Histochemistry of Single Molecules: Methods and Protocols (Methods in Molecular Biology, 2566)

351 Pages·2022·15.85 MB·English

by  Carlo Pellicciari (editor), Marco Biggiogera (editor), Manuela Malatesta (editor)

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