advancing life sciences
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Institute for Life Sciences
News and features: Researching biofilms in infant feeding tubes
Spotlight on: Pioneering research enabled by disruptive technologies
Publications: A sample of research outputs from our PhD students
July 2019
ADVANCING LIFE SCIENCES
ADVANCING LIFE SCIENCES
Find out more: www.southampton.ac.uk/ifls
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WELCOME CONTENTS
LifeSciencesareessentialtoourwellbeing,theeconomyandtheprotectionofanenvironmentcriticaltooursurvival.TheLifeSciencescommunityattheUniversityofSouthamptonisattheforefrontofapproachestoaddresstheseglobalchallenges,breakingthetraditionalmouldofsolvingproblemswithintheconfinesofadiscipline.
Wehaveanestablishedreputationforworkingcollaboratively,bytakingdisruptiveapproachesandriskthroughinterdisciplinaryteamscience.Withinterdisciplinarycultureattheheartofourcommunity,wefocusonfourareasofexcellence:HealthandMedicine,andLivingSystems,alongsideDisruptiveLifeTechnologiesandInsightsthroughData.Thelatterprovidetheadvancedtoolstodriveourunderstandingatthefrontiers.
Inpreviousreports,wehavefocusedontheexpansionofourimpactinregionalactivitiesandhowwehavecontributedtogovernmentstrategy.Inthisreport,wecontinuetohighlightourimpactthroughourengagementwithTheRosalindFranklinInstituteandTheAlanTuringInstitute,aswellasshowcasingourcurrentcollaborations,technologicalbreakthroughsanddemonstratingtheincreasingimportanceofdatainallofourresearch.
YoucanalsoseeaselectionofrecentpublicationsfromourcohortofinterdisciplinaryPhDstudentsastheydevelopintoindependentresearchersandfutureleaders.
Professor Peter JS Smith DirectoroftheInstituteforLifeSciences
TheLifeSciencesareakeycomponentoftheUKstrategyforgrowth,underpinningourengagementwithhealthandthebioscienceshereattheUniversityofSouthampton.
Thisyear’sreportfromtheInstituteforLifeSciences(IfLS)highlightsthecentralroleitcontinuestoplayintermsofourinstitutionalaspirationsandachievements,asadynamic,consistentandcollaborativechampionofourlifesciencesportfolio.
Professor Mark SpearingPresidentandVice-Chancellor(Interim)UniversityofSouthampton
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FEATURE: Cross-Institute Engagement Pioneeringresearchenabledbydisruptivetechnologies
12Living SystemsCatalysingourexpertiseinecologyandevolution
18PublicationsAsampleofpublicationsfromourinterdisciplinarypostgraduatestudents
08 Health and Medicine Collaboratingattheforefrontof
cancerimmunology
Front cover image: First-of-a-kind soft tissue-optimised micro-computed tomography (μCT) scanner in Southampton for 3D X-ray histology.
10Life TechnologiesRevolutionisingbiomedicalimaging
14Insights through DataTransformingprecisionmedicinethroughdataanalytics
16 News in BriefAround-upofnewsfromacrosstheInstituteforLifeSciences
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Southampton is renowned both nationally and internationally for the strength and breadth of its interdisciplinary life sciences research, and is particularly proud of its revolutionary collaboration between medical, health and natural sciences.
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PIONEERING RESEARCH ENABLED BY DISRUPTIVE TECHNOLOGIES
Fromidentifyingindicatorstopredictacceleratedageing,tousingmathematicalmodellingtounderstandbreastcancer,andfromdevelopinghighresolutionmicroscopytoolstousingchemistryprocessestocreatenewantibiotics,Southampton’slifesciencesportfoliospansmanyareasacrosstheUniversity.
TheglobalrecognitionoftheUniversityasahubofexpertiseinthelifescienceshasledtotheorganisationbecomingapartneroftwoleadingUKinstitutionsthatarepioneeringresearch–TheRosalindFranklinInstituteandTheAlanTuringInstitute.
Southampton’s involvementTheUniversity’sInstituteforLifeSciencesDirectorandBoardMemberofTheRosalindFranklinInstitute,ProfessorPeterJSSmith,stronglywelcomesSouthampton’sinvolvementinthesetwoinnovativeinstitutions.
Hesaid:“Itisagreatpleasuretobecomeacorepartofthesetwomajorinstitutes.Itreflectsthestrengthwehaveinlifesciencesresearchacrossmanydisciplines.
“AtSouthampton,wearecapableofcontributingtoanumberofthecorethemesofTheRosalindFranklinInstitute,particularlywithourresearchindisruptiveadvancesinimagingtechnologiesfromthelargescaledowntotheatomicscale.
“WewillfeedintoprojectsthatTheRosalindFranklinInstituteisundertakingandwillbeattheforefrontofcutting-edgetechnologydevelopmentthatwillhelpdriveourownresearchforward.”
The Rosalind Franklin InstituteTheRosalindFranklinInstituteisdedicatedtotransforminglifesciencethroughinterdisciplinaryresearchandtechnologydevelopment.Itaimstoproducetechnologiesthatwillallowustoseethebiologicalworldinnewways,fromsinglemoleculestoentiresystems,speedingupdrugdesignanddevelopment,andpushingforwardourunderstandingofhumanhealthanddisease.
TheUniversityofSouthamptonisoneoftenuniversitiesatthecoreofTheRosalindFranklinInstitute,whowillworkwithindustrialandacademicpartnerstofosterinterdisciplinaryresearch,atscale,withrealimpact.
The Alan Turing InstituteTheAlanTuringInstituteistheUK’snationalinstitutefordatascienceandartificialintelligence.Itsgoalsaretoundertakeworld-leadingresearchintheseareas,applythisresearchtorealworldproblems,driveeconomicimpactandsocietalgood,leadthetrainingofanewgenerationofscientists,andshapethepublicconversationarounddata.SeveralmembersoftheIfLSarenowTuringFellowswithaccesstoopportunitiesandthewidernetwork.
Image: Extreme ultraviolet light generated by femtosecond lasers is used by Professor Jeremy Frey and Dr Bill Brocklesby for nanoscale imaging of neurons.
