2024
Olfactory sensory neuron population expansions influence projection neuron adaptation and enhance odour tracking
Takagi S, Sancer G, Abuin L, Stupski S, Roman Arguello J, Prieto-Godino L, Stern D, Cruchet S, Álvarez-Ocaña R, Wienecke C, van Breugel F, Jeanne J, Auer T, Benton R. Olfactory sensory neuron population expansions influence projection neuron adaptation and enhance odour tracking. Nature Communications 2024, 15: 7041. PMID: 39147786, PMCID: PMC11327376, DOI: 10.1038/s41467-024-50808-w.Peer-Reviewed Original ResearchConceptsOlfactory sensory neuronsPopulation expansionSpecies-specific expansionSensory neuronsProjection neuronsConnections of sensory neuronsOlfactory sensory neuron numbersSpecies-specific behaviorsD. sechelliaDrosophila sechelliaEcologically-relevantProportion of neuronsEnvironmental cuesMultigenic changesEvolutionary expansionIncreased synaptic connectivityFunctional impactPN sensitivityNeuronal adaptationOdor trackingNeuronsSechelliaLateral inhibitionInhibitionSpeciesAn atlas of human vector-borne microbe interactions reveals pathogenicity mechanisms
Hart T, Sonnert N, Tang X, Chaurasia R, Allen P, Hunt J, Read C, Johnson E, Arora G, Dai Y, Cui Y, Chuang Y, Yu Q, Rahman M, Mendes M, Rolandelli A, Singh P, Tripathi A, Ben Mamoun C, Caimano M, Radolf J, Lin Y, Fingerle V, Margos G, Pal U, Johnson R, Pedra J, Azad A, Salje J, Dimopoulos G, Vinetz J, Carlyon J, Palm N, Fikrig E, Ring A. An atlas of human vector-borne microbe interactions reveals pathogenicity mechanisms. Cell 2024, 187: 4113-4127.e13. PMID: 38876107, PMCID: PMC11959484, DOI: 10.1016/j.cell.2024.05.023.Peer-Reviewed Original ResearchCell invasionHost-microbe interactionsArthropod-borne pathogensHost sensingMicrobe interactionsTranscriptional regulationLyme disease spirocheteMicrobial interactionsExtracellular proteinsMicrobial pathogenesisEpidermal growth factorTissue colonizationEnvironmental cuesBacterial selectivityIntracellular pathogensPutative interactionsNext-generation therapeuticsPathogensFunctional investigationsInteractomeVector-borne diseasesImmune evasionPathogenic mechanismsStrainUnmet medical needReconstructing axial progenitor field dynamics in mouse stem cell-derived embryoids
Bolondi A, Law B, Kretzmer H, Gassaloglu S, Buschow R, Riemenschneider C, Yang D, Walther M, Veenvliet J, Meissner A, Smith Z, Chan M. Reconstructing axial progenitor field dynamics in mouse stem cell-derived embryoids. Developmental Cell 2024, 59: 1489-1505.e14. PMID: 38579718, PMCID: PMC11187653, DOI: 10.1016/j.devcel.2024.03.024.Peer-Reviewed Original ResearchNeuro-mesodermal progenitorsFate outcomesStem cell-based modelsEmbryonic trunkEnvironmental cuesMorphological phenotypesDownstream lineagesMolecular recordCell-based modelsCell typesTranscriptional signatureComplex tissuesAxial progenitorsLineagesDevelopmental timeNeural lineagesTransient progenitor populationProgenitor populationsDevelopmental windowPhylogenySpatial–temporal order–disorder transition in angiogenic NOTCH signaling controls cell fate specification
Kang T, Bocci F, Nie Q, Onuchic J, Levchenko A. Spatial–temporal order–disorder transition in angiogenic NOTCH signaling controls cell fate specification. ELife 2024, 12 DOI: 10.7554/elife.89262.3.Peer-Reviewed Original ResearchCell fate specificationStalk cellsCell type-specificTip cellsNotch signalingFate specificationStalk cell differentiationMorphogenic processesDensity of fibronectinType-specificCell typesCell-cell communicationComplex morphogenic processesResponse to elevated levelsCell fateCell identityDynamics of spatial patternsDepletion of fibronectinEnvironmental cuesSignaling moleculesBlood vessel sproutingSprout extensionAngiogenic morphogenesisSignaling pathwayHypoxic micro-environmentSkeletal muscle TET3 promotes insulin resistance through destabilisation of PGC-1α
