Circadian Rhythms and Biological Clocks Part B

389 Pages·2015·13.16 MB·English

by  Sehgal

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
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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