Destination Science

Destination Science bynicolekresge

illustrationbyclaremallison

An innovative collaboration program opens Janelia’s doors

to visiting scientists from around the world.

I20 Spring2014/HHMIBulletin

inmarch2013 ,LillianFritz-LaylinpackedacoolerfullofhumanimmunecellsandhoppedonaplanefromSanFranciscotoVirginia.Onceshearrived,shespentalmosteverydayinasmall,darkroominEricBetzig’slabatHHMI’sJaneliaFarmResearchCampus,watchingthecellscrawlacrossamicroscope’sstage.Amonthlater,shereturnedtotheWestCoastwithmorethan10terabytesofdataandinformationthatwouldchangethewayawholefieldlooksatcellmovement.

Fritz-Laylin,apostdoctoralresearcherinHHMIInvestigatorDycheMullins’labattheUniversityofCalifornia,SanFrancisco,studies“fast”immunecells,whichziparoundabout100timesquickerthanmostothercells.Theyneedthisspeedtorespondtoinfectionsandotherproblemsbeforethingsgetoutofhand.She’dliketoknowhowtheygetaroundsoswiftly.Unfortunately,microscopesthatcancapturethedetailsofcellsmovingatthisspeedarefewandfarbetween.ExceptinBetzig’slab.He’sbuiltseveralmicroscopesthatcanvisualizelivecells,upclose,inthreedimensions.Anavidcollaborator,BetziginvitedFritz-Laylintobringhercellstohislab.

Whatthemicroscoperevealedwasstriking.Atypicalcellmovesbyoozing:extendingathinsurface-attachededge,whilesimultaneouslyretractingitsbackside.Thefastcells,asseenmovingin3-D,weredifferent.Theywerecoveredinlarge,dynamicprojectionsthatextendedandretractedinalldirections[seeWebExtramovie].Fritz-Laylinsuspectsthefastcellsareusingforcesproducedbytherearretractions—likeatubeoftoothpastebeingsqueezedfromthebottom.

TheJaneliaVisitorProgramwelcomesscientistssuchasFritz-LaylinfromaroundtheworldtotheAshburn,VA,campustodoresearch.Todate,morethan180visitingscientistsfromtheUnitedStatesand23othercountrieshaveparticipatedintheprogramsinceitlaunchedwhenJaneliaopenedin2006.

Somecollaborationslastafewweeks;othersgoonforyears.Someinvolvehugeendeavorslikemappingallthenervecellsintheflybrain.Otherstacklesmallerproblemslikesleuthingouttheneuronsthataffecthungerinmice.Bybringingtogetherpeoplewithdifferentexpertise,thecollaborationsaccomplishmorethanasinglelabcouldhavedoneonitsown.

“Scientistscomehereandgetaccesstoequipment,budget,scientificreagents,andtheabilitytodothings

theycouldn’tdoattheirhomeinstitutions,”saysJaneliaExecutiveDirectorGerryRubin.“It’saveryspecialopportunitythatdoesn’treallyexistelsewhere.”

“Wereallywanttomakesurethatourstate-of-the-artinstrumentationoranynewtechniquethatwe’vedevelopedcanreachthecommunityatlarge,”explainsScienceProgramManagerZarixiaZavala-Ruiz.

Fly FightersOneoftheveryfirstvisitorstoJaneliawaslongtimeHHMIInvestigatorDavidAnderson.HisCaliforniaInstituteofTechnologylabgroupistryingtounderstandhowthebrainprocessesemotionalbehaviorsuchasfear,anxiety,andaggression.Overthreeyears,AndersontraveledtoRubin’slabeverycoupleofmonthstodevelopanassaytolearnwhetherthefruitflyDrosophila melanogasterexperiencesfear.

“Iwouldspendaweekhereandthere,buriedinthelaboratory,runningmyexperiments,”Andersonrecalls.“IreallyenjoyedtheopportunitytogetawayfrommyadministrativeresponsibilitiesatCaltechandimmersemyselfindoingbenchsciencewithmyowntwohands.”

Anderson’sinitialprojectgrewintoasecond,largeronefocusedonaggression.Hispostdoc,EricHoopfer,movedtoJaneliatocarryoutthefive-yearproject,whichcenteredonacollectionof8,000transgenicDrosophilalines.CreatedbyRubinandhisteam,eachlinehasadifferentsetofnervecellsthatcanbeturnedonandoff.Theentirecollectioncoverstheestimated150,000neuronsthatmakeupthecentralnervoussystemintheadultfruitfly.Atthetime,thelineswereanextremelyhotcommodityforscientistsinterestedinnervecellfunction.