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Cross-Institute Engagement
Cross-Institute Engagement
Here we look at how some of our researchers are taking disruptive approaches to solve life science questions.
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Tackling antibiotic resistanceResearchbyProfessorSymaKhalidandherteaminChemistrywillhaveabigimpactonthecurrent,globalfightagainstantimicrobialresistance.
SymawillbeusingSouthampton’shighperformancecomputer–Iridis5–aswellasthenationalSupercomputer–ARCHER–tohelpdesignnewantibotics.
Theteamiscreatingaccuratecomputermodelsofmolecularassemblieswithinbiologicalsystemstobetterunderstandhowbacteriarespondtoantibiotics,inordertodevelopimproved,morepotentdrugs.
Shesaid:“WorkingwithTheRosalindFranklinInstitutewillfacilitatecross-disciplinarystudies,sowecancombineourcomputationalworkwithdatafromcolleagueswhodowet-laboratorysciencetoprovidegreaterinsights.”
Lens-less imaging at the nanoscaleAcollaborationbetweenChemistryandSouthampton’sZeplerInstitutehopestobringaninnovativemicroscopytoolapplicationthathasthepotentialtolookatbiologicalsystemsatamuchhigherresolutionanddefinition.
ProfessorJeremyFrey,fromChemistry,andDrBillBrocklesby,fromtheZeplerInstitute,areamongthefirstresearchersintheworldtodemonstratelens-lessimagingonactualbiologicalsamplesusingextremeultravioletlight,whichgivesmuchhigherresolutionthanopticalmicroscopy.
Jeremysaid:“Usuallymetalcoatingsorfluorescentdyesneedtobeaddedtosamplesbeforeimagesaretaken,butwehavebeendevelopingacoherentlightsourceoverthepastfewyearsthatenablesustotakemeasurementsfromsampleswithouthavingtodotoomuchtothesamplebeforehand.
“Thisisopeningupawholenewwayoflookingatthesub-cellularstructure,revealinginformationthathasn’tbeenseenatthislevelbefore.BytakingthisnoveltechnologytoTheRosalindFranklinInstitute,wewillhaveaccesstomuchlargerequipmentthatwillenableustoimprovetheresolutionofourlens-lessimagingtothenanoscale.”
Billadded:“Wearehopingthattheimagesthatwecannowproduceofnanoscalebiologicalstructurescanmakeacaseforinvestmentinthenextgenerationofthesetools.Wewillbecreatingapathwaythatcouldmakethisimagingequipmentmorecompactallowingittoberolledoutforusemoregenerallyinbiology.”
Theseadvanceswillcontributetothegeneralthemesofcorrelativemicroscopy–afocusofdevelopmentatTheRosalindFranklinInstitute.
Using mathematical modelling in predicting breast cancerDrPhilipGreulichisoneoftheUniversity’sfirstTuringFellowsandisinvestigatinghowstemcellsdivideanddifferentiate,whichiscrucialforunderstandinghowcancerdevelops.
CollaboratingwithDrSalahElias,alsofromtheIfLS,PhilipisusingmathematicalmodellingtestedonSalah’sexperimentaldata,toexplorewhetherthedirectioninwhichbreasttissuecellsdivide,candeterminethecellfateandwhattypeofcellitwillbecome.
Hesaid:“Ithasbeenshownthattheorientationofbreastcancercelldivisionismuchmorerandomthanthatofhealthycells.Wewanttofindoutifthiscouldbeapredictortocausecancerorifithasnorelation.BeingaTuringFellowIwillbeabletosharemyexpertiseinmathematicalmodelling,andIwillhaveaccesstoresearcherswhoworkwithlargehigh-dimensionaldatasetswhocanhelpmeanalysethecomplexdatainvolvedinmyresearch.”
Predicting the ageing processTuringFellowandIfLSmemberDrNickFuggle,fromtheMRCLifecourseEpidemiologyUnit,islookingatindicatorsthatcanpredictthoseatriskofacceleratedbiologicalageingwithafocusonmusculoskeletalhealth.
Byusingclinicalparameters,epigeneticmarksandspecialistimaging,heistryingtoidentifywhomaybeatriskofconditionssuchasosteoporosis,osteoarthritisandsarcopenia(muscleloss).Thiswouldallowearlyinterventionandameliorationoftheriskofthesediseasesofmusculoskeletalageing.
Hesaid:“TheTuringFellowshiphasallowedmetobuildrelationshipsandcollaborationsacrossTheAlanTuringInstitute.Ihaveconnectedwithcolleagueswhohavediverse,interdisciplinaryinterestsinmachinelearning,healthservices,epigeneticsandimageprocessing,whichisresultinginasubstantialbroadeningofmyresearchhorizons.”
“Itisagreatpleasuretobecomeacorepartofthesetwomajorinstitutes.Itreflectsthestrengthwehaveinlifesciencesresearchacrossmanydisciplines.”
Professor Peter JS Smith Director of the Institute for Life Sciences
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For more than 40 years, scientists at the University of Southampton have been at the very forefront of cancer immunology research and have an international reputation for bench to bedside results.
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programmeinapplicationsoftopologyspecificallytocancerimmunology.”
Studying at the boundaries of Maths and MedicineIfLSstudentJosephEganisamathematicalmodellerbasedattheCCI,whoisusinghismathematicalskillstohelpthecancerimmunologistsbetterunderstandtheinteractionsbetweencellsoftheimmunesystemandtumourcells.
HewasinspiredbytheinterdisciplinaryresearchattheCCIanddecidedtotakeupthePhD,whichcrossestheboundariesofMathsandMedicine.
Hesaid:“I’mreallyinterestedinusingmymathematicalmodellingskillsinareal-worldsetting.Iworkwithateamofleadingimmunologists,andtheideaofbeingabletodevelopmodelsbasedontheirexperiments,andforthesemodelstothenguidefutureexperiments,isincrediblyexciting.”
Attracting leading international researchersSouthampton’sinterdisciplinarycultureandinternationalreputationfortranslational
researchwereinstrumentalinattractingProfessorSallyWardandProfessorRaimundObertotheCCI.
