlzheimer’sdisease.

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ExpressionofGFP‐taggedhumankeratin18inaprimaryrathepatocyte.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAcademicStaff

PROFESSOR PAUL YOUNG Phone:0733654646Email:[emailprotected]

VIROLOGYUNIT

AntiviralTargetsofDengueandWestNileVirusesWehavebeeninvestigatingthreeseparateproteinsthatareencodedbydengueandWestNilevirusesastargetsforantiviraldrugdesign.ThesearethevirionsurfaceproteinE,whichmediatesviralfusionwiththecellularmembrane,theviralproteaseNS3,whoseactivityiscrucialtothecleavageoftheviralpolyproteinprecursorandNS1,akeyplayer inviralRNA replication. Inorder togainaclearerunderstandingof themolecularbasisofthekeyfunctionalactivitiesoftheseproteins,aseriesofprojectsareavailablethatusesite‐directedmutagenesisof recombinantproteins asone approach to investigate the role that specificresiduesanddomainsintheseproteinsmayplayintheirrespectiveactivities.

KoalaRetrovirusasaModelforCancerInductionWehaverecentlyidentifiedadirectassociationbetweenhighbloodlevelsofaretrovirusofkoalasandtheincidenceofcancer in this iconic species.Furthermore,wehave shown that thisvirus isanendogenouselement in the koala genome. Projects are available thatwill investigate the location of the retroviralinsertions in the koala genome, the methylation status of these insertions and their transcriptionalactivation.

ConstrainedAlphaHelicalPeptidomimeticsasInhibitorsofViralFusionRespiratorysyncytialvirusisthemostimportantrespiratorypathogenofyoungchildren,howevertherearefewdiseasecontroloptionscurrentlyavailable.WehaveidentifiedakeydomainwithintheRSVFproteinthatappearstoplayapivotalroleintheprocessofviralfusionwiththeoutercellmembrane.Thisdomaincomprisespartofanextendedamphipathicalphahelix.IncollaborationwithProfessorDavidFairlieoftheIMBweareinvestigatingthepossiblyofstructurallyconstrainingshortpeptidemimicsofthisdomainandtestingtheirpotentialasinhibitorsoffusionactivity.Thisprojectwillentailpeptidesynthesis,recombinantproteinexpressionandcellculturebasedstudies.

SCMB ACADEMIC STAFF WITH JOINT APPOINTMENTS

PROFESSOR DEBRA BERNHARDT SCMBandAIBNGroupLeaderPhone:0733463939Email:[emailprotected]Website:www.aibn.uq.edu.au/debra‐bernhardt

Mygroupresearchgroupisinterestedinthestudyofmatterusingtheoreticalandcomputationalmethodsthatcanultimatelybeusedtoaddressawiderangeofpracticalproblems.Applicationsofinterestincludetransport in nanopores, fluctuations in nanoscale systems, melting, solubility, separation of gases,lubrication,designof ionic liquids,designandassessmentofmaterialsforenergyconversionandstorage,carbondioxidesequestrationandcatalysis. Ourgrouphasworld leadingexpertise invarious theoreticaland computationalmethods ranging fromquantum chemical calculations to the statisticalmechanicsofnonequilibrium systems, access to high performance computing facilities and an international team ofcollaborators.

Possibleprojectsinclude:

TransportinnanoporoussystemsNanoporoussolidsareusedasadsorbentsinpollutioncontrol,industrialseparations,storageoffluidsandcatalysis. Simulations can be used to assist in the design of bettermaterials, and to understand thefundamentalnatureoftheadsorptionandtransportprocesses.Oneofthekeyfactorsdeterminingflowoffluidsthroughnanoporesistheirstickorslipbehaviournearthewalls.Wehaverecentlydevelopedanewapproachforstudyingthisbehaviourthatshouldbemoreefficientforcomplexsystems.

ComputationalstudiesofionicliquidsIonic liquidshaveexceptional solvationpropertiesandelectricalconductivity,meaning theyhaveawiderangeofindustrialapplications.Bycombiningdifferentions,ionicliquidscanbedesignedtooptimizetheirproperties. However, the science of ionic liquids is new and therefore prediction of their properties isproblematic.Toaddressthis,wearetakingadvantageofrecentdevelopmentsinnonequilibriumstatisticalmechanicstocreateefficientalgorithmstodeterminekeypropertiesofionicliquids.

StatisticalmechanicsofnonequilibriumfluidsAnysystemthatisflowing,stirred,hasatemperaturegradientacrossitorissubjecttoanexternalfieldisinanonequilibriumstate. Thepropertiesofthesesystemsarenotwelldevelopedwhenthesystemsarefar from equilibrium. In this project theory and computationalmethods will be used to expand ourfundamentalunderstandingofthesesystems.

QuantummechanicsforthedesignofnewmaterialsNewmaterialsare required for solarenergyapplications, catalysis,adsorbents forpollutants, storageoffuels,newpolymers, fuel cellsetc.Quantummechanicsenables thepropertiesof thesematerials tobepredictedinanefficientandcosteffectivemanner.Projectsareavailablethatwillfocusonthepredictionof material properties using a range of computational quantum chemical methods.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBStaffwithJointAppointments

DR GRAHAM LEGGATT Phone:0731765937Email:[emailprotected]

Mylaboratorystudiestheimmuneresponsetonon‐melanomaskincancers.

Projectsinclude:

(1)Tcell‐‐‐basedimmunotherapyofskincancerafterlymphodepletion.(2)TheroleofIFN‐‐‐ginsuppressingimmuneresponsestoskinprecancers.(3)Mechanismsoflymphocytetraffickingtoskinprecancers.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBStaffwithJointAppointments

PROFESSOR MICHAEL MONTEIRO Phone:0733466164Email:[emailprotected]

LivingPolymersPolymers made by living radical polymerization have well‐defined chain length and architecture. Thestructuresthatcanbesynthesisedareblock,star,branched,gradientandevendendrimer.Theadvantageof such a technique is the wide range of functional monomers that can be incorporated in thesearchitectures, allowing materials from biomedical applications to coatings to electronic devices to beprepared.

NanostructuresforDrugDeliveryThe aim of the project is to synthesis the next generation of nanostructures built from linear polymerchains.TheprojectwillattempttomakeawiderangeofarchitecturesthatarecurrentlyunavailableandincollaborationwithCellBiologistsusetheseasvehiclesfordrugandvaccinedeliverydevices.(ARCDicoverygranted2009)

‘Smart’NanoreactorsforEnvironmentallyFriendlyOrganicandPolymerReactionsNanoreactors provide the ideal setting where selected chemical reactions can take place with highefficiency incontrolledenvironments.Theaimof thisproject is touse these ‘smart’nanoreactors in thesynthesisofmoleculesandmacromoleculeswithhighchemicalselectivityandrapidly.Thisopensamethodforthesynthesisofnewcompoundsandpolymerspreviouslyunaccessibly.(ARCDicoverygranted2009)

SmartNanostructuresforDrugDeliveryThe aim of this project is to synthesis polymers with complex architectures on the nanoscale in anenvironmentally friendlymedium,water.Once thesewell‐definednanostructureshavebeenmade theirstructure‐property relationship will be evaluated using structural characterization techniques such aselectronmicroscopyforsizeandmorphology,andwillbefunctionalisedforuseasdrugandgenedeliverydevices.

