2025
Pantothenate kinase is an effective target for antifungal therapy
Regan J, DeJarnette C, Reitler P, Gihaz S, Srivastava A, Ge W, Tucker K, Peters T, Meibohm B, Ben Mamoun C, Fortwendel J, Hevener K, Palmer G. Pantothenate kinase is an effective target for antifungal therapy. Cell Chemical Biology 2025, 32: 710-721.e6. PMID: 40378822, DOI: 10.1016/j.chembiol.2025.04.007.Peer-Reviewed Original ResearchConceptsPantothenate kinasePathogenic yeast Candida albicansDisseminated C. albicans infectionYeast Candida albicansIn vivo antifungal efficacyChemical-genetic approachBroad-spectrum antifungalAntifungal therapeuticsCoA productionCandida albicansMammalian hostsAntifungal therapyCoenzyme ASmall molecule inhibitorsAntifungal efficacyPanKEssential cofactorChemical probesMolecule inhibitorsKinaseLiving organismsPantothenateMouse modelEffective targetVirulence
2024
Mass Spectrometry Analysis of Nucleic Acid Modifications: From Beginning to Future
Xie Y, Brás‐Costa C, Lin Z, Garcia B. Mass Spectrometry Analysis of Nucleic Acid Modifications: From Beginning to Future. Mass Spectrometry Reviews 2024 PMID: 39308031, PMCID: PMC11928337, DOI: 10.1002/mas.21907.Peer-Reviewed Original ResearchMass spectrometryRegulate gene expressionMS-based methodsNucleic acidsNucleic acid structuresGenomic methodsTranscriptome researchModification statusGenetic informationNucleic acid modificationsProtein translationNucleic acid sample preparationBiological functionsGene expressionMS analysisSample preparationAcid structuresBiological moleculesModified speciesHigh-throughputDiverse modificationsLiving organismsAccurate quantitative informationAcid modificationGenomeNative architecture of a human GBP1 defense complex for cell-autonomous immunity to infection
Zhu S, Bradfield C, Maminska A, Park E, Kim B, Kumar P, Huang S, Kim M, Zhang Y, Bewersdorf J, MacMicking J. Native architecture of a human GBP1 defense complex for cell-autonomous immunity to infection. Science 2024, 383: eabm9903-eabm9903. PMID: 38422126, PMCID: PMC12091997, DOI: 10.1126/science.abm9903.Peer-Reviewed Original ResearchConceptsGuanylate-binding proteinsCaspase-4Surface of Gram-negative bacteriaGuanosine triphosphate hydrolysisImmunity to infectionInnate immunity to infectionCryo-electron tomographyGram-negative bacteriaImmunity proteinSignaling platformsMembrane insertionHuman cellsNative structureCombat infectionsLipopolysaccharide releaseGasdermin DExtended conformationLiving organismsProteinDefense complexCellsNative architectureGBP1BacteriaInfectionR2V-PPI: Enhancing Prediction of Protein-Protein Interactions Using Word2Vec Embeddings and Deep Neural Networks
Oviya I, N S, Raja K. R2V-PPI: Enhancing Prediction of Protein-Protein Interactions Using Word2Vec Embeddings and Deep Neural Networks. 2024, 00: 1-7. DOI: 10.1109/icaect60202.2024.10469595.Peer-Reviewed Original ResearchProtein-protein interactionsProtein sequencesPrediction of protein-protein interactionsPredicting Protein-Protein InteractionsRaw protein sequencesS. cerevisiae datasetAmino acid residuesIndividual amino acid residuesLarge-scale approachAcid residuesIndividual residuesNeighbouring residuesSequenceProteinResiduesLiving organismsDeep learning modelsDrug discoveryLearning modelsTraditional encoding methodStructural informationState-of-the-art machine learning modelsAdvanced deep learning modelsState-of-the-artDeep neural networksLocal and dynamic regulation of neuronal glycolysis in vivo
Wolfe A, Koberstein J, Smith C, Stewart M, Gonzalez I, Hammarlund M, Hyman A, Stork P, Goodman R, Colón-Ramos D. Local and dynamic regulation of neuronal glycolysis in vivo. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2314699121. PMID: 38198527, PMCID: PMC10801914, DOI: 10.1073/pnas.2314699121.Peer-Reviewed Original ResearchConceptsGlycolytic stateEnergy stressEnergy metabolismConditions of energy stressDynamic regulationNeuronal functionIndividual cell typesMitochondrial localizationGenetic analysisSubcellular regionsRegulatory enzymeCell-autonomousNeuronal identityGlycolysisCell typesMetabolic stateImaging dynamic changesMetabolismLiving organismsIn vivoCellsEnergy landscapeIndividual neuronsEnzymeDynamic changes
2021
Two-Photon Fluorescent Probes for Detecting Enzyme Activities in Live Tissues
Juvekar V, Lee H, Kim H. Two-Photon Fluorescent Probes for Detecting Enzyme Activities in Live Tissues. ACS Applied Bio Materials 2021, 4: 2957-2973. PMID: 35014386, DOI: 10.1021/acsabm.1c00063.Peer-Reviewed Original ResearchConceptsEnzyme activityDetectable enzyme activityEnzymatic probesEnzyme regulationBiological significanceEfficient detection toolAbnormal enzyme activityEnzymeAlzheimer's diseasePhysiological functionsLiving organismsTwo-photon microscopyProbe developmentBiological systemsEnzyme sensorEnzyme investigationsMinimal perturbationFluorescent probeLiving systemsReal-time bioimagingBiosynthesesTwo-photon fluorescent probeActivityDetection toolsLiving tissues
2019
Lysosome‐Targeted Bioprobes for Sequential Cell Tracking from Macroscopic to Microscopic Scales
Park G, Lee J, Levitz A, Fakhri G, Hwang N, Henary M, Choi H. Lysosome‐Targeted Bioprobes for Sequential Cell Tracking from Macroscopic to Microscopic Scales. Advanced Materials 2019, 31: e1806216. PMID: 30740778, PMCID: PMC6574216, DOI: 10.1002/adma.201806216.Peer-Reviewed Original ResearchConceptsMechanism of actionEfficient cellular labellingLive cell trackingCytoplasmic membraneCell trackingOptical propertiesLiving cellsNear-infraredCell-based therapeuticsHost tissuesTrackingCellular analysisLipophilic cationsChemical treatmentCellular effluxLiving organismsTarget cellsCellsCellular retentionExcellent cell permeationTarget tissues
2012
Genome-wide analysis of transcriptional changes in the thoracic muscle of the migratory locust, Locusta migratoria, exposed to hypobaric hypoxia
Zhao D, Zhang Z, Harrison J, Kang L. Genome-wide analysis of transcriptional changes in the thoracic muscle of the migratory locust, Locusta migratoria, exposed to hypobaric hypoxia. Journal Of Insect Physiology 2012, 58: 1424-1431. PMID: 22985864, DOI: 10.1016/j.jinsphys.2012.08.006.Peer-Reviewed Original ResearchConceptsAnalysis of transcriptional changesHypoxia-inducible factorGenome-wide analysisPentose phosphate pathwayThoracic musclesPhosphate pathwayEndoplasmic reticulumMitochondrial biogenesisTranscriptional changesTranscriptional profilesDysfunctional proteinsTarget genesMitochondrial activityBiological response to hypoxiaMigratory locustLiving organismsResponse to hypoxiaLocusta migratoriaHigh-altitude regionsBiological responsesOxidative stressBiogenesisImpact of hypobaric hypoxiaPentoseInvertebrates
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