Salamanders: Methods and Protocols

471 Pages·2022·15.981 MB·English

by  Ashley W. Seifert, Joshua D. Currie

Methods in
Molecular Biology 2562
Ashley W. Seifert
Joshua D. Currie Editors
Salamanders
Methods and Protocols
M M B
ETHODS IN OLECULAR IO LO GY
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School of Lifeand MedicalSciences
University ofHertfordshire
Hatfield, Hertfordshire, UK
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Salamanders
Methods and Protocols
Edited by
Ashley W. Seifert
Department of Biology, University of Kentucky, Lexington, KY, USA
Joshua D. Currie
Department of Biology, Wake Forest University, Winston-Salem, NC, USA
Editors
AshleyW.Seifert JoshuaD.Currie
DepartmentofBiology DepartmentofBiology
UniversityofKentucky WakeForestUniversity
Lexington,KY,USA Winston-Salem,NC,USA
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-0716-2658-0 ISBN978-1-0716-2659-7 (eBook)
https://doi.org/10.1007/978-1-0716-2659-7
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Preface
For nearly threecenturies,salamanders haveremainedkeyresearch organisms fordevelop-
mental,evolutionary,andecologicalstudies.Buildingonadvancesingeneticmodelsystems
(e.g., Drosophila,C.elegans,and Mus),the last20 yearshasseen adizzyingacceleration of
molecularandgenomictechniquesthathavemadetheir wayintoamphibianresearch.This
breadthanddepthhavemadesalamanderandnewtmodelsidealresearchorganismstostudy
processesaffectingbiologicalscalesfrommoleculestoecosystems.
OurgoalineditingthisneweditionofMethodsinSalamanderResearchwastoassemble
a definitive desk reference for researchers either new to using salamanders for research or
expert labs that want to bring new techniques and approaches to bear on their scientific
questions.Thechapterscontainedinthisvolumehighlightnewvoicesinthisfieldalongside
the experience and perspective of veteran salamander scientists. We want to extend a
heartfeltthankstoallthisvolume’sauthorsfor theireffortsinthefaceofpandemic-related
disruptions. We hope this reference will be a catalyst for researchers using amphibians to
dialoguewiththeauthorsandthebroadercommunityinordertoextendtheboundariesof
salamander research.
Lexington,KY,USA AshleyW.Seifert
Winston-Salem,NC,USA JoshuaD.Currie
v
Contents
Preface ..................................................................... v
Contributors................................................................. xi
1 SalamandersasKeyModelsforDevelopmentand
RegenerationResearch ..... ........ ....... ....... ........ ....... ........ 1
MalcolmMaden
PART I LABORATORY COLONY HUSBANDRY
2 EstablishingaNewResearchAxolotlColony........ ........ ....... ........ 27
AnastasiaS.YandulskayaandJamesR.Monaghan
3 HealthMonitoringforLaboratorySalamanders ..... ...... .... ..... ........ 41
MarcusJ.CrimandMarciaL.Hart
4 Husbandry,CaptiveBreeding,andFieldSurveyofChinese
GiantSalamander(Andriasdavidianus) .. ... ...... ....... .. .... ... ........ 75
WanshengJiang,HaifengTian,andLuZhang
PART II TRADITIONAL MOLECULAR TECHNIQUES
5 Whole-MountInSituHybridization(WISH)forSalamander
EmbryosandLarvae ....... ........ ....... ....... ........ ....... ........ 95
SruthiPurushothamanandAshleyW.Seifert
6 HybridizationChainReactionFluorescenceInSituHybridization
(HCR-FISH)inAmbystomamexicanumTissue...... ........ ....... ........ 109
AlexM.Lovely,TimothyJ.Duerr,DavidF.Stein,
EvanT.Mun,andJamesR.Monaghan
7 EthylCinnamate-BasedTissueClearingStrategies ......... .. ...... ......... 123
WouterMasselinkandEllyM.Tanaka
8 InductionandCharacterizationofCellularSenescenceinSalamanders ........ 135
QinghaoYu,HannahE.Walters,andMaximinaH.Yun
9 MethodsforStudyingAppendicularSkeletalBiologyinAxolotls...... ........ 155
CamiloRiquelme-Guzma´nandTatianaSandoval-Guzma´n
10 FluorescenceInSituHybridizationofDNAProbeson
MitoticChromosomesoftheMexicanAxolotl ...... ........ ....... ........ 165
MelissaKeinathandVladimirTimoshevskiy
11 TheUseofSmallMoleculestoDissectDevelopmentaland
RegenerativeProcessesinAxolotls.......... ....... ........ ....... ..... ... 175
Ste´phaneRoy
12 COMETAssayforDetectionofDNADamageDuring
AxolotlTailRegeneration........... ....... ....... ........ ....... ........ 183
BelfranCarbonell,JenniferA´lvarez,GloriaA.Santa-Gonza´lez,
andJeanPaulDelgado
vii
viii Contents
PART III EXPERIMENTAL MANIPULATIONS AND SURGERIES
13 InVivoandExVivoViewofNewtLensRegeneration....... ....... ........ 197
GeorgiosTsissios,AnthonySallese,WeihaoChen,AlyssaMiller,
HuiWang,andKatiaDelRio-Tsonis
14 BeadImplantationandDeliveryofExogenousGrowthFactors....... ........ 209
RenaKashimoto,SayaFurukawa,SakiyaYamamoto,
andAkiraSatoh
15 TheAccessoryLimbModelRegenerativeAssayandItsDerivatives ........... 217
MichaelRaymondandCatherineD.Mccusker
16 EmbryonicTissueandBlastemaTransplantations.... ........ ....... ........ 235
MarittaSchuez,ThomasKurth,JoshuaD.Currie,
andTatianaSandoval-Guzma´n
17 RetinoicAcid–InducedLimbDuplications.......... ........ ....... ........ 249
MalcolmMadenandTreyPolvadore
18 IsolationandCharacterizationofPeritonealMacrophages
fromSalamanders......... ......... ....... ....... ........ ....... ........ 259
AnthonySallese,GeorgiosTsissios,J.Rau´lPe´rez-Estrada,
ArielleMartinez,andKatiaDelRio-Tsonis
PART IV BIOINFORMATICS AND GENOMICS
19 NavigationandUseofCustomTrackswithintheAxolotl
GenomeBrowser .......... ........ ....... ....... ........ ....... ........ 273
SergejNowoshilowandEllyM.Tanaka
20 ChromosomeConformationCaptureforLargeGenomes .... .... ... ...... .. 291
AkaneKawaguchiandEllyM.Tanaka
PART V TRANSGENICS AND LINEAGE-TRACING
21 AxolotlTransgenesisviaInjectionofI-SceIMeganucleaseor
Tol2TransposonSystem.... ........ ....... ....... ........ ....... ........ 321
MarittaSchuezandTatianaSandoval-Guzma´n
22 APracticalGuideforCRISPR-Cas9-InducedMutationsinAxolotls .......... 335
KonstantinosSousounis,KatharineCourtemanche,
andJessicaL.Whited
23 ApplyingaKnock-InStrategytoCreateReporter-Tagged
KnockoutAllelesinAxolotls ........ ....... ....... ........ ....... ........ 351
LiqunWang,Yan-YunZeng,YanmeiLiu,andJi-FengFei
24 BaculovirusProductionandInfectioninAxolotls.... ........ ....... ........ 369
PrayagMurawala,CatarinaR.Oliveira,HelenaOkulski,
MaximinaH.Yun,andEllyM.Tanaka
25 CellDissociationTechniquesinSalamanders........ ........ ....... ........ 389
GabrielaJohnson,NadjibDastagir,ZacharyBeal,
AndrewHart,andJamesGodwin
Contents ix
PART VI PHYSIOLOGICAL AND ORGANISMAL TECHNIQUES
26 AxolotlMetabolism:MeasuringMetabolicRate ..... ........ ....... ........ 407
MosheKhurgel
27 ArtificialInseminationinAxolotl .... ....... ....... ........ ....... ........ 417
YukaTaniguchi-SugiuraandEllyM.Tanaka
28 ScreeningSalamandersforSymbionts ....... ....... ........ ....... ........ 425
ElliVickersandRyanKerney
29 AssessingLeukocyteProfilesofSalamandersandOtherAmphibians:
AHerpetologists’Guide.... .... .... .... ... ....... ........ ....... ........ 443
AndrewK.DavisandJohnC.Maerz
PART VII EPILOGUE
30 BestPracticestoPromoteDataUtilityandReusebythe
Non-TraditionalModelOrganismCommunity...... ........ ....... ........ 461
GarrettS.DunlapandNicholasD.Leigh
31 NowthatWeGotThere,WhatNext? ....... ....... ........ ....... ........ 471
EllyM.Tanaka
Index ...................................................................... 481
Contributors
JENNIFERA´LVAREZ • GrupoGene´ticaRegeneraci(cid:1)onyCa´ncer,InstituteofBiology,University
ofAntioquia,Medellin,Colombia
ZACHARYBEAL • MountDesertIslandBiologicalLaboratory(MDIBL),KathrynW.Davis
Center forRegenerativeBiologyandAging,BarHarbor,ME,USA
BELFRANCARBONELL • GrupoGene´ticaRegeneraci(cid:1)onyCa´ncer,InstituteofBiology,
UniversityofAntioquia,Medellin,Colombia
WEIHAOCHEN • CellularMolecularandStructuralBiologyProgram,MiamiUniversity,
Oxford,OH,USA;DepartmentofChemical,PaperandBiomedicalEngineering,Miami
University,Oxford,OH,USA
KATHARINECOURTEMANCHE • DepartmentofStemCellandRegenerativeBiology,Harvard
University,Cambridge,MA,USA
MARCUS J.CRIM • IDEXXBioAnalytics,Columbia,MO,USA
JOSHUA D.CURRIE • DepartmentofBiology,WakeForestUniversity,Winston-Salem,NC,
USA
NADJIBDASTAGIR • MountDesertIslandBiologicalLaboratory(MDIBL),KathrynW.Davis
Center forRegenerativeBiologyandAging,BarHarbor,ME,USA
ANDREWK.DAVIS • OdumSchoolofEcology,TheUniversityofGeorgia,Athens,GA,USA;D.
B.WarnellSchoolofForestryandNaturalResources,TheUniversityofGeorgia,Athens,
GA,USA
KATIADELRIO-TSONIS • DepartmentofBiology,MiamiUniversity,Oxford,OH,USA;
Center forVisualSciencesatMiamiUniversity,Oxford,OH,USA;CellularMolecular
andStructuralBiologyProgram,MiamiUniversity,Oxford,OH,USA
JEANPAULDELGADO • GrupoGene´ticaRegeneraci(cid:1)onyCa´ncer,InstituteofBiology,
UniversityofAntioquia,Medellin,Colombia
TIMOTHYJ.DUERR • DepartmentofBiology,Northeastern University,Boston,MA,USA
GARRETTS.DUNLAP • BiologicalandBiomedicalSciences,HarvardMedicalSchool,
Cambridge,MA,USA
JI-FENGFEI • KeyLaboratoryofBrain,CognitionandEducationSciences,Ministryof
Education,InstituteforBrainResearchandRehabilitation,SouthChinaNormal
University,Guangzhou,China;DepartmentofPathology,GuangdongProvincialPeople’s
Hospital,GuangdongAcademyofMedicalSciences,Guangzhou,China
SAYAFURUKAWA • DepartmentofBiologicalScienceFacultyofScience,OkayamaUniversity,
Okayama,Japan
JAMESGODWIN • MountDesertIslandBiologicalLaboratory(MDIBL),KathrynW.Davis
Center forRegenerativeBiologyandAging,BarHarbor,ME,USA
ANDREWHART • MountDesertIslandBiologicalLaboratory(MDIBL),KathrynW.Davis
Center forRegenerativeBiologyandAging,BarHarbor,ME,USA
MARCIAL.HART • IDEXXBioAnalytics,Columbia,MO,USA
WANSHENG JIANG • JishouUniversity,Zhangjiajie,Hunan,China
GABRIELAJOHNSON • MountDesertIslandBiologicalLaboratory(MDIBL),Kathryn
W.DavisCenter forRegenerativeBiologyandAging,BarHarbor,ME,USA
RENAKASHIMOTO • OkayamaUniversity,GraduateschoolofNaturalScienceand
Technology,Okayama,Japan
xi