2025
Highly stable planar asymmetric suspended membranes for investigating protein dynamics and membrane fusion
Bera M, Kalyana Sundaram R, Coleman J, Chatterjee A, Thoduvayil S, Pincet F, Ramakrishnan S. Highly stable planar asymmetric suspended membranes for investigating protein dynamics and membrane fusion. Nature Protocols 2025, 1-25. PMID: 40461798, DOI: 10.1038/s41596-025-01192-2.Peer-Reviewed Original ResearchMembrane fusionSingle-vesicle fusion assayMembrane fusion eventsProtein dynamics analysisMembrane fusion mechanismFluorescently labeled proteinsProtein-lipid interactionsSNARE proteinsTotal internal reflection fluorescenceFusion eventsMolecular chaperonesInvestigate protein dynamicsTime-lapse imagingCellular signalingLipid asymmetryFusion assayBiological processesLipid membranesProtein dynamicsMembrane model systemsLiving cellsMembrane environmentNear-native environmentMolecular componentsReflection fluorescenceNew dimensions in the molecular genetics of insect chemoreception
Talross G, Carlson J. New dimensions in the molecular genetics of insect chemoreception. Trends In Genetics 2025 PMID: 40340097, DOI: 10.1016/j.tig.2025.04.003.Peer-Reviewed Original ResearchMolecular geneticsChemosensory systemOdorant receptor genesRNA editingChemoreceptor expressionInsect chemoreceptionEpigenetic mechanismsLong noncoding RNAsOlfactory receptor neuronsNoncoding RNAsMolecular componentsReceptor geneTaste receptorsRNAReceptor neuronsChemoreceptionDrosophilaGenesNew insightsInsectsSpread diseaseMolecular Components of Vesicle Cycling at the Rod Photoreceptor Ribbon Synapse
Hanke-Gogokhia C, Zapadka T, Finkelstein S, Arshavsky V, Demb J. Molecular Components of Vesicle Cycling at the Rod Photoreceptor Ribbon Synapse. Advances In Experimental Medicine And Biology 2025, 1468: 325-330. PMID: 39930217, DOI: 10.1007/978-3-031-76550-6_54.Peer-Reviewed Original ResearchConceptsSynaptic vesicle exocytosisSynaptic vesicle recyclingPhotoreceptor ribbon synapseVesicle exocytosisVesicle recyclingVesicle cycleVesicle releaseRibbon synapseProtein synthesisProperties of synaptic transmissionMolecular componentsMouse rodsSynaptic terminalsRod cellsProteinVesiclesRod photoreceptorsDim lightSynaptic transmissionInner segmentsCellsExocytosisEndocytosisOuter segmentsEnergy production
2023
Comparative connectomics and escape behavior in larvae of closely related Drosophila species
Zhu J, Boivin J, Pang S, Xu C, Lu Z, Saalfeld S, Hess H, Ohyama T. Comparative connectomics and escape behavior in larvae of closely related Drosophila species. Current Biology 2023, 33: 2491-2503.e4. PMID: 37285846, DOI: 10.1016/j.cub.2023.05.043.Peer-Reviewed Original ResearchConceptsRelated Drosophila speciesDrosophila speciesEscape behaviorDrosophilid speciesRelated speciesMelanogasterSantomeaVentral nerve cordPlausible mechanistic explanationCommon partnerBehavioral traitsMolecular componentsNoxious cuesComparative connectomicsUnderlying neural circuitsSpeciesDownstream partnersMDIVMechanistic explanationCentralspindlin proteins Pavarotti and Tumbleweed along with WASH regulate nuclear envelope budding
Davidson K, Nakamura M, Verboon J, Parkhurst S. Centralspindlin proteins Pavarotti and Tumbleweed along with WASH regulate nuclear envelope budding. Journal Of Cell Biology 2023, 222: e202211074. PMID: 37163553, PMCID: PMC10174194, DOI: 10.1083/jcb.202211074.Peer-Reviewed Original ResearchConceptsNuclear envelope buddingActin nucleation activityNuclear export pathwayNE buddingExport pathwayWiskott-Aldrich syndrome proteinProtein quality controlActin-bundling activityNew molecular componentsCargo recruitmentSyndrome proteinRegulatory complexMitochondrial integritySynapse developmentCell differentiationStructural roleMolecular componentsNuclear washesLarge cargoBuddingPavarottiBudsMachineryTumbleweedNew entry point
2022
Maf family transcription factors are required for nutrient uptake in the mouse neonatal gut
Bara A, Chen L, Ma C, Underwood J, Moreci R, Sumigray K, Sun T, Diao Y, Verzi M, Lechler T. Maf family transcription factors are required for nutrient uptake in the mouse neonatal gut. Development 2022, 149 PMID: 36504079, PMCID: PMC10112929, DOI: 10.1242/dev.201251.Peer-Reviewed Original ResearchConceptsNutrient uptakeTranscription factorsMaf family transcription factorsMajor transcriptional changesFamily transcription factorsLoss of Blimp1Transcription factor MafBMaf proteinsCell fateTranscriptional regulatorsTranscriptional changesRNA-seqMaster regulatorEnterocyte genesFatty acid oxidationGene expressionPeroxisome numberAdult intestineMetabolic pathwaysMolecular componentsSubsequent degradationMaf factorsC-MafSimilar defectsIntestinal enterocytes
2020
Drosophila Wash and the Wash regulatory complex function in nuclear envelope budding
Verboon JM, Nakamura M, Davidson KA, Decker JR, Nandakumar V, Parkhurst SM. Drosophila Wash and the Wash regulatory complex function in nuclear envelope budding. Journal Of Cell Science 2020, 133: jcs243576. PMID: 32503943, PMCID: PMC7358131, DOI: 10.1242/jcs.243576.Peer-Reviewed Original ResearchConceptsNuclear envelope buddingBud formationImportant cellular processesNew molecular componentsNuclear lamina disruptionLarge macromolecular complexesDrosophila WashNE buddingRegulatory complexMolecular machineryCellular processesLamin BMacromolecular complexesCellular eventsNuclear membraneEgress mechanismsMolecular componentsArp2/3BuddingLamina disruptionDisease biologyModel systemProteinComplex functionsNew avenues
2018
Neurotransmitter signaling through heterotrimeric G proteins: insights from studies in C. elegans.
Koelle MR. Neurotransmitter signaling through heterotrimeric G proteins: insights from studies in C. elegans. WormBook 2018, 2018: 1-52. PMID: 26937633, PMCID: PMC5010795, DOI: 10.1895/wormbook.1.75.2.Peer-Reviewed Original ResearchConceptsHeterotrimeric G proteinsC. elegansG proteinsRic-8 proteinsNew molecular componentsG protein signalingG alpha proteinsNeurotransmitter releaseGenetic screenMammalian orthologsSmall molecule neurotransmittersIndividual receptor typesProtein signalingReceptor homologG alphaElegansDistant cellsAlpha proteinAdditional GPCRsGenetic studiesIndividual neural circuitsGαMolecular componentsGαqGαoStructural basis and energy landscape for the Ca2+ gating and calmodulation of the Kv7.2 K+ channel
Bernardo-Seisdedos G, Nuñez E, Gomis-Perez C, Malo C, Villarroel Á, Millet O. Structural basis and energy landscape for the Ca2+ gating and calmodulation of the Kv7.2 K+ channel. Proceedings Of The National Academy Of Sciences Of The United States Of America 2018, 115: 2395-2400. PMID: 29463698, PMCID: PMC5873240, DOI: 10.1073/pnas.1800235115.Peer-Reviewed Original ResearchConceptsC-lobeKey biological signalsPrincipal molecular componentsAssociation of helicesTransmembrane regionStructural basisFunction of CaKv7.2 channelsBasal cytosolic CaConformational rearrangementsN-lobeInactive stateKey controllerMolecular componentsCytosolic CaIntracellular CaKv7.2HelixInactive channelsM-currentBiological signalsCalcification stateMillisecond timeNeuronal excitabilityPopulated excited statesThe Molecular Composition and Function of the Nuclear Periphery and Its Impact on the Genome
Lusk C, King M. The Molecular Composition and Function of the Nuclear Periphery and Its Impact on the Genome. 2018, 35-62. DOI: 10.1007/978-3-319-71614-5_2.Peer-Reviewed Original ResearchNuclear peripheryNuclear subcompartmentsIntegral inner nuclear membrane proteinsInner nuclear membrane proteinSpecific genic regionsRepressive histone marksNuclear membrane proteinsGene-poor chromatinModern genomic analysesGenome stabilityHistone marksNuclear architectureGenic regionsTranscriptional outputNuclear laminsGene positionMembrane proteinsGenomic analysisDevelopmental inputsMolecular insightsMolecular componentsGenomeModel systemMolecular compositionCurrent understandingGenetic determinants and epigenetic effects of pioneer-factor occupancy
