Mitochondrial Medicine: Volume 2: Assessing Mitochondria (Methods in Molecular Biology, 2276) PDF
Preview Mitochondrial Medicine: Volume 2: Assessing Mitochondria (Methods in Molecular Biology, 2276)
Methods in Molecular Biology 2276 Volkmar Weissig Marvin Edeas Editors Mitochondrial Medicine Volume 2: Assessing Mitochondria Second 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. Mitochondrial Medicine Volume 2: Assessing Mitochondria Second Edition Edited by Volkmar Weissig Department of Pharmaceutical Sciences, Midwestern University, Glendale, AZ, USA Marvin Edeas Cochin Hospital, Cochin Institute, INSERM U1016, PARIS, France Editors VolkmarWeissig MarvinEdeas DepartmentofPharmaceuticalSciences CochinHospital MidwesternUniversity CochinInstitute,INSERMU1016 Glendale,AZ,USA PARIS,France ISSN1064-3745 ISSN1940-6029 (electronic) MethodsinMolecularBiology ISBN978-1-0716-1265-1 ISBN978-1-0716-1266-8 (eBook) https://doi.org/10.1007/978-1-0716-1266-8 ©SpringerScience+BusinessMedia,LLC,partofSpringerNature2021 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,theauthors,andtheeditorsaresafetoassumethattheadviceandinformationinthisbookarebelievedto betrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditorsgiveawarranty, expressedorimplied,withrespecttothematerialcontainedhereinorforanyerrorsoromissionsthatmayhavebeen made.Thepublisherremainsneutralwithregardtojurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations. ThisSpringerimprintispublishedbytheregisteredcompanySpringerScience+BusinessMedia,LLC,partofSpringer Nature. Theregisteredcompanyaddressis:1NewYorkPlaza,NewYork,NY10004,U.S.A. Preface ItisourdistinctpleasuretopresentthesecondeditionofMiMBMitochondrialMedicineto the ever increasing number of scientists and physicians who are as fascinated by this tiny organelleasweare.WestartedworkingonthefirsteditioninSeptember2014andwereable to bring about one year later two volumes with a total of 70 chapters to the market. As of today(July2020),195KdownloadshavebeenrecordedforVolumeI1and90Kdownloads for volume II2. In light of the rapidly growing and expanding field of Mitochondrial Medicine,wereadilyacceptedtheinvitationtocompileasecondedition,whichwestarted toworkoninMarch2019.Thissecondeditionasofferedhereinvolvesatotalof88chapters with45ofthemwrittenbynewcontributorswhowerenotpartofourfirstedition.Thefirst and secondeditionscombinedsubsequentlypresentworkfrom115mitochondriallabora- tories from around the globe. We therefore believe these five volumes combined to be the most comprehensive source of know-how in the wide-ranging field of Mitochondrial Medicine. Dividing 87 chapters equally over three volumes proved to be a bit challenging. We chosethesubtitleTargetingMitochondriafor volumeI,AssessingMitochondriafor volume II,andManipulatingMitochondriaandDiseaseSpecificApproachesfor volumeIIIwhileof course being well aware of significant overlaps between these three areas of research. For example, it is quiteobvious that mitochondria are being targeted for the purpose of either assessing them or to manipulate them. We therefore ask all authors not to be too critical regarding the placement of their particular chapter. The reader we believe will anyway choose to download a chapter of his/her interest quite independently of its placement in oneofthethreevolumes. All chapters in these three volumes were written for graduate students, postdoctoral associates, independent investigators in academia and industry as well as physicians by leading experts in their particular field. We are extremely grateful to them for having