Featured Publications
Automated time-lapse data segmentation reveals in vivo cell state dynamics
Genuth M, Kojima Y, Jülich D, Kiryu H, Holley S. Automated time-lapse data segmentation reveals in vivo cell state dynamics. Science Advances 2023, 9: eadf1814. PMID: 37267354, PMCID: PMC10413672, DOI: 10.1126/sciadv.adf1814.Peer-Reviewed Original ResearchConceptsCell statesSingle-cell RNA sequencing dataCell state dynamicsCell behaviorEmbryonic development proceedsCell state transitionsRNA sequencing dataCollective cell behaviorIndividual cell behaviorsZebrafish tailbudLeft-right asymmetryCell tracking dataCollective cell motionGene expressionSequencing dataMolecular processesIndividual embryosDevelopment proceedsEmbryosCell motionParallel identificationBilateral symmetryReproducible patternTailbudState transitionsOrganization of Embryonic Morphogenesis via Mechanical Information
Das D, Jülich D, Schwendinger-Schreck J, Guillon E, Lawton AK, Dray N, Emonet T, O'Hern CS, Shattuck MD, Holley SA. Organization of Embryonic Morphogenesis via Mechanical Information. Developmental Cell 2019, 49: 829-839.e5. PMID: 31178400, PMCID: PMC6590525, DOI: 10.1016/j.devcel.2019.05.014.Peer-Reviewed Original ResearchConceptsEmbryonic organizerCell motionCell polarityTransgenic perturbationsEmbryonic morphogenesisMorphogen signalingTail organizerZebrafish embryosCell movementMechanical informationCell adhesionCell contractilityNeighboring cellsLocal biochemicalEmbryosMorphogenesisSecondary consequenceAdditional mechanismCellsMorphogensTranscriptionSignalingSystematic analysisOrganizersComputational modelingPatterned Disordered Cell Motion Ensures Vertebral Column Symmetry
Das D, Chatti V, Emonet T, Holley SA. Patterned Disordered Cell Motion Ensures Vertebral Column Symmetry. Developmental Cell 2017, 42: 170-180.e5. PMID: 28743003, PMCID: PMC5568629, DOI: 10.1016/j.devcel.2017.06.020.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBody PatterningCell MovementComputer SimulationModels, BiologicalSpineTailZebrafishZebrafish ProteinsCross-Scale Integrin Regulation Organizes ECM and Tissue Topology
Jülich D, Cobb G, Melo AM, McMillen P, Lawton AK, Mochrie SG, Rhoades E, Holley SA. Cross-Scale Integrin Regulation Organizes ECM and Tissue Topology. Developmental Cell 2015, 34: 33-44. PMID: 26096733, PMCID: PMC4496283, DOI: 10.1016/j.devcel.2015.05.005.Peer-Reviewed Original ResearchConceptsExtracellular matrixCadherin-2Integrin α5Cell-cell adhesionFluorescence cross-correlation spectroscopyECM protein fibronectinSomite boundariesCross-correlation spectroscopyAdjacent cell membranesBody elongationECM assemblyIntegrin associationIntegrin activationPhysical associationActive conformationFibronectin fibrillogenesisProtein fibronectinTissue assemblyIntegrin conformationTissue topologyInactive integrinsCell membraneCross-scale mechanismsStereotypic patternAnimal tissues
2016
A Sawtooth Pattern of Cadherin 2 Stability Mechanically Regulates Somite Morphogenesis
McMillen P, Chatti V, Jülich D, Holley SA. A Sawtooth Pattern of Cadherin 2 Stability Mechanically Regulates Somite Morphogenesis. Current Biology 2016, 26: 542-549. PMID: 26853361, PMCID: PMC4822709, DOI: 10.1016/j.cub.2015.12.055.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCadherinsExtracellular MatrixMesodermMorphogenesisSomitesZebrafishZebrafish ProteinsConceptsECM assemblyGenetic mosaicsPosterior somitesDifferential cadherin expressionExtracellular matrixCell-ECM adhesionFN matrix assemblyBoundary formationVertebrate gastrulationSomite boundariesSomite morphogenesisCytoskeletal contractilityParaxial mesodermEmbryonic precursorsCDH activityMatrix assemblyCadherin expressionCDH2SomitesTissue boundariesIntegrin α5SomitogenesisCell sortingCell aggregatesAssembly
2013
Cell-Fibronectin Interactions Propel Vertebrate Trunk Elongation via Tissue Mechanics
Dray N, Lawton A, Nandi A, Jülich D, Emonet T, Holley SA. Cell-Fibronectin Interactions Propel Vertebrate Trunk Elongation via Tissue Mechanics. Current Biology 2013, 23: 1335-1341. PMID: 23810535, PMCID: PMC3725194, DOI: 10.1016/j.cub.2013.05.052.Peer-Reviewed Original ResearchConceptsCell migrationTrunk elongationExtracellular matrixCell-FN interactionsTransgenic rescue experimentsECM protein fibronectinElongation defectsParaxial mesodermBody elongationEmbryonic developmentTissue homeostasisTail budTissue mechanicsΑ-subunitRescue experimentsProtein fibronectinSystem-level analysisCell adhesionFN matrixIntegrin α5Concomitant lossTissue integrityCell motionITGαvFibronectinRegulated tissue fluidity steers zebrafish body elongation
