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 explanation
2019
Attentional bias in depression: understanding mechanisms to improve training and treatment
Mennen AC, Norman KA, Turk-Browne NB. Attentional bias in depression: understanding mechanisms to improve training and treatment. Current Opinion In Psychology 2019, 29: 266-273. PMID: 31521030, PMCID: PMC6980447, DOI: 10.1016/j.copsyc.2019.07.036.Peer-Reviewed Original ResearchConceptsNegative attentional biasAttentional biasReal-time neurofeedbackTraining attentionAttention systemNegative stimuliNegative thoughtsClinical psychologyExtant findingsBehavioral interventionsRecent researchPotential mechanistic explanationDiverse bodyDepressionTheoretical progressPsychologyBiasNeurofeedbackMoodStimuliMechanistic explanationMindSymptomsThoughtTraining
2018
Elevated hepatic expression of H19 long noncoding RNA contributes to diabetic hyperglycemia
Zhang N, Geng T, Wang Z, Zhang R, Cao T, Camporez JP, Cai SY, Liu Y, Dandolo L, Shulman GI, Carmichael GG, Taylor HS, Huang Y. Elevated hepatic expression of H19 long noncoding RNA contributes to diabetic hyperglycemia. JCI Insight 2018, 3: e120304. PMID: 29769440, PMCID: PMC6012507, DOI: 10.1172/jci.insight.120304.Peer-Reviewed Original ResearchConceptsHepatic glucose productionGenome-wide methylationExpression of Hnf4aGluconeogenic transcription factorsDiabetic hyperglycemiaH19 depletionTranscriptome analysisTranscription factorsExpression of H19Molecular mechanismsDiet-induced diabetic miceExcessive hepatic glucose productionType 2 diabetesInsulin-dependent suppressionElevated hepatic expressionH19 knockdownH19Promoter methylationMechanistic explanationMethylationDiabetic patientsRNADiabetic miceInsulin resistanceH19 overexpression
2017
Deconstruction of the Ras switching cycle through saturation mutagenesis
Bandaru P, Shah NH, Bhattacharyya M, Barton JP, Kondo Y, Cofsky JC, Gee CL, Chakraborty AK, Kortemme T, Ranganathan R, Kuriyan J. Deconstruction of the Ras switching cycle through saturation mutagenesis. ELife 2017, 6: e27810. PMID: 28686159, PMCID: PMC5538825, DOI: 10.7554/elife.27810.Peer-Reviewed Original ResearchConceptsInactive stateNucleotide exchange factorsDeep mutational scanningVertebrate lineageSequence conservationRas proteinsEvolutionary analysisHigh conservationExchange factorMutational toleranceRas dynamicsMutational effectsSelection pressureMutational scanningGlobal selection pressureSaturation mutagenesisMutational dataRas sequencesProteinBiochemical analysisBiochemical networksMechanistic explanationRegulatorMutationsConservation
2016
Transmission bottlenecks and RNAi collectively influence tick-borne flavivirus evolution
Grubaugh ND, Rückert C, Armstrong PM, Bransfield A, Anderson JF, Ebel GD, Brackney DE. Transmission bottlenecks and RNAi collectively influence tick-borne flavivirus evolution. Virus Evolution 2016, 2: vew033. PMID: 28058113, PMCID: PMC5210029, DOI: 10.1093/ve/vew033.Peer-Reviewed Original ResearchSimilar selective pressuresMicro-evolutionary forcesGreat genetic plasticityArthropod-borne RNA virusesVirus populationsLong-term evolutionary trendsGenetic bottleneckSelective constraintsFlavivirus evolutionEcological nichesGenetic plasticitySelective pressureVertebrate hostsPopulation dynamicsArthropod-borne virusesRNA virusesEvolutionary trendsArthropod vectorsMolecular levelMechanistic explanationTransmission bottleneckHostHeterogeneous populationUnique rateRNAiHeme oxygenase 1 protects ethanol-administered liver tissue in Aldh2 knockout mice
Matsumoto A, Thompson D, Chen Y, Vasiliou V, Kawamoto T, Ichiba M. Heme oxygenase 1 protects ethanol-administered liver tissue in Aldh2 knockout mice. Alcohol 2016, 52: 49-54. PMID: 27139237, DOI: 10.1016/j.alcohol.2016.02.004.Peer-Reviewed Original ResearchConceptsAldh2 knockout miceStress-related proteinsOxidative stress-related proteinsAlanine transaminaseAnti-oxidative proteinsKnockout miceHealthy individualsHepatic tumor necrosis factor alphaLiver tissueProtective factorsTumor necrosis factor alphaSerum alanine transaminaseRecent epidemiological studiesNecrosis factor alphaWild-type miceHeme oxygenase-1Cytochrome P450 2E1ALDH2 proteinProteinAldehyde dehydrogenase 2 geneHepatic malondialdehydeMechanistic explanationInflammatory cytokinesEthanol administrationMechanistic hypothesesBCOR regulates myeloid cell proliferation and differentiation
Cao Q, Gearhart M, Gery S, Shojaee S, Yang H, Sun H, Lin D, Bai J, Mead M, Zhao Z, Chen Q, Chien W, Alkan S, Alpermann T, Haferlach T, Müschen M, Bardwell V, Koeffler H. BCOR regulates myeloid cell proliferation and differentiation. Leukemia 2016, 30: 1155-1165. PMID: 26847029, PMCID: PMC5131645, DOI: 10.1038/leu.2016.2.Peer-Reviewed Original ResearchConceptsMyeloid cell proliferationHox genesCell proliferationFunction mutationsUbiquitin ligase subunitRNA expression profilingPolycomb groupEnhanced cell proliferationOverexpression allelesHOXA genesExpression profilingGene expressionConditional lossMyeloid differentiationMurine cellsFamily complexesNormal hematopoiesisGenesBone marrow cellsBCOR expressionProtein levelsMechanistic explanationDifferentiation rateAML patient samplesMutations
2015
Proteomics and Transcriptomics of BJAB Cells Expressing the Epstein-Barr Virus Noncoding RNAs EBER1 and EBER2
Pimienta G, Fok V, Haslip M, Nagy M, Takyar S, Steitz JA. Proteomics and Transcriptomics of BJAB Cells Expressing the Epstein-Barr Virus Noncoding RNAs EBER1 and EBER2. PLOS ONE 2015, 10: e0124638. PMID: 26121143, PMCID: PMC4487896, DOI: 10.1371/journal.pone.0124638.Peer-Reviewed Original ResearchConceptsMRNA-seq dataHost cell nucleusBJAB cellsCell proliferationGene expression featuresPro-survival effectsProtein adaptersAlternative splicingMRNA transcriptomeUpregulated proteinsSILAC dataRich elementsAkt activationPI3K-AktBiochemical assaysCell nucleiEBV latencySwitch eventsProteinMaintenance of latencyCell linesVEGFA proteinMechanistic explanationUpregulated oncogenesPIK3AP1
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