NanopolymerCompositesPreparedinWaterThe aim of this project is to synthesis polymers with complex architectures (as shown above) on thenanoscale inanenvironmentally friendlymedium,water.Thesynthesiswill involveusingawiderangeofLivingradicalpolymerizationstowardsadeepermechanisticunderstandingofthereactionpathways.Oncethesewell‐definednanostructureshavebeenmadetheirstructure‐propertyrelationshipwillbeevaluatedusingstructuralcharacterizationtechniquessuchaselectronmicroscopyforsizeandmorphology,andwillbefunctionalisedforuseasdrugandgenedeliverydevices.

MechanismsinLivingRadicalPolymerizationUnderstandingthemechanismsinlivingradicalpolymerizationallowsforbetterdesignofthelivingagentsandtheoptimaluseof livingpolymerizations. Theprojectwill involvethedeterminationofthe initiationmechanisms involved in Atom Radical Transfer and Reversible Addition‐Fragmentation chain Transferpolymerizations. Thiswill enable us to determine the dominantmechanisms andwhat factors controladdition,fragmentationandtransferreactionsfortheselivingprocesses.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBStaffwithJointAppointments

PROFESSOR MATT TRAU DeputyDirector(AIBN)Phone:0733464173Email:[emailprotected]Website:www.aibn.uq.edu.au/matt‐trau

Our Centre for Biomarker Research and Development is located in the Australian Institute forBioengineering andNanotechnology (AIBN) and has access to state‐of‐the‐art chemistry synthesis, andcharacterisation facilities.Studentsworking in theCentrewillhave theopportunity tocreatenanoscaledbiosensors for applications in cancer, infectiousdisease and point‐of‐caredevices. Studentswill alsobegiventheopportunitytoworkwithleadinggeneticists,epigeneticistsandclinicalresearcherstotestthesedevices inclinicalsettings.TheCentrehasafocusondevelopingdiagnosticdevicesforearlydetectionofdiseasessuchascancer,when it ismost responsive to treatmentwhichalsoprovides thegreatestsocialandeconomicbenefitstosociety.Nanotechnologyoffersthepromiseofminiaturized,inexpensive,flexibleandrobust“plug‐and‐play”molecularreadingsystemswhichcanbeeffectivelydeployedtodetectdiseasesinaclinicalsetting.Currentprojectsavailableinclude:

1)MicrofluidicDevicesforCapturingRareCirculatingTumourCellsTheprogressionofcancer inpatients ischaracterizedbycells that invade locallyand travel through thebloodstreamtometastasizeintheotherpartsofthebody.Thesecells,accountfor1orfewercellsin106bloodcellsandareknownascirculating tumourcells (CTCs).Developmentofadvanced technologies forcapturingCTCs in blood in the early stage of themetastasis processwould transform the treatmentofcancer.ThisprojectstrivestobuildandtestamicrofluidicdevicetoenableselectivecaptureanddetectionofCTCsusingthree‐dimensionalmicrostructuredelectrodeswithinthedevice.

2)Nanodevices/NanobiosensorsforCancerBiomarkerProteinsDetectinglowconcentrationsbiomarkersinserumispotentiallyusefulforthediagnosisandprognosisofadisease.Thedevelopmentofadetectionmethodthatisrapidandcheapcouldrevolutionizethetreatmentofdiseases suchas cancer. In thisproject,weaim to fabricatenanobiosensorswithnanostructured3D‐electrodes todetectsingleproteinmolecules inblood.Studentswillachievehandsonexperience in thedesign,fabricationandapplicationofthemicrofluidicdevicesandelectrochemicalmicro(nano)biosensors.

3)DNANanomachineryforEarlyBreastCancerDetectionSubsetsofnon‐coding(nc)RNAsserveaspotentialbiomarkersofdiseases.Thisprojectinvolvesdesigning,developingandevaluatingnovelDNAnanomachinerytoperformtasksthatarecurrentlybeyondthereachof existingmolecular readout technologies.We aim to use these nanomachines as a new technologyplatform to rapidlydetectncRNAbiomarkers inbreast cancerpatients.This interdisciplinaryprojectwillprovide an opportunity for students to acquire diverse skills in chemistry, molecular biology andbioengineering.

4)Point‐of‐CareDiagnosticsPoint‐of‐care(POC)diagnosticshavethepotentialtorevolutioniseglobalhealthcarebyenablingdiseasestoberapidlydiagnosed‘onthespot’usingminimalspecialisedinfrastructure.POCdevicesneedtobehighlysensitive,specific,practical,costeffectiveandportableiftheyaretobeusedinresourcelimitedsettings.WearefocusedonnovelandsimplemolecularassaystogeneratenewPOCdiagnostictechnologies.Studentswillbeinvolvedindesigning,developingandevaluatingmethodstorapidlydetectpathogenicDNAusingdevicessuchasmobiletelephones.Thisinterdisciplinaryprojectwillprovideanopportunitytoacquirediverseskillsinchemistry,molecularbiology,bioengineering,andbiotechnology.

SCMB RESEARCH FELLOWS

DR ELIZABETH KRENSKE ARCFutureFellow

Phone:0733654632Email:[emailprotected]

ComputationalExplorationsofOrganicReactivity

We use advanced computational techniques to investigate aspects ofmolecular reactivity thatare invisible to theexperimentalist.Quantummechanical calculations (e.g. DFT) are applied to explore themechanisms of newly‐discovered synthetic transformations, to explainhow stereocontrol is achieved, and to design new reactions.We areespecially active in discovering previously‐unknown mechanisms ofstereocontrolinvolvingnon‐covalentinteractions.

Honoursprojects in this laboratory involve collaborationswith leadingsynthetic chemistsboth inAustraliaand internationally,andwillequipthestudentwithmodellingskillsthatshouldproveequallyadvantageouseitherasacomplementtofurtherresearchinsyntheticchemistryorasanentrypointtoadvancedtheoreticalresearch.

DR MEGAN O’MARA

Phone:0733657562Email:[emailprotected]

Investigatingmembranetransportusingmoleculardynamicssimulationtechniques

Regulation and control ofmembrane transport is an integral part of normal cellfunction, fromnutrientuptaketosignallingandremovalofmetabolicby‐products.The ABC multidrug transporter, P‐glycoprotein, exports over 120 distinct drugs,chemotherapeuticagentsandendogenoussubstrates.Itiswellestablishedthattheexpression of P‐glycoprotein in cancer lines is a major cause of chemotherapyresistance, however the molecular details of drug uptake and transport by P‐glycoprotein remain unclear. Recent investigations have also demonstrated thatplatelet‐activatingfactor(PAF),apotentphospholipidactivatorofleukocyte‐inducedinflammation; and amyloid‐� peptide (A‐� peptide), the major component ofamyloidplaquesinAlzheimer’sdisease,aretwoendogenoustransportsubstratesofP‐glycoprotein. These results suggest that the transport activity of P‐glycoproteinmayplayaroleininitiatingbothinflammatoryprocessesandAlzheimer’sdisease,as

wellasinthedevelopmentofchemotherapyresistantcancers.

TheaimofthisprojectistounderstandthemoleculardetailsofbothendogenousanddrugsubstrateinteractionswithP‐glycoproteinandthecellmembrane,usingcomputationaltoolssuchasmoleculardynamicssimulationsandfreeenergycalculations.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBResearchFellows

DR BENJAMIN SCHULZ Phone:0733654875Email:[emailprotected]

MolecularSystemsGlycobiology

Myresearchfocusesonthemechanismsandbiologicalrolesofproteinglycosylation.

Project1:DrugresistanceandN‐glycosylationinbreastcancerDocetaxel isan importantchemotherapeuticdrug for treatmentofbreastcancer,although tumourscandevelop resistance.This study seeks tounderstandhowprotein glycosylationallow tumours tobecomeresistanttodocetaxel.Thisprojectwillusecellculture,massspectrometryproteomicsandbioinformatics.

Project2:EngineeringglycoproteinsforimprovedexpressionMany proteins currently used as pharmaceuticals or in biotechnology are glycoproteins, such aserythropoietin (EPO) andmonoclonal antibodies. This projectwill further develop a low‐cost bacterialexpressionsystems.usingsite‐directedmutagenesis,proteinexpression,purificationandcharacterization.

Project3:EvolvabilityandrobustnessofproteinglycosylationN‐glycosylationofproteinshelpsthemtofoldcorrectly,andisalsoimportantinregulatingtheactivitiesofmatureglycoproteinsand iscatalyzedbyanenzymecalledOTase.Thisprojectwillexperimentallymodelthisco‐evolutionbymutatingtheaccessoryproteinsofOTaseandquantifyingtheeffectofthesemutationsonproteinglycosylationatasystemslevel.

DR ANNETTE SHEWAN Phone:0733654634Email:[emailprotected]

EpithelialMorphogenesisandCancerCellBiology

Understandingthemechanisticbasisofepithelialmorphogenesis isamajorchallenge inmodernbiology,withclearramificationsforhumanhealthanddisease.Theformationofatissuerequirestimelyandwell‐orchestrated interactions of different cells within their microenvironment. These cellular interactionsunderpin developmental processes and support normal tissue form and function. Crucial to normalepithelialtissuefunctionistheestablishmentofcellularpolarity.Epithelialtumourscanariseasaresultoflossofpolarityand it isbecoming increasingapparentthatthe interactionoftransformedcellswiththeirmicroenvironmentisinstrumentalintumourgrowthandmetastasis.Myprogramisfocussedonunravellingthemolecularmechanismsthatunderpintheestablishmentandmaintenanceofcellularpolarity.Theover‐archinggoalistobuildacomprehensiveunderstandingofhowdisruptionofcellularpolaritycontributestocellulartransformation,whichultimatelyresultsincancercelldisseminationandtumourprogression.

ResearchProjectsavailableinthefollowingareas:‐Molecularmechanismsofepithelialpolarityandcellulartransformation.‐Polarityproteincontrolofplasmamembraneasymmetry:establishingthefence.‐Proteintraffickingincellpolarity.‐Molecularregulationoftissuegrowthbypolarityproteinnetworks.Techniques Employed:Mammalian cell culture (2‐D & 3‐D), DNA cloning and mutagenesis, QRT‐PCR,miRNAassays,cellularsignalling,protein‐proteininteractions,RNAitechniques,transformationassays,epi‐fluorescenceandconfocalmicroscopy.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBResearchFellows

DR PAVLA SIMERSKA Phone:0733654636Email:[emailprotected]

EnzymaticligationmethodsfordrugandvaccinedeliveryTheaimof thisproject is todevelopefficientenzymatic ligation techniques for the synthesisofdrugandvaccinetherapeutics.Manypeptideshavebeenidentifiedaspotentialnewmedicinesbutonlyafewhaveprogressedintoclinicmainly due to their rapid enzymatic breakdown, problematic delivery and/or their poor inherentimmunogenicity.Thisprojectwilladdressthemajorissuesinpeptidedeliverythroughastrategyinvolvingenvironmentally friendly enzymatic transformations for coupling of sugars and/or lipids to thetherapeutic peptides of interest. These peptidemodifications are designed to improve peptideabsorption,metabolicstability,andconcentrationofpeptidesattheiractivesitesbyutilizingcarbohydrateand/oraminoacidtransportsystems.Theapplicationof the enzymatic synthesis provides access tocomplexcarbohydratestructuresthatcanbyusedtotarget carbohydrate receptors such asasialoglycoprotein. Available projects includedevelopment of enzymatic peptide ligations forsynthesis of group A streptococcal vaccinecandidatesusingglycosidasesandpeptidasesandenzymaticglycosylationsofpainregulatingpeptidesforCNSdeliveryusingglycosyltransferases.

DR MARIUSZ SKWARCZYNSKI Phone:0733469894Email:[emailprotected]

NanovaccinesRecent developments in nanomedicine/vaccinology have found that the size and morphologicalcharacteristicsofnanoparticlevaccinesaffecttheirefficacy.Preliminary investigationshavedemonstratedthat 20 nm polymer‐basednanoparticles that displayed peptide epitopeson their surfacewere able toinduceverystrongimmuneresponsesagainstthoseepitopes.Wehavealsoshownthatthisresponsewassizedependent.Thisprojectaimsto furtherexploretheeffectofsizeandmorphologyontheefficacyofnanoparticlevaccines.Project aims: 1) Produce polymer‐peptide chimeras that possess the desired epitope. 2) Establishreproducible self‐assemblymethod to synthesise the construct into nanoparticles. 3) Produce and self‐assemble multi‐epitope vaccine constructs.4) Fully characterise nanoparticles includingthesurfacearrangementoftheepitopes.

Peptides

Peptidetherapeutics

Enzyme

Glycosylation

Lipidation

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBResearchFellows

DR MAKRINA TOTSIKA

Phone:0733653830Email:[emailprotected]

Myresearchfocusesonthemolecularmechanismsemployedbypathogenicbacteriaduringinfectionofthehost.Currentprojectsinclude:1.ThemultidrugresistantEscherichiacolipandemic:howmolecularinsightintobacterialpathogenesiscanleadtonoveltherapiesE.colisequencetype131isa‘high‐risk’groupofmultidrugresistantpathogensthatemergedrecentlyandspreadrapidlyworldwide.ThepathogenicsuccessofE.coliST131isnotfullyunderstood.Usingrelevantcellandanimalinfectionmodelscombinedwithbacterialgenomicsandgeneticengineering,weunravelleduniqueaspectsofE.coliST131pathogenesisand identifiednoveladhesion inhibitorsthatpreventedandtreatedchronicbladder infectionwithE.coliST131 inmice.Students working in this project will gain strong experience in bacterial genetics andmolecular biology techniques,workingwithbacterialgenomesandusingcellandanimalinfectionmodelstoenhanceourunderstandingofE.coliST131pathogenesis,andaddresstheurgentandcurrentlyunmetneedfornovelalternativestoantimicrobialtreatmentofUTIthatarerefractorytoantibiotics.2.UnderstandinghowbacteriabecomestickyBacteriaproducestickyfibers,termedadhesins,whichmediatebacterialattachmenttobioticorabioticsurfaces(e.g.hostcellsorcatheters)andareessentialforcolonisationoftheirecologicalniche.Gram‐negativebacteriaexpressalarge repertoireof adhesins, including fimbrial and autotransporter (AT) adhesins.Although adhesin assemblyhasbeen studied extensively, recent findings implicate periplasmic enzymes in the early assembly steps. We useuropathogenicE.coli(UPEC)asaGram‐negativemodelorganismtodissectthecontributionofdifferentperiplasmicproteinsintheassemblyoffimbrialandATadhesins.Studentsworkinginthisprojectwillusegenetics,molecularandcellularmicrobiology,biochemistryandproteomicstoadvanceourunderstandingofhowbacteriaproduceadherencefactorsthataid inhostcolonization.Thiscanhelp identifynoveltargetsforanti‐virulenceapproachesasalternativeinfectiontherapeutics.

