Mitochondrial Medicine: Volume 2: Assessing Mitochondria (Methods in Molecular Biology, 2276)

455 Pages·2021·13.811 MB·English

by  Volkmar Weissig (editor), Marvin Edeas (editor)

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
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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
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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