2022
Clone Phylogenetics Reveals Metastatic Tumor Migrations, Maps, and Models
Chroni A, Miura S, Hamilton L, Vu T, Gaffney SG, Aly V, Karim S, Sanderford M, Townsend JP, Kumar S. Clone Phylogenetics Reveals Metastatic Tumor Migrations, Maps, and Models. Cancers 2022, 14: 4326. PMID: 36077861, PMCID: PMC9454754, DOI: 10.3390/cancers14174326.Peer-Reviewed Original ResearchDynamic evolutionary historyMolecular phylogenetic analysisMolecular evolutionary analysisTumor cell migrationEvolutionary historyEvolutionary analysisPhylogenetic analysisDispersal routesCell migrationTumor evolutionTumor genetic heterogeneityGenetic heterogeneityMetastatic cellsClonesTumor migrationMigration historyGeneral patternPhylogeneticsFundamental questionsEvolution of metastasesMigrationEvolutionCellsHybridsVariation
2021
Decoding Cell Death: From a Veritable Library of Babel to Vade Mecum?
Hughes LD, Wang Y, Meli AP, Rothlin CV, Ghosh S. Decoding Cell Death: From a Veritable Library of Babel to Vade Mecum? Annual Review Of Immunology 2021, 39: 791-817. PMID: 33902311, DOI: 10.1146/annurev-immunol-102819-072601.Peer-Reviewed Original Research
2020
Is There a ‘Social’ Brain? Implementations and Algorithms
Lockwood PL, Apps MAJ, Chang SWC. Is There a ‘Social’ Brain? Implementations and Algorithms. Trends In Cognitive Sciences 2020, 24: 802-813. PMID: 32736965, PMCID: PMC7501252, DOI: 10.1016/j.tics.2020.06.011.Peer-Reviewed Original ResearchConceptsSocial behaviorNeural processesMotor facultiesInformation processingInfluential frameworkSocial specificitiesAlgorithmic levelGreater integrationPsychologyNeuroscienceBehaviorDifferent levelsImportant new insightsEmpirical approachMarrProcessingFundamental questionsBrainResearchMonkeysFrameworkHumans
2017
Don’t let sleeping dogmas lie: new views of peptidoglycan synthesis and its regulation
Zhao H, Patel V, Helmann J, Dörr T. Don’t let sleeping dogmas lie: new views of peptidoglycan synthesis and its regulation. Molecular Microbiology 2017, 106: 847-860. PMID: 28975672, PMCID: PMC5720918, DOI: 10.1111/mmi.13853.Peer-Reviewed Original ResearchConceptsCell wall biogenesisCell wall synthesisWall biogenesisWall synthesisBacterial cell wall biogenesisCell wall synthesis processRod-shaped bacteriaBacterial cell wall synthesisSingle-molecule trackingPeptidoglycan synthesisCell wallMolecule trackingIntense research focusBiogenesisBacteriaCircumstantial evidencePowerful antibioticsFundamental questionsRegulationTechnical limitationsBiochemistryNew dataTemporal mappingSynthesisOld observations
2016
Axon regeneration in C. elegans: Worming our way to mechanisms of axon regeneration
Byrne AB, Hammarlund M. Axon regeneration in C. elegans: Worming our way to mechanisms of axon regeneration. Experimental Neurology 2016, 287: 300-309. PMID: 27569538, PMCID: PMC5136328, DOI: 10.1016/j.expneurol.2016.08.015.Peer-Reviewed Original ResearchConceptsC. elegansC. elegans researchC. elegans modelSimple nervous systemMammalian nervous systemConserved genomeElegansElegans modelRegeneration responseAxon regenerationCellular mechanismsRegeneration researchTransparent bodyNervous systemRegenerationGenomeFundamental questionsSpeciesMechanismTechnical advancesRegeneration studiesPotential future directions
2015
Epigenetic Mechanisms of Serotonin Signaling