Liu B, Xie D, Huang X, Jin S, Dai Y, Sun X, Li D, Bennett A, Diano S, Huang Y. Skeletal muscle TET3 promotes insulin resistance through destabilisation of PGC-1α. Diabetologia 2024, 67: 724-737. PMID: 38216792, PMCID: PMC10904493, DOI: 10.1007/s00125-023-06073-5.Peer-Reviewed Original ResearchConceptsTen-eleven translocationMuscle insulin sensitivityRNA-seqPGC-1aRegulation of muscle insulin sensitivityType 2 diabetesAnalysis of RNA-seqResponse to environmental cuesGenome-wide expression profilingWild-typeHFD-fedHFD-induced insulin resistanceHigh-fat diet (HFD)-inducedExpression levelsMaintenance of glucoseSkeletal muscle insulin sensitivityAccession numbersSkeletal muscleEnhanced glucose toleranceFamily dioxygenasesMitochondrial respirationSkeletal muscle of humansEnvironmental cuesMitochondrial functionBiological processes
2023
“Don't [ruminate], be happy”: A cognitive perspective linking depression and anhedonia
Rutherford A, McDougle S, Joormann J. “Don't [ruminate], be happy”: A cognitive perspective linking depression and anhedonia. Clinical Psychology Review 2023, 101: 102255. PMID: 36871425, DOI: 10.1016/j.cpr.2023.102255.Peer-Reviewed Original ResearchConceptsPositive affectNegative affectSustained negative affectCognitive constructsCognitive theoryCognitive perspectiveLack of pleasureCognitive deficitsSpecific thoughtsIntervention effortsDifferent theoretical lensesAffectRuminationAnhedoniaDeficitsExtant literatureMemoryDepressionHallmark featureComputational modelingTheoretical lensesEnvironmental cuesLess focusDebilitating disorderCues
2022
Muscarinic antagonists impair multiple aspects of operant discrimination learning and performance
Yousuf H, Girardi E, Crouse R, Picciotto M. Muscarinic antagonists impair multiple aspects of operant discrimination learning and performance. Neuroscience Letters 2022, 794: 137025. PMID: 36529388, PMCID: PMC9812939, DOI: 10.1016/j.neulet.2022.137025.Peer-Reviewed Original ResearchConceptsOperant discriminationOperant discrimination learningCue-reward associationsLong-term memoryMultiple training sessionsPost-session injectionsCue associationsReward-related respondingMemory processesDiscrimination learningMaladaptive formsImpaired consolidationFood rewardSuccessful learningNose pokesDifferent learningPre-session injectionsTraining sessionsRewardTaskMemoryLearningMultiple aspectsEnvironmental cuesMuscarinic acetylcholine receptor family
2021
BACH1, the master regulator of oxidative stress, has a dual effect on CFTR expression
NandyMazumdar M, Paranjapye A, Browne J, Yin S, Leir SH, Harris A. BACH1, the master regulator of oxidative stress, has a dual effect on CFTR expression. Biochemical Journal 2021, 478: 3741-3756. PMID: 34605540, PMCID: PMC8589331, DOI: 10.1042/bcj20210252.Peer-Reviewed Original ResearchMeSH KeywordsBasic-Leucine Zipper Transcription FactorsCell Line, TumorCell ProliferationCystic Fibrosis Transmembrane Conductance RegulatorEpithelial CellsGene Expression ProfilingGene Expression RegulationGlutamate-Cysteine LigaseGlutathioneHeme Oxygenase-1HumansHydrogen PeroxideNF-E2-Related Factor 2Oxidative StressOxygenPromoter Regions, GeneticRNA, Small InterferingSignal TransductionConceptsCis-regulatory elementsTranscription factorsCFTR expressionMaster regulatorHigher-order chromatin structureOrder chromatin structureMultiple cis-regulatory elementsFine-tune expressionSpecific transcription factorsCystic fibrosis transmembrane conductance regulator (CFTR) geneCFTR gene expressionCell-specific expressionTransmembrane conductance regulator geneOxidative stressArchitectural proteinsChromatin structureLocus architectureTune expressionBTB domainCNC homolog 1SiRNA screenRegulator geneGene promoterEnvironmental cuesPhysiological oxygenCo-stimulation with opposing macrophage polarization cues leads to orthogonal secretion programs in individual cells