Leadersinthefieldofantibody-relatedtherapeutics,thepairrelocatedtotheCCItoheadupajointinterdisciplinarylaboratory.ThislaboratorycombinesSally’sexpertiseinfindingnewwaystoengineerantibodiestohelpthemdestroycancercellsandunderstandhowimmuneresponsescanbemodulatedfortherapy,andRaimund’sresearchindevelopingnewsuper-resolutionimagingtechniquestostudythefateoftherapeuticanti-cancerantibodiesastheyattackcancercells.
Theirpre-clinicalresearchhasalreadyhelpedthemsecuretwokeygrantstosupporttheirresearch–£2.2mfromCancerResearchUKand£2.7mfromtheWellcomeTrust.
Sallysaid:“WewereimpressedwiththestrongethosofinterdisciplinarityatSouthampton.TheCCIandtheIfLSaregreatexamplesofhowthiscanbeembeddedwithinorganisations.WehavealreadybeenliaisingwithmembersoftheIfLSaboutpotentialwaysofworkingtogetherinthefuture.”
Findoutmore: www.southampton.ac.uk/youreit
TheCentreforCancerImmunology(CCI)–theUK’sfirstdedicatedcentreforcancerimmunologyresearch-wasdevelopedbytheUniversitytobringtogetherworld-leadingscientiststoimproveourunderstandingofhowimmunitytotumourscanbestimulatedandtoexpandclinicaltrialsanddevelopmorelifesavingdrugsinthisexcitingandpromisingareaofcancerresearch.
AttheheartoftheCCIistheethosofinterdisciplinarityandtranslationalmedicine–principlesthataresupportedbytheUniversity’sInstituteforLifeSciences(IfLS)withwhichtheCCIhasacloseaffiliation.
CCIDirectorandDeputyDirectoroftheIfLSProfessorTimElliottsaid:“ThesetwoprinciplesarepillarsoftheIfLSandIwaskeentoensurethattheyarecentraltotheresearchstrategyoftheCCI.Ourresearchincancerimmunologyreliesonscientistsfrommanydifferentfields
workingcloselytogethertosolvekeychallengesanddriveforwardresearchinthisarea;anditsapplicationtotreatingcancerreliesonintegratedteamsofdoctors,scientists,nursesandclinicaltrialsexperts.”
A close collaborationTimsaid:“TheIfLShascreatedanenvironmentwhereresearchersunderstandthevalueofworkingacrossdisciplines.Thishashelpedusestablishrealinterdisciplinaryconnectionsthatareenablingustochannelourdiscoveriesfromourlabstopatientsfortheveryfirsttime.
“TheIfLShashelpedtobrokerimportantinterdisciplinaryconnectionsforus.Combiningourimmunologyexpertisewithworld-leadingengineers,computerscientists,chemistsandmathematicians,allowsustotacklebigquestionslikehowthehumanimmunesystemreactstocancer,ininnovativeways.”
Embedding in the CCIIfLSmemberandProfessorofPureMathematicsJacekBrodzkiisthefirstresearchsabbaticalfellowtospendayearembeddedintheCCI,usinghisskillsintopologicalmodellingtechniquestobetterinformandunderstandbigdatainscientificexperiments.
Jaceksaid:“Cancerimmunologyresearchisbasedoncutting-edgeexperimentsthatcreatevastamountsofreallycomplexandmultidimensionaldatawhichisnoteasytoanalyseusingthestandardmethods.Topologicaldataanalysisprovidesnewinsightsintotheoutcomesofexperimentsandsuggestsnewwaystoorganiseandinterpretthedata.
“Mysabbaticaloffersmethecrucialopportunitytospeakdirectlytotheexpertstounderstandtheunderlyingproblemsandmotivationsfortheexperiments.IamplanningtodevelopnewmethodologiestosupporttheworkattheCentre,andsetupanewresearch
COLLABORATING AT THE FOREFRONT OF CANCER IMMUNOLOGY
“TheCentreforCancerImmunologyisuniqueinitsinterdisciplinaryandtranslationalapproachtocancerresearchinvolvingresearchersfrommanydifferentdisciplinesrangingfrommathematicianstoclinicalresearchers.CollaboratingwithIfLSresearchersprovidesexceptionalopportunitiesforgroundbreakingresearch.”
Professor Raimund Ober Professor of Imaging and Biomedical Engineering, Centre for Cancer Immunology, Southampton
Professor Tim Elliott Professor Sally Ward
Professor Jacek Brodzki and Joseph Egan
The Centre for Cancer Immunology
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Health and Medicine
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REVOLUTIONISING BIOMEDICAL IMAGING
“Thisresearchisanexcellentexampleofhowfundingofasmallpilotprojectlaysthefoundationresultingseveralyearslaterinmajorgrantfunding.Thisisafantasticcollaborativeachievement.”
Professor Peter JS Smith Director of the IfLS
“CouplingexpertisefromMedicineandEngineeringacrossthedisciplinaryboundarieshasbeenfundamentaltothisprojectandhasresultedinsignificantresearchfundingandcommercialengagement.”
Professor John Holloway Associate Dean (Research) in Medicine
“Thisprojectbuildsonourlong-standingcollaborativecommitmenttohigh-resolutionX-rayimagingatSouthampton.Inthefieldofimagingconventionallymountedbiomedicalsamples,theteamsatSouthamptonareclearlyworldleaders.”
Ian Haig VP Engineering, X-ray Special Projects Nikon X-Tek Systems Ltd
Over the last two decades, high-resolution 3D imaging of hard tissues such as bones and teeth by X-ray micro-computed tomography (µCT) has become a routine tool in biomedical and pre-clinical research.
Untilrecentlyithasbeenthoughtimpossibletogeneratesimilarhigh-resolutionµCTimagesfromsofttissuesthathavenotbeenspeciallypreparedforincreasedX-raycontrast.