Holloway T, González-Maeso J. Epigenetic Mechanisms of Serotonin Signaling. ACS Chemical Neuroscience 2015, 6: 1099-1109. PMID: 25734378, PMCID: PMC4838281, DOI: 10.1021/acschemneuro.5b00033.Peer-Reviewed Original ResearchConceptsEpigenetic mechanismsHeritable epigenetic modificationsNumerous physiological responsesSignal transduction mechanismsReceptor-dependent signalingEpigenetic marksHistone modificationsGene functionEpigenetic modificationsDNA methylationCellular phenotypesGene expressionTransduction mechanismsPhysiological responsesFundamental roleDiverse setComplex interactionsCentral nervous systemRecent advancesFundamental questionsIntense researchMethylationNervous systemSignalingMechanism
2014
Reticulon 4 Is Necessary for Endoplasmic Reticulum Tubulation, STIM1-Orai1 Coupling, and Store-operated Calcium Entry
Jozsef L, Tashiro K, Kuo A, Park EJ, Skoura A, Albinsson S, Rivera-Molina F, Harrison KD, Iwakiri Y, Toomre D, Sessa WC. Reticulon 4 Is Necessary for Endoplasmic Reticulum Tubulation, STIM1-Orai1 Coupling, and Store-operated Calcium Entry. Journal Of Biological Chemistry 2014, 289: 9380-9395. PMID: 24558039, PMCID: PMC3969502, DOI: 10.1074/jbc.m114.548602.Peer-Reviewed Original ResearchConceptsSTIM1-Orai1 couplingER morphologyRedistribution of STIM1Store-operated calcium entryER tubulationER sheetsElevated cytoplasmicReticulon 4Functional consequencesRTN4SOCETubulationCalcium entryRecent advancesFundamental questionsSTIM1CytoplasmicHomeostasisApoptosisRegulationMechanisticallyFirst timeCellsMorphology
2011
Developmental Biology of the Placenta
Hui P. Developmental Biology of the Placenta. Current Clinical Pathology 2011, 15-39. DOI: 10.1007/978-1-61779-394-3_2.Peer-Reviewed Original ResearchX-chromosome inactivationGenomic imprintingMammalian biologyChromosome inactivationDevelopmental biologyEutherian mammalsTransient organCell typesHormonal regulationTissue remodelingRecent findingsBiologyMaternal uterusBiological fluctuationsGenomeDelicate balanceFundamental questionsImmunological propertiesMammalsEmbryosProliferative disordersImprintingRegulationInactivationMaternal neoplasmLung Stem Cell Self-Renewal Relies on BMI1-Dependent Control of Expression at Imprinted Loci
Zacharek SJ, Fillmore CM, Lau AN, Gludish DW, Chou A, Ho JW, Zamponi R, Gazit R, Bock C, Jäger N, Smith ZD, Kim TM, Saunders AH, Wong J, Lee JH, Roach RR, Rossi DJ, Meissner A, Gimelbrant AA, Park PJ, Kim CF. Lung Stem Cell Self-Renewal Relies on BMI1-Dependent Control of Expression at Imprinted Loci. Cell Stem Cell 2011, 9: 272-281. PMID: 21885022, PMCID: PMC3167236, DOI: 10.1016/j.stem.2011.07.007.Peer-Reviewed Original ResearchMeSH KeywordsAdult Stem CellsAnimalsCell SurvivalCells, CulturedCyclin-Dependent Kinase Inhibitor p16Gene Expression ProfilingGene Expression Regulation, DevelopmentalGenes, p16Genetic LociGenomic ImprintingLungMiceMice, Mutant StrainsNuclear ProteinsPolycomb Repressive Complex 1Proto-Oncogene ProteinsRegenerationRepressor ProteinsRNA, Small InterferingS-Phase Kinase-Associated ProteinsConceptsImprinted lociBronchioalveolar stem cellsStem cellsAdult tissue-specific stem cellsTissue-specific stem cellsLung epithelial stem cellsSelf-renewal defectLung epithelial cell injuryLung stem cellsDevelopmental processesEpithelial stem cellsExpression of p57Bmi1 knockout miceLung cellsGenesAdult cellsLociExpressionCellsAllelesRegulationKnockout miceEpithelial cell injuryFundamental questionsCDKN1C
2010
Regulation of Adaptive Immunity by the Innate Immune System