Muñoz-Rojas AR, Kelsey I, Pappalardo JL, Chen M, Miller-Jensen K. Co-stimulation with opposing macrophage polarization cues leads to orthogonal secretion programs in individual cells. Nature Communications 2021, 12: 301. PMID: 33436596, PMCID: PMC7804107, DOI: 10.1038/s41467-020-20540-2.Peer-Reviewed Original ResearchConceptsCo-stimulated macrophagesFunctional diversitySingle-cell RNA sequencingGlobal transcriptional programSuch functional diversityTranscriptional programsTissue homeostasisRNA sequencingEnvironmental cuesGene resultsExclusive expressionInflammatory stimuli LPSCell heterogeneityIndividual cellsPolarization cuesIndividual macrophagesTissue repairCytokine genesDiversityInnate immune cellsFighting infectionsCellsMacrophagesCuesTranscription
2020
Adaptive tuning of cell sensory diversity without changes in gene expression
Kamino K, Keegstra JM, Long J, Emonet T, Shimizu TS. Adaptive tuning of cell sensory diversity without changes in gene expression. Science Advances 2020, 6: eabc1087. PMID: 33188019, PMCID: PMC7673753, DOI: 10.1126/sciadv.abc1087.Peer-Reviewed Original ResearchConceptsPhenotypic diversityGene expressionCell variationDiversity of phenotypesChemoreceptor TarPosttranslational modificationsAllosteric couplingEnvironmental cuesChemotaxis networkCovalent modificationEnvironmental changesDiversitySensory diversityCell populationsCellsExpressionSuch betsPhenotypeEscherichiaPopulationPrevious studiesModificationVariationSignalsChemoreceptors
2018
Diversity and Evolution of Sensor Histidine Kinases in Eukaryotes
Kabbara S, Hérivaux A, de Bernonville T, Courdavault V, Clastre M, Gastebois A, Osman M, Hamze M, Cock J, Schaap P, Papon N. Diversity and Evolution of Sensor Histidine Kinases in Eukaryotes. Genome Biology And Evolution 2018, 11: 86-108. PMID: 30252070, PMCID: PMC6324907, DOI: 10.1093/gbe/evy213.Peer-Reviewed Original ResearchConceptsTwo-component systemHistidine kinaseHK proteinsEukaryotic supergroupsPhylogenetic analysisMajor eukaryotic supergroupsSensor histidine kinaseIndependent phylogenetic analysesEukaryotic speciesGenomic resourcesEukaryotic organismsPhylogenetic distributionPhylogenetic lineagesPhysiological traitsPhylogenetic treeHK genesSensor proteinsTransduction systemEnvironmental cuesUnprecedented overviewSingle kingdomEukaryotesProteinStructural diversityEvolutionary pathRictor/TORC2 mediates gut-to-brain signaling in the regulation of phenotypic plasticity in C. elegans
O’Donnell M, Chao P, Kammenga J, Sengupta P. Rictor/TORC2 mediates gut-to-brain signaling in the regulation of phenotypic plasticity in C. elegans. PLOS Genetics 2018, 14: e1007213. PMID: 29415022, PMCID: PMC5819832, DOI: 10.1371/journal.pgen.1007213.Peer-Reviewed Original ResearchMeSH KeywordsAdaptation, PhysiologicalAnimalsAnimals, Genetically ModifiedBrainCaenorhabditis elegansCaenorhabditis elegans ProteinsGene Expression Regulation, DevelopmentalIntestinal MucosaIntestinesMechanistic Target of Rapamycin Complex 2Neuronal PlasticityPhenotypeRapamycin-Insensitive Companion of mTOR ProteinSensory Receptor CellsSignal TransductionTemperatureConceptsQuantitative trait lociDauer larval stageTarget of rapamycinNematode C. elegansExternal cuesInsulin-like peptidesNeuronal functionDAF-7Phenotypic plasticityDaf-28Developmental decisionsC. elegansTrait lociCellular stressorsBacterial foodGenetic variationForaging behaviorRictor/Reproductive growthLarval developmentEnvironmental cuesNeuroendocrine gene expressionGene expressionLarval stagesFood signals