PioneeringresearchbyaninterdisciplinaryteamofInstituteforLifeSciences(IfLS)membershasrevolutionisedthisareaofbiomedicalimagingbydevelopingaµCTscannercapableofproducingnon-invasive3Dscansofsofttissuebiopsiesatmicroscopicresolutions.ItrevealsfeatureshundredsoftimesmoredetailedthanconventionalCTscans-comparableto2Dlightmicroscopyimagesfromconventionaltissuesections.
ThefirstgenerationofthisscannerhasbeenoperationalinSouthamptonforthelastthreeyearsandavarietyofsofttissuesamplesincludinglung,colonandliverhavebeenimagedandanalysed.TheworkisattractinginternationalinterestfrombiomedicalresearchersandclinicianskeentotryµCTintheirwork.
Theresearchhasfurtherstrengthenedandestablishednewrelationshipswithindustrialpartners,includingNikonX-TekSystemsLtdandDECTRISLtd.TheteamatSouthamptonhasreceivednearly£2mofWellcomeTrustfundingandsupportfromindustrytodevelop,standardiseanddriveuptakeoftheirinnovativeμCTtechnologyfor3DX-rayhistology.
The historyFiveyearsago,thehighlyinterdisciplinaryteamofresearchersfromMedicineandEngineering,togetherwiththeBiomedicalImagingUnit(BIU)andtheµ-VISX-rayImagingCentre,receivedproof-of-conceptfundingfromtheIfLS.
DrPhilippSchneider,AcademicDirectoroftheµ-VISX-rayImagingCentre,said:“ThatinitialIfLSfundingencouragedustocomeclosertogetherasacohesiveunit,tofurtherdevelopourresearch,andgeneratemicroscopic3D
imagesoflungtissuefromwhichwecouldgatherproof-of-principledatatodemonstratewhatweweretryingtoachieve.”
DrPeterLackie,AcademicLeadintheBIU,said:“Thepilotdatawecreatedwascrucialandground-breaking.Itwasthefirsttimethatanyonehaddonethis3Dscanningofsofttissueinstandardwaxblocks,anditallowedustobidforfurtherfundingculminatinginthelargeWellcomeTrustgrants.”
Potential impactThishigh-resolutionwayofscanningsofttissuesistheimagingofthefuture.Itopensupawealthofnewinformationtobiologists,biomedicalscientists,medicalresearchersandclinicians,enablingthemtoseeandquantitativelyanalysethemicrostructuresofsofttissuebiopsiesintheir3Dcontext.
Theselungtissuescanshavealreadyhelpedmedicalresearcherstounderstandmoreaboutrespiratorydiseases.Theyhaverevealedimportantdetailsoftheprocessesinvolvedinlungfibrosisandchronicobstructivepulmonarydiseasethatwillhelpinformfuturetreatments.
ManageroftheBIUDrAntonPagesaid:“Theresearchisacriticalpartofourinternationallycompetitive3DbiomedicalimagingcapabilityatSouthampton.”ProfessorIanSinclair,SeniorAdvisoroftheµ-VISX-rayImagingCentre,said:“Wehavealreadyhadinterestfrommedicaland
biomedicalresearchers,andcliniciansacrossEuropewhowouldliketoemploythistechnology.”
CollaborationTheteam’smaincollaboratorduringtheprojecthasbeenNikonX-TekSystems,whoco-fundedtwoPhDstudents,anddevelopedthescannerthatwasusedfortheinitialworkfundedbyaWellcomeTrustPathfindergrant.
InadditiontothesystematSouthampton,otheridenticalprototypeshavebeeninstalledatGreatOrmondStreetHospital(GOSH)LondonandMemorialSloanKetteringCancerCentreinNewYorkandarebeingusedtodevelopotherapplicationsofµCTinmedicine.
Theteamhasalsoliaisedwithexperthistopathologistsaroundtheworld,receivingpositivefeedbackaboutthe3Dmicrostructuresandthediagnosticallyrelevantinformationtheirscansreveal.
The futureTheirsecondWellcomeTrustgrantaimstoincreasethescanner’sthroughput;standardisetheimageacquisitionandprocessingworkflows;raiseawarenessanddriveuptakeof3DX-rayhistology;andfurtherbenchmarkstate-of-the-artX-raysourceanddetectortechnologytobeintegratedinthefuture.TheyarelookingforwardtocollaboratingwithUniversitycolleaguestofullyexploittheirnoveldata,usingmachinelearningtoolsandartificialintelligencefordiagnosisofdiseasesandpatientstratification.
DECTRISLtdistheworldleadingHybridPhotonCounting(HPC)detectormanufacturerforscientificapplicationsandwillprovideaHPCdetectortogeneratezeroelectronicnoiseandfastimagingathighresolutionandmaximumsharpness.
Findoutmore: www.xrayhistology.org
3D X-ray histology: Setting up a μCT scan of a standard human biopsy specimen.
Image: First-of-a-kind soft tissue-optimised micro-computed tomography(µCT) scanner in Southampton for 3D X-ray histology. https://doi.org/10.1016/j.ajpath.2019.05.004
Life Technologies
CATALYSING OUR EXPERTISE IN ECOLOGY AND EVOLUTION
Withspeciesunderthreatandhabitatsbeingdestroyed,wearehavingtotakeacloselookathowwecanprotectourecosystemsandsustainourlivingsystemsforthefuture.
AtSouthampton,wehavesignificantresearchstrengthsinecologyandevolutionthatarehavinganimpactonunderstandingtheresilienceofspeciesfromthesmallestorganismtothemostcomplexecosystem.
ThisexpertiseacrosstheUniversityisbeingdrawntogetherbytheInstituteforLifeSciences(IfLS)tocreateastrong,cohesivenetworkofresearchandeducation–theEvolutionGroupthatisfacilitatinginterdisciplinaryworkbetweendiverseareasincludingOceanandEarthSciences(OES),BiologicalSciences,Mathematics,ElectronicsandComputerScienceandEngineering.
Southampton’s expertiseDirectoroftheIfLSProfessorPeterJSSmithsaid:“AcrosstheUniversitytherearetremendousskillsetsintheareasofecologyandevolutionandweareseizingtheopportunitytobringthisgrouptogetherasonecohesivecommunity.
“AspartofSouthampton’slifesciencesstrategy,wewanttheUniversitytoberecognisedasahubofexpertiseintheseareas.Bydrawingtogetherallofthesegroups,theywillbeinastronger,unifiedpositiontoexpandtheirresearchimpact,enablemorecollaborativeopportunities,andfurtherincreasetheirsignificantgrantincome.”
Workingtogethertotargeteco-evolutionarysynergies,IfLSmemberDrThomasEzardisco-ordinatingtheevolutionaryaspectswithDrJasminGodboldco-ordinatingontheecologyside.
Thomassaid:“TheUniversityisdemonstratingtheimpactoftheexcellentresearchthatisbeingcarriedoutinvariousareasofevolution.Inthelastthreeyears,wehavewonmorethan£2.5mfromtheNaturalEnvironmentResearchCouncil(NERC)andtheBiotechnologyandBiologicalSciencesResearchCouncil(BBSRC).Wearealsoakeypartofaninternationalmultidisciplinaryteamtakingpartina$8.5mprojectsupportedbytheJohnTempletonFoundationwhichrecognisestheimportanceofintegratedsciencesacrossdisciplines.”
Studying the adaptive response of batsIfLSmemberDrOrlyRazgourisaNERCIndependentResearchFellowandLecturerinEcologywhoisexploringtheevolutionaryandecologicalresponsestoglobalchangetounderstandhowwecanbettermanagetheenvironmentandconservebiodiversity.
Sheprimarilyfocusesonlookingattheeffectofenvironmentalchangeonbatsandthewaytheyhaverespondedtothesechanges.
Shesaid:“Batsaregoodindicatorsbecausetheyareawidespread,diversegroupoforganismsthatenableustostudythepotentialresponsesofbothbirdsandmammals.MyresearchisinvestigatinghowenvironmentalchangehasaffectedbatspeciesacrossEurope,AfricaandtheMiddleEasttohelpidentifythetraitsthatmakethemparticularlyvulnerabletofuturechange.
“Byunderstandinghowtheyadaptandhowtheabilitytoadaptdiffersbetweenpopulations,wecanlookatwhereweneedtofocusourconservationefforts.”
Orlyrecognisestheimportanceofinterdisciplinaryworkinherresearch.Shesaid:“Thesearebigglobalissuesthatrequireanalysisanddatafromdifferentdisciplinesinordertofullyunderstandtheproblemsandwhattheresponsestothoseproblemsare.
“IamworkingwithotherevolutionarybiologistsfromacrosstheUniversitytotryanddevelopmathematicalmodelsofevolutionandadaptiveresponses.Thesedifferentstrengthsfromdifferentfacultiesarevitaltoadvancemyresearch.”
Crop domestication as a model for evolutionAssociateProfessorinBiologyDrMarkChapmanisusingBrassicacropstodeliveranewunderstandingofhowevolutionworks.
AspartofhisNERCandBBSRCprojectwithDrThomasEzard,fromOES,MarkisexaminingBrassicas,suchasturnipsandcabbages,tofindouthowpopulationsdivergeandbecomeseparatespecies.Heislookingathowindividualplantschangetobestmatchtheprevailingenvironment–knownasphenotypicplasticity.
Hesaid:“Wehaveseenthatwildturnipsgrowninacultivated-likeenvironmentstarttoresemblecultivatedturnips,andtheirgeneexpressionstartstoaltertoo.Soweareaskingourselvesifwildspecieshavebeenselectedbyhumansbecauseofthisplasticity?
“ByanalysingseveralBrassicacropsandtheirwildrelatives,wecanseeifthesamechangeshappenindifferentspecies,givingusanewunderstandingofevolutionandhowimportantthedifferenttypesofplasticityareindrivingevolutionarydivergenceamongspecies.”
Safeguarding the future of our planet is the biggest challenge facing society today.
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01 DrJasminGodboldandDrAdamReedmeasuringthesizeofamudstarattheUniversity’sBiodiversityEcosystemFuturesFacility.
02 DrOrlyRazgoursamplingbatsinSpaintostudyadaptationsalongclimaticgradients.
03 DrMarkChapmanandpostdoctoralresearchfellowJasmineSabanprepareDNAsamplesforgenomesequencing.
04 FossilisedplanktonbeingstudiedinDrThomasEzard’slab
05 Examiningthephenotypesofplantsindifferentgrowthenvironments.
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Living Systems
Southampton’s unique in-depth expertise in multi-omic technologies, combined with access to patient cohorts from world-leading collaborative clinical partners, is helping to transform precision medicine across the disease spectrum from cancer immunology to respiratory conditions.
Thenewly-establishedIntegrativeMolecularPhenotypingCentre(IMPC)isbringingtogether’omicexpertsfromacrosstheUniversitytousemulti-omicdata,incombinationwithclinicaldata,tobetterunderstanddiseaseandenablemorepersonalisedandeffectivehealthcaretreatmentanddiagnosis.
ThenewCentre,whichispartoftheInstituteforLifeScience(IfLS),willdriveforwardinterdisciplinaryresearchusingmolecularphenotypingtoexploreindividualvariabilityingenes,environmentandlifestyle.Thiswillallowdoctorsandresearcherstopredictmoreaccuratelywhichtreatmentandpreventionstrategiesforaparticulardiseasewillworkinwhichgroupsofpeople.
Southampton’s unique positionDrPaulSkipp,AssociateProfessorinProteomics,isleadingthedevelopmentoftheCentrethatdrawstogetherexpertisefromMedicine,BiologicalSciences,MathematicsandEngineering.Hesaid:“Southamptonisinauniquepositionbecausewehaveexpertsinnumerous’omictechnologiesanddatascienceandhaveexcellentcollaborationwithourclinicalpartnersbothintheUKandacrossEurope.
“Itisonlybyworkingtogetherthatwecanreallyunderstandthemechanismsbehinddiseases.Notonlyarewecarryingouttheinnovative
researchhere,butourestablishedclinicallinksmeanwecantranslatethatresearchintotheclinicandthroughtothepatient.
