CV – Burcu Şimşir
BURCUŞİMŞİR
(865)2743884,bsimsir@vols.utk.edu
EDUCATION
DoctorofPhilosophyinCivilandEnvironmentalEngineeringExpectedAugust2016
UniversityofTennessee,Knoxville,TN,USA
DissertationTitle:EcologyofOrganohalide-RespiringDehalococcoidia:
CommunityInteractions,StrainDiversityand
AdaptiveEvolution(Advisor:Dr.FrankE.Löffler)
DissertationCommittee:FrankE.Löffler,GaryS.Sayler,
KostasT.Konstantinidis,QiangHe,TerryC.Hazen
BachelorofScienceinEnvironmentalEngineeringJuly2010
MiddleEastTechnicalUniversity(METU),Ankara,Turkey
BachelorofScienceinChemicalEngineeringJun2006
UniversityofAnkara,Ankara,Turkey(transferredafter1stgrade)
RESEARCHINTEREST
Environmentalmicrobiology,molecularbiology,omics,bioinformatics,anaerobic
environmentalbiotechnology,wastewatertreatment,renewableenergyandpollutionprevention
RESEARCHEXPERIENCE
GraduateResearchAssistant2010-Present
UniversityofTennessee,Knoxville,TN,USA(withDr.FrankE.Löffler)
• CollaboratedwithanengineerfromGeosnytecConsultanttoexplorenatural
attenuationpotentialofachlorinatedsolvent-contaminatedsitebyapplying
acombinationofhydrogeologicalandmicrobiologicalanalyses.
• Identifyimportantcommunitymembersindechlorinatingmixedculturesandexplore
functionalinteractionsbetweenDehalococcoidesandothercommunity
membersusinganaerobicdechlorinatingculturesandcomparative
metagenome/transcriptomeanalyses.
• CollaboratewithDr.JunYantocarryoutaprojectaimedtoexploreDehalococcoides
nutrientrequirements(e.i.,corrinoidcofactor)usingvariousdechlorinatingmixed
culturesandDehalococcoidespurecultures.
• Investigatediversityofreductivedechalogenasegenesapplyingampliconsequencing
andcomparativesequenceanalyses.
• ExploreDehalococcoidesadaptiveevolutionprocessapplyingcomparativemetagenome
analysesofcontaminatedvsnon-contaminatedsitematerials.
GraduateResearchAssistant2011-Present
OakRidgeNationalLaboratory,OakRidge,TN,USA(withDr.FrankE.Löffler)
EnergyandEnvironmentalSciencesDivision,BiosciencesDivision.
• Contributetoaprojectaimedatdesigningahigh-throughputqPCRtoolformonitoring
andpredictingreductivedechlorinationactivityoforganohalide-respiringChloroflexi.
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RESEARCHEXPERIENCECONTINUED
OakRidgeNationalLaboratory,OakRidge,TN,USA(withDr.FrankE.Löffler),continued
• Conduct454-pyrosequencing,metagenomesequencingtoidentifycommunity
compositionsandmicrobialinteractionsofdechlorinatingcultures.
• CollaboratewithDr.KarunaChaureyandDr.RobertHettichtocarryoutcomparative
transcriptomicsandproteomicsanalysesofDehalococcoidesculture.
VisitingGraduateStudentJanuary2012,July2013
GeorgiaInstituteofTechnology,Atlanta,GA,USA(withDr.KostasKonstantinidis)
• Learnedbioinformaticstoolstoanalyze16SrRNAgene,metagenome,
transcriptomesequencedata.
• Collaboratewithagraduatestudent,DespinaTsementiz,fromKonstantinidisLab
tocarryoutcomparativemetagenomeandtranscriptomesequenceanalyses.
UndergraduateResearchAssistant2008-2010
MiddleEastTechnicalUniversity,Ankara,Turkey(withDr.GökselN.Demirer)
• Investigatedanaerobicbiohydrogenproductionfrompotato-cornflakeprocessing
wasteandwastewater.
• InvolvedinanEUproject,investigatednutrientrecoveryfromanaerobicdigestion
residueswithdifferentcompositions.
• Collaboratedwithfellowundergraduateandgraduatestudentstoexplorepossible
carbonfootprintdeductioninMETUDepartmentofEnvironmentalEngineeringby
applyinginnovativepollutionpreventiontechniques.