Hoopfersystematicallyturnedonsetsofneuronsintheflybrainhopingtotransformnormallydocilefliesintoaggressivefighters.“Inthevastmajorityofdays,they’ddo

“The ability to do this project has been a great help to my career.”—erichoopfer

nothing,”headmits.Butonceinawhile,theflieswouldstartgoingaftereachother.

“Thereareveryspecificpopulationsofneuronsthatareinvolvedinaggression,andlookingforthemislikelookingforaneedleinahaystack,”Hoopferexplains.Heendedupscreeningabout3,000flylines.Twentyofthoselinescontainedneuronsthatincreasedaggression.

BackatCaltechnow,Hoopferiswritinguphisresultsandstartingtofigureouthowthelabeledneuronscontributetoaggressivebehavior.“Theabilitytodothisprojecthasbeenagreathelptomycareer,”hesays.“ThelinesthatIfoundarebasicallytoolsthatI’llbeabletousetostartmyownindependentresearchgroup.Thereareyearsofworktobedonefiguringouthowjustthese20lineswork.”

Hunger CircuitryJaneliaGroupLeaderScottSternsonalsolikestocollaborate.EvenbeforehesetuphislabatJanelia,hehadalistofscientistshewantedtoworkwith.SoitwasperfectlynaturalforhimtoproposeaprojectwithneuroscientistAnirvanGhoshwithinafewhoursofmeetinghim.

Sternsonstudieshunger.Backin2010whenhefirstmetGhosh,hewaswalkingneuronbyneuronthroughthepathsthatsensewhenamouse’sbrainneedsfuel,hopingtocreateamapofthecircuitrythatcontrolshunger.Unfortunately,thecircuitsweren’tlinear.Instead,thenervecells’axons—thefinger-likeregionsthattransmitsignalstoneighboringneurons—branchintodifferentpartsofthebrain,makingithardtofigureoutwhichforkintheroadtofollow.Sternsonknewhecoulddeterminethecorrectpathbyblockingtheaxons’outputpoints,calledsynapses,andseeingifthatmadethemousehungry.Butheneededhelptargetingthesynapses.

That’swhereGhoshcamein.HewasstudyingthemolecularbiologyofsynapsesattheUniversityofCalifornia,SanDiego.Sternsonrealizedthatbycollaborating,theymightbeabletobuilda“circuitbreakingtool”thatcouldhomeinonselectedsynapsesandturnthemoff.ThepairdecidedtobasetheirtoolonamoleculecalledhM4D,whichturnsoffnervecellsinthepresenceofadrugcalledclozapine-N-oxide(CNO).

Fortheproject,GhoshrecruitedTevStachniak,apostdoctoralfellowfromMcGillUniversityinMontrealwhowasinterestedinneuralcircuits.WithguidancefrombothGhoshandSternson,StachniaktinkeredwithhM4Dandeventuallygotittospecificallytargetthesynapsesofinterest.TheeffectsofCNOlastaboutanhour,justenoughtimetotestthecircuitbreaker’simpactonmousefeedingbehavior.

Theproject,whichiswindingdown,wasagreatsuccess.Stachniakdiscoveredthatpartofthehungerpathwayinvolvesneuronsthatmediatereward-motivatedbehavioringeneral,hintingattheexistenceofacorecircuitsharedbythesebehaviors.Thetool,describedinapublicationinpressatNeuron,canbeusedtotargetsynapsesinvolvedinothercircuitsaswell,makingitwidelyusefulforneuroscientists.Ghosh,whomovedtoRocheastheGlobalHeadofNeuroscienceDiscoveryin2011,isstartingtothinkaboutusingsimilartoolsinmorecomplexanimalssuchasprimates.AndSternson,ofcourse,isalreadyontohisnextcollaboration.

Brain MapsTheonlywayGroupLeaderAlbertCardonawillaccomplishhisambitiousprojectisifheengageslotsofvisitingscientists.Hewantstocreateaneuralwiringmapofthefruitflylarvabrain.That’sabout12,000neurons,3,000,000synapses,and50person-yearsofwork.Sofar,he’sbroughtin39scientists

Visiting scientists have come to Janelia from 23 countries to collaborate on projects.

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from19labsaroundtheworld.HeteachesthemhowtotracetheneuronsinelectronmicrographscreatedbyRickFetter,aprincipalscientistatJanelia,fromaDrosophilalarvathatwasslicedintoabout5,000sections,each50nanometersthick.

OneofhisvisitorsisKatharinaEichler,aPhDstudentfromAndreasThum’slabattheUniversityofKonstanzinGermany.She’sbeenworkingwithCardonaforaboutsixmonths,spendingherdayshunchedoveracomputerandclickingacursorontheblack-and-whitemicrographs.Sheexpectstobedoingthisforatleastanothersixmonths.

