Correlative Light and Electron Microscopy IV (Volume 162) (Methods in Cell Biology, Volume 162) PDF
Preview Correlative Light and Electron Microscopy IV (Volume 162) (Methods in Cell Biology, Volume 162)
Methods in Cell Biology Correlative Light and Electron Microscopy IV Volume 162 Series Editors Leslie Wilson Department of Molecular, Cellular and Developmental Biology University of California Santa Barbara, California Phong Tran University of Pennsylvania Philadelphia, USA & Institut Curie, Paris, France Methods in Cell Biology Correlative Light and Electron Microscopy IV Volume 162 Edited by Thomas Mu¨ller-Reichert Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universita¨t Dresden, Dresden, Germany Paul Verkade School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, United Kingdom AcademicPressisanimprintofElsevier 50HampshireStreet,5thFloor,Cambridge,MA02139,UnitedStates 525BStreet,Suite1650,SanDiego,CA92101,UnitedStates TheBoulevard,LangfordLane,Kidlington,OxfordOX51GB,UnitedKingdom 125LondonWall,London,EC2Y5AS,UnitedKingdom Firstedition2021 Copyright©2021ElsevierInc.Allrightsreserved. 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Practitionersandresearchersmustalwaysrelyontheirownexperienceandknowledgeinevaluatingand usinganyinformation,methods,compounds,orexperimentsdescribedherein.Inusingsuchinformation ormethodstheyshouldbemindfuloftheirownsafetyandthesafetyofothers,includingpartiesforwhom theyhaveaprofessionalresponsibility. Tothefullestextentofthelaw,neitherthePublishernortheauthors,contributors,oreditors,assumeany liabilityforanyinjuryand/ordamagetopersonsorpropertyasamatterofproductsliability,negligenceor otherwise,orfromanyuseoroperationofanymethods,products,instructions,orideascontainedinthe materialherein. ISBN:978-0-12-822058-0 ISSN:0091-679X ForinformationonallAcademicPresspublications visitourwebsiteathttps://www.elsevier.com/books-and-journals Publisher:ZoeKruze EditorialProjectManager:LeticiaM.Lima ProductionProjectManager:DennyMansingh CoverDesigner:MilesHitchen TypesetbySPiGlobal,India Contents Contributors.............................................................................................................xi Preface toCLEM IV: Broaden the horizon..........................................................xix CHAPTER 1 50 Shades of CLEM: How to choose the right approach for you..........................................................1 Nadav Scherand Ori Avinoam 1. What is CLEM?.............................................................................1 2. The microscopist’sdilemma..........................................................2 3. Sample preservation.......................................................................5 4. Case studies....................................................................................6 5. How tochoose your shade of CLEM: Closing remarks...............8 Acknowledgments...............................................................................9 References...........................................................................................9 CHAPTER 2 The Histo-CLEM Workflow for tissues of model organisms...................................................................13 Ana Laura Sousa, Joana RodriguesLo´ios, Pedro Faı´sca, and Erin M.Tranfield 1. Introduction..................................................................................14 2. Generaldesign ofthe Histo-CLEM Workflow...........................16 3. Applicationexample....................................................................28 4. Concluding remarks.....................................................................34 Acknowledgments.............................................................................34 References.........................................................................................35 CHAPTER 3 Fluorescentplatinumnanoclustersascorrelative light electron microscopy probes..............................39 Hugh Tanner,Lorna Hodgson, Judith Mantell, and PaulVerkade 1. Introduction..................................................................................40 2. CLEM probes...............................................................................41 3. Instrumentation,materials, and reagents.....................................45 4. Methods........................................................................................47 5. Generationand validation ofthe probe.......................................49 6. Use ofPtNCs...............................................................................57 v vi Contents 7. Discussion and outlook................................................................62 Acknowledgments.............................................................................63 References.........................................................................................64 CHAPTER 4 Refining a correlative light electron microscopy workflow using luminescent metal complexes.........69 Jonathan R. Shewring,Lorna Hodgson, Helen L. Bryant, Per A.Bullough,Julia A. Weinstein,and Paul Verkade 1. Introduction..................................................................................70 2. Transition metal Ircomplex 1.....................................................71 3. Instrumentation andmaterials......................................................72 4. Methods........................................................................................74 5. Results..........................................................................................76 6. Discussion....................................................................................83 Acknowledgments.............................................................................84 References.........................................................................................84 CHAPTER 5 Sample preparation for energy dispersive X-ray imaging of biological tissues....................................89 NicoleM.Pirozzi,JeroenKuipers,andBenN.G.Giepmans 1. Introduction..................................................................................90 2. Routinechemical fixation oftissues...........................................91 3. Resin...........................................................................................101 4. Contrasting.................................................................................102 5. Grids and sample holder............................................................106 6. Other considerations..................................................................107 7. Conclusion..................................................................................111 8. Materials.....................................................................................111 Acknowledgments...........................................................................112 Author contributions........................................................................113 References.......................................................................................113 CHAPTER 6 HPM live μ for a full CLEM workflow......................115 XavierHeiligenstein, Maritde Beer, (cid:1) ^ (cid:1) (cid:1) JeromeHeiligenstein,FrederiqueEyraud,LaurentManet, Fabrice Schmitt, Edwin Lamers, Joerg Lindenau, Mariska Kea-te Lindert, JeanSalamero, Grac¸a Raposo, Nico Sommerdijk, Martin Belle, andAnatAkiva 1. Introduction................................................................................117 2. High pressure freezing principles..............................................117 3. Designingthe HPM liveμ.........................................................120 Contents vii 4. Integrationof the HPM live μin aCLEM workflow...............131 5. Aliveimaging,cryo-fluorescence,in-resinfluorescenceand EM workflow:Validationat each step......................................135 6. Perspectives................................................................................144 Acknowledgments...........................................................................145 Author contributions........................................................................145 References.......................................................................................145 