MENTORINGEXPERIENCE
GraduateMentor,UniversityofTennessee,Knoxville,TN,USA
Mentoredundergraduateandgraduatestudentsinthelaboratory,taughtanaerobicculturegrowth
techniques,moleculartoolsandguidedthestudentsininterpretationandpresentationoffindings.
PamDexter,undergraduatestudent,MicrobiologySummerNSFREUProgram,Summer2015
Researchproject:Isolationofcorrinoidproducingmicroorganisms
MatthewEntler,graduatestudent,GenomeScience&Tech.,UniversityofTennesseeFall2014
Researchproject:Exploringdiversityofreductivedehalogenasegenes
JefferyM.Colfer,undergraduatestudent,Microbiology,UniversityofTennesseeSummer2012-Fall2013
Researchproject:Investigationofdehalogenationofchlorofluorocarbons
HONORSANDAWARDS
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GraduateSchoolFellowshiptopursueaPhD,UniversityofTennessee2010–Present
GraduateSchoolSenateTravelAward,UniversityofTennesseeFall2015
GeosyntecAnnualStudentPaperCompetition,winner2014
YoungScientistTravelGrant,TerraGenomeResearchCoordinationNetworkFall2013
GraduateSchoolSenateTravelAward,UniversityofTennesseeSpring2013
GraduatedMagnaCumLaude(2ndintheDept.),MiddleEastTechnicalUniversityJuly2010
EightHighHonorStudentCertificatesfromundergraduatestudies2005–2010
FirstplaceinthebestprojectcompetitioninEnvironmentalEngineeringDesignI,METUFall2009
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GRANTS
NIEHSSuperfundResearchProgram2014-2017
“BiogeochemicalControlsoverCorrinoidBioavailabilitytoOrganihalide-RespiringChloroflexi”
PIs:F.E.Löffler,J.Yan,S.R.Campagna.TotalFunds:$860,000
PUBLICATIONS
• Şimşir,B.,J.Yan,D.GravesandF.E.Löffler.NaturalAttenuationinStreambedSedimentReceivingChlorinated
SolventsfromUnderlyingFractureNetworks(2016,submitted).
• Yan,J.,B.Şimşir,A.T.Farmer,M.Bi,Y.Yang,S.R.Campagna,andF.E.Löffler.Thecorrinoidcofactorofreductive
dehalogenasesaffectsdechlorinationratesandextentsinorganohalide-respiringDehalococcoidesmccartyi,
ISMEJ.,2015,doi: 10.1038/ismej.2015.197
Manuscriptsinpreparation:
• Şimşir,B.,D.Tsementzi,K.Cusick,K.T.Konstantinidis,andF.E.Löffler.MetatranscriptomicsRevealsInteractions
BetweenFree-Living,PleomorphicSpirochetes(FLiPS)andDehalococcoidesmccartyi.
• ŞimşirB.,J.YanandF.E.Löffler.GeochemicalconditionsaffectcorrinoidpoolsthatcontrolDehalococcoides
mccartyireductivedechlorinationactivity.
• ŞimşirB.,J.YanandF.E.Löffler.BiostimulationwithDMBovercomesincompletedetoxificationinacisdichloroethenedechlorinatingconsortia.
• ŞimşirB.,Y.Yang,D.Tsementzi,J.Chowdhary,J.Yan,K.T.KonstantinidisandF.E.Löffler.
EffectsofChlorinatedAcceptorsandCorrinoidCofactoronDehalococcoidesmccartyistraindiversity.
• Tsementzi,D.,B.Şimşir,andF.E.Löffler,K.Konstantinidis.Comperativemetagenomicsidentifiedunexpectedly
highabundantDehalococcoidiafromphylumChloroflexiincreeksediment.
• Şimşir,B.,T.H.Erguder,G.N.Demirer.Effectsofironbioavailabilityandalkali-heatpretreatmentsonbiohydrogen
productionfrompotato-cornflakeprocessingwastes.
PublicationsinInternationalConferenceProceedings:
• ErguderT.H.,L.Ozkan,B.Şimşir,G.N.Demirer.“Agro-industrialwastesasresourcesofcleanenergy;hydrogen”.
1stInt.SymposiumonMicrobialResourceManagementinBiotechnology:ConceptsandApplications,Ghent,
BELGIUM.30June-01July2011.
• Şimşir,B.,T.H.Erguder,G.N.Demirer.“Anaerobicbiohydrogenproductionfrompotato-cornflakeprocessing
wastesandwastewater”,InternationalSymposiumonEngineeringandArchitecturalScienceofBalkan,Caucasus
andTurkicRepublics.Isparta,TURKEY.22-24October2009.
CONFERENCEPRESENTATIONS
ORALPRESENTATIONS
1. Şimşir,B.,J.Yan,F.E.Löffler.BiogeochemicalconditionscontrolcorrinoidpoolsthataffectDehalococcoides
mccartyireductivedechlorinationactivity.ConferenceonRemediationofChlorinatedandRecalcitrant
Compounds,(Battelle),PalmSpring,CA,USA,May22-26,2016.
2. Şimşir,B.,J.Yan,F.E.Löffler.GeochemicalconditionsaffectcorrinoidpoolsthatcontrolDehalococcoidesmccartyi
reductivedechlorinatioactivity.NIEHSSRPAnnualMeeting,SanJuan,PuertoRico,November18-20,2015.
3. Şimşir,B.,K.Chourey,R.Hettich,K.M.Ritalahti,andF.E.Löffler.Themoleculartoolbox:currentandfuture
applicationstoimprovemicrobialremedies.ThirdInternationalSymposiumonBioremediationandSustainable
EnvironmentalTechnologies,Miami,FL,USA,May18-21,2015.
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CONFERENCEPRESENTATIONSCONTINUED
ORALPRESENTATIONS
4. Şimşir,B.,D.Tsementzi,K.Cusick,K.M.Ritalahti,K.T.Konstantinidis,andF.E.Löffler.InsightsIntoMutualistic
InteractionsBetweenFree-Living,PleomorphicSpirochetes(FLiPS)andDehalococcoidesmccartyi.9th
InternationalSymposiumonSubsurfaceMicrobiology(ISSM),PacificGrove,CA,USA,October5-10,2014.
5. Şimşir,B.,J.Yan,K.M.Ritalahti,andF.E.Löffler.2014.Reductivedechlorinatingconsortia:Unravelingcommunity
interactionsthatcontrolDehalacoccoidesactivity.9thInternationalConferenceonRemediationofChlorinated
andRecalcitrantCompounds(Battelle),Monterey,CA,USA,May19-22,2014.
6. Yan,J.,B.Şimşir,K.M.Ritalahti,andF.E.Löffler.ExploringDehalococcoidesmccartyicorrinoidrequirementto
enhancereductivedechlorinationactivity.9thInternationalConferenceonRemediationofChlorinatedand
RecalcitrantCompounds(Battelle),Monterey,CA,USA,May19-22,2014.
7. Chourey.K.,R.Hettich,K.M.Ritalahti,B.Şimşir,andF.E.Löffler.Developmentofametaproteomicsplatformto
detectreductivedechlorinationbiomarkerproteinsinenvironmentalsamples. 9thInternationalConferenceon
RemediationofChlorinatedandRecalcitrantCompounds(Battelle),Monterey,CA,USA,May19-22,2014.
8. ErguderTH.,OzkanL.,Şimşir,B.,DemirerGN.,“Agro-industrialwastesasresourcesofcleanenergy;hydrogen”.
1stInt.SymposiumonMicrobialResourceManagementinBiotechnology:ConceptsandApplications,Ghent,
BELGIUM,30June-01July2011
9. Şimşir,B.,T.H.ErguderandG.N.Demirer.2009.AnerobicBiohydrogenProductionfromPotato-CornFlake
ProcessingWastesandWastewater.InternationalSymposiumonEngineeringandArchitecturalScienceof
Balkan,CaucasusandTurkicRepublics.Isparta,TURKEY,22-24October2009.
POSTERPRESENTATIONS
1. Şimşir,B.,J.Yan,C.LebronandF.E.Löffler.TheB12-qChip:ahigh-throughputqPCRtoolformonitoringand
predictingreductivedechlorinationactivityoforganohalide-respiringChloroflexi.NIEHSSuperfundResearch
ProgramAnnualMeeting.SanJuan,PR,November18-20,2015.
