Histochemistry of Single Molecules: Methods and Protocols (Methods in Molecular Biology, 2566) PDF
Preview Histochemistry of Single Molecules: Methods and Protocols (Methods in Molecular Biology, 2566)
Methods in Molecular Biology 2566 Carlo Pellicciari · Marco Biggiogera Manuela Malatesta Editors Histochemistry of Single Molecules Methods and Protocols 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. Histochemistry of Single Molecules Methods and Protocols Second Edition Edited by Carlo Pellicciari Department of Biology and Biotechnology, University of Pavia, PAVIA, Italy Marco Biggiogera Department of Biology and Biotechnology, University of Pavia, PAVIA, Italy Manuela Malatesta Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, VERONA, Italy Editors CarloPellicciari MarcoBiggiogera DepartmentofBiologyand DepartmentofBiologyandBiotechnology Biotechnology UniversityofPavia UniversityofPavia PAVIA,Italy PAVIA,Italy ManuelaMalatesta DepartmentofNeurosciences, BiomedicineandMovementSciences UniversityofVerona VERONA,Italy ISSN1064-3745 ISSN1940-6029 (electronic) MethodsinMolecularBiology ISBN978-1-0716-2674-0 ISBN978-1-0716-2675-7 (eBook) https://doi.org/10.1007/978-1-0716-2675-7 ©TheEditor(s)(ifapplicable)andTheAuthor(s),underexclusivelicensetoSpringerScience+BusinessMedia,LLC,part ofSpringerNature2023 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. Cover Illustration: Combined lectin- and immune-histochemistry on a semithin cryosection of normal human urothelium. For labelling the proteins, the primary polyclonal rabbit antibody against transmembrane proteins uroplakinsand Alexa Flour 588 conjugated secondary goat anti-rabbit antibody were used (red fluorescence), while for labelling the sugar residues, the FITC-conjugated Amaranthus caudatus agglutinin (ACA) was used (green fluorescence).ColocalizationofuroplakinsandACAbindingisseenasorangetoyellowfluorescence.NuclearDNA wascounterstainedwithDAPI(bluefluorescence).(CourtesyofDasˇaZupancˇicˇ,MatejaErdaniKreftandRokRomih.) ThisHumanaimprintispublishedbytheregisteredcompanySpringerScience+BusinessMedia,LLC,partofSpringer Nature. Theregisteredcompanyaddressis:1NewYorkPlaza,NewYork,NY10004,U.S.A. Preface Asadistinctivefeature,histochemicaltechniquesallowlocalizingdifferentchemicalspecies intheveryplace(inatissue,oracelloranorganelle)theyexist,aresynthesized,orfunction invivo;thismakeshistochemistryauniquetoolforbasicandappliedbio-medicalresearch, whereitprovidestopologicalevidenceofthebiochemicalandmoleculardata. Thestoryofhistochemistrygoesalongwaybackand,inthelast150years,hasevolved inparallelwiththedetectioninstruments,fromlightandelectronmicroscopytocytometry and super-resolution microscopy. Since the year 2000, about 325,000 articles, in which histochemistrywasused,havebeenpublishedinqualifiedinternationaljournals(according to the Web of Science database). This demonstrates that histochemistry is central for inves- tigating very different research subjects (from cell and tissue biology to anatomy and pathology,fromzoologyandbotanytoecology,fromdevelopmentalbiologytonanotech- nology),whereitisprincipallyappliedtolocateandquantifysinglemoleculesormolecular complexesinsitu,intheattempttorelatestructuralorganizationandfunction. ThissecondeditionofHistochemistryofSingleMoleculesaimsatupdatingandimproving the first edition’s overview of histochemical techniques, through a series of discursive chapters and lab-tested protocols for the detection of specific molecules or metabolic processes,atlightandelectronmicroscopy. The book opens with a review chapter on the evolution of histochemical markers in cytometry, and then it is divided into seven parts dealing with an assortment of chemical targets. Part I is on vital histochemistry, and it includes four chapters on autofluorescence imaging,lysosomeimagingbycarbondots,thedetectionofoxidativeandnitrosativestress, andtheidentificationofadipogenicandosteogenicdifferentiationoflivingstemcells.Part