Iwasaki A, Medzhitov R. Regulation of Adaptive Immunity by the Innate Immune System. Science 2010, 327: 291-295. PMID: 20075244, PMCID: PMC3645875, DOI: 10.1126/science.1183021.Peer-Reviewed Original ResearchConceptsInnate immune recognitionB lymphocyte-mediated immune responsesImmune responsePattern recognition receptorsImmune recognitionAntigen-specific adaptive immune responsesLymphocyte-mediated immune responsesMicrobial pathogensInnate immune systemAdaptive immune responsesRecognition receptorsHost defenseField of immunologyAdaptive immunityImmune systemFundamental questionsReceptorsRegulationPathwayPathogensInvasionDefenseInjuryInfectionDiscovery
2008
Multidimensional Visual Statistical Learning
Turk-Browne NB, Isola PJ, Scholl BJ, Treat TA. Multidimensional Visual Statistical Learning. Journal Of Experimental Psychology Learning Memory And Cognition 2008, 34: 399-407. PMID: 18315414, DOI: 10.1037/0278-7393.34.2.399.Peer-Reviewed Original ResearchConceptsVisual statistical learningStatistical learningFeature dimensionDifferent feature dimensionsVisual stimuliStatistical regularitiesParticular colorTest itemsColor patchesColor pairsMultidimensional objectsLearningStimuliObjectsObserverDimensionsItemsFundamental questionsPrevious experimentsAwarenessRecent studiesColorIntentMultidimensional sequences
2006
Genomic analysis of the hierarchical structure of regulatory networks
Yu H, Gerstein M. Genomic analysis of the hierarchical structure of regulatory networks. Proceedings Of The National Academy Of Sciences Of The United States Of America 2006, 103: 14724-14731. PMID: 17003135, PMCID: PMC1595419, DOI: 10.1073/pnas.0508637103.Peer-Reviewed Original ResearchConceptsTranscription factorsMaster transcription factorRegulatory networksRegulatory hierarchyProtein-protein interaction networkMost transcription factorsExpression of thousandsExpression level changesGenomic analysisProtein interactionsInteraction networksTarget genesDirect targetGenesEukaryotesProkaryotesCellsFundamental questionsBiologyTargetExpression
2004
Connecting two-component regulatory systems by a protein that protects a response regulator from dephosphorylation by its cognate sensor
Kato A, Groisman EA. Connecting two-component regulatory systems by a protein that protects a response regulator from dephosphorylation by its cognate sensor. Genes & Development 2004, 18: 2302-2313. PMID: 15371344, PMCID: PMC517523, DOI: 10.1101/gad.1230804.Peer-Reviewed Original ResearchMeSH KeywordsAllelesBacterial ProteinsBase SequenceGene Expression Regulation, BacterialMagnesiumMolecular Sequence DataPhosphorylationPromoter Regions, GeneticProtein Processing, Post-TranslationalProtein Structure, TertiarySalmonella entericaSignal TransductionTranscription FactorsTranscription, GeneticConceptsTwo-component systemResponse regulatorPhosphorylated formTwo-component regulatory systemTranscription of PmrAResponse regulator PmrAPhoP/PhoQPmrA/PmrBPmrA proteinTarget promotersCognate sensorProtein bindsSignal transductionCellular responsesDephosphorylationRegulatory systemPmrAProteinTranscriptionMultiple signalsRegulatorHigh affinityPmrA.Fundamental questionsPhoP
2003
Closing the loop: The PmrA/PmrB two-component system negatively controls expression of its posttranscriptional activator PmrD
