2025
Molecular basis of cell fate plasticity — insights from the privileged cells
Scalf S, Wu Q, Guo S. Molecular basis of cell fate plasticity — insights from the privileged cells. Current Opinion In Genetics & Development 2025, 93: 102354. PMID: 40327951, DOI: 10.1016/j.gde.2025.102354.Peer-Reviewed Original ResearchSupervised fine-tuning of pre-trained antibody language models improves antigen specificity prediction
Wang M, Patsenker J, Li H, Kluger Y, Kleinstein S. Supervised fine-tuning of pre-trained antibody language models improves antigen specificity prediction. PLOS Computational Biology 2025, 21: e1012153. PMID: 40163503, PMCID: PMC12013870, DOI: 10.1371/journal.pcbi.1012153.Peer-Reviewed Original ResearchConceptsSupervised fine-tuningImmune responseMolecular basis of antigen recognitionSARS-CoV-2 spike proteinLanguage modelSARS-CoV-2 vaccinesAdaptive immune responsesSpecific predictionsMolecular basisSpