Morphogen Gradients: Methods and Protocols

303 Pages·2018·13.178 MB·English

by  Julien Dubrulle

Methods in
Molecular Biology 1863
Julien Dubrulle Editor
Morphogen
Gradients
Methods and Protocols
M M B
ETHODS IN OLECULAR IO LO GY
SeriesEditor
JohnM.Walker
School of Lifeand MedicalSciences
University ofHertfordshire
Hatfield, Hertfordshire,AL109AB,UK
Forfurther volumes:
http://www.springer.com/series/7651
Morphogen Gradients
Methods and Protocols
Edited by
Julien Dubrulle
Integrated Microscopy Core, Baylor College of Medicine, Houston, TX, USA
Editor
JulienDubrulle
IntegratedMicroscopyCore
BaylorCollegeofMedicine
Houston,TX,USA
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-8771-9 ISBN978-1-4939-8772-6 (eBook)
https://doi.org/10.1007/978-1-4939-8772-6
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Preface
Duringembryonicdevelopmentandtissuegrowth,progenitorcellsreceivecuesfromtheir
environment that instruct them to differentiate according to their spatial location. This
positionalinformationisconveyedbymoleculescalledmorphogensthatformaconcentra-
tion gradient across the tissue. These morphogens, whether they are secreted peptides,
metabolites, or diffusible transcription factors, are produced from a source and travel
throughtheresponsivefieldbypassivediffusion,advection,oractivecell-to-celltransport.
Differentconcentrationsofthemorphogentriggerdifferentresponsesinthereceivingcells,
leadingtoaspatialarrangementofcellswithspecificidentitiesthatdependontheirdistance
fromthesource.
The study of morphogen gradients combines biophysics, cell and developmental biol-
ogy, and applied mathematics approaches to understand how they form, what their
biologicalfunctionsare,andtopredicttheirbehaviorinspaceandtime.Thisbookpresents
methods focusing on the visualization of morphogen gradients, the analysis of their bio-
physicalandbiologicalproperties,andthetheoreticalaspectsunderlyingtheir functions.
Houston,TX,USA JulienDubrulle
v
Contents
Preface ..................................................................... v
Contributors................................................................. ix
PART I VISUALIZATION OF MORPHOGEN GRADIENTS
1 AnalysisofExpressionGradientsofDevelopmentalRegulators
inArabidopsisthalianaRoots ............................................ 3
Marı´aFlorenciaErcoli,RodrigoVena,CamilaGoldy,
JavierF.Palatnik,andRamiro E.Rodrı´guez
2 DetectionandQuantificationoftheBicoidConcentrationGradient
inDrosophilaEmbryos.................................................. 19
FengHe,HonggangWu,DavidCheung,andJunMa
3 ImagingCytonemesinDrosophilaEmbryos ............................... 29
LijuanDuandSougataRoy
4 MeasuringDorsoventralPatternandMorphogenSignalingProfiles
intheGrowingNeuralTube ............................................. 47
MarcinZagorskiandAnnaKicheva
PART II ANALYSIS OF BIOPHYSICAL PROPERTIES AND FUNCTIONS
OF MORPHOGENS
5 FluorescenceCorrelationandCross-CorrelationSpectroscopy
inZebrafish ............................................................ 67
XueWenNg,KarunaSampath,andThorstenWohland
6 FRAPAnalysisofExtracellularDiffusioninZebrafishEmbryos............... 107
GaryH.SohandPatrickMu¨ller
7 GenerationofEctopicMorphogenGradientsintheZebrafish
Blastula................................................................ 125
MaraysadeOlivera-Melo,Peng-FeiXu,NathalieHoussin,
BernardThisse,andChristineThisse
8 PolarizingRegionTissueGraftingintheChickEmbryoLimbBud ........... 143
HollyStaintonandMatthewTowers
9 AnalysisofPLETHORAGradientFormationbySecreted
PeptidesDuringRootDevelopment ...................................... 155
HidefumiShinoharaandYoshikatsuMatsubayashi
10 LiveImagingofmRNATranscriptioninDrosophilaEmbryos................ 165
CarminaAngelicaPerez-Romero,HuyTran,MathieuCoppey,
AleksandraM.Walczak,Ce´cileFradin,andNathalieDostatni
vii
viii Contents
11 LiveFly:AToolboxfor theAnalysisofTranscriptionDynamics
inLiveDrosophilaEmbryos ............................................. 183
HuyTran,CarminaAngelicaPerez-Romero,TeresaFerraro,
Ce´cileFradin,NathalieDostatni,MathieuCoppey,
andAleksandraM.Walczak
PART III MODELING OF MORPHOGEN BEHAVIORS AND ACTIVITIES
12 Discrete-StateStochasticModelingofMorphogenGradient
Formation ............................................................. 199
HamidTeimouriandAnatolyB.Kolomeisky
13 SimulationofMorphogenandTissueDynamics............................ 223
MichaelD.Multerer,LucasD.Wittwer,AnnaStopka,DianaBarac,
ChristineLang,andDagmarIber
14 MechanismsandMeasurementsofScaleInvarianceofMorphogen
Gradients .............................................................. 251
YanHuangandDavidUmulis
15 ScalingofMorphogeneticPatterns........................................ 263
Manan’IarivoRasolonjanaharyandBakhtierVasiev
16 ModellingTime-DependentAcquisitionofPositionalInformation ........... 281
LaurentJutras-Dube´,AdrienHenry,andPaulFranc¸ois
Index ...................................................................... 303
Contributors
DIANA BARAC (cid:1) DepartmentofBiosystemsScienceandEngineering,ETHZurich,Basel,
Switzerland
DAVIDCHEUNG (cid:1) DivisionofDevelopmentalBiology,CincinnatiChildren’sResearch
Foundation,Cincinnati,OH,USA;DivisionofBiomedicalInformatics,Cincinnati
Children’sResearchFoundation,Cincinnati,OH,USA
MATHIEUCOPPEY (cid:1) InstitutCurie,PSLResearchUniversity,CNRS,SorbonneUniversite´,
PhysicoChimie,Paris,France
MARAYSADEOLIVERA-MELO (cid:1) DepartmentofCellBiology,UniversityofVirginiaSchoolof
Medicine,Charlottesville,VA,USA
NATHALIEDOSTATNI (cid:1) InstitutCurie,PSLResearchUniversity,CNRS,SorbonneUniversite´,
NuclearDynamics,Paris,France
LIJUANDU (cid:1) DepartmentofCellBiologyandMolecularGenetics,UniversityofMaryland,
CollegePark,MD,USA
MARI´AFLORENCIAERCOLI (cid:1) IBR(InstitutodeBiologı´aMolecular yCelulardeRosario),
CONICET,UniversidadNacionaldeRosario,Rosario,Argentina
TERESAFERRARO (cid:1) EcoleNormaleSupe´rieure,PSLResearchUniversity,CNRS,Sorbonne
Universite´,LaboratoiredePhysiqueThe´orique,Paris,France;InstitutdeBiologieParis-
Seine,SorbonneUniversite´,CNRS,DevelopmentalBiology,Paris,France
CE´CILEFRADIN (cid:1) InstitutCurie,PSLResearchUniversity,CNRS,SorbonneUniversite´,
NuclearDynamics,Paris,France;McMasterUniversity,Hamilton,ON,Canada
PAULFRANC¸OIS (cid:1) McGillUniversity,Montreal,QC,Canada
CAMILAGOLDY (cid:1) IBR(InstitutodeBiologı´aMolecular yCelulardeRosario),CONICET,
UniversidadNacionaldeRosario,Rosario,Argentina
FENGHE (cid:1) DivisionofMedicalGeneticsandGenomics,Children’sHospital,Zhejiang
UniversitySchoolofMedicine,Hangzhou,Zhejiang,China;InstituteofGenetics,Zhejiang
UniversitySchoolofMedicine,Hangzhou,Zhejiang,China;KeyLaboratoryofPollinating
InsectBiologyoftheMinistryofAgriculture,InstituteofApiculturalResearch,Chinese
AcademyofAgriculturalSciences,Beijing,China
ADRIENHENRY (cid:1) McGillUniversity,Montreal,QC,Canada
NATHALIEHOUSSIN (cid:1) DepartmentofCellBiology,UniversityofVirginiaSchoolofMedicine,
Charlottesville,VA,USA
YANHUANG (cid:1) AgriculturalandBiologicalEngineering,PurdueUniversity,WestLafayette,
IN,USA
DAGMARIBER (cid:1) DepartmentofBiosystemsScienceandEngineering,ETHZurich,Basel,
Switzerland
LAURENTJUTRAS-DUBE´ (cid:1) McGillUniversity,Montreal,QC,Canada
ANNAKICHEVA (cid:1) InstituteofScienceandTechnologyAustria(ISTAustria),Klosterneuburg,
Austria
ANATOLYB.KOLOMEISKY (cid:1) DepartmentofChemistryandCenter forTheoreticalBiological
Physics,RiceUniversity,Houston,Texas,USA
CHRISTINELANG (cid:1) DepartmentofBiosystemsScienceandEngineering,ETHZurich,Basel,
Switzerland
ix
x Contributors
JUNMA (cid:1) DivisionofMedicalGeneticsandGenomics,Children’sHospital,Zhejiang
UniversitySchoolofMedicine,Hangzhou,Zhejiang,China;InstituteofGenetics,Zhejiang
UniversitySchoolofMedicine,Hangzhou,Zhejiang,China;DivisionofDevelopmental