“Byusingmolecularsignaturesfrommulti-omicsdata-genomics,transcriptomics,proteomics,glycomicsandmetabolomics-incombinationwithclinicaldata,wecanenablebettertailoringofexistingtreatments,andpavethewayforthedevelopmentofnewtherapeuticsanddiagnosticsforimprovedpatientoutcome.
“However,thedatathatwearegeneratingfromthisresearchishuge.TheIMPCwillenableustodevelopcriticalnewapproachestointegrateandanalysethisdataandextracttheinformationweneedfromthesebigdatasets.
“ThecombinationofalltheworkwearedoingatSouthampton,particularlyintheareasofcancer,respiratoryandinfectiousdisease,ischangingthewaywelookatdiseaseandplacesusasleadersinprecisionmedicine.”
Research impactSouthamptonisalreadymakinganimpactinmolecularphenotypingandprecisionmedicine:
TopoMD - isagroupofscientistsandmathematiciansfromtheUniversitywhoseexcitingresearchispromisingtorevolutionisehealthcarebyallowinghighresolutioninvestigationofmolecularmechanismsunderlyingdisease,andthereforeenabling
developmentoftargetedtreatmentsforapplicationinpersonalisedmedicine.Theyareusingrevolutionarytopologicalalgorithmstoplottheshapeofapatient’sgeneexpressionandcompareittotheshapeofgeneexpressioncharacteristicofdiseasesforpreciseandaccuratediagnosis.
Asthma –usingclinicaland’omicsdatafromhundredsofadultsandchildrenwithsevereasthmaweareabletounderstandmoreaboutdifferenttypesofasthmatoensurebetterdiagnosisandtreatmentforeachpersonanduncovernewinformationandideasthatcouldleadtothecreationofeffectivenewtreatments.Theteamhasrecentlyidentifiednovelmolecularsub-typesofasthmathatareusedinclinicaltrialstobetterpredicttherapeuticefficacy.
Cancer -incollaborationwiththeSouthamptonCentreforCancerImmunology,theteamisusingmulti-omicsapproachestoidentifyhumanleukocyteantigen(HLA)class-Iandclass-IIpeptidespresentedtoT-cellsinanumberofcancerswhicharecrucialfordesigninginnovativepersonalisedtherapeuticsandvaccinesagainstcancerandotherdiseases.
Breast cancer – usingmolecularphenotypingdatacollectedfrom3,000patientsoverfiveyears,wearediscoveringnewbiomarkersforassessingtheriskofdevelopingsecondarybreastcancer,breastcancerrecurrenceandhowdietandlifestylefactorscouldinfluencetheoutcomeofthedisease.
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TRANSFORMING PRECISION MEDICINE THROUGH DATA ANALYTICS
Image: Dr Paul Skipp15
Insights Through Data
ThreeyearsagoChriswonanationalaward-theprizeforbestresearchposterattheNationalNursesNutritionGroupannualconference.
Morerecently,hehasdevelopedarepresentativefeedingmodeltohelpsimulatebiofilmcontaminationoninfantfeedingdeviceswithinalaboratorysetting;istalkingabouthisworkatTheAmericanSocietyforMicrobiology’s(ASM)Annualconference,inSanFrancisco,forwhichhehasbeenawardedtheirASMStudentandPostdoctoralTravelAward;andisrunningaclinicaltrialatSouthampton’sPrincessAnneHospitalneonatalunit,collectingusedtubestogaina
deeperunderstandingonthetruediversityofcontaminants.
Hesaid:“Thedatafromtheclinicaltrialisbeinganalysedandisstartingtouncoverfascinatinginformationaboutthetruediversityofmicro-organismsfound,andhowdifferentspecificcareregimesarealteringthesepopulations.
“Therepresentativefeedingmodelaimstogetadeeperunderstandingofcontamination,butalsoprovideatoolforhealthcareprofessionalstomodelandunderstandhowdifferentfeedingandcareregimescouldhaveimpactsoncontamination.”
Chris’postgraduatethesisresearch,fundedbytheIfLS,HealthSciencesandBiologicalSciences,isnearingcompletion.Hesaid:“TheopportunitytoundertakesuchaprojectisonlypossibleduetothesupportandinfrastructureprovidedtomeaspartofmystudentshipandisarealtestimonytothequalityofresearchthatcanbeconductedattheUniversity.
“TheexperienceIhavegained,combinedwiththeopportunitiesaffordedme,hasallowedmetoenjoymyresearchexperience,andIamexcitedtocontinuemyresearchcareerintothefuture.”ChrisissupervisedbyDrSandraWilks,ProfessorBillKeevilandProfessorMandyFader.
InterdisciplinaryresearchersintheInstituteforLifeScience(IfLS)havereceivedthreeprojectgrantsfromtheGlobalChallengesResearchFund(GCRF)-a£1.5billionfundannouncedbytheUKGovernmenttosupportcutting-edgeresearchthataddressesthechallengesfacedbydevelopingcountries.
The IfLS-related projects are:
− AcademicsfromEngineeringandPhysicalSciences,HealthSciencesandMedicineareworkingonathree-yearprojecttoimproveaccesstoartificiallimbsinlowerandmiddleincomecountries.TwostudiesarebeingcarriedoutwithclinicianandeducationpartnersinCambodia,aimingtodevelopdigitaltoolstoincreaseprostheticandorthoticservices,trainprosthetist-orthotistsandensurefundingisspentmoreefficiently.
− Infectionresearchers,engineersandbioinformaticiansfromSouthamptonandUniversityCollegeLondonhavedevelopedanew3Dsystemtostudyhumaninfectioninthelaboratory.ThespheresareallowingresearcherstocarryoutaprojectinDurban,SouthAfrica,tofurtherinvestigatewhathappensinthehumanbodywhentuburculosisdevelops.Theirlong-termaimistoidentifynewantibiotictreatmentsandvaccines.