DR GEORGE VAMVOUNIS

Phone:0733667989Email:[emailprotected]

PhotoswitchablePlasticElectronicsOrganicphotochromicmoleculesreversiblychangecolourwithlight,i.e.photoswitch,asshowninFigure1.

Figure 1: A typical photochromic molecule (azobenzene) thatchanges colour in the presence of light due to a change inconformation.

These photochromic molecules have shown promise forinexpensiveoptical‐basedstoragemedia,wherethe trans‐

isomercouldbethe“0”logicelementandthecis‐isomercouldbethe“1”logicelement.AsillustratedinFigure1,UVlightisusedtowrite(toformthecisisomer)whilevisiblelightisusedtoread(toobservethecolour).Thisopticalreadprocessactuallytransformsthemoleculebacktothetrans‐conformation,thusdestroyingthestateofthemolecule.Interestingly,thechangeinopticalpropertiesoforganicphotochromicmoleculesalsocorrespondstoachangeintheelectronicproperties(chargetransport)ofthematerial,wheretheyswitchfrominsulatingtosemi‐conductingstates.In thisproject,youwill systematically synthesizephotochromicmolecules tomaximize thedifferencebetween theinsulatingtosemiconductivestatesforuseinmemorydevices.Specifically,youwillpreparephotochromicmolecules(givingyouexperience insyntheticOrganicChemistry),studytheirstructural,thermal,electronicandphotophysicalproperties (giving you experience in PhysicalChemistry) and possibly incorporate intoprototype plastic electronicdevices.

trans-azobenzene

UVlight

Visible light

N N

cis-azobenzene

SCMB AFFILIATE STAFF

PROFESSOR PAUL ALEWOOD GROUPLEADER,IMB

Phone:0733462982

Email:[emailprotected]

Theresearch interestsofourgroup include thediscoveryandtotalsynthesisofpeptide toxinsfrom Australia’s venomous creatures, the chemical synthesis of proteins and bioactive peptides,development ofnew synthetic and analytical methods, heterocyclicchemistry, proteomics and bio‐‐‐organic and medicinalchemistry. Special emphasis is placed on determining the structure‐‐‐functionrelationshipsofnaturaland/ordesignedmolecules.

Alpha‐‐‐conotoxinsthattargetchronicpainConotoxins are small bioactive highly structured peptides from the venom ofmarine cone snails(genus Conus). Over the past 50 million years these molluscs have developed a complex venomco*cktail foreachspecieswitheachvenomcomprisedof100‐‐‐2000distinctcysteine‐‐‐richpeptidesfor prey capture anddefence. This project focuses on the important andwell‐‐‐studied class of a‐‐‐conotoxins which contain twodisulfide bridges, 12‐‐‐16 residues and are potent and selectiveantagonists of nicotinic acetylcholine receptors. Specifically, we have found that there is an ‘a‐‐‐conotoxin‐‐‐like’ class of conotoxins that target theGABA‐‐‐B GPCR and are effective as blockers ofchronic pain. In this project wewill identify, synthesise andcharacterise some new leads in thisclass, develop peptidomimetics and evaluate them in vitro and in vivoas leadcandidatesfordrugdevelopment.

PROFESSOR ROB CAPON GROUPLEADER,IMB

Phone:33462979Email:[emailprotected]Website:http://capon.imb.uq.edu.au

Biodiscovery:BiodiversityandBiology,toBioactivesandBeyondMy research group focuses on the detection, isolation, characterization, identification and evaluation of novelbioactive metabolites from Australian marine and terrestrial biodiversity. These metabolites span all knownbiosynthetic structure classes including many molecules new to science, andtheir study requires the use ofsophisticated chromatographic, spectroscopic and chemical technologies. Natural products uncovered during ourinvestigationsrepresentvaluablenewleadsinthesearchfordrugswithapplicationinthefieldsofhumanandanimalhealthandcropprotection,havepotentialasmolecularprobestobetter interrogateandunderstand livingsystems,andcouldfindapplicationasbiologicalcontrolagents.

AvailableHonoursprojects:TargetingMultidrugEffluxinCancer:Thisprojectwilldevelopourrecent(unpublished)discoveryofamarine

fungal alkaloid thatinhibit P‐glycoprotein (P‐gp)mediatedmultidrug resistance in human cancers. The projectwilloptimizeapracticalsynthesis,preparealibraryofanalogues,assessanddocumentchemicalpropertiesandevaluateP‐gpinhibitoryactivityagainsthumancoloncancercelllines.

TargetingAlzheimer’sDisease:Thisprojectwilldevelopour recent (patented)discoveryofauniqueclassofmarine sponge alkaloid that inhibit kinases critical to the development of neurodegenerative diseases (e.g.Alzheimer’s). The projectwill optimize a practical synthesis, prepare a library of analogues, assess and documentchemicalpropertiesandevaluatekinaseinhibitoryactivity.

Targeting Cane Toads: This projectwill develop our recent (patented) discovery of a pheromonal attractant

capableoftrappingcanetoadtadpoles.Theprojectwilloptimizetheproductionandchemicalderivatizationofthepheromone, and the design and formulation of delivery devices, which will be evaluated in field trials.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAffiliateStaff

ASSOCIATE PROFESSOR NICK DAVIS-POYNTER UNITHEAD,SASVRC/CMVCPhone:0736368138Email:[emailprotected]Website:http://www.sasvrc.qld.gov.au?Projects.html

Duringthecourseofmillionsofyearsofevolution,herpesviruseshavepiratednumerousgenes fromthehost. Our group is determining the contribution of such genes to the herpesvirus lifecycle – from thecellular to the whole animal level. Many herpesviruses, including cytomegaloviruses (CMVs), encodehom*ologuesofcellularGprotein‐coupledreceptors(GPCR).TheGPCRshavediversebiologicaleffects,duetotheirpotentialtoinvokeacascadeofintracellularsignallingpathways.Theprojectwill investigateoneoftheviralGPCRofmouseCMV(termedM33andM78),hom*ologuesofwhich are expressed by all cytomegaloviruses. Disruption of either of these genes results in profoundattenuationinvivoandalsoaffectreplicationincertaincelltypesintissueculture,suggestingtheymaybenovel targets forantiviraldrugs. Weare investigating theeffectsofspecificmutationsofM33andM78upontheirbiologicalfunctions. Mutationswillbegeneratedbysite‐directedmutagenesisandtheeffectscharacterised using transfected cells and/or genetically modified mouse CMV. The student willconsequentlygainexperienceofarangeofmolecularbiology/virologytechniques.WearealsodeterminingwhetherthehumanCMVGPCRarefunctionallysimilartothoseofmouseCMV.Theresultsofthesestudieswill improvetheunderstandingofthefunctionoftheGPCRforthevirusandindicate whether viral GPCR may be a suitable target for anti‐viral drug development. For moreinformation,contactNickorvisitthewebsite.

DR ANNETTE DEXTER ASSOCIATEGROUPLEADER,AIBNPhone:0733463199Email:[emailprotected]Short designer peptides are attractive building blocks for the preparation of novel functional nano‐materials.Peptidesofferstimuli‐responsiveness,biocompatibility,predictablefoldingandthecapacityforsustainableproduction.Byemployingakeystructuralmotifofnativeproteins,theamphipathicalpha‐helix,wehavedeveloped lineagesofdesignerpeptides thatshowpromiseas responsivehydrogels forwoundhealing, tissue engineering and drug delivery or separately, as environmentally‐friendly switchablesurfactants.