Biology,CincinnatiChildren’sResearchFoundation,Cincinnati,OH,USA;Divisionof
BiomedicalInformatics,CincinnatiChildren’sResearchFoundation,Cincinnati,OH,
USA;LaboratoryofSystemsDevelopmentalBiology,InstituteofGenetics,Zhejiang
UniversitySchoolofMedicine,Hangzhou,Zhejiang,China
YOSHIKATSUMATSUBAYASHI (cid:1) DivisionofBiologicalScience,GraduateSchoolofScience,
NagoyaUniversity,Nagoya,Japan
PATRICKMU¨LLER (cid:1) FriedrichMiescherLaboratoryoftheMaxPlanckSociety,Tu¨bingen,
Germany
MICHAELD.MULTERER (cid:1) DepartmentofBiosystemsScienceandEngineering,ETHZurich,
Basel,Switzerland
XUEWENNG (cid:1) DepartmentofChemistryandCentreforBioimagingSciences,National
UniversityofSingapore,Singapore,Singapore
JAVIERF.PALATNIK (cid:1) IBR(InstitutodeBiologı´aMolecular yCelulardeRosario),
CONICET,UniversidadNacionaldeRosario,Rosario,Argentina;CentrodeEstudios
Interdisciplinarios,UniversidadNacionaldeRosario,Rosario,Argentina
CARMINAANGELICAPEREZ-ROMERO (cid:1) InstitutCurie,PSLResearchUniversity,CNRS,
SorbonneUniversite´,NuclearDynamics,Paris,France;McMasterUniversity,Hamilton,
ON,Canada
MANAN’IARIVORASOLONJANAHARY (cid:1) DepartmentofMathematicalSciences,Universityof
Liverpool,Liverpool,UK
RAMIROE.RODRI´GUEZ (cid:1) IBR(InstitutodeBiologı´aMolecular yCelulardeRosario),
CONICET,UniversidadNacionaldeRosario,Rosario,Argentina;CentrodeEstudios
Interdisciplinarios,UniversidadNacionaldeRosario,Rosario,Argentina
SOUGATAROY (cid:1) DepartmentofCellBiologyandMolecularGenetics,UniversityofMaryland,
CollegePark,MD,USA
KARUNASAMPATH (cid:1) DivisionofBiomedicalSciences,WarwickMedicalSchool,Universityof
Warwick,Coventry,UK
HIDEFUMISHINOHARA (cid:1) DivisionofBiologicalScience,GraduateSchoolofScience,Nagoya
University,Nagoya,Japan
GARYH.SOH (cid:1) FriedrichMiescherLaboratoryoftheMaxPlanckSociety,Tu¨bingen,Germany
HOLLY STAINTON (cid:1) DepartmentofBiomedicalScience,UniversityofSheffield,Sheffield,UK
ANNASTOPKA (cid:1) DepartmentofBiosystemsScienceandEngineering,ETHZurich,Basel,
Switzerland
HAMID TEIMOURI (cid:1) DepartmentofPhysicsandFASCenter forSystemsBiology,Harvard
University,Cambridge,MA,USA
BERNARDTHISSE (cid:1) DepartmentofCellBiology,UniversityofVirginiaSchoolofMedicine,
Charlottesville,VA,USA
CHRISTINETHISSE (cid:1) DepartmentofCellBiology,UniversityofVirginiaSchoolofMedicine,
Charlottesville,VA,USA
MATTHEWTOWERS (cid:1) DepartmentofBiomedicalScience,UniversityofSheffield,Sheffield,UK
HUYTRAN (cid:1) InstitutCurie,PSLResearchUniversity,CNRS,SorbonneUniversite´,Nuclear
Dynamics,Paris,France;EcoleNormaleSupe´rieure,PSLResearchUniversity,CNRS,
SorbonneUniversite´,PhysiqueThe´orique,Paris,France
Contributors xi
DAVIDUMULIS (cid:1) AgriculturalandBiologicalEngineering,PurdueUniversity,West
Lafayette,IN,USA;WeldonSchoolofBiomedicalEngineering,PurdueUniversity,West
Lafayette,IN,USA
BAKHTIERVASIEV (cid:1) DepartmentofMathematicalSciences,UniversityofLiverpool,Liverpool,
UK
RODRIGO VENA (cid:1) IBR(InstitutodeBiologı´aMolecular yCelulardeRosario),CONICET,
UniversidadNacionaldeRosario,Rosario,Argentina
ALEKSANDRAM.WALCZAK (cid:1) EcoleNormaleSupe´rieure,PSLResearchUniversity,CNRS,
SorbonneUniversite´,LaboratoiredePhysiqueThe´orique,Paris,France
LUCASD.WITTWER (cid:1) DepartmentofBiosystemsScienceandEngineering,ETHZurich,Basel,
Switzerland
THORSTENWOHLAND (cid:1) DepartmentofChemistryandCentreforBioimagingSciences,
NationalUniversityofSingapore,Singapore,Singapore;DepartmentofBiologicalSciences,
NationalUniversityofSingapore,Singapore,Singapore
HONGGANGWU (cid:1) StateKeyLaboratoryofBrainandCognitiveSciences,Instituteof
Biophysics,ChineseAcademyofSciences,Beijing,China;UniversityofChineseAcademyof
Sciences,Beijing,China
PENG-FEIXU (cid:1) DepartmentofCellBiology,UniversityofVirginiaSchoolofMedicine,
Charlottesville,VA,USA
MARCINZAGORSKI (cid:1) InstituteofScienceandTechnologyAustria(ISTAustria),
Klosterneuburg,Austria