foundthetimetoeitherupdatetheirchapterfromthefirsteditionortowriteanewchapter. We will not forget that for many if not all of our contributors the worldwide COVID-19 pandemic posed additional and unexpected hurdles towards finishing their manuscript in duetime.Thankyoutoall! TheideaforouroriginalbookproposalleadingtothefirsteditionofMiMBMitochon- drial Medicine originated in our efforts to organize a series of annual conferences on TargetingMitochondria(www.targeting-mitochondria.com),thetenthoneofwhichmean- whilehastakenplaceinNovember2019inBerlin,Germany.Duetotheongoingpandemic, our11thconference(October29–30,2020)willbeavirtualonebutwearesureitwillnot belessexcitingthanallthepreviouseditions. Last but not least we would like to sincerely thank John Walker, the series editor of MethodsinMolecularBiology,forhavinginvitedustocompilethissecondeditionandforhis 1https://link.springer.com/book/10.1007/978-1-4939-2257-4. 2https://link.springer.com/book/10.1007/978-1-4939-2288-8. v vi Preface unlimited guidanceand help throughout theentire process. We alsoowe sincere thanks to PatrickMarton,theExecutiveEditoroftheSpringerProtocolSeries,foralwayshavingbeen availableinassistingusthroughouttheentireproject. Glendale,AZ,USA VolkmarWeissig Paris,France MarvinEdeas Contents Preface ..................................................................... v Contributors................................................................. xi 1 MitochondrialDysfunctioninMitochondrialMedicine:Current Limitations,Pitfalls,andTomorrow....................................... 1 NaigGueguen,GuyLenaers,PascalReynier, VolkmarWeissig,andMarvinEdeas 2 Preparationof“Functional”Mitochondria:AChallengingBusiness........... 31 StefanLehr,SonjaHartwig,andJorgKotzka 3 IsolationandQualityControlofFunctionalMitochondria................... 41 SonjaHartwig,JorgKotzka,andStefanLehr 4 PurificationofFunctionalPlateletMitochondria UsingaDiscontinuousPercollGradient ................................... 57 JacobL.Le´ger,NicolasPichaud,andLucH.Boudreau 5 MechanicalPermeabilizationasaNewMethodforAssessment ofMitochondrialFunctioninInsectTissues................................ 67 AlessandroGaviraghi,YanAveiro,StephanieS.Carvalho, RodiesleyS.Rosa,MatheusP.Oliveira,andMarcusF.Oliveira 6 AnalysisofMitochondrialRetrogradeSignalinginYeastModelSystems....... 87 NicolettaGuaragnella,MaˇsaZˇdralevic´,ZdenaPalkova´, andSergioGiannattasio 7 NativeGelElectrophoresisandImmunoblottingtoAnalyze ElectronTransportChainComplexes ..................................... 103 GiselaBeutnerandGeorgeA.PorterJr. 8 MeasuringMitochondrialHydrogenPeroxideLevelsand GlutathioneRedoxEquilibriuminDrosophilaNeuronSubtypes UsingRedox-SensitiveFluorophoresand3DImaging....................... 113 LoriM.Buhlman,PetrosP.Keoseyan,KathrynHoulihan, andAmberN.Juba 9 AssessmentofMitochondrialCellMetabolismbyRespiratory ChainElectronFlowAssays.............................................. 129 FlaviaRadogna,De´borahGe´rard,MarioDicato,andMarcDiederich 10 Whole-CellandMitochondrialdNTPPoolQuantification fromCellsandTissues................................................... 143 JuanC.Landoni,LiyaWang,andAnuSuomalainen 11 Single-ParticleTrackingMethodinFluorescenceMicroscopy toMonitorBioenergeticResponsesofIndividualMitochondria .............. 153 CamilleColin,EmmanuelSuraniti,EmmaAbell,AudreySe´mont, NesoSojic,PhilippeDiolez,andSte´phaneArbault vii viii Contents 12 InvestigationofMitochondrialADP-Ribosylation ViaImmunofluorescence ................................................ 