ExamplesofavailableHonoursprojectsincludethefollowing:Peptidehydrogelsforburnhealing—preparingandtestinghydrogelsfordeliveryofproteinactivestoburnwounds,whileprovidingamoistwoundbedconducivetoimprovedhealing.

Peptides as surfactants for eco‐friendly industrial fluids—formulating and testing cutting fluidemulsionsforlubricationinmetal‐workingandrecyclabilityoftheoilandwatercomponents.

Bioproduction of peptides as hetero‐ or hom*oconcatemers—design, expression and downstreamprocessingofa*gellingpeptideforbiomedicaluse.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAffiliateStaff

ASSOCIATE PROFESSOR RALF DIETZGEN QUEENSLANDALLIANCEFORAGRICULTUREANDFOODINNOVATION(QAAFI)QueenslandAgriculturalBiotechnologyCentre(QABC),StLuciaCampusPhone:0733466503Email:[emailprotected]Website:http://www.qaafi.uq.edu.au//?page=157981

MolecularPlant‐MicrobeInteractionsMyresearch interest is inthediscoveryandbiodiversityofgenes,proteinsandregulatoryRNAs inplantsand viruses and their interactions in agricultural systems. Increased knowledge of these molecularinteractionswillenable improvedcropperformanceandbetterdiseasecontrol.Special interests includethe characterisation of plant‐adapted rhabdoviruses and tospoviruses, virus diagnosis and molecularevolution,RNAsilencingpathwaysforpestanddiseaseresistance,andfunctionalgenomicsandmolecularmarkersintropicalhorticulture.

TheprojectPlantvirusmovementon cytoskeletalhighwaysandbyways seeks to investigate thefunctionsofthecell‐to‐cellmovementprotein(Mv)ofaplant‐adaptedrhabdovirus.Planthostfactorsthatareknowntointeractwithexpressedrhabdoviralmovementproteinswillbeinvestigatedbyliveplantcellimaging using advanced protein localisation and interaction techniques and laser scanning confocalmicroscopy. Gateway cloning technology compatible with binary vectors for bimolecular fluorescencecomplementationwill be used to validate interactions,while fusionswith autofluorescent proteinswillallowaccuratedeterminationoftheirintracellularlocation.Protein‐proteininteractionswillbevalidatedbyinfiltrationofchemicalsthatinterruptcomponentsoftheplantcytoskeleton.GFP‐taggedviralMPwillalsobeusedtodeterminethemechanismofvirusmovementtoneighbouringcellseitherasribonucleoproteincomplexorasvirionsthroughtubulesacrossplasmodesmatausing isolatedMP‐expressingplantcells, ie.Protopla.

PROFESSOR DAVID FAIRLIE CHEMISTRYANDHUMANTHERAPEUTICS,IMBEmail:[emailprotected]Website:http://fairlie.imb.uq.edu.auOurbiologyresearchprograms investigatethepathogenesisandtreatmentofdiseases.Biochemistryandpharmacology studentsusenew compounds (inventedby chemists inour group) to interrogatehumanproteins, human cells, and rodentmodels of human disease to elucidatemechanisms of physiologicalprocesses,diseasedevelopment, anddrug action. Students learnmultiple techniques relevant to eitherprotein/gene expression, enzymology, protein‐protein interactions, intracellular signaling, or rat/mousemodelsofhumandiseases.Researchersgaininsightstoprocessespivotaltohumanphysiologyoraberrantindisease,anddevelopinterdisciplinaryskillsinoneormoreofbiochemistry,pharmacology,immunology,oncology,virology,parasitology,orneurobiology.Amongprojectsin2013are:(1)Gprotein‐coupledreceptorsignalinginhumancellsthatmediatediseases(2)Pharmacologyinrodentmodelsofinflammatorydiseases(3)Inhibitingenzymesincancer,inflammatoryorneurodegenerativediseases(4)Understandingrelationshipsbetweenobesity,diabetesandinflammation(5)Targetingviralproteinsthatareessentialforinfectiousdisease

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAffiliateStaff

DR MARY FLETCHER QUEENSLANDALLIANCEFORAGRICULTUREANDFOODINNOVATION(QAAFI)NaturalToxins,Health&FoodSciencesPrecinct,CoopersPlainsPhone:0732766089Email:[emailprotected]Research interestsfocusonthe identificationandanalysisofnaturaltoxins inarangeofplants,fungiandagricultural products and their impact on livestock and agricultural production. Such toxins have thepotential to form residues in agricultural products and pose a risk to consumers.Honours projects areavailablein:1.TheprevalenceofindospicineinIndigoferaplantspeciesbyLC‐MS/MSIndospicine isanunusualaminoacid inthat itisnot incorporated intoproteins,but ispresentasthefreeaminoacidandaccumulatesintissuesofanimalsfedIndigoferaplantmaterial.Thisprojectinvestigatestheprevalenceof indospicine inarangeof Indigoferaplantspeciespresent inAustralianrangelandsby liquidchromatography‐tandemmassspectrometry(LC‐MS/MS).2.EffectofUVlightonthecontrolofmycotoxinsinmaizeAflatoxin inafungaltoxin(mycotoxin)producedbyfungionagriculturalcropssuchasmaize.Thisprojectwill investigate thecontrolof the toxinbypost‐harvestdrying insunlightand storageonmaize infectedwithAspergillusfungusandaflatoxin.Thisprojectwillprovideinsightintoareasofinternationalfoodsafetyandaflatoxinanalysisandcontrol.

PROFESSOR ROBERT G GILBERT RESEARCHPROFESSOR,CNAFSPhone:0733654809Email:[emailprotected]

Biosynthesis‐structure‐propertyrelationsforstarchandglycogenStarch providesmore than half theworld population’s calorific intake; glycogen is our body’s glucosebuffer.Theseareat firstsightsimplehom*opolymersofglucose,but theirstructurespansmany levelsofcomplexity,withfeaturesrangingfromnmtomm.Thesestructuralfeaturesstrongly influencenutritionalvalue forhumans,andhowwellglycogen iseffective incontrollingbloodsugar(andhencepropensitytodiabetes). In synthetic polymer science and technology, the paradigm for understanding materialproperties, and producingmaterialswith improved properties, iswell established as synthesis controlsstructurecontrolsproperties.Wearenowdoingtheequivalentforstarchandglycogen:onechangesthegenetics(biosynthesis)totrytoobtaincerealswithdesirableproperties—betterdigestibilityformanagingand reducingobesity,diabetes and colo‐rectal cancers—anddrug targets fordiabetes through glycogensynthesisenzymes.Thisprojectwillgreatlyexpandcurrentknowledge,throughouruniqueexperimentalandtheoreticaltools,toexaminethestructureofthesepolymersandthentorelatethestructuralfeaturestobothbiosynthesisandtoproperties.

Project1:Genetics/structurerelations:simulationsProject2:Genetics/structurerelations:experiment

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAffiliateStaff

PROFESSOR GLENN KING GROUPLEADER,IMBPhone:0733462025Email:[emailprotected]Website:http://www.imb.uq.edu.au/index.html?page=56210

VenomicsasadrugandinsecticidediscoveryplatformAnimalvenomsare increasingly important indrugdiscoveryeffortsas theyconstituteavastand largelyuntapped sourceofpharmacologicallyactivemolecules.Spidersareby far themost successfulgroupofvenomousanimalsand theirvenomsarepredicted tocontainmore than10milliondifferentbiologicallyactivepeptides.Ourgroupisexploringspidervenomsasasourceofnovelpeptidestoprovideleadsforthedevelopment of new drugs and insecticides. As a major part of this initiative, we have developed astructuralvenomicspipelinethatallowsproteinstructurestobedeterminedviaNMRatanunprecedentedrate.AvailableHonoursprojects:

Screening spider venoms for peptides targeted at ion channels involved in sensing pain, andexaminationoftheiranalgesicpotentialinanimals.

