Circadian Rhythms and Biological Clocks Part B PDF
Preview Circadian Rhythms and Biological Clocks Part B
METHODS IN ENZYMOLOGY Editors-in-Chief JOHN N. ABELSON and MELVIN I. SIMON Division of Biology California Institute of Technology Pasadena, California ANNA MARIE PYLE Departments of Molecular, Cellular and Developmental Biology and Department of Chemistry Investigator Howard Hughes Medical Institute Yale University Founding Editors SIDNEY P. COLOWICK and NATHAN O. KAPLAN AcademicPressisanimprintofElsevier 125LondonWall,London,EC2Y5AS,UK 525BStreet,Suite1800,SanDiego,CA92101-4495,USA 225WymanStreet,Waltham,MA02451,USA TheBoulevard,LangfordLane,Kidlington,OxfordOX51GB,UK Firstedition2015 Copyright©2015ElsevierInc.Allrightsreserved. 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ISBN:978-0-12-803380-7 ISSN:0076-6879 ForinformationonallAcademicPresspublications visitourwebsiteatstore.elsevier.com CONTRIBUTORS RaviAllada DepartmentofNeurobiology,NorthwesternUniversity,Evanston,Illinois,USA MarchevaB DivisionofEndocrinology,MetabolismandMolecularMedicine,FeinbergSchoolof Medicine,Chicago,andDepartmentofNeurobiology,NorthwesternUniversity,Evanston, Illinois,USA DavidM.Bannerman DepartmentofExperimentalPsychology,UniversityofOxford,Oxford,UnitedKingdom MathiasBasner DivisionofSleepandChronobiology,DepartmentofPsychiatry,PerelmanSchoolof Medicine,UniversityofPennsylvania,Philadelphia,Pennsylvania,USA LaurenceA.Brown NuffieldLaboratoryofOphthalmology,NuffieldDepartmentofClinicalNeurosciences, UniversityofOxford,Oxford,UnitedKingdom StevenA.Brown InstituteofPharmacologyandToxicology,UniversityofZurich,Zurich,Switzerland PeekC.B DivisionofEndocrinology,MetabolismandMolecularMedicine,FeinbergSchoolof Medicine,Chicago,andDepartmentofNeurobiology,NorthwesternUniversity,Evanston, Illinois,USA LevineD.C DivisionofEndocrinology,MetabolismandMolecularMedicine,FeinbergSchoolof Medicine,Chicago,andDepartmentofNeurobiology,NorthwesternUniversity,Evanston, Illinois,USA DavidF.Dinges DivisionofSleepandChronobiology,DepartmentofPsychiatry,PerelmanSchoolof Medicine,UniversityofPennsylvania,Philadelphia,Pennsylvania,USA RachelS.Edgar DepartmentofClinicalNeurosciences,UniversityofCambridgeMetabolicResearch Laboratories,NIHRBiomedicalResearchCentre,WellcomeTrust-MRCInstituteof MetabolicScience,UniversityofCambridge,Addenbrooke’sHospital,Cambridge,United Kingdom DorotheeFischer InstituteforMedicalPsychology,CentreforChronobiology,MedicalFaculty, Ludwig-Maximilians-University,Munich,Bavaria,Germany xi xii Contributors GarretA.FitzGerald InstituteforTranslationalMedicineandTherapeutics,SmilowCenterforTranslational Research,PerelmanSchoolofMedicine,UniversityofPennsylvania,Philadelphia, Pennsylvania,USA MatthieuFlourakis DepartmentofNeurobiology,NorthwesternUniversity,Evanston,Illinois,USA RussellG.Foster NuffieldLaboratoryofOphthalmology,NuffieldDepartmentofClinicalNeurosciences, UniversityofOxford,Oxford,UnitedKingdom Ying-HuiFu DepartmentofNeurology,UniversityofCalifornia,SanFrancisco,SanFrancisco, California,USA LudmilaGaspar InstituteofPharmacologyandToxicology,UniversityofZurich,Zurich,Switzerland NamniGoel DivisionofSleepandChronobiology,DepartmentofPsychiatry,PerelmanSchoolof Medicine,UniversityofPennsylvania,Philadelphia,Pennsylvania,USA PhilipHaines InstituteforTranslationalMedicineandTherapeutics,SmilowCenterforTranslational Research,PerelmanSchoolofMedicine,UniversityofPennsylvania,Philadelphia, Pennsylvania,USA MarkW.Hankins SleepandCircadianInstitute(SCNi),NuffieldDepartmentofClinicalNeurosciences (NuffieldLaboratoryofOphthalmology),UniversityofOxford,Oxford,UnitedKingdom MegumiHatori