CHAPTER 7 High-throughputscreeningofmitoticmammalian cells for electron microscopy using classic histological dyes......................................................151 RobertKiewisz,ThomasM€uller-Reichert,andGunarFabig 1. Introduction................................................................................152 2. Methods......................................................................................154 3. Instrumentationand materials....................................................164 4. Discussion..................................................................................165 Acknowledgments...........................................................................168 References.......................................................................................168 CHAPTER 8 On-section correlative light and electron microscopyoflargecellularvolumesusingSTEM tomography...............................................................171 KorbinianBuerger,KerstinN.Schmidt,JantinaFokkema, Hans C.Gerritsen, OlgaMaier,Uwe de Vries, Yulia Zaytseva, Reinhard Rachel, and Ralph Witzgall 1. Introduction................................................................................173 2. Methods......................................................................................175 3. Instrumentationand materials....................................................180 4. Results........................................................................................183 5. Discussion..................................................................................196 6. Conclusion..................................................................................199 Acknowledgments...........................................................................200 References.......................................................................................200 CHAPTER 9 An accelerated procedure for approaching and imagingofopticallybrandedregionofinterestin tissue........................................................................205 Katlijn Vints, PieterBaatsen,and Natalia V. Gounko 1. Introduction................................................................................206 2. Rationale....................................................................................208 3. Methods......................................................................................209 viii Contents 4. Instrumentation andmaterials....................................................217 5. Discussion and conclusion.........................................................218 Acknowledgments...........................................................................219 References.......................................................................................219 CHAPTER 10 Cryo-fluorescence microscopy of high-pressure frozen C. elegans enables correlative FIB-SEM imaging of targeted embryonic stages in the intact worm...............................................................223 Irene Y. Chang, Mohammad Rahman,Adam Harned, Orna Cohen-Fix,and Kedar Narayan 1. Introduction................................................................................225 2. Anote onselecting the right cryoprotectant.............................226 3. Rationale....................................................................................232 4. Methods......................................................................................233 5. Instrumentation andmaterials....................................................244 6. Discussion..................................................................................247 Acknowledgments...........................................................................248 References.......................................................................................249 CHAPTER 11 Correlative super-resolution fluorescence and electron cryo-microscopy based on cryo-SOFI.......253 Vojteˇch Prazˇa´k,KayGr€unewald,and Rainer Kaufmann 1. Introduction................................................................................254 2. Rationale....................................................................................255 3. Materials.....................................................................................255 4. Methods......................................................................................257 5. Discussion..................................................................................268 Acknowledgments...........................................................................270 References.......................................................................................270 CHAPTER 12 Cryo-correlative light and electron microscopy workflow for cryo-focused ion beam milled adherent cells...........................................................273 SteffenKlein,MoritzWachsmuth-Melm,SophieL.Winter, AndronikiKolovou,and Petr Chlanda 1. Introduction................................................................................274 2. Rationale....................................................................................275 3. Materials.....................................................................................276 4. Methods......................................................................................278 Contents ix 5. Results anddiscussion...............................................................297 Acknowledgments...........................................................................300 References.......................................................................................301 CHAPTER 13 Super-resolution correlative light-electron microscopyusingaclick-chemistryapproachfor studying intracellular trafficking.............................303 TeodoraAndrian, ThomasBakkum, Daphne M. vanElsland, Erik Bos, Abraham J. Koster, Lorenzo Albertazzi, Sander I. van Kasteren, and Sı´lvia Pujals 1. Introduction................................................................................305 2. Methods......................................................................................310 3. Instrumentationand materials....................................................319 4. Discussion..................................................................................320 Acknowledgments...........................................................................324 References.......................................................................................325 CHAPTER 14 Step-by-step guide to post-acquisition correlation of confocal and FIB/SEM volumes using Amira software...............................................333 Allon Weiner 1. Introduction................................................................................334 2. Precursor techniques..................................................................336 3. Software and hardware..............................................................338 4. Step-by-step guide......................................................................338 5. Summaryand discussion...........................................................347 Acknowledgments...........................................................................348 References.......................................................................................348 CHAPTER 15 Visualization and co-registration of correlative microscopy data with the ImageJ plug-in Correlia...353 Matthias Schmidt, Florens Rohde, and Ulf-DietrichBraumann 1. Introduction................................................................................355 2. Models for image co-registration..............................................358 3. Correlia......................................................................................359 4. Two real-life examples..............................................................370 5. Summaryand conclusions.........................................................385 Acknowledgments...........................................................................386 References.......................................................................................386
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