2017
Light sensing by opsins and fungal ecology: NOP‐1 modulates entry into sexual reproduction in response to environmental cues
Wang Z, Wang J, Li N, Li J, Trail F, Dunlap JC, Townsend JP. Light sensing by opsins and fungal ecology: NOP‐1 modulates entry into sexual reproduction in response to environmental cues. Molecular Ecology 2017, 27: 216-232. PMID: 29134709, PMCID: PMC5797489, DOI: 10.1111/mec.14425.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceConserved SequenceEcological and Environmental PhenomenaFungal ProteinsGene Expression Regulation, FungalGene Knockout TechniquesGene Regulatory NetworksGenes, FungalLightModels, BiologicalMultienzyme ComplexesNADH, NADPH OxidoreductasesNeurospora crassaOpsinsOxidation-ReductionOxidative StressPhenotypePhylogenyProtein Structure, SecondaryReproductionUp-RegulationConceptsNOP-1Opsin-like proteinFungal ecologyPlant-associated fungiRapid environmental changeOxidative stress responseKey amino acidsFungal genomesComparative transcriptomicsSexual reproductionOrganismal functionNeurospora crassaEnvironmental cuesGenetic basisSensory rhodopsinStress responseNAD/NADPTransmembrane movementRetinal binding siteGenesAmino acidsFungiEnvironmental changesSexual developmentOpsinSmooth muscle cell differentiation: Mechanisms and models for vascular diseases
Deng Y, Lin C, Zhou H, Min W. Smooth muscle cell differentiation: Mechanisms and models for vascular diseases. Frontiers In Biology 2017, 12: 392-405. DOI: 10.1007/s11515-017-1473-z.Peer-Reviewed Original ResearchVSMC differentiationVascular diseaseVSMC behaviorEnvironmental cuesVSMC phenotypeMolecular mechanismsPhenotypic switchingPhenotype modulationMature cellsNew therapeutic targetsSynthetic stateProgenitor cellsSmooth muscle cellsMuscle cellsCritical roleVascular-related diseasesTherapeutic targetDifferentiationCardiovascular diseaseCardiovascular conditionsCellsContractile stateDiseaseComprehensive understandingPhenotypeDeath begets a new beginning
Bosurgi L, Hughes LD, Rothlin CV, Ghosh S. Death begets a new beginning. Immunological Reviews 2017, 280: 8-25. PMID: 29027219, PMCID: PMC5658037, DOI: 10.1111/imr.12585.BooksConceptsCell deathBillions of cellsApoptotic cell deathEnvironmental cuesSpecific functionsHomeostatic conditionsTissue microenvironmentApoptotic cellsDead cellsTissue repairGrowth factorCellsPhagocytosisPerpetual featureSevere tissue injuryDeathInductionAppropriate responseMicroenvironmentPhagocytesCues
2016
Phosphoproteomic Analysis Reveals a Novel Mechanism of CaMKIIα Regulation Inversely Induced by Cocaine Memory Extinction versus Reconsolidation
Rich MT, Abbott TB, Chung L, Gulcicek EE, Stone KL, Colangelo CM, Lam TT, Nairn AC, Taylor JR, Torregrossa MM. Phosphoproteomic Analysis Reveals a Novel Mechanism of CaMKIIα Regulation Inversely Induced by Cocaine Memory Extinction versus Reconsolidation. Journal Of Neuroscience 2016, 36: 7613-7627. PMID: 27445140, PMCID: PMC4951572, DOI: 10.1523/jneurosci.1108-16.2016.Peer-Reviewed Original ResearchMeSH Keywords1-(5-Isoquinolinesulfonyl)-2-MethylpiperazineAmygdalaAnimalsBenzylaminesCalcium-Calmodulin-Dependent Protein Kinase Type 2CocaineConditioning, OperantCuesEnzyme InhibitorsExtinction, PsychologicalHEK293 CellsHumansMaleMemoryPhosphorylationProteomicsRatsRats, Sprague-DawleySelf