Donaghey J, Thakurela S, Charlton J, Chen JS, Smith ZD, Gu H, Pop R, Clement K, Stamenova EK, Karnik R, Kelley DR, Gifford CA, Cacchiarelli D, Rinn JL, Gnirke A, Ziller MJ, Meissner A. Genetic determinants and epigenetic effects of pioneer-factor occupancy. Nature Genetics 2018, 50: 250-258. PMID: 29358654, PMCID: PMC6517675, DOI: 10.1038/s41588-017-0034-3.Peer-Reviewed Original ResearchMeSH KeywordsA549 CellsBinding SitesCell LineageCells, CulturedComputational BiologyDNAEpigenesis, GeneticEpistasis, GeneticGATA4 Transcription FactorGene Expression RegulationGene Regulatory NetworksGenes, SwitchHEK293 CellsHep G2 CellsHepatocyte Nuclear Factor 3-betaHumansOctamer Transcription Factor-3Protein BindingTranscription FactorsConceptsCell typesAlternative cell typesGenomic occupancyDNA accessibilityPioneer factorsDNA replicationDNA methylationDNA sequencesEpigenetic effectsGene expressionDevelopmental transitionsMolecular componentsGenetic determinantsFOXA2TF activityGATA4Specific bindingExpressionSubsequent lossOccupancyEnrichmentMethylationLociLow enrichmentBinding
2017
The Mitochondrial Permeability Transition Pore: Molecular Structure and Function in Health and Disease
Jonas E, Porter G, Beutner G, Mnatsakanyan N, Park H, Mehta N, Chen R, Alavian K. The Mitochondrial Permeability Transition Pore: Molecular Structure and Function in Health and Disease. Biological And Medical Physics, Biomedical Engineering 2017, 69-105. DOI: 10.1007/978-3-319-55539-3_3.Peer-Reviewed Original ResearchMitochondrial permeability transition porePermeability transition poreCell deathTransition poreMitochondrial inner membraneInner mitochondrial membraneC subunitATP synthaseInner membraneOuter membraneMitochondrial membraneCardiac developmentRegulatory mechanismsOxidative phosphorylationATP productionMitochondrial functionMolecular componentsMitochondrial efficiencyOsmotic dysregulationCell functionLarge conductanceRecent findingsPersistent openingMembraneIon transport
2015
The Mitochondrial Permeability Transition Pore, the c‐Subunit of the F1Fo ATP Synthase, Cellular Development, and Synaptic Efficiency
Jonas E, Porter G, Beutner G, Mnatsakanyan N, Alavian K. The Mitochondrial Permeability Transition Pore, the c‐Subunit of the F1Fo ATP Synthase, Cellular Development, and Synaptic Efficiency. 2015, 31-64. DOI: 10.1002/9781119017127.ch2.Peer-Reviewed Original ResearchMitochondrial permeability transition poreMitochondrial membrane permeabilizationPermeability transition poreATP synthaseC subunitCell deathOuter mitochondrial membrane permeabilizationTransition poreF1Fo-ATP synthaseInner mitochondrial membraneMembrane channel activityMitochondrial permeability transitionMetabolic plasticityPT poreOuter membraneCellular developmentMembrane permeabilizationMitochondrial membraneRegulatory mechanismsOxidative phosphorylationAdenosine triphosphate (ATP) productionMitochondrial functionPermeability transitionMolecular componentsTriphosphate productionCell death disguised: The mitochondrial permeability transition pore as the c-subunit of the F1FO ATP synthase
Jonas EA, Porter GA, Beutner G, Mnatsakanyan N, Alavian KN. Cell death disguised: The mitochondrial permeability transition pore as the c-subunit of the F1FO ATP synthase. Pharmacological Research 2015, 99: 382-392. PMID: 25956324, PMCID: PMC4567435, DOI: 10.1016/j.phrs.2015.04.013.BooksConceptsMitochondrial permeability transition poreATP synthaseC subunitCell deathF1Fo-ATP synthaseInner mitochondrial membranePermeability transition poreMitochondrial permeability transitionOuter membraneMitochondrial membraneRegulatory mechanismsOxidative phosphorylationATP productionTransition poreMitochondrial functionPermeability transitionMolecular componentsOsmotic dysregulationLarge conductancePathological roleRecent findingsPersistent openingSynthaseIon transportMembrane
2014
Pivoting between Calmodulin Lobes Triggered by Calcium in the Kv7.2/Calmodulin Complex
Alaimo A, Alberdi A, Gomis-Perez C, Fernández-Orth J, Bernardo-Seisdedos G, Malo C, Millet O, Areso P, Villarroel A. Pivoting between Calmodulin Lobes Triggered by Calcium in the Kv7.2/Calmodulin Complex. PLOS ONE 2014, 9: e86711. PMID: 24489773, PMCID: PMC3904923, DOI: 10.1371/journal.pone.0086711.Peer-Reviewed Original ResearchConceptsC-lobeC-terminal segmentPrincipal molecular componentsAssociation of CaMChannel traffickingKv7.2 channelsMolecular mechanismsMolecular eventsEndoplasmic reticulumN-lobeMolecular componentsHelix BCalmodulin complexHelix A.CalmodulinData highlightKv7.2Calmodulin lobesM channelsComplementary approachesNeuronal excitabilityFluorometric assayTraffickingReporterReticulum