SchoolofMedicine,KeioUniversity,Shinjuku-ku,Tokyo,Japan CharlotteHelfrich-Fo€rster NeurobiologyandGenetics,Theodor-BoveriInstitute,Biocenter,UniversityofWu€rzburg, Wu€rzburg,Germany ErikD.Herzog DepartmentofBiology,WashingtonUniversity,St.Louis,Missouri,USA Pei-KenHsu DepartmentofNeurology,andHowardHughesMedicalInstitute,UniversityofCalifornia, SanFrancisco,SanFrancisco,California,USA YanmeiHuang DepartmentofNeuroscience,SacklerPrograminBiomedicalSciences,TuftsUniversity SchoolofMedicine,Boston,MA,USA StevenHughes Sleep and Circadian Institute (SCNi), Nuffield Department of Clinical Neurosciences (Nuffield Laboratory of Ophthalmology), University of Oxford, Oxford, United Kingdom Contributors xiii BassJ DivisionofEndocrinology,MetabolismandMolecularMedicine,FeinbergSchoolof Medicine,Chicago,andDepartmentofNeurobiology,NorthwesternUniversity,Evanston, Illinois,USA F.RobJackson DepartmentofNeuroscience,SacklerPrograminBiomedicalSciences,TuftsUniversity SchoolofMedicine,Boston,MA,USA AartiJagannath SleepandCircadianInstitute(SCNi),NuffieldDepartmentofClinicalNeurosciences (Nuffield Laboratory of Ophthalmology), University of Oxford, Oxford, United Kingdom RamseyK.M DivisionofEndocrinology,MetabolismandMolecularMedicine,FeinbergSchoolof Medicine,Chicago,andDepartmentofNeurobiology,NorthwesternUniversity,Evanston, Illinois,USA LenaK.Keller InstituteforMedicalPsychology,CentreforChronobiology,MedicalFaculty,Ludwig- Maximilians-University,andDepartmentofChildandAdolescentPsychiatry, PsychosomaticsandPsychotherapy,UniversityHospitalMunich,Munich,Bavaria, Germany Istva´nZ.Kiss DepartmentofChemistry,SaintLouisUniversity,St.Louis,Missouri,USA PerelisM DivisionofEndocrinology,MetabolismandMolecularMedicine,FeinbergSchoolof Medicine,Chicago,andDepartmentofNeurobiology,NorthwesternUniversity,Evanston, Illinois,USA JoanaL.Matera InstituteforMedicalPsychology,CentreforChronobiology,MedicalFaculty, Ludwig-Maximilians-University,Munich,Bavaria,Germany CristinaMazuski DepartmentofBiology,WashingtonUniversity,St.Louis,Missouri,USA SarahC.McLoughlin InstituteforTranslationalMedicineandTherapeutics,SmilowCenterforTranslational Research,PerelmanSchoolofMedicine,UniversityofPennsylvania,Philadelphia, Pennsylvania,USA JohannaH.Meijer DepartmentofNeurophysiology,LeidenUniversityMedicalCenter,Leiden, TheNetherlands StephanMichel DepartmentofMolecularCellBiology,LeidenUniversityMedicalCenter,Leiden, TheNetherlands xiv Contributors NikolayB.Milev DepartmentofClinicalNeurosciences,UniversityofCambridgeMetabolicResearch Laboratories,NIHRBiomedicalResearchCentre,WellcomeTrust-MRCInstituteof MetabolicScience,UniversityofCambridge,Addenbrooke’sHospital,Cambridge, UnitedKingdom FannyS.Ng DepartmentofNeuroscience,SacklerPrograminBiomedicalSciences,TuftsUniversity SchoolofMedicine,Boston,MA,USA JohnS.O’Neill MRCLaboratoryofMolecularBiology,Cambridge,UnitedKingdom SatchidanandaPanda RegulatoryBiologyLaboratory,SalkInstituteforBiologicalStudies,LaJolla,CA,USA StuartN.Peirson NuffieldLaboratoryofOphthalmology,NuffieldDepartmentofClinicalNeurosciences, UniversityofOxford,Oxford,UnitedKingdom DavidPritchett NuffieldLaboratoryofOphthalmology,NuffieldDepartmentofClinicalNeurosciences, UniversityofOxford,Oxford,UnitedKingdom LouisJ.Pta´cˇek DepartmentofNeurology,andHowardHughesMedicalInstitute,UniversityofCalifornia, SanFrancisco,SanFrancisco,California,USA AkhileshB.Reddy DepartmentofClinicalNeurosciences,UniversityofCambridgeMetabolicResearch Laboratories,NIHRBiomedicalResearchCentre,WellcomeTrust-MRCInstituteof MetabolicScience,UniversityofCambridge,Addenbrooke’sHospital,Cambridge,United Kingdom GuillaumeRey