− ResearchersinSouthamptonandMalaysiaarecarryingoutapioneeringstudythatcouldleadtothedevelopmentofavaccinetopreventheadandneckcancer.TeamsbasedattheNIHRCRUKSouthamptonExperimentalCancerMedicineCentreandCancerResearchMalaysia,arestudyingprecancerouslesionsinthemouthwhich,ifleftuntreated,canprogressintoheadandneckcancer.Theyarefocusingontestingthelesionsformarkerswhichcanthenbetargetedbyvaccinationandisthefirststudyaimedatcreatingavaccinetopreventaformofcancerdeveloping.
InstituteforLifeSciences(IfLS)memberProfessorRoxanaCarare,togetherwithDrChristopherKippsattheUniversityHospitalSouthamptonNHSFoundationTrust,areleadingthecreationofanewinterdisciplinaryresearchcentretoaddressnationalchallengesinthefieldsofdementiaandbrainageing.
Theunderstandingofdementiaandneurodegenerativedisease,togetherwithimprovedtherapiesanddeliveryofcareforpeoplewiththeseconditions,isapressingneedintheUK,andtheSouthCoastregionisrecognisedasanareawheretheseproblemsareparticularlyacute.
TheInterdisciplinaryDementiaandAgeingCentre(IDeAC)isbringingtogetherlocalexpertisefromacrosstheresearchspectrumtoformadedicatedinterdisciplinarydementiaandageingresearchcentretoaddresstheproblemsinthiscomplexfield.
TheIDeACnetwork,whichisworkingcloselywiththeIfLS,includesbasicscientists,clinicians,healthandsocialcaredeliveryresearchers,epidemiologists,imagers,mathematicians,andcomputinganddatascientists.
Roxanaisinternationallyrenownedforherresearchintothecausesofdementiaandfindingnewtherapeutictargetstohelpthemanypeopleaffectedbythedisease.Shesaid:“Thereisconsiderablelocalexpertiseinageinganddementiaandouraimistobringthistogetherintoanetwork.IDeACwillseektoenergise,co-ordinateandfocuseffortstoputusinastrongpositiontoattractandsustainfundingforanationallyrecognisedcentre.”
Christopherisabehaviouralneurologistwithexpertiseindementiadiagnosis,clinicaltrialsanddementiaservicedelivery.Hesaid:“Onethirdofuswillbedirectlyaffectedbydementiaatsomepointinourlives.Weneedtoadvanceourknowledgeateverypointalongthedementiapathwayfrombasicsciencetotheorganisationofclinicalservicestosupportpatientsandtheircarers.ThisisanexcellentopportunitytomakethishappeninSouthampton.”
RESEARCHING BIOFILMS IN INFANT FEEDING TUBES
ADDRESSING THE CHALLENGES IN DEVELOPING COUNTRIES
NEW RESEARCH CENTRE TO TACKLE DEMENTIA AND BRAIN AGEING
Institute for Life Sciences (IfLS) PhD student Chris Winnard’s research into the development of biofilms in neonatal nasogastric tubes has been going from strength to strength.
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The team is developing technologies to improve access to prosthetics.
Image: Team discussing infant feeding tubes in the Neonatal Unit, Princess Anne Hospital.
Image: Human arteries with amyloid (red) in Alzheimer’s disease.
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In Brief
Institute for Life Science (IfLS) PhD students work on novel interdisciplinary research projects with support from a supervisory team across the project disciplines. This supportive interdisciplinary environment, shaped by the IfLS and host faculties, creates a unique training and development experience for the next generation of leaders.
A sample of publications from our interdisciplinary postgraduate students: 2018-2019
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Health and Medicine
AshtonJJ,BorcaF, Mossotto E,CoelhoT,BatraA,AfzalNA,PhanHTT,StantonM,EnnisS&BeattieRM(2019).Increasedprevalenceofanti-TNFtherapyinpaediatricinflammatoryboweldiseaseisassociatedwithadeclineinsurgicalresectionsduringchildhood.Alimentary Pharmacology Therapeutics49(4),398–407.DOI:10.1111/apt.15094
Jevons LA, HoughtonFD&TareRS(2018).Augmentationofmusculoskeletalregeneration:roleforpluripotentstemcells.Regenerative Medicine 13(2),189-206.DOI:10.2217/rme-2017-0113
Scarpa E, JaneczekAA,HailesA,deAndrésMC,DeGraziaA,OreffoROC,NewmanTA&EvansND(2018).PolymersomenanoparticlesfordeliveryofWnt-activatingsmallmolecules.Nanomedicine 14(4),1267-1277.DOI:10.1016/j.nano.2018.02.014
Sri S, Pegasiou CM,CaveCA,HoughK,WoodN,Gomez-NicolaD,DeinhardtK,BannermanD,PerryVH&Vargas-CaballeroM(2019).Emergenceofsynapticandcognitiveimpairmentinamature-onsetAPPmousemodelofAlzheimer’sdisease.Acta Neuropathologica Communications 7,25.DOI:10.1186/s40478-019-0670-1
Sutton EJ,BradshawRT,OrrCM,FrendéusB,LarssonG,TeigeI,CraggMS,TewsI&EssexJW(2018).Evaluatinganti-CD32bF(ab)conformationusingmoleculardynamicsandsmall-angleX-Rayscattering.Biophysical Journal 115(2),289-299.DOI:10.1016/j.bpj.2018.03.040
Life Technologies
Anderson WJ,NowinskaK,HutterT,MahajanS&FischlechnerM(2018).Tuningplasmonslayer-by-layerforquantitativecolloidalsensingwithsurface-enhancedRamanspectroscopy.Nanoscale 10,7138-7146.DOI:10.1039/C7NR06656B
Boags AT,SamsudinF&KhalidS(2019).Bindingfrombothsides:TolRandfull-lengthOmpAbindandmaintainthelocalstructureoftheE coli cellwall.Structure27,713-724.e2.DOI:10.1016/j.str.2019.01.001
Boags AT,SamsudinF&KhalidS(2019).DetailsofhydrophobicentanglementbetweensmallmoleculesandBraun’slipoproteinwithinthecavityofthebacterialchaperoneLolA.Scientific Reports 9,3717.DOI:10.1038/s41598-019-40170-z