AdministrationSerineSignal TransductionSulfonamidesConceptsRelapse-like behaviorMemory extinctionSubsequent cue-induced reinstatementAddiction treatmentDrug-associated memoriesCocaine-associated memoryCue-induced reinstatementRelapse prevention therapySelf-administer cocaineLong-term abstinenceReconsolidation disruptionAbstinence effortsAudiovisual cuesEssential therapeutic goalCocaine memoryMemory strengtheningAmygdala inhibitionDrug useReconsolidationExtinction enhancementAddictive disordersRelapse preventionMemoryCuesEnvironmental cuesCystic Fibrosis Lung Immunity: The Role of the Macrophage
Bruscia EM, Bonfield TL. Cystic Fibrosis Lung Immunity: The Role of the Macrophage. Journal Of Innate Immunity 2016, 8: 550-563. PMID: 27336915, PMCID: PMC5089923, DOI: 10.1159/000446825.Peer-Reviewed Original ResearchConceptsLung homeostasisCystic fibrosis pathophysiologyTranscriptional shiftMortality of patientsEnvironmental cuesAdaptive immune networkModifier genesMΦ functionMajor morbidityExcessive inflammationMΦ phenotypeLung infectionCF lungCFTR dysfunctionMajor playersHomeostasisDiseaseMacrophagesIntrinsic changesGenesImmune networkPhenotypeMorbidityInflammationPatientsShort-lived myeloid cell lifespan is regulated by a long non-coding RNA
Kotzin J, Spencer S, McCright S, Uthaya Kumar D, Mowel W, Makiya M, Klion A, Williams A, Flavell R, Henao-Mejia J. Short-lived myeloid cell lifespan is regulated by a long non-coding RNA. The Journal Of Immunology 2016, 196: 202.28-202.28. DOI: 10.4049/jimmunol.196.supp.202.28.Peer-Reviewed Original ResearchLong non-coding RNAsNon-coding RNAsNovel long non-coding RNAAllele-specific mannerPro-survival cytokinesLocus-specific regulationPro-apoptotic genesExtracellular signalsMyeloid cellsEnvironmental cuesPrecise regulationGene expressionRegulatory mechanismsCell homeostasisImmune cell homeostasisLncRNAsShort lifespanPotential therapeutic targetCell lifespanRNATherapeutic targetCellsLifespanRegulationHost response
2014
Calcium-sensing receptor 20 years later
Alfadda TI, Saleh AM, Houillier P, Geibel JP. Calcium-sensing receptor 20 years later. American Journal Of Physiology - Cell Physiology 2014, 307: c221-c231. PMID: 24871857, PMCID: PMC4121584, DOI: 10.1152/ajpcell.00139.2014.Peer-Reviewed Original ResearchConceptsCellular ion transport mechanismsG protein-coupled receptor familyProtein-coupled receptor familyEnvironmental cuesExtracellular environmentOrgan physiologyReceptor familySense changesDifferent tissuesCellular levelCalcium-sensing receptorIon transport mechanismsPhysiologyReceptor physiologyAmino acid concentrationsDisease statesReceptorsSystemic physiologyDiversity of locationsReceptor mutationsDifferent organ systemsImportant roleMembersFamilyHomology
2013
Interactions between VEGFR and Notch signaling pathways in endothelial and neural cells
Thomas JL, Baker K, Han J, Calvo C, Nurmi H, Eichmann AC, Alitalo K. Interactions between VEGFR and Notch signaling pathways in endothelial and neural cells. Cellular And Molecular Life Sciences 2013, 70: 1779-1792. PMID: 23479133, PMCID: PMC3648205, DOI: 10.1007/s00018-013-1312-6.Peer-Reviewed Original ResearchConceptsCell fate decisionsDifferent cell contextsTyrosine kinase VEGF receptorsExtracellular matrix moleculesCell interaction mechanismsMetazoan speciesFate decisionsGrowth factorCanonical NotchVascular endothelial growth factorNotch receptorsCell contextEnvironmental cuesDynamic regulationMolecular relationshipsKey regulatorNotch pathwayMatrix moleculesNeural cellsCell contactAdjacent cellsPathwayVEGF receptorsCellsNeurovascular interactions
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