2. Şimşir,B.,Yan,J.,Chouray,K.,VillalobosSolis,M.I.,Ritalahti,K.,Hettich,R.L.,F.E.Löffler.High-throughputqPCR
andenvironmentalproteomicstoassessmicrobialactivitiesatcomplicatedchlorinatedsolventsites.Chlorinated
SolventsinGroundwaterTechnicalExchangeMeeting,Arlington,VA,USA,Dec10-12,2014.
3. Şimşir,B.,D.Tsementzi,K.T.Konstantinidis,andF.E.Löffler.ComparativeMetagenomicsunraveladaptive
evolutionprocessesinDehalococcoidesmccartyi.2ndThünenSymposiumonSoilMetagenomics,Braunschweig,
Germany,December11-13,2013.
4. Şimşir,B.,J.Yan,K.M.Ritalahti,andF.E.Löffler.Definingtheessentialcommunitysupporting
Dehalococcoidesreductivedechlorinationactivity.RemediationTechnologySummit(RemTEC13),Westminster,
CO,USA,March4-6,2013.
5. Şimşir,B.,D.Graves,andF.E.Löffler.Naturalattenuationofchlorinatedsolventsinstreambedsediment.
RemediationTechnologySummit(RemTEC13),Westminster,CO,USA,March4-6,2013.
6. Şimşir,B.,K.M.RitalahtiandF.E.Löffler.DefiningtheessentialcommunitysupportingDehalococcoides
reductivedechlorinationactivity.AmericanSocietyforMicrobiologyKY-TNBranchMeeting,Maryville,TN,
October26-27,2012.
INTERNSHIPEXPERIENCES
ATACEngineeringConsultancyConstructionMiningandTradingLtd.Co.,Istanbul,Turkey2009
• Workedwithanenvironmentalengineerinaprojectaimedtodevelopahydraulicstreamoverflow
modelforasite.Firstdefinedtherainwaterbasinsandstreambedsofthesite,andcalculatedthetotal
rainfallcouldhappenintothestreambedsusingthesite’sprecipitationrecords,lastlyusedArcGIS
(geographicinformationsystem)todevelopthemodel.
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INTERNSHIPEXPERIENCESCONTINUED
TAI,TurkishAerospaceIndustriesInc.,Ankara,Turkey2008
• Spentfourweeksinvariouswastewaterandwatertreatmentunits,learnedchemical,
physicalandbiologicalprocessesappliedineachtreatmentunit.
• Conductedwaterqualityanalysesofwastewatersamplesfromprocessstreamlines,
inchemistryandbiologylaboratories.
• Workedwithenvironmentalengineersandwitnessedhowtheoreticalknowledgefrom
coursesareappliedforlargescaleprocessdevelopmentandhowengineersapproachedand
anticipatedpotentialproblemsandimprovements.
EDUCATIONALEXPERIENCES
PollutantFate,ModelingandRiskAssessment,UT,Knoxville(withDr.QiangHe)Spring2012
• Collaboratedwithfourfellowgraduatestudentsindevelopingamodelformethane
emissionstotheatmospherefromdeepwateroil/gasspills.Amathematicalmodel
wasdevelopedincludingallphysical,chemical,andbiologicalprocesses
describingmethanefateafterspills.
EnvironmentalEngineeringDesignI&II,METU,Turkey(withDr.İpekİmamoğlu)Fall2009,Spring2010
• Collaboratedwithfivefellowundergraduatestudentsduringtwosemesters,
leadedthegroupinpreparationofaproposalfordevelopinganintegrated
environmentalmanagementplanforIlginSugarFactory,Konya,Turkey.
• Foundedanimaginarycompany,namedGreeNetworkCorporationandpreparedaproject
proposalconductingallprofessionalsteps,includingsiteinvestigation,logicalframework,
legislativeframework,technicalframeworkanalyses(e.i,design),detailedtechnical
processcalculations,costanalyses,automatedmonitoringsystemdevelopment.
• GreeNetworkCo.developedanintegratedenvironmentalmanagementplanfor
IlginSugarFactoryincludedwastewatertreatmentsystem,agasemissioncontrol
systemandacleanerproductionstrategytogetherwithanenvironmentalawarenessprogram.