EichlerandtheothervisitingscientistsdotheirmappingusingaWebapplicationcalledCATMAID(CollaborativeAnnotationToolkitforMassiveAmountsofImageData)thatislikeaGoogleMapsforthebrain.Theroads—neurons,inthiscase—arealreadyonthemap.“It’sjustliketheOpenStreetMap.orgprojectthataskscontributorsworldwidetoannotatetheplacetheyliveinwiththeirknowledgeofthelocalgeography,”saysCardona.Oncethescientistslearntheprogram,theycanloginfromtheirowncomputersandtraceneuronsfromanywhereintheworld.

MostofthescientistsstaywithCardonaforonetosixmonths,learninghowtomaptheflybrain.Eichlerisanexceptionbecauseshe’sdecidedtocompleteherPhDatJaneliaincollaborationwiththeUniversityofKonstanz.EichlercouldhavedonetheprojectinGermany,but,sheexplains,“Ithinkit’simportanttobeherebecauseit’sreallyhelpfultobeabletotalktopeoplewhohaveworkedwithacertainneuronorareaofthebrainbefore.”

Eichler’sstudyingthemushroombodies—apairofstructuresinvolvedinolfactorylearningandmemory.

BythetimesheleavesJanelia,shehopestohavetracedalloftheapproximately320nervecellsthatmakeupthestructures.

Sofar,Eichlerandtherestoftheteamhavemappedabout12percentofthenervoussystem.Butthisisnotthebestmeasureoftheirprogress.“Biologicallyspeaking,therearesomanyquestionsyoucananswerwithafractionofareconstruction,”saysCardona.“Youdon’thavetofinishthewholethingtoextractenormousvalue.Youextractvalueasyougo.”Eichlerhasalreadyproventhis:eventhoughshe’sonlyabouthalfwaythroughhermapping,she’salreadyshowinghowtheconnectionsbetweenthemushroombodyneuronscontributetothevariousrolesthestructureplaysintheflybrain.

Massive Sequencing ExperimentsSachaNelsonandhispostdocKenSuginohadabigideathatneededsomebigresources.ResourceslikeimmensecomputationalpowerandinstrumentationthatcouldonlybefoundataplacelikeJanelia.

Thepairhadfiguredouthowtoisolategeneticallysimilarcellsfromamouse’sbrain,pooltheRNAfromthecells,anddeterminetheRNA’ssequence.Theresultwasatranscriptionalprofile—auniquefingerprint—thatcouldbeusedtodistinguishdifferentcelltypes.IftheycouldcreateadatabaseofRNAproducedbyeachofthecelltypesinthemousebrain,itwouldbeanincredibleresourceforneuroscientists.

“Ultimately,ifthisdatabasewerebigenough,anyscientistcouldjustlookupafavoriteneuronandreadoutthatneuron’sprofile,”explainsJaneliaGroupLeaderAdamHantman.Thatinformationcouldhelpthescientistfigureoutwhattheneurondoesandhowitdoesit.

Theproblemwasthat,bySuginoandNelson’sestimate,thebrainhasbetween5,000and10,000differentcelltypes.SequencingeachofthosecelltypeswouldrequiremoreresourcesthanwereavailableinasmallacademiclabsuchasNelson’satBrandeisUniversity.SoNelsonstartedcastingaroundforcollaborators.“IlookedforpeopleatJanelia,”hesays,“whowereinterestedinusingthescaleavailabletheretodothemassivesequencingexperimentsthatwerenotpracticaltocontinueinmyownlab.”

That’showtheyteamedupwithHantmanandJaneliaGroupLeaderSeanEddy.Hantmanneededhelpcharacterizingsomemousebraincellshewasstudying.Eddy,ontheotherhand,wasinterestedinthegenomicimplicationsoftheproject.“Itwouldbereallycoolifyoucouldgeteachcelltypeandsay,‘Thisisthegeneticprogramthisguyisrunning,andthisistheprogramthatguyisrunning,’”heexplains.“Thenyoucouldstarttoaskhowtranscriptionregulationworks,howitevolved,andhowisitdifferentbetweenspecies.”

Eddyalsohappenedtohavetwopostdocs,LeeHenryandFredDavis,whowereworkingonasimilartechniquetopurifyflybraincellsandsequencetheirRNA.Thus,thebigprojectgotevenbigger.Thenewgoalwastosequenceallthecelltypesinboththemouseandflybrains.

Aswordgotoutabouttheproject,manyJaneliascientistsapproachedtheteam,askingthemtocreate

Janelia’s Albert Cardona welcomes visiting researchers like Germany’s Katharina Eichler to map the fly brain.