Kato A, Latifi T, Groisman EA. Closing the loop: The PmrA/PmrB two-component system negatively controls expression of its posttranscriptional activator PmrD. Proceedings Of The National Academy Of Sciences Of The United States Of America 2003, 100: 4706-4711. PMID: 12676988, PMCID: PMC153620, DOI: 10.1073/pnas.0836837100.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceArtificial Gene FusionBacterial ProteinsBase SequenceBinding SitesDNA, BacterialFeedbackGene Expression Regulation, BacterialGenes, BacterialModels, GeneticMolecular Sequence DataMutationPlasmidsPromoter Regions, GeneticProtein BindingSalmonella typhimuriumTranscription FactorsConceptsPmrA proteinTwo-component systemResponse regulator PmrAAppropriate cellular responsesPmrA/PmrBPhoQ proteinPhoP proteinRegulatory circuitsPosttranscriptional levelPromoter upstreamNegative regulationCellular responsesPmrB proteinCellular levelProteinPmrASalmonella entericaGenesMultiple signalsPmrDFeedback loopSingular exampleExpressionPhoPFundamental questions
2002
Evolutionary Rate in the Protein Interaction Network
Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW. Evolutionary Rate in the Protein Interaction Network. Science 2002, 296: 750-752. PMID: 11976460, DOI: 10.1126/science.1068696.Peer-Reviewed Original ResearchConceptsProtein interaction networksInteraction networksMost cellular functionsRate of evolutionHigh-throughput screenMolecular evolutionEvolutionary ratesYeast SaccharomycesCellular functionsEvolutionary changeSelection pressureProtein resultsProteinMore interactorsInteractorsFundamental questionsSaccharomycesCoevolutionEvolutionOrganismsReciprocal changesFunctionSimilar ratesGreater proportionScreen
2001
In Vitro Selection of Kinase and Ligase Deoxyribozymes
Li Y, Breaker R. In Vitro Selection of Kinase and Ligase Deoxyribozymes. Methods 2001, 23: 179-190. PMID: 11181037, DOI: 10.1006/meth.2000.1119.Peer-Reviewed Original ResearchConceptsDNA ligationModern living systemsDNA kinaseEnzymatic functionRandom sequence populationVitro SelectionProtein enzymesConstruction of DNADNA constructsDNA phosphorylationDNADeoxyribozymesKinaseLiving systemsFundamental roleChemical reactionsAdenylationFundamental questionsBiocatalysisPhosphorylationEnzymeBiotechnologySelection strategyDiscoveryDetailed overview
1997
Distinct cortical areas associated with native and second languages
Kim K, Relkin N, Lee K, Hirsch J. Distinct cortical areas associated with native and second languages. Nature 1997, 388: 171-174. PMID: 9217156, DOI: 10.1038/40623.Peer-Reviewed Original ResearchConceptsSecond languageFunctional magnetic resonance imagingMultiple language functionsLanguage-specific regionsCortical areasEssential human capacitiesFrontal cortical areasLanguage acquisitionNative languageBilingual subjectsMultiple languagesDistinct cortical areasLanguageLanguage functionBroca's areaCortical representationHuman capacityHuman brainHuman cortexAcquisition stageSeparation of activitiesMagnetic resonance imagingResonance imagingFundamental questionsAdulthood
1991
Ultraviolet Mutagenesis of a Shuttle Vector Plasmid in Repair Proficient and Deficient Human Cells
Seidman M, Brash D, Settharam S, Kraemer K, Bredberg A. Ultraviolet Mutagenesis of a Shuttle Vector Plasmid in Repair Proficient and Deficient Human Cells. 1991, 183-192. DOI: 10.1007/978-1-4615-3732-8_23.ChaptersDNA sequence dataRecombinant DNA revolutionStudy of mutagenesisDeficient human cellsMechanisms of mutagenesisMammalian genomesNature of mutationsMammalian cellsShuttle vector plasmidSequence dataProkaryotic systemDNA revolutionShuttle vectorHuman cellsMutagenesisVector plasmidRepair proficientMutagenic agentsUltraviolet mutagenesisGenomeCellsFundamental questionsEnormous bodyGeneticsPlasmid
1984
Objectivity and Prejudice
BERG D. Objectivity and Prejudice. American Behavioral Scientist 1984, 27: 387-402. DOI: 10.1177/000276484027003009.Peer-Reviewed Original Research
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