Lawton AK, Nandi A, Stulberg MJ, Dray N, Sneddon MW, Pontius W, Emonet T, Holley SA. Regulated tissue fluidity steers zebrafish body elongation. Development 2013, 140: 573-582. PMID: 23293289, PMCID: PMC3561786, DOI: 10.1242/dev.090381.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnimals, Genetically ModifiedBiomechanical PhenomenaBody PatterningCadherinsCell AdhesionCell CountCell MovementCell PolarityComputer SimulationEmbryo, NonmammalianEmbryonic DevelopmentFibroblast Growth FactorsGene Expression Regulation, DevelopmentalModels, BiologicalTailTime FactorsWnt Signaling PathwayZebrafishZebrafish Proteins
2012
Crosstalk between Fgf and Wnt signaling in the zebrafish tailbud
Stulberg MJ, Lin A, Zhao H, Holley SA. Crosstalk between Fgf and Wnt signaling in the zebrafish tailbud. Developmental Biology 2012, 369: 298-307. PMID: 22796649, PMCID: PMC3423502, DOI: 10.1016/j.ydbio.2012.07.003.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceDNA PrimersFibroblast Growth FactorsGene Expression Regulation, DevelopmentalGene Regulatory NetworksGlycogen Synthase Kinase 3Glycogen Synthase Kinase 3 betaMAP Kinase Signaling SystemModels, BiologicalPhosphatidylinositol 3-KinasesPhosphorylationProto-Oncogene Proteins c-aktSignal TransductionTailWnt Signaling PathwayZebrafishZebrafish ProteinsConceptsZebrafish tailbudCell fate specificationCell fate changesCo-regulated genesWnt antagonist Dkk1Reciprocal positive regulationFate specificationFate changesNascent transcriptionAxis elongationProtein phosphorylationPhosphorylation of GSK3βPI3-kinaseFGF pathwayMesodermal developmentTail elongationPositive regulationTarget genesAntagonist DKK1TailbudFibroblast growth factorWntPhosphorylation levelsTranscriptionGSK3β phosphorylationThe Her7 node modulates the network topology of the zebrafish segmentation clock via sequestration of the Hes6 hub
Trofka A, Schwendinger-Schreck J, Brend T, Pontius W, Emonet T, Holley SA. The Her7 node modulates the network topology of the zebrafish segmentation clock via sequestration of the Hes6 hub. Development 2012, 139: 940-947. PMID: 22278920, PMCID: PMC3274355, DOI: 10.1242/dev.073544.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBasic Helix-Loop-Helix Transcription FactorsBiological ClocksBody PatterningComputer SimulationDimerizationDNAGene Expression Regulation, DevelopmentalGene Knockdown TechniquesGene Regulatory NetworksRecombinant Fusion ProteinsRepressor ProteinsTranscription FactorsZebrafishZebrafish ProteinsConceptsZebrafish segmentation clockSegmentation clockBinds DNACis-regulatory sequencesDNA-binding heterodimersTranscriptional negative feedbackGenetic experimentsHer7Regulatory sequencesDNA bindingHes6Vivo assaysDNAHomodimerHeterodimersDistinct preferenceEmergent functionsNetwork hubsNegative feedbackComputational analysisClockDimersSequestrationProteinRegulation
2009
Control of extracellular matrix assembly along tissue boundaries via Integrin and Eph/Ephrin signaling
Jülich D, Mould AP, Koper E, Holley SA. Control of extracellular matrix assembly along tissue boundaries via Integrin and Eph/Ephrin signaling. Development 2009, 136: 2913-2921. PMID: 19641014, DOI: 10.1242/dev.038935.Peer-Reviewed Original Research
2005
Integrinα5 and Delta/Notch Signaling Have Complementary Spatiotemporal Requirements during Zebrafish Somitogenesis
Ju¨lich D, Geisler R, Consortium T, Holley S. Integrinα5 and Delta/Notch Signaling Have Complementary Spatiotemporal Requirements during Zebrafish Somitogenesis. Developmental Cell 2005, 8: 575-586. PMID: 15809039, DOI: 10.1016/j.devcel.2005.01.016.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsAnimals, Genetically ModifiedBody PatterningCell PolarityExtracellular MatrixFibronectinsGene Expression Regulation, DevelopmentalIn Situ HybridizationIntegrin alpha5Intracellular Signaling Peptides and ProteinsMembrane ProteinsMolecular Sequence DataMorphogenesisPhenotypePoint MutationReceptors, NotchRecombinant Fusion ProteinsSignal TransductionSomitesZebrafishZebrafish ProteinsConceptsFibronectin matrix assemblyDelta/Notch signalingMatrix assemblyNotch pathway mutantsEntire body axisZebrafish somitogenesisVertebrate embryogenesisPathway mutantsDouble mutantSomite defectsSomite formationPosterior somitesGenetic controlSomitogenesisNotch signalingNotch pathwayEpithelial transitionSpatiotemporal requirementsBody axisCell polarizationSegmentation defectsPoint mutationsMutantsComplete lossSkeletal muscle