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Learn more about collaborative projects with international visiting scientists at

www.hhmi.org/bulletin/spring-2o14.

23HHMIBulletin/Spring2014

RNAprofilesforthemouseandflybraincellstheywerestudying.Asaresult,inSeptember2012—oneandahalfyearsafteritstarted—thevisitorprojectmorphedintoalarger-scale,permanentprojectcalledNeuroSeq.

Sugino,Henry,andDavisarenowfull-timeemployeesatJaneliaontheNeuroSeqteam.NelsonisbackinhislabatBrandeis,overseeingtheprojectfromafar.Theteamisalsospendingone-thirdofitstimehelpingJaneliascientistsaskspecificquestionsaboutbraincells.SternsonhasalreadyapproachedthemtolearnhowchangesinfeedingaffecttheRNAproducedbycertaincellsinthemousebrain.

A New Adventure WeeklyJaneliaGroupLeaderEricBetzigcallstheVisitorProgramhis“secretweapon.”Withoutit,hewouldn’tbeabletosharethecutting-edge,butverylarge,immobilemicroscopeshebuilds.Peoplehavetocometohim.“Weneedtoshowthatthetoolsareuseful,”heexplains.“AndIneedoutsidecollaboratorstodothat.”

OneofhiscreationsistheBesselbeammicroscopethatFritz-Laylinused.It’sahulkingassemblyoflasersandlensesthatusesathinsheetoflight—similartoascanneratacheckoutcounter—toacquiretensofthousandsofimagesfromalivingspecimen.Bypiecingtogethertheframes,Betzigcanassembledazzlingthree-dimensionalmoviesthatshowtheinnerworkingsofcells.

In2012and2013,Betzigaveragedabout20visitorsperyear.AquickglanceathiscalendarforJanuary2014showsfourcollaboratorsvisitingbacktoback:aresearcherfromDukeUniversity,ascientistfromtheNationalInstitutesofHealth,acollaboratorfromJohnsHopkinsUniversity,andfinally,agroupfromHarvardUniversity.

Typically,visitors—whorangefromindividualscientiststoteamsofspecialists—arriveonSundayandjumpintodata

collectionfirstthingMondaymorning.ThemicroscopesarecomplicatedenoughthattheyhavetobeoperatedbyBetzig’spostdocs,whoarewillingtowork18-hourdaystomakesurethecollaboratorsleavewithasmuchdataaspossible.

Betzigwillsayyestoanycollaborationthatcouldbenefitfromhismicroscopes.“Thevarietyofthingswe’velookedatisalloverthemap,”hesays.“We’vegonefrombacteriauptohugefish,andeverythinginbetween.Everyweekisanewadventure.”Twovisitors—onefromHarvardandonefromtheUniversityofCalifornia,SanFrancisco—areevenusingtheVisitorProgramtobuildtheirownlightsheetmicroscopesincollaborationwithBetzigandJanelia’sInstrumentDesign&Fabricationteam.

Adding On“IthinkeverybodybenefitsfromtheVisitorProgram,”saysJaneliaScientificProgramDirectorUlrikeHeberlein.“Janeliabenefitsfromhavingreallywonderfulandsmartpeoplecontributetotheintellectualdiscourse.Thevisitorsbenefitfrombeinginthisreallyfantasticenvironmentwheretheycantrythingstheyotherwisemightneverbeabletodo.”

WhenHeberleinfirstcametoJaneliatwoyearsago,shethoughttheVisitorProgrammightbenefitfromalittlemorestructure.“Iwantedtohavemorerulesandcriteriaforwhatgetsfundedandwhatdoesn’t,”sheexplains.Shesoonshelvedthatidea.“Itturnsoutthattherealbeautyofthisprogramistheflexibility,”shesays.

Ratherthanchangingtheprogram,Heberleinhasdecidedtoaddtoit.Thisspring,JanelialauncheditsVisitorGraduateFellowship.Aimedatstudentsfromaroundtheworld,theprogramwillallowtheyoungscientiststocreatecollaborativeprojectsthatwillbecomepartoftheirthesisresearch.

And,liketheVisitorProgram,theskyisthelimit.EvenlongshotprojectsfindahomeatJanelia.

“We’rewillingtosay,‘Well,this[visitorproject]mayonlyhavea20percentchanceofworking,butifitworksit’sgoingtobereallytransformational,sowe’lldoit,’”saysRubin.“Wehaveahigh-risk,high-rewardattitudetowardtheseprojects.”

Ken Sugino, Adam Hantman, and Sean Eddy collaborated to produce a massive library of RNA profiles of mouse and fly brain cells.

“We need to show that the tools are useful. And I need outside collaborators to do that.”—ericbetzig

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