• TheGreeNetworkCo.’sproposalcompetedwithother8proposals,presentedto
ownerofIlginSugarFactory,environmentalauditorsfromtheRepublicofTurkey
MinistryofEnvironment,andfacultyfromMETUDepartmentofEnvironmental
Engineeringandotheruniversities.TheprojectdesignedbyGreeNetworkCo.wasawarded
asthewinnerinthefirstsemesterandtookthesecondplaceinthesecondsemester.
GreenPerspectiveProject,METU,Turkey(withDr.GökselN.Demirer)2008-2010
• Asbeingintheleadingteam,workedtogetherwithfellowgraduateand
undergraduatestudentsinapilotproject,aimedtominimizethecarbon
emissionsfromMETUDepartmentofEnvironmentalEngineering.
• Equipment,strategy,materialchangesweremadeinthedepartment
withtheaimsofefficientwateruse,energyefficiency,greenpurchasing,
integratedlaboratorywastemanagement,recycling,solidwastemanagement.
• Varioussponsorshipswerereceivedfrombigcompanies
(e.g.,EczacibasiHoldingInc.).Exampleapplication:replacementofallof
thewaterclosetthankswithwaterefficientones,prevented210tonsofannual
cleanwaterconsumption.
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SOCIALEXPERIENCES
TurkishStudentAssociationofUniversityofTennessee,vicepresident2011–present
Dancer,EthnicUSFolkDanceGroupofKnoxville,TN,USA2012–2015
TennesseeIstanbulCulturalCenter,Knoxville,instructorJanuary2013-Jun2014
VoluntarilytaughtTurkishandintroducedTurkishCulturetoAmericans,whowere
interestedinTurkishcultureand/orhadprofessionalreasonstolearnTurkish.Learnersfrom
variousbackgrounds,weremiddleschool/collegestudents,doctors,professors(ages:14-65).
CouncilonInternationalEducationalExchange(CIEE),host2008-2010
HostedthreeAmericanexchangestudents,whostudiedinMETUforasemester
YouthServiceCentre,Hötensleben,GermanySummer2008
Involvedvoluntarilyinacommunityproject,aimingatrestorationof
TheDDRBorderMemorialofHötensleben
AssistantBasketballCoach2006-2007
SocialScienceHighSchoolMen`sBasketballTeam,Ankara,Turkey
LicensedBasketballPlayer1999-2007
Teams:AnkaragücüSportClub,MTA,AriCollege,BilimCollege,METU
MEMBERSHIP
AmericanSocietyofMicrobiology(ASM)
SELECTEDSKILLS
MicrobiologyandMolecularBiologyTechniques
Anaerobicculturemaintenance,anaerobicmicroorganismisolation,cloning,plasmid,DNA,RNAisolation,
PCR-qPCRprimerdesign,andamplicon,metagenome,metatranscriptomesequencing.
TechnicalSkills
16SrRNAamplicon,metagenome,metatranscriptomesequence-dataanalysesusingbioinformaticstools
Programinglanguages/computersystems,engineeringandmathematicalpackages:MatLAB,Linux,R,JMP.
HOBBIES
Basketball,running,crossfit,painting,writingessaysandshortstories,readingbooks,music.
REFERENCES
• FrankE.Löffler,GovernorsChairProfessor,DepartmentofMicrobiology,DepartmentofCiviland
EnvironmentalEngineering,UniversityofTennessee,706SERF,1414CircleDrive,Knoxville,TN,
37996-2000.Phone:(+1)865-974-4004,e-mail:frank.loeffler@utk.edu
• GökselN.Demirer,Professor,DepartmentofEnvironmentalEngineering,MiddleEastTechnical
University,DepartmentofEnvironmentalEngineering,Ankara,Turkey.Phone:(+90)312-210-5867
e-mail:goksel@metu.edu.tr
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REFERENCESCONTINUED
• GarySayler,Professor,DepartmentofMicrobiology,CenterforEnvironmentalBiotechnology,University
ofTennessee,676DabneyHall,CircleDrive,Knoxville,TN,37996-1605.Phone:(+1)865-974-8086,
e-mail:sayler@utk.edu
• QiangHe,AssociateProfessor,DepartmentofCivilandEnvironmentalEngineering,Universityof
Tennessee,325JohnD.TickleBuilding,851NeylandDr.Knoxville,TN,37996-2313.
Phone:(+1)865-974-6067,e-mail:qhe2@utk.edu
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