II, Carbohydrate Histochemistry, is comprises an updated overview on lectin histochemis- try, followed by two chapters on the histochemical and immunohistochemical labelling of proteoglycans, and on combined lectin- and immuno-histochemistry for fluorescence microscopy. Five chapters form Part III, Protein Histochemistry: in the first four chapters, immunohistochemistry is used to detect proteins marking myogenic differentiation or autophagy at light microscopy, or milk proteins at electron microscopy, while in the last one potassium permanganate is rediscovered as a stain for basic proteins on ultrathin sectionsattransmissionelectronmicroscopy.PartIV,LipidHistochemistry,offersanupdate of basics in fixation and tissue processing, and gives protocols for the staining of myelin in the nervous system or of lipid droplets in mouse oocytes and embryos. Part V, Nuclear Histochemistry,containsaprotocolforassessingDNAdamageincervicalepithelialcellsand twocontrastingmethodsfor transmissionelectronmicroscopy:auranyl-freetechniquefor nuclearstructuresandastainingprocedureforthespecificvisualizationofRNAbyterbium citrate vapors. Part VI is on plant histochemistry: threechapters describe protocols for the detection of different molecules in plant cell walls, one is on starch staining with iodine solution, and the last one on plant secretory structures. The book ends with Part VII, Histochemistry for Nanoscience: this part, which was not present in the first edition, includes protocols for the visualization of chemically different nanoconstructs in animal andplantcellsatbright-field,fluorescence,andtransmissionelectronmicroscopy. v vi Preface These28chaptersdemonstratethathistochemicaltechniquesmaybeeffectivelyusedto visualize, with high specificity, a plethora of molecules in differently processed tissues and cells, thus confirming that histochemistry still ranks high among the methodological approachesinlifescienceresearch. Pavia,Italy CarloPellicciari Pavia,Italy MarcoBiggiogera Verona,Italy ManuelaMalatesta Contents Preface ..................................................................... v Contributors................................................................. xi 1 HistochemistryinAdvancedCytometry:FromFluorochromes toMassProbes ..... ....... ........ ....... ....... ........ ....... ........ 1 GiulianoMazziniandMarcoDanova PART I VITAL HISTOCHEMISTRY 2 AutofluorescenceLabel-FreeImagingoftheLiverReticularStructure......... 29 AnnaC.Croce,GiuseppinaPalladini,AndreaFerrigno, andMariapiaVairetti 3 LysosomeImagingBasedonFluorescentCarbonDots....... ....... ........ 37 ShuoGuo,YuanqiangSun,andZhaohuiLi 4 OxidativeandNitrosativeStressDetectioninHumanSperm UsingFluorescentProbes........... ....... ...... ........ ....... ..... .... 45 SaraEscada-RebeloandJoa˜oRamalho-Santos 5 SimultaneousLabelingofAdipogenicandOsteogenicDifferentiating StemCellsforLiveConfocalAnalysis ....... ....... ........ ....... ........ 53 PatriziaVaghi,AmandaOldani,PaolaFulghieri,LidiaPollara, EnzaMariaValente,andVirginieSottile PART II CARBOHYDRATE HISTOCHEMISTRY 6 LectinHistochemistry:HistoricalPerspectives,StateoftheArt, andFutureDirections ...... ........ ....... ....... ........ ....... ........ 65 SusanAnnBrooks 7 HistochemicalandImmunohistochemicalMethodsfor the IdentificationofProteoglycans ... ... ...... .... .... ........ ....... ........ 85 DavidSa´nchez-Porras,JuanVaras,CarlosGodoy-Guzma´n, FabiolaBermejo-Casares,Sebastia´nSanMartı´n,andVı´ctorCarriel 8 CombinedLectin-andImmuno-histochemistry(CLIH)for FluorescenceMicroscopy ........... ....... ....... ........ ....... ........ 99 DaˇsaZupancˇicˇ,MatejaErdaniKreft,andRokRomih PART III PROTEIN HISTOCHEMISTRY 9 ImmunofluorescenceLabelingofSkeletalMuscleinDevelopment, Regeneration,andDisease .......... ....... ....... ........ ....... ........ 