Discoveryofnovelinsecticidalandantimalarialcompounds.

Structuralandfunctionalcharacterisationofvenompeptides.

Characterisationoftheinteractionbetweenvenompeptidesandtheirionchanneltargets.

Examination of the genetic basis underlying the remarkable diversity and evolution of venompeptides.

DevelopingmethodsforautomatedproteinstructuredeterminationviaNMR.

DR KIRSTEN SPANN SIRALBERTSAKZEWSKIVIRUSRESEARCHCENTRECLINICALMEDICALVIROLOGYCENTRE,RESPIRATORYVIRUSRESEARCHUNITPhone:0736368718Email:[emailprotected]RespiratorySyncytialVirus (RSV)andmetapneumovirus (MPV)aresignificantcausesof lower respiratorytractdiseaseininfants,youngchildrenandimmune‐compromisedadults.Theyarealsolinkedtoboththeinceptionsandexacerbationofasthma.TherearenovaccinesorcommerciallyavailabletargetedantiviralsforeitherRSVorMPV.Weare interested inthepathogenesisoftheseviruses inassociationwithasthmaandacutedisease,andalsotheidentificationofantiviraltargets.

Project1: Therehas been a recent surge in research concerninghumanmicroRNAs (miRNA) andhow

thesesmallRNAspeciesregulatehumangeneexpressioninrelationtodisease.Pathogenssuchasvirusesalso regulatemiRNAs,which, in turn, regulatehuman genes involved in the immune response.We areinterestedinhowRSVregulatesmiRNAsinhumancellsduringinfection.RSVencodesspecificproteinsthatare involved in suppressing the innateantiviral response to infection.Weare interesting in investigatingwhichmiRNAs are regulated by the RSV immune‐suppressive proteins and howmimicking or inhibitingthesemiRNAsmayaffectRSVreplication.

Project2:Asthmaticadultsandchildrenmayhaveadefect intheir innateantiviralresponsethatmakesthemmore susceptible to viral infection anddisease thanhealthy individuals. This hasbeen shown forrhinovirus infection,howeverweare investigatingdefects intheantiviralresponseofasthmatic(andalsoallergic) individuals toRSVandMPV,whichareparamyxoviruses.Weare interesting innotonly intrinsicdefectsoftheairwayepitheliumofasthmatics,butalsotherolethevirusesplayinregulatingtheantiviralresponsethatmayunderlietheriskofasthma.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAffiliateStaff

ASSOCIATE PROFESSOR RICK STURM GROUPLEADER,IMBPhone:0733462038Email:[emailprotected]Website:www.imb.uq.edu.au/index.html?page=11690

MoleculargeneticsofpigmentationandmelanomaMelanocytes produce themelanin pigments responsible for skin, hair and eye colour. Darker forms ofmelaninprotecttheskin fromsolarradiationexposure,howevermelanocytesarealsothecelltype fromwhichmalignantmelanomacanoriginate.Wearestudyingthehumanpigmentationsystemtounderstandthe genetic basis of cellular differentiation, tissue‐specific gene expression and cellular transformationinducedbysolarUVlight.AvailableHonoursprojects:Genetics of human pigmentation including comparing individuals of high and low mole number, andlookingatgenescontrollingmolemorphology.Cell biology of human pigmentation, whereby the laboratory is growing primary cultures of humanmelanocytesaloneortogetherwithkeratinocytestoassayfunctionofgenes.

Specificprojectslistedonwww.imb.uq.edu.au/index.html?page=11690

DR MATT SWEET GROUPLEADER,IMBPhone:0733462082Email:[emailprotected]

PathogenSurveillance,InnateImmunityandInflammationMy group focuses on understanding how the innate immune system detects and responds to invadingmicroorganisms. Innate immune cells such as macrophages express a broad repertoire of patternrecognitionreceptors,forexamplemembersoftheToll‐likeReceptor(TLR)familythatdetectanumberofpathogen‐associatedmolecularpatterns including LPS,CpGDNAandbacterial lipoproteins.Macrophageactivation via TLRs regulates expressionof genes involved in antimicrobial responses, inflammation andprimingoftheadaptiveimmuneresponse.Whensuchresponsesaredysregulated,bothacuteandchronicinflammatorydiseasecanresult.WestudyTLRsignallingpathwaysandthefunctionofnovelTLR‐regulatedgenes in the context of infectious and inflammatory diseases. Key collaborators within SCMB includeProfessorAlMcEwan,Dr.KateStaceyandProfessorMarkSchembri.AvailableHonoursprojectsfor2014include:(1)UnderstandingtheroleofhistonedeacetylasesinTLR‐activatedinflammatorypathways;(2)Characterizinghumanmacrophageanti‐microbialpathways;and(3)CharacterizationofnovelTLRtargetgenes.

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAffiliateStaff

ASSOCIATE PROFESSOR ROHAN TEASDALE GROUPLEADER,IMBPhone:0733462056Email:[emailprotected]Website:http://www.imb.uq.edu.au/index.html?page=11682&pid=11669

EndosomalDynamicsandPathogenInvasioThe endosomal/lysosomal system ofmammalian cells is a highly dynamic organelle and the traffickingpathwayswithin theendosomalsystemare fundamental forawidevarietyofkeycellularprocesses.Mygroup is developing cellular and computational approaches to identify novel mammalian proteinsassociated with the endosomal system. This includes the retromer complex that has recently beenidentifiedasacausalagentforType2diabetesandneurodegenerativedisease.Numerousinfectiouspathogensexploitspecificendocyticpathwaystoinvadethehost.Characterizationofpathogenentrypathways isessential forunderstanding infectiousdiseasesbuthas alsoproven tobe apowerful tool for gaining insight into normal cellular processes. We are currently investigating themoleculardetailsofthesepathwaysandhowtheyaremodulatedinresponsetoinfectionwithSalmonella,a leading cause of human gastroenteritis and Chlamydia, amajor sexually transmitted pathogen.Onceinside the cell, thesepathogens actively alter thehost cellsmembrane traffickingpathways to create areplicativenichethatenablesthepathogentosurviveandavoidtheinnateimmunesysteminthesecells.AvailableHonoursprojects:

Defining theessentialhostproteins required for intracellularbacterialpathogen infection.Thesehostproteinsrepresentattractivetherapeutictargets.

RNAiscreeningtofurtherdefineessentialproteins forarangeofendosomeassociatedpathwaystargetedbybacterialpathogens.

Definingthemolecularandcellularpropertiesofretromer’sfunctioninneurodegenerativediseasesincludingParkinson’sandAlzheimer’s.