DepartmentofClinicalNeurosciences,UniversityofCambridgeMetabolicResearch Laboratories,NIHRBiomedicalResearchCentre,WellcomeTrust-MRCInstituteof MetabolicScience,UniversityofCambridge,Addenbrooke’sHospital,Cambridge,United Kingdom TillRoenneberg InstituteforMedicalPsychology,CentreforChronobiology,MedicalFaculty, Ludwig-Maximilians-University,Munich,Bavaria,Germany MatthiasSchlichting NeurobiologyandGenetics,Theodor-BoveriInstitute,Biocenter,UniversityofWu€rzburg, Wu€rzburg,Germany SukanyaSengupta DepartmentofNeuroscience,SacklerPrograminBiomedicalSciences,TuftsUniversity SchoolofMedicine,Boston,MA,USA Contributors xv ShuK.E.Tam NuffieldLaboratoryofOphthalmology,NuffieldDepartmentofClinicalNeurosciences,and DepartmentofExperimentalPsychology,UniversityofOxford,Oxford,UnitedKingdom UthamK.Valekunja DepartmentofClinicalNeurosciences,UniversityofCambridgeMetabolicResearch Laboratories,NIHRBiomedicalResearchCentre,WellcomeTrust-MRCInstitute ofMetabolicScience,UniversityofCambridge,Addenbrooke’sHospital,Cambridge, UnitedKingdom Ce´lineVetter ChanningDivisionofNetworkMedicine,BrighamandWomen’sHospital,Harvard MedicalSchool,Boston,Massachusetts,USA EvaC.Winnebeck InstituteforMedicalPsychology,CentreforChronobiology,MedicalFaculty, Ludwig-Maximilians-University,Munich,Bavaria,Germany SamanthaYou DepartmentofNeuroscience,SacklerPrograminBiomedicalSciences,TuftsUniversity SchoolofMedicine,Boston,MA,USA PREFACE Inthe10yearssinceapreviouscircadianvolumeofMethodsinEnzymology waspublished,thecircadianfieldhasevolvedwiththeintroductionofnew concepts, new approaches, and, of course, many new investigators. As the previousvolumewasprecededbyanexplosionofdiscoveriesandinforma- tion about how clocks work in diverse organisms, from cyanobacteria to humans,onemighthavepredictedagradualplateauingofactivity,butthis wasclearlynotthecase.Importantly,thenewdiscoverieshavecontinuedto comefromspeciesacrossthephylogenetictree,andsothefieldremainstruly interdisciplinary,whichisreflectedintwovolumes,CircadianRhythmsand Biological Clocks Part A and B. Wecontinuetoseeadvancesinthemethodsusedtomeasureandanalyze rhythms,to identifynew circadiangenes,andto characterizeknown clock components. In fact, clocks are now being modulated with a goal of ther- apeutic application. At the same time, there is considerable focus on the molecularmechanismsthroughwhichrhythmsaretransmittedbytheclock. Majorclockproteinsaretranscriptionfactorsthateffectivelydriverhythmic expression of many genes, which generally vary from tissue to tissue. The mechanism by which such rhythmic transcription occurs is a subject of intense investigation, and sophisticated techniques have been brought to bearonit.However,itisalsoevidentthatposttranscriptionalorevenpost- translational mechanisms alone can drive the cycling of RNA or protein. Indeed,proteinsmaynotevenneedtocycleintermsoflevelsastheiractivity canberegulatedthroughcyclicmodifications,suchasphosphorylation.Sev- eralclockproteinsarekinases,andincyanobacteria,theentireclockcanbe reconstituted as a rhythmic phosphorylation cycle. In addition, 24-h oscil- lations that are independent not only of transcription but also of known clock elements have been proposed for redox pathways in the cell. Thus, whilegenome-wideanalysesareallowingidentificationofRNAsexpressed rhythmicallyindifferenttissues,andeveninsmallgroupsofbrainneurons, proteomicstudieshavebeeninitiatedtopinpointrhythmsatthislevel.Allof these have required development and use of the appropriate, anatomical, molecular, biochemical, and statistical tools described