C. elegans: Methods and Applications PDF
Preview C. elegans: Methods and Applications
Methods in Molecular Biology 2468 Gal Haspel · Anne C. Hart Editors C. elegans Methods and Applications Third Edition M M B ETHODS IN OLECULAR IO LO GY SeriesEditor JohnM.Walker School of Lifeand MedicalSciences University ofHertfordshire Hatfield, Hertfordshire, UK Forfurther volumes: http://www.springer.com/series/7651 For over 35 years, biological scientists have come to rely on the research protocols and methodologiesinthecriticallyacclaimedMethodsinMolecularBiologyseries.Theserieswas thefirsttointroducethestep-by-stepprotocolsapproachthathasbecomethestandardinall biomedicalprotocolpublishing.Eachprotocolisprovidedinreadily-reproduciblestep-by- step fashion, opening with an introductory overview, a list of the materials and reagents neededtocompletetheexperiment,andfollowedbyadetailedprocedurethatissupported with a helpful notes section offering tips and tricks of the trade as well as troubleshooting advice. These hallmark features were introduced by series editor Dr. John Walker and constitutethekeyingredientineachandeveryvolumeoftheMethodsinMolecularBiology series. Tested and trusted, comprehensive and reliable, all protocols from the series are indexedinPubMed. C. elegans Methods and Applications Third Edition Edited by Gal Haspel Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, USA Anne C. Hart Department of Neuroscience, Brown University, Providence, RI, USA Editors GalHaspel AnneC.Hart DepartmentofBiologicalSciences DepartmentofNeuroscience NewJerseyInstituteofTechnology BrownUniversity Newark,NJ,USA Providence,RI,USA ISSN1064-3745 ISSN1940-6029 (electronic) MethodsinMolecularBiology ISBN978-1-0716-2180-6 ISBN978-1-0716-2181-3 (eBook) https://doi.org/10.1007/978-1-0716-2181-3 ©TheEditor(s)(ifapplicable)andTheAuthor(s),underexclusivelicensetoSpringerScience+BusinessMedia,LLC,part ofSpringerNature2006,2015,2022 Thisworkissubjecttocopyright.AllrightsaresolelyandexclusivelylicensedbythePublisher,whetherthewholeorpart of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting,reproductionon microfilmsorinanyotherphysicalway,andtransmissionorinformation storageand retrieval,electronicadaptation, computersoftware,orbysimilar ordissimilar methodologynow knownorhereafter developed. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublicationdoesnotimply, evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotectivelawsandregulations andthereforefreeforgeneraluse. Thepublisher,theauthorsandtheeditorsaresafetoassumethattheadviceandinformationinthisbookarebelievedto betrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditorsgiveawarranty, expressedorimplied,withrespecttothematerialcontainedhereinorforanyerrorsoromissionsthatmayhavebeen made.Thepublisherremainsneutralwithregardtojurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations. CoverIllustrationCaption:“InstrumentsofDiscovery”,adigitalcollagebyGalHaspel(2021). ThisHumanaimprintispublishedbytheregisteredcompanySpringerScience+BusinessMedia,LLC,partofSpringer Nature. Theregisteredcompanyaddressis:1NewYorkPlaza,NewYork,NY10004,U.S.A. Preface “Worms are not model animals; they are pioneer organisms and a discovery mechanism.” (paraphrasingDr.M.Chalfie#Worm21) C.elegans,andthecommunityofresearchersusingthispioneerorganism,haveproven to be a discovery engine for the rules of life, from molecules and genes, through cellular physiology, metabolism and aging, neurobiology to behavior, individuality and interaction with the environment. This nematode was also used to pioneer methods that became common practice for diverse researchers, from fluorescent proteins and optogenetic tools, to genomic sequencing and editing, confocal microscopy, expansion microscopy, and 3D reconstructionofneurons,amongmanyothers. WebelievethatthecollegialspiritoftheC.eleganscommunity,explicitlyenvisionedand cultivatedasthecommunityexpanded,haspromotedtheseinnovationsanddiscoveries.We aimtoabidebythisspiritbyeditingthiscollection,whichsharesexperience,knowledge,and perhapswisdom. The first two chapters provide practical advice for setting up research programs with C. elegans, either for a new research group or for a short-term project such as a teaching laboratory. The following chapters are written in a familiar format that, if successful, will resembleshadowinganexperiencedresearcherastheyruntheir favorite,well-honedexper- imental protocol, with a list of materials and equipment to prepare, step-by-step instruc- tions,andusefulnotes.Somechaptersfromthelasteditionwereupdatedandincludedhere, whileothersthatdidnotrequireupdatescanbefoundinthatcollection. Wethankourmentors,mentees,andcollaboratorsforteachinguseverythingweknow. Newark,NJ,USA GalHaspel Providence,RI,USA AnneC.Hart v Contents Preface ..................................................................... v Contributors................................................................. ix 1 StartingaC.elegansResearchLaboratory:PracticalAdvice................... 1 AnneC.HartandHeatherL.Bennett 2 TheBasicsofSettingupSuccessfulTeachingLabsandShort-Term ProjectswithC.elegans.................................................. 25 ElizabethE.Glater 3 CryopreservationofC.elegansandOtherNematodeswithDimethyl SulfoxideandTrehalose.................................................. 43 KevinF.O’Connell 4 GeneticMethodsforCellularManipulationinC.elegans .................... 51 MenachemKatz 5 ObservingandQuantifyingFluorescentReporters.......................... 73 SreeparnaPradhanandMichaelHendricks 6 MicrobialRhodopsinOptogeneticTools:ApplicationforAnalyses ofSynapticTransmissionandofNeuronalNetworkActivity inBehavior............................................................. 89 AmelieBergs,ThiloHenss,CasparGlock,JatinNagpal, andAlexanderGottschalk 7 OptogeneticPerturbationofIndividualC.elegansPharyngealNeurons WhileMonitoringFeedingBehavior ...................................... 117 NicholasF.TrojanowskiandChristopherFang-Yen 8 AntibodyStainingforNematodeswithHeat-inducedAntigenRetrieval (HIAR)................................................................ 133 CurtisM.Loer 9 ExCel:Super-ResolutionImagingofC.eleganswithExpansion Microscopy............................................................. 141 Chih-Chieh(Jay)Yu,DanielleM.OrozcoCosio, andEdwardS.Boyden 10 AFusionPCRMethodforExpressingGeneticToolsinC.elegans............ 205 EduardBokman,YifatEliezer,andAlonZaslaver 11 ApproachesforCRISPR/Cas9GenomeEditinginC.elegans................ 215 CharlotteJ.MartinandJohnA.Calarco 12 TargetedandRandomTransposon-AssistedSingle-CopyTransgene InsertioninC.elegans................................................... 