PROFESSOR BRANDON WAINWRIGHT GROUPLEADER,IMBPhone:0733462053Email:[emailprotected]

MolecularGeneticsofHumanDiseaseOur research group is focused on elucidatingmolecular pathology of human genetic disease, primarilythroughtheanalysisofthesinglegenedisorder,cysticfibrosisandthroughthediscoveryofPatched,thegeneresponsibleforboththeinheritedandsporadicformsofbasalcellcarcinomaoftheskin.Asaresultofthese studieswehave aparticular interest in the interfacebetweendevelopmentalbiologyandhumangenetics,andintherapeuticstrategiessuchasgenetherapy.Projectsinclude:

Thedownstreamtargetsofpatched/hedgehogsignalling

Structure/functionanalysisofPatched

DissectionoftherolesofSonic,IndianandDeserthedgehogindevelopmentandneoplasia

Thecontrolofthehostresponsedefectincysticfibrosismutantmice

Genesmodulatedbythecysticfibrosisgene

Correctionofthehostresponse(inflammation)defectinG551DCFTRmutantmice

Chemistry&MolecularBiosciencesHonoursProjects2014|SCMBAffiliateStaff

PROFESSOR ANDREW WHITTAKER GROUPLEADER,AIBNPhone:0733463885Email:[emailprotected]Web:www.uq.edu.au/polymer‐chemistry/Ourresearchgroupdevelopspolymericmaterialstoimprovehumanhealth.Ourlargegroupofresearchershaveprogramsof researchacross the spectrum frombench top‐to‐bedside. Specificallywework in thefieldsofsensingofdisease,deliveryofdrugsandregenerationoftissue.Theprojects listedbelowarealldoneincollaborationwithexpertsinclinicalapplicationofbiomaterials,andwillprovideasolidfoundationinpracticalandtheoreticalaspectsoftheuseofpolymericmaterialsasbiomaterials.Honoursprojectsareavailableinthefollowingareas(forprojectdetails,pleaseseeourwebsiteorcontactAndrewbyemail).Thewebsitelistsotherprojects.

1. Functionalisationofthesurfacesoftitaniumalloysforimprovedosseointegration2. Developmentofnovelpolymerscaffoldstoaidtherepairofthespinalcord3. Developmentoflow‐fouling,anti‐microbialsurfacecoatings4. Novelpolymermolecularimagingagents(MRI)forearlydiseasedetection5. Peptidehydrogelsforcelldelivery6. Deliveryoftherapeuticdrugstothespinalcord

AFFILIATED INSTITUTIONS

HonoursprojectsmayalsobeavailableinthefollowingUQInstitutesthathavestronglinkswiththeSchoolofChemistry&MolecularBiosciences:

ADVANCED WATER MANAGEMENT CENTRE Website:www.awmc.uq.edu.au

AUSTRALIAN INSTITUTE FOR BIOENGINEERING & NANOTECHNOLOGY Website:www.aibn.uq.edu.au

CENTRE FOR ADVANCED IMAGING Website:www.cai.uq.edu.au/honours‐projects

INSTITUTE FOR MOLECULAR BIOSCIENCE Website:www.imb.uq.edu.au

UNIVERSITY OF QUEENSLAND CENTRE FOR CLINICAL RESEARCH Website:www.uqccr.uq.edu.au

UNIVERSITY OF QUEENSLAND DIAMANTINA INSTITUTE Website:www.di.uq.edu.auHonoursscholarships:www.di.uq.edu.au/scholarshipsContact:PostgraduateAdministrationOfficeron(07)31763197oremail[emailprotected]

EXTERNAL INSTITUTIONS (Including SCMB ADJUNCT

ACADEMIC STAFF)

CSIRO QUEENSLANDBIOSICENCESPRECINCT,UQSTLUCIACAMPUS

PROFESSOR JOHN MANNERS CSIROPlantIndustryEmail:[emailprotected]

PotentialHonoursProjectfor2014 FungalpathogenspeciesFusariumandinteractionswithbothArabidopsisandwheat

PROFESSOR MARK MORRISON CSIROMicrobialBiologyandMetagenomicsResearchEmail:[emailprotected]

PotentialHonoursProjectsfor2014 Bacterialmousetraps:theroleofserpinsingutbacteria

Howdomicrobesmakechocolate?

QUEENSLAND INSTITUTE OF MEDICAL RESEARCH HOSPITALSCOMPLEX,HERSTON

PROFESSOR JEFF GORMAN Head,QIMRProteinDiscoveryCentreConvenor,ProteomicsAustraliaEmail:[emailprotected]

PotentialHonoursProjectfor2014 High‐PerformanceProteomicAnalysisofViralProteinPost‐TranslationalModificationsandInteractions

withHostCells

DR LUTZ KRAUSE Head,BioinformaticsLaboratoryPhone:0738453745Email:[emailprotected]

PotentialHonoursProjectsfor2014 Discoveryofbiomarkersfordiseaseonset,prognosisandpersonalizedtreatment

ComparativeandEvolutionaryGenomicsofHumanParasites–IdentifyingParasiteSpecificGenes,DrugandVaccineTargets

Roleofthehumangutmicrobiotainhealthanddisease

Chemistry&MolecularBiosciencesHonoursProjects2014|ExternalInstitutions

ProjectNext‐generation‐sequencingandepigenetics–Characterizinganewlydiscoveredgeneinvolvedinepigeneticgeneregulation

DevelopSupportVectorMachinebasedpredictorofcandidatevaccineanddrugtargetsagainstthehumanparasitesSchistosomaspp.

Findingtheneedleinahaystack–Developmentofaweb‐toolforannotatinggenomicvariations

SIR ALBERT SAKZEWSKI VIRUS RESEARCH CENTRE CLINICALMEDICALVIROLOGYCENTRE,RESPIRATORYVIRUSRESEARCHUNIT

ASSOCIATE PROFESSOR IAN M MACKAY GroupLeaderEmail:[emailprotected]

PotentialHonoursProjectsfor2014 Humanrhinovirusesandenterovirusesinasthma:identification,molecularanalysisandclinicalimpact

Genomedeductionandepidemiologyofarecentlyidentifiedparechovirus

HONOURS IN INDUSTRY

Opportunitiesexistintheseindustriesandmore:

biotechnology chemical

pharmaceutical

foodprocessing pathology

AsaChemistryorMolecularBiosciencesstudent,youmaybeabletoundertakehonourswithcompanieswithwhomSCMBalreadyhasaworkingrelationship.Inaddition,ifthereisaparticularcompanyyouwouldliketoworkwith,youarewelcometoproposeittous.Tofindoutmore,expressinterestonlineatscmb.uq.edu.au/honsorbyscanningthisQRcode.

WouldyouliketoundertakepartofyourhonoursprojectinacompanyoutsideUQ?