165 Ann-KatrinHoppandMichaelO.Hottiger 13 AssessmentofMitochondrialCa2+Uptake................................. 173 Andra´sT.Deak,ClaireJean-Quartier,AlexanderI.Bondarenko, LukasN.Groschner,RolandMalli,WolfgangF.Graier, andMarkusWaldeck-Weiermair 14 AssessmentofMitochondrialMembranePotentialandNADH RedoxStateinAcuteBrainSlices ......................................... 193 AndreyY.Vinokurov,ViktorV.Dremin,GennadiiA.Piavchenko, OlgaA.Stelmashchuk,PlamenaR.Angelova,andAndreyY.Abramov 15 EvaluationofMitochondriaContentandFunctioninLive CellsbyMulticolorFlowCytometricAnalysis.............................. 203 Hsiu-HanFan,Tsung-LinTsai,IvanL.Dzhagalov, andChia-LinHsu 16 AnalysisofMitochondrialDysfunctionDuringCellDeath................... 215 VladimirGogvadzeandBorisZhivotovsky 17 ModifiedBlueNativeGelApproachforAnalysisofRespiratory Supercomplexes ........................................................ 227 SergiyM.Nadtochiy,MeganNgai,andPaulS.Brookes 18 Patch-ClampRecordingoftheActivityofIonChannels intheInnerMitochondrialMembrane .................................... 235 PiotrBednarczyk,RafałP.Kampa,ShurGałecka, AleksandraSe˛k,AgnieszkaWalewska,andPiotrKoprowski 19 AssessmentofMitochondrialProteinGlutathionylation asSignalingforCOPathway ............................................. 249 AnaS.Almeida,Cla´udiaFigueiredo-Pereira, andHelenaL.A.Vieira 20 3DOpticalCryo-ImagingMethod:ANovelApproach toQuantifyRenalMitochondrialBioenergeticsDysfunction ................. 259 ShimaMehrvar,AmadouK.S.Camara,andMahsaRanji 21 SimultaneousQuantificationofMitochondrialATPandROS ProductionUsingATPEnergyClampMethodology........................ 271 LipingYu,BrianD.Fink,andWilliamI.Sivitz 22 High-ThroughputImageAnalysisofLipid-Droplet-Bound Mitochondria .......................................................... 285 NathanaelMiller,DaneWolf,NourAlsabeeh,KianaMahdaviani, MayukoSegawa,MarcLiesa,andOrianS.Shirihai 23 CellEnergyBudgetPlatformforMultiparametric AssessmentofCellandTissueMetabolism................................. 305 DmitriB.PapkovskyandAlexanderV.Zhdanov 24 Fluorescence-BasedAssayForMeasuringOMA1Activity.................... 325 JuliaTobacykandLeeAnnMacMillan-Crow 25 StudyingMitochondrialNetworkFormationbyInVivo andInVitroReconstitutionAssay ........................................ 333 WanqingDu,XiangjunDi,andQianPeterSu Contents ix 26 ExtractionofFunctionalMitochondriaBasedonMembrane Stiffness ............................................................... 343 MdHabiburRahman,QinruXiao,ShiruiZhao, An-ChiWei,andYi-PingHo 27 AProtocolforUntargetedMetabolomicAnalysis:From SamplePreparationtoDataProcessing.................................... 357 AmandaL.SouzaandGaryJ.Patti 28 AMethodforAnalysisofNitrotyrosine-ContainingProteins byImmunoblottingCoupledwithMassSpectrometry ...................... 383 MatejKohutiarandAdamEckhardt 29 InVivoVisualizationandQuantificationofMitochondrial MorphologyinC.elegans................................................ 397 R.deBoer,R.L.Smith,W.H.DeVos,E.M.M.Manders, andH.vanderSpek 30 AssessingImpactofPlatinumComplexesonMitochondrial Functions.............................................................. 409 SuxingJinandXiaoyongWang 31 InSilicoModelingoftheMitochondrialPumpingComplexes withMarkovStateModels ............................................... 425 RogerSpringett 32 MonitoringtheMitochondrialPresequenceImportPathway InLivingMammalianCellswithaNewMolecularBiosensor................. 441 MaximeJacoupy,EmelineHamon-Keromen, andOlgaCorti Index ...................................................................... 453
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