Moura CC,BourdakosKN,TareR,OreffoROC&MahajanS(2019).Live-imagingofbioengineeredcartilagetissueusingmultimodalnon-linearmolecularimaging.Scientific Reports 9,5561.DOI:10.1038/s41598-019-41466-w
Moura CC,LanhamSA,MonfortT,BourdakosKN,TareR,OreffoROC&MahajanS(2018).Quantitativetemporalinterrogationin3Dofbioengineeredhumancartilageusingmultimodallabel-freeimaging.Integrative Biology 10,635-645.DOI:10.1039/C8IB00050F
Núñez JA,GoringA,JavaheriB,RaziH,Gomez-NicolaD,HesseE,PitsillidesAA,ThurnerPJ,SchneiderP&ClarkinCE(2018).RegionaldiversityinthemurinecorticalvascularnetworkisrevealedbysynchrotronX-raytomographyandisamplifiedwithage.European Cells and Materials35,281-299.DOI:10.22203/eCM.v035a20
YangX,LennardKR,HeC,WalkerMC,BallAT,Doigneaux C,TavassoliA,&vanderDonkWA(2018).Alanthipeptidelibraryusedtoidentifyaprotein–proteininteractioninhibitor.Nature Chemical Biology 14,375–380.DOI:10.1038/s41589-018-0008-5
Living Systems
Ratto F,SimmonsBI,SpakeR,Zamora-GutierrezV,MacDonaldMA,MerrimanJC,TremlettCJ,PoppyGM,PehKS-H&DicksLV(2018).Globalimportanceofvertebratepollinatorsforplantreproductivesuccess:ameta-analysis.Frontiers in Ecology and the Environment 16(2),82-90.DOI:10.1002/fee.1763
Insights through Data
AshtonJJ,BonduelleQ,Mossotto E,CoelhoT,BatraA,AfzalNA,VadgamaB,EnnisS&BeattieRM(2018).Endoscopicandhistologicalassessmentofpaediatricinflammatoryboweldiseaseovera3-yearfollow-upperiod.Journal of Paediatric Gastroenterology and Nutrition 66(3),402-409.DOI:10.1097/MPG.0000000000001729
The Life Sciences Building
IfLS Student Publications 2018-19
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AshtonJJ,BorcaF,Mossotto E, PhanHTT,EnnisS&BeattieRM(2018).Analysisandhierarchicalclusteringofbloodresultspriortodiagnosisinpaediatricinflammatoryboweldisease.Inflammatory Bowel Diseases izy369.DOI:10.1093/ibd/izy369
AshtonJJ,Mossotto E, EnnisS&BeattieRM(2019).Personalisingmedicineininflammatoryboweldisease—currentandfutureperspectives.Translational Pediatrics 8(1),56-69.DOI:10.21037/tp.2018.12.03
Lee KM,BiedermannS&MitraR(2018).Optimaldesignforexperimentswithpossiblyincompleteobservations.Statistica Sinica 28,1611-1632.DOI:10.5705/ss.202015.0225
Lee KM,BiedermannS&MitraR(2018).Optimaldesignwhenoutcomevaluesarenotmissingatrandom.Statistica Sinica 28,1821-1838.DOI:10.5705/ss.202016.0526
Lee KM,BiedermannS&MitraR(2019).D-optimaldesignsformultiarmtrialswithdropouts.Statistics in Medicine 38(15),2749-2766.DOI:10.1002/sim.8148
Mossotto E,AshtonJJ,O’GormanL,PengellyR,BeattieRM,MacArthurB&EnnisS(2019).GenePy-ascoreforestimatinggenepathogenicityinindividualsusingnext-generationsequencingdata.BMC Bioinformatics20,254.DOI:10.1186/s12859-019-2877-3
Testori M,HoyleR&EisenbarthH(2019).Howgroupcompositionaffectscooperationinfixednetworks:canpsychopathictraitsinfluencegroupdynamics?Royal Society Open Science 6,181329.DOI:10.1098/rsos.181329
Testori M, HarrisT,HoyleR&EisenbarthH(2019).TheeffectofpsychopathyoncooperativestrategiesinaniteratedPrisoner’sDilemmaexperimentwithemotionalfeedback.Scientific Reports9,2299.DOI:10.1038/s41598-019-38796-0
Wang T,BredeM,IanniA&MentzakisE(2018).Socialinteractionsinonlineeatingdisordercommunities:anetworkperspective.PLoS ONE13(7),e0200800.DOI:10.1371/journal.pone.0200800
Wang T, BredeM,IanniA&MentzakisE(2019).Characterizingdynamiccommunicationinonlineeatingdisordercommunities:amultiplexnetworkapproach.Applied Network Science 4,12.DOI:10.1007/s41109-019-0125-4
Wang T,MentzakisE,BredeM&IanniA(2019).EstimatingdeterminantsofattritionineatingdisordercommunitiesonTwitter:aninstrumentalvariablesapproach.Journal of Medical Internet Research 21(5),e10942.DOI:10.2196/10942
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Page title“Southampton’s mental health research
activity brings together doctors, psychologists, neuroscientists and health
scientists to deliver translational research that will positively impact on people’s lives.
Our expertise in child development, psychological interventions and affective neuroscience combine to deliver cutting
edge research that has the potential to improve mental health treatments and
wellbeing across the lifespan.”
Professor Matthew Garner Institute for Life Sciences and SoNG member
and Head of Psychology University of Southampton
“Globalchallengeswillonlybemetwhenresearchersworktogetherincross-disciplinarypartnerships.Ourfuture-lookingIfLSstudentshipschemefosterssuchcollaborationstodevelopthenextgenerationofresearchleaders.Weareimmenselyproudofouroutstandingstudentsandfullyexpectthemtobethemoversandshakersoftheirchosencareers.”
Professor Mandy Fader ProVice-Chancellor(InternalPartnerships)
Image: Changing Minds through Neuroscience Inspired Fashion is a collaboration between Peter Symonds College, the
University’s Winchester School of Art and the Southampton Neuroscience Group (SoNG) which aims to raise awareness of
mental health. Dress designed by Stephanie Orlowski. It is shaped like a butterfly with repeated prints of brain scans from
a stroke patient and is worn with a “cocoon” cape.