Experienceacommercialworkplace

Makecontactstohelpyouwithyourcareer

Receive support and guidance from UQ as well as yourindustrysupervisor

Chemistry&MolecularBiosciencesHonoursProjects2014|HonoursinIndustry

‘HonoursinIndustry’projectisawin‐win‐winforastudent,acompanyandforUQ

QiQiHedecided inthethirdyearofherBScstudiestodoHonoursasawaytoobtainresearchandotherskillsvaluedbyemployers. Interested in the synthesis of different kinds of newcompounds related to carbohydrate chemistry, Qi QiapproachedAssociateProfessorVitoFerrooftheSchoolofChemistry&MolecularBiosciences(SCMB)aboutatopic.Using his industry contacts, Assoc Prof Ferro found aproject for Qi Qi with Brisbane‐based biopharmaceuticaland drug discovery company, Alchemia Ltd, as part ofSCMB’snew‘HonoursinIndustry’program.“We had encounteredwhat looked like an interesting chemical reaction, but did not have the time toexplorethisduetoothercommercialprojects,”Alchemia’sVice‐President,Discovery,DrWimMeutermans,said.“Itseemedan idealhonoursproject intermsofbroadskilldevelopment(synthesis,purification,structuredetermination)”.QiQiwasawardeda$2,000HonoursscholarshipbySCMBandundertookherprojectunderthesupervisionofbothAssocProfFerroatUQandDrNorbertWimmeratAlchemia.“My project involved solving a real problem of the decomposition of a promising compound in thecompoundlibraryatAlchemia,”saidQiQi.“Itwasreallyinteresting,anditgavemeachancetoapplywhatIhadlearntinmybachelordegreeprogram.“WorkingatAlchemia’splantexposedmetonewresearchtechniquesandvaluablepracticalskillsthatarespecificallyusedinindustrynowadays.”QiQiadded thattheexperiencegaveheran insight into industrialcultureandhow toworkonherowninitiativeandaspartofateam.DrMeutermansagreedthatworkingonanindustryreallifeproblemgaveQiQiasenseofdirectapplicabilitytoit.DrMeutermans said thatQiQi undertook to evaluate anunusual chemical rearrangement involving anundefinedkineticintermediate.“Qi Qi successfully determined the structure, and it provided valuable information for our discoveryefforts,”saidDrMeutermans.Qi Qi said that during her studies, she received “tremendous support” from her UQ and Alchemiasupervisors.“Theyhelpedmetoplanwhat Ishoulddotosucceedtosolvetheproblem inmyHonoursproject.Theyalso instructedme in the lab, sharing theirknowledgeof chemistry,assistingmewithdifferentkindsofresearchtechniquesandteachingmevaluablepracticalskills.”QiQigraduatedwithFirstClassHonoursandwasplanningtogoontoaPhDorworkasaresearch

assistant.

Chemistry&MolecularBiosciencesHonoursProjects2014|HonoursinIndustry

PROFESSOR JAMES DE VOSS DR JOANNE BLANCHFIELD

Phone:0733653825 Phone:0733653622Email:[emailprotected] Email:[emailprotected]

Includingaplacementat:

IntegriaHealthcare,EightMilePlains,BrisbaneResearcharea:AnalyticalChemistryasappliedtothePharmaceuticalindustry,withparticularemphasisoncomplementarymedicineProject1:Basedinananalyticallaboratory

Project2:Basedinamanufacturingfacility

Chemistry&MolecularBiosciencesHonoursProjects2014|HonoursinIndustry

PROFESSOR ROSS BARNARD

Email:[emailprotected]

Includingaplacementat:

CookMedical,EightMilePlains,BrisbaneProjectScope:Cook Australia, a US owned and based company,developsandmanufacturesmedicaldevicesfornationaland internationalmarkets.TheAustralianarmofthiscompanymanufacturesanextensiverangeofhealthcaredevicesthatincludesstateoftheartproductsforeachstepintheIVFprocess.TheR&D/EngineeringdepartmentatCookAustraliahaveestablishedaprojectto investigatethewashingand drying processing of products. This process step is successfully producing product cleaned ofsubstancestoxictohumanembryos.

Areas of specific interest are the:Detergents ‐ chemistry of cleaning and rinsibility,Water – chemical

activityofwater,andWater‐physicalprocessofwashingsmallboretubes(needlesandcatheters).

SirrometWines,MtCottonWitheveryvintage,newchallengesemergeinwinemaking.Overthepast5years Queensland vintage weather conditions have varied enormouslyrequiring constantvigilanceand innovationby thewinemaker tomaintainconsistencyofqualityandwinestyle.Projectscope:Investigating thechemicalbasisoftaste,colour,mouthfeel,and ‘pinking’ in redwine,browning inwhitewineandcoppercasseformation.Assessmentof levelsof phenolics,N, P, K, Fe,Cu, pH, alcohol, resveratrol and stability of proteins andeffectsofyeastcharacteristicsandlevels,grapevarieties,altitude,soil,vintage,climateandconditions.Analysisanddevelopmentofextractstoenrichredwines.

School of Chemistry & Molecular Biosciences CHEMISTRY ... CHEM_MBS Project... · BSc Honours Projects 2014 CHEMISTRY, BIOCHEMISTRY & MOLECULAR BIOLOGY and MICROBIOLOGY & PARASITOLOGY - [PDF Document] (2024)

FAQs

What is biochemistry and molecular biology Honours? ›

This honours area emphasises projects that study how these molecules pass information and energy within and between cells, and from generation to generation, and how these processes impact form and function.

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What is the biochemistry and molecular biology program? ›

Concentrates on the chemical and physical properties of biological molecules, the complex array of chemical reactions occurring in cells, and the function and regulation of genes.

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What is School of Chemistry and Molecular Biosciences Indian Scholarship? ›

The School of Chemistry and Molecular Biosciences at The University of Queensland (UQ) invites outstanding students who are citizens of India, to apply for a postgraduate coursework scholarship to cover 25% of tuition fees in the Master of Biotechnology, Master of Molecular Biology or Master of Bioinformatics programs, ...

What is biochemistry all about in PDF notes? ›

Biochemistry studies all the processes within a living cell. With their all molecular compounds and contents, understanding how all these processes contribute to health and disease of living cells or organisms are major focus of Biochemistry.

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Is biochemistry and molecular biology a hard major? ›

Biochemistry can be a challenging subject for many students because the material is broad and complex. It's a multidisciplinary science that calls for expertise in a variety of fields including chemistry, biology and mathematics.

Which is better molecular biology or biochemistry? ›

If you're more interested in life at the molecular scale, molecular biology may be for you. If you're intrigued by the chemical reactions that create and influence life, consider looking into a biochemistry program.

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How much do biochemistry and molecular biology jobs pay in the US? ›

Molecular Biology Salary

	Annual Salary	Hourly Wage
Top Earners	$102,500	$49
75th Percentile	$98,500	$47
Average	$80,687	$39
25th Percentile	$69,000	$33

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Do biochemists make medicine? ›

For example, in medicine, biochemists and biophysicists develop tests used to detect infections, genetic disorders, and other diseases. They also develop new drugs and medications, such as those used to treat cancer or Alzheimer's disease.

What do molecular biology majors do? ›

Isolate, analyze, and synthesize proteins, enzymes, DNA, and other molecules. Research the effects of substances such as drugs, hormones, and food on tissues and biological processes. Prepare technical reports, research papers, and recommendations based on their research.

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What is molecular biology and biotechnology Honours? ›

Molecular Biology and Biotechnology focuses down to the levels of the molecules that support life and uses cutting-edge technology to understand mechanisms driving cell division and disease.

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What is BSc molecular biology course? ›

The BSc (Hons) in Molecular Biology involves an introduction to the foundations of molecular and cellular biology and then focuses on topics such as chromosome structure and function, molecular genetics, molecular cell biology, biotechnology, bioinformatics, molecular virology and gene expression.

Is molecular biology a good course? ›

Molecular Biology has wide-ranging applications in healthcare and is emerging as an excellent career option.

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What are the 4 major components of biochemistry? ›

There are four classes of biochemical compounds: carbohydrates, proteins, lipids (fats), and nucleic acids.

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What is the 5 importance of biochemistry? ›

Biochemistry combines biology and chemistry to study living matter. It powers scientific and medical discovery in fields such as pharmaceuticals, forensics and nutrition. With biochemistry, you will study chemical reactions at a molecular level to better understand the world and develop new ways to harness these.

School of Chemistry & Molecular Biosciences CHEMISTRY ... CHEM_MBS Project... · BSc Honours Projects 2014 CHEMISTRY, BIOCHEMISTRY & MOLECULAR BIOLOGY and MICROBIOLOGY & PARASITOLOGY - [PDF Document] (2024)

FAQs

What is biochemistry and molecular biology Honours? ›

What is BSc molecular biology course? ›

References