2013
Tumor protein D52 controls trafficking of an apical endolysosomal secretory pathway in pancreatic acinar cells
Messenger SW, Thomas DD, Falkowski MA, Byrne JA, Gorelick FS, Groblewski GE. Tumor protein D52 controls trafficking of an apical endolysosomal secretory pathway in pancreatic acinar cells. AJP Gastrointestinal And Liver Physiology 2013, 305: g439-g452. PMID: 23868405, PMCID: PMC3761242, DOI: 10.1152/ajpgi.00143.2013.Peer-Reviewed Original ResearchConceptsImmature secretory granulesApical exocytosisTumor protein D52Endosomal compartmentsEndolysosomal compartmentsMinor regulated pathwayZymogen granule formationAcinar cellsEndosomal intermediatesISG maturationSerine 136Phosphorylation sitesTrans-GolgiSecretory pathwayAspartate substitutionContent proteinsRegulatory proteinsBrefeldin ASynaptotagmin-1Molecular componentsPancreatic acinar cellsGranule formationExocytosisLysosomal membraneLAMP1
2012
Obligate Symbionts Activate Immune System Development in the Tsetse Fly
Weiss BL, Maltz M, Aksoy S. Obligate Symbionts Activate Immune System Development in the Tsetse Fly. The Journal Of Immunology 2012, 188: 3395-3403. PMID: 22368278, PMCID: PMC3311772, DOI: 10.4049/jimmunol.1103691.Peer-Reviewed Original ResearchConceptsSymbiotic bacteriaImmune system developmentNovel evolutionary adaptationImmunity-related genesObligate symbiontsSymbiotic microbesObligate mutualistsViviparous modeProper immune system functionEvolutionary adaptationPhagocytic hemocytesMolecular mechanismsCell extractsMolecular componentsSusceptible phenotypeNonpathogenic Escherichia coliEscherichia coliTsetse fliesImmune systemFliesAtypical expressionHemocytesImmune system functionPhenotypeTsetse
2006
Estrogen Receptor-Mediated Rapid Signaling
Moriarty K, Kim KH, Bender JR. Estrogen Receptor-Mediated Rapid Signaling. Endocrinology 2006, 147: 5557-5563. PMID: 16946015, DOI: 10.1210/en.2006-0729.Peer-Reviewed Original ResearchConceptsMembrane estrogen receptorsPlasma membrane-associated formSplice variantsMembrane-associated formTranscriptional activationMultimolecular complexesRapid signalingSignaling cascadesMolecular componentsSpecific tissuesER splice variantsMolecular levelSpecific fashionEnzymatic pathwaysEstrogen receptorEstrogen responseNuclear responsePathwayPhysiological outcomesReceptorsComplexesSignalingVariantsVascular endotheliumRapid response
2004
Visualizing a Circadian Clock Protein Crystal Structure of KaiC and Functional Insights
Pattanayek R, Wang J, Mori T, Xu Y, Johnson CH, Egli M. Visualizing a Circadian Clock Protein Crystal Structure of KaiC and Functional Insights. Molecular Cell 2004, 15: 375-388. PMID: 15304218, DOI: 10.1016/j.molcel.2004.07.013.Peer-Reviewed Original ResearchConceptsClock protein complexesAuto-phosphorylation siteGlobal gene expressionCircadian biological clockHomohexameric complexEvolutionary relationshipsProtein complexesCircadian clockworkATP bindingFunctional insightsCircadian proteinsKaiCProtein crystal structuresCentral poreGene expressionMolecular componentsBiochemical mechanismsBiological clockCrystal structureDouble donutComplex formationProteinCircadian rhythmicityMutationsCyanobacteria
2000
Substrate–cytoskeletal coupling as a mechanism for the regulation of growth cone motility and guidance
Suter D, Forscher P. Substrate–cytoskeletal coupling as a mechanism for the regulation of growth cone motility and guidance. Developmental Neurobiology 2000, 44: 97-113. PMID: 10934315, DOI: 10.1002/1097-4695(200008)44:2<97::aid-neu2>3.0.co;2-u.Peer-Reviewed Original ResearchConceptsGrowth cone motilityCone motilityGuidance cuesGrowth conesDifferent guidance cuesDynamic cytoskeletonCell adhesion moleculeSignal transducerAxon guidanceMolecular componentsCytoskeletonMotile structuresMotility deviceAppropriate target cellsDifferent functionsRespective receptorsAdhesion moleculesProteinAxonal growthMotilityGrowth cone movementTarget cellsNeuronal processesRecent evidenceCone movement
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