113 MarieE.Esper,KasunKodippili,andMichaelA.Rudnicki vii viii Contents 10 ImmunohistochemicalDetectionoftheAutophagyMarkersLC3 andp62/SQSTM1inFormalin-FixedandParaffin-EmbeddedTissue......... 133 SabinaBerezowskaandJose´A.Galva´n 11 ImmunohistochemicalDetectionoftheChaperone-Mediated AutophagyMarkersLAMP2AandHSPA8inFormalin-Fixedand Paraffin-EmbeddedTissues ......... ....... ....... ........ ....... ........ 141 TerezaLosmanova´,MarioP.Tschan,Jose´A.Galva´n, andSabinaBerezowska 12 ImmunogoldLabelingofMilkProteinsatTransmission ElectronMicroscopy ....... ........ ....... ....... ........ ....... ........ 149 PaoloD’Incecco 13 RediscoverPotassiumPermanganateasaStainforBasicProteins onUltrathinSectionsatTransmissionElectronMicroscopy.......... ...... .. 159 LorenaZannino,ClaudioCasali,andMarcoBiggiogera PART IV LIPID HISTOCHEMISTRY 14 TissueFixationandProcessingfor theHistologicalIdentification ofLipids........... ....... ........ ....... ....... ........ ....... ........ 175 DavidSa´nchez-Porras,FabiolaBermejo-Casares, Ram(cid:1)onCarmona, TamaraWeiss,FernandoCampos,andVı´ctorCarriel 15 StainingMethodsforNormalandRegenerativeMyelininthe NervousSystem .... ....... ........ ....... ....... ........ ... .... ...... .. 187 O´scarD.Garcı´a-Garcı´a,TamaraWeiss,Jesu´sChato-Astrain, StefaniaRaimondo,andVı´ctorCarriel 16 NileRedandBODIPYStainingofLipidDropletsinMouse OocytesandEmbryos...... ........ ....... ....... ........ ....... ........ 205 SimonaBisogno,ŁukaszGa˛sior,andGraz˙ynaE.Ptak PART V NUCLEAR HISTOCHEMISTRY 17 ChromatinDispersionTesttoAssesDNADamageinCervical EpithelialCells ..... ....... ........ ....... ....... ........ ....... ........ 215 ElvaI.Corte´s-Gutie´rrez,Jose´L.Ferna´ndez,MarthaI.Da´vila-Rodrı´guez, CarlosGarcı´adelaVega,andJaimeGosa´lvez 18 Uranyl-FreeStainingasaSuitableContrastingTechniquefor NuclearStructuresatTransmissionElectronMicroscopy ..... ....... ........ 225 MariaAssuntaLacavallaandBarbaraCisterna 19 SpecificRNAVisualizationatElectronMicroscopyviaTerbium CitrateVapors...... ....... ........ ....... ....... ........ ....... ........ 233 ClaudioCasali,LorenaZannino,andMarcoBiggiogera PART VI PLANT HISTOCHEMISTRY 20 LocalizingMoleculesinPlantCellWallsUsingFluorescenceMicroscopy...... 243 LloydA.Donaldson Contents ix 21 RatiometricFluorescentSafranin-OStainingAllowsthe QuantificationofLigninContentsInMuro......... ........ ....... ........ 261 OrianeMorel,CorentinSpriet,Ce´dricLion,FabienBaldacci-Cresp, GarancePontier,MarieBaucher,ChristopheBiot,SimonHawkins, andGodfreyNeutelings 22 LiveFluorescenceVisualizationofCelluloseandPectinin PlantCellWalls..... ....... ........ ....... ....... ........ ....... ........ 269 YoussefChebliandAnjaGeitmann 23 StainingStarchwithIodineSolution........ ....... ........ ....... ...... .. 281 ShengnanZhao,YinhuiRen,andCunxuWei 24 HistochemicalAnalysisofPlantSecretoryStructures......... ....... ........ 291 DiegoDemarco PART VII HISTOCHEMISTRY FOR NANOSCIENCE 25 AlcianBlueStainingtoVisualizeIntracellularHyaluronic Acid-BasedNanoparticles........... ....... ....... ........ ....... ........ 313 MathieuRepellin,FlaviaCarton,GiovannaLollo, andManuelaMalatesta 26 PrussianBlueStainingtoVisualizeIronOxideNanoparticles ........ ........ 321 ValeriaBitonto,FrancescaGarello,ArnaudScherberich, andMiriamFilippi 27 DiaminobenzidinePhotooxidationtoVisualizeFluorescent NanoparticlesinAdheringCulturedCellsatTransmission ElectronMicroscopy ....... ....... ..... ... ....... ........ ....... ........ 333 ManuelaCostanzoandManuelaMalatesta 28 FluorescentLabelingofLigninNanocapsuleswithFluorol Yellow088......... ....... ........ ....... ....... ........ ....... ........ 345 FrancoCheli,SaraFalsini,MariaCristinaSalvatici, SandraRistori,SilviaSchiff,EmilioCorti,IreneCostantini, CristinaGonnelli,FrancescoSaverioPavone,andAlessioPapini Index ...................................................................... 355
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