239 SoniaElMouridiandChristianFrøkjær-Jensen 13 MutationMappingandIdentificationbyWhole-GenomeSequencing......... 257 HaroldE.Smith vii viii Contents 14 LipidExtractionandAnalysis............................................. 271 HenryH.HarrisonandJenniferL.Watts 15 IsolatingCaenorhabditiselegansfromtheNaturalHabitat ................... 283 ClotildeGimond,NausicaaPoullet,andChristianBraendle 16 MicrofluidicDevicesforBehavioralAnalysis,Microscopy,andNeuronal ImaginginCaenorhabditiselegans ........................................ 293 RossC.Lagoy,EricLarsen,DanLawler,HamiltonWhite, andDirkR.Albrecht 17 NeuronalMicrosurgerywithanYb-DopedFiberFemtosecondLaser ......... 319 MariaB.Harreguy,TracyS.Tran,andGalHaspel 18 AnImagingSystemforMonitoringC.elegansBehaviorandAging ........... 329 MatthewA.ChurginandChristopherFang-Yen 19 MethodsforModulatingandMeasuringNeuromuscularExertion inC.elegans............................................................ 339 KileyJ.HughesandAndre´sG.Vidal-Gadea 20 RecordingandQuantifyingC.elegansBehavior ............................ 357 NavinPokalaandStevenW.Flavell 21 PrimeronMathematicalModelinginC.elegans............................ 375 AyushRanawadeandErelLevine Index ...................................................................... 387 Contributors DIRKR.ALBRECHT • DepartmentofBiomedicalEngineering,WorcesterPolytechnicInstitute, Worcester,MA,USA;DepartmentofBiologyandBiotechnology,WorcesterPolytechnic Institute,Worcester,MA,USA HEATHERL.BENNETT • DepartmentofBiology,TrinityCollege,Hartford,CT,USA AMELIEBERGS • BuchmannInstituteforMolecularLifeSciences,GoetheUniversity, Frankfurt,Germany;InstituteofBiophysicalChemistry,GoetheUniversity,Frankfurt, Germany EDUARDBOKMAN • DepartmentofGenetics,SilbermanInstituteofLifeScience,EdmondJ. SafraCampus,TheHebrewUniversityofJerusalem,Jerusalem,Israel EDWARDS.BOYDEN • McGovern InstituteforBrainResearchandKochInstitute,MIT, Cambridge,MA,USA;DepartmentofBiologicalEngineering,MIT,Cambridge,MA, USA;DepartmentofBrainandCognitiveSciences,MIT,Cambridge,MA,USA;Howard HughesMedicalInstitute,Cambridge,MA,USA;DepartmentofMediaArtsandSciences, MIT,Cambridge,MA,USA;KLisaYangCenter forBionics,andCenter for NeurobiologicalEngineering,MIT,Cambridge,MA,USA CHRISTIAN BRAENDLE • Universite´Coˆted’Azur,CNRS,Inserm,IBV,Nice,France JOHNA.CALARCO • DepartmentofCellandSystemsBiology,UniversityofToronto,Toronto, ON,Canada MATTHEWA.CHURGIN • DepartmentofBioengineering,SchoolofEngineeringandApplied Science,UniversityofPennsylvania,Philadelphia,PA,USA SONIAELMOURIDI • BiologicalandEnvironmentalScienceandEngineeringDivision (BESE),KAUSTEnvironmentalEpigeneticsProgram(KEEP),KingAbdullah UniversityofScienceandTechnology(KAUST),Thuwal,SaudiArabia YIFATELIEZER • DepartmentofGenetics,SilbermanInstituteofLifeScience,EdmondJ. SafraCampus,TheHebrewUniversityofJerusalem,Jerusalem,Israel CHRISTOPHERFANG-YEN • DepartmentofBioengineering,SchoolofEngineeringand AppliedScience,UniversityofPennsylvania,Philadelphia,PA,USA;Departmentof Neuroscience,PerelmanSchoolofMedicine,UniversityofPennsylvania,Philadelphia,PA, USA STEVENW.FLAVELL • DepartmentofBrain&CognitiveSciences,PicowerInstitutefor Learning&Memory,MassachusettsInstituteofTechnology,Cambridge,MA,USA CHRISTIAN FRØKJÆR-JENSEN • BiologicalandEnvironmentalScienceandEngineering Division(BESE),KAUSTEnvironmentalEpigeneticsProgram(KEEP),KingAbdullah UniversityofScienceandTechnology(KAUST),Thuwal,SaudiArabia CLOTILDEGIMOND • Universite´Coˆted’Azur,CNRS,Inserm,IBV,Nice,France ELIZABETHE.GLATER • PomonaCollege,Claremont,CA,USA CASPARGLOCK • BuchmannInstituteforMolecularLifeSciences,GoetheUniversity, Frankfurt,Germany;InstituteofBiophysicalChemistry,GoetheUniversity,Frankfurt, Germany;Max-Planck-InstituteforBrainResearch,Frankfurt,Germany ALEXANDERGOTTSCHALK • BuchmannInstituteforMolecularLifeSciences,Goethe University,Frankfurt,Germany;InstituteofBiophysicalChemistry,GoetheUniversity, Frankfurt,Germany ix x Contributors MARIAB.HARREGUY • FederatedDepartmentofBiologicalSciences,NewJerseyInstituteof TechnologyandRutgersUniversity,Newark,NJ,USA HENRYH.HARRISON • SchoolofMolecularBiosciences,WashingtonStateUniversity, Pullman,WA,USA ANNEC.HART • DepartmentofNeuroscienceandRobertJ.andNancyD.CarneyInstitute forBrainScience,BrownUniversity,Providence,RI,USA GALHASPEL • FederatedDepartmentofBiologicalSciences,NewJerseyInstituteof TechnologyandRutgersUniversity,Newark,NJ,USA MICHAELHENDRICKS • DepartmentofBiology,McGillUniversity,Montreal,QC,Canada THILO HENSS • BuchmannInstituteforMolecularLifeSciences,GoetheUniversity, Frankfurt,Germany;InstituteofBiophysicalChemistry,GoetheUniversity,Frankfurt, Germany KILEYJ.HUGHES • SchoolofBiologicalSciences,IllinoisStateUniversity,Normal,IL,USA MENACHEMKATZ • DepartmentofBiology,Technion-IsraelInstituteofTechnology,Haifa, Israel ROSSC.LAGOY • DepartmentofBiomedicalEngineering,WorcesterPolytechnicInstitute, Worcester,MA,USA ERICLARSEN • DepartmentofBiomedicalEngineering,WorcesterPolytechnicInstitute, Worcester,MA,USA DANLAWLER • DepartmentofBiomedicalEngineering,WorcesterPolytechnicInstitute, Worcester,MA,USA ERELLEVINE • DepartmentofBioengineering,NortheasternUniversity,Boston,MA,USA CURTISM.LOER • FletcherJonesProfessorofBiology,DepartmentofBiology,Universityof SanDiego,SanDiego,CA,USA CHARLOTTEJ.MARTIN • DepartmentofCellandSystemsBiology,UniversityofToronto, Toronto,ON,Canada JATINNAGPAL • BuchmannInstituteforMolecularLifeSciences,GoetheUniversity, Frankfurt,Germany;InstituteofBiophysicalChemistry,GoetheUniversity,Frankfurt, Germany;APCMicrobiomeIreland,UniversityCollegeCork,Cork,Ireland KEVIN F.O’CONNELL • LaboratoryofBiochemistryandGenetics,NationalInstituteof Diabetes&DigestiveandKidneyDiseases,Bethesda,MD,USA DANIELLEM.OROZCOCOSIO • McGovernInstituteforBrainResearchandKochInstitute, MIT,Cambridge,MA,USA;DepartmentofBrainandCognitiveSciences,MIT, Cambridge,MA,USA NAVINPOKALA • DepartmentofBiologicalandChemicalSciences,TheobaldScienceCenter, NewYorkInstituteofTechnology,OldWestbury,NY,USA NAUSICAAPOULLET • Universite´Coˆted’Azur,CNRS,Inserm,IBV,Nice,France;URZ, INRAE,Petit-Bourg(Guadeloupe),France SREEPARNAPRADHAN • PicowerInstituteforLearningandMemory,MassachusettsInstitute ofTechnology,Cambridge,MA,USA AYUSH RANAWADE • DepartmentofBioengineering,NortheasternUniversity,Boston,MA, USA HAROLDE.SMITH • NationalInstituteofDiabetesandDigestiveandKidneyDiseases, NationalInstitutesofHealth,Bethesda,MD,USA TRACY S.TRAN • FederatedDepartmentofBiologicalSciences,NewJerseyInstituteof TechnologyandRutgersUniversity,Newark,NJ,USA
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