here. Rhythmsinmoleculesleadtorhythmsincellularandorganismalphys- iology.Asclocksarefoundthroughoutthebody,theycontrolmanyphys- iologicalprocessesandbehaviors.Inthebrain,rhythmsofelectricalactivity xvii xviii Preface aresynchronizedacrossclockcellsandtransmittedacrosscircadiancircuits, likely comprised of neurons and glia, to generate rhythmic behavior. Cel- lularrhythms,suchasinmitochondrialrespiration,mayoccurineverycell in mammals. In addition, each organ/system, such as the cardiovascular system,hasitsowncircadianphysiologythatcanbemeasuredthroughappli- cation of specific methods. Interestingly, while the light:dark cycle is the most powerful entraining stimulus for the clock in the brain, which then synchronizes other body clocks, rhythmic gene expression in peripheral tissues like the liver responds most strongly to the time of feeding. Thus, aberrant feeding schedules can have adverse effects on metabolic function, but the time of feeding can even be manipulated to produce beneficial consequences. Overall, it is increasingly evident that circadian rhythms are critical for organismalfitness.Severalapproachesarenowbeingusedtoassesscircadian functioninhumans,itscontrolbygeneticfactors,anditsrelevancetohuman health.Disruptedrhythmshavebeenassociatedwithneurologicalandpsy- chiatricdisordersandstudiesarenowunderwaytoaddressthesignificanceof suchassociation.Thesevolumesprovidesmethodologicalinsightintocirca- dian physiology and behavior in model organisms and in humans and touches upon the pathological implications of circadian dysfunction. While I took on the job of putting these volumes together, the actual creditshouldgotoallthecontributingauthors,whotooktimeoutoftheir extremelybusylivestomakethevolumerepresentativeofthebestworkin the circadian field. Iam incrediblygrateful for their efforts andtheir coop- eration.Also,allofthiswasmadepossiblebytheconstanthelpofEditorial ProjectManager,SarahLay,whowasarealpleasuretoworkwiththrough- out the process. AMITA SEHGAL CHAPTER ONE Measuring Synchrony in the Mammalian Central Circadian Circuit Erik D. Herzog*,1, István Z. Kiss†, Cristina Mazuski* *DepartmentofBiology,WashingtonUniversity,St.Louis,Missouri,USA †DepartmentofChemistry,SaintLouisUniversity,St.Louis,Missouri,USA 1Correspondingauthor:e-mailaddress:[email protected] Contents 1. Introduction 4 1.1 Whatissynchrony? 4 1.2 Whatiscircadiansynchrony? 4 1.3 Goalsofthisreview 5 2. MonitoringSCNRhythmswithCellularResolution 6 3. IsolatingDatafromSingleCells 6 4. DefiningaRhythm 9 4.1 Plottingrhythmicdataforvisualinspection 9 5. PeriodSynchrony:MethodstoExtractandComparePeriodsBetweenCells 10 5.1 Docellssharethesameperiod? 15 6. PhaseSynchrony:MethodstoExtractandComparePhaseRelationships BetweenCells 16 7. PerturbationsRevealSynchronizationMechanisms 17 8. MethodsAwaitingApplicationinCircadianBiology 17 9. Step-by-StepInstructionsforMeasuringSynchronyinSCNSlice 18 9.1 Bioluminescencerecordingsusingacharge-coupleddevicecamera 18 9.2 Imageprocessing 18 9.3 Single-celltracking 18 9.4 Datapresentation 19 Acknowledgments 19 References 19 Abstract Circadianclockscontroldailyrhythmsinphysiologyandbehavioracrossallphyla.These rhythmsareintrinsictoindividualcellsthatmustsynchronizetotheirenvironmentand toeachothertoanticipatedailyevents.Recentadvancesinrecordingfromlargenum- bersofcellsformanycircadiancycleshaveenabledresearcherstobegintoevaluatethe mechanisms and consequences of intercellular circadian synchrony. Consequently, methodshavebeenadaptedtoestimatetheperiod,phase,andamplitudeofindividual MethodsinEnzymology,Volume552 #2015ElsevierInc. 3 ISSN0076-6879 Allrightsreserved. http://dx.doi.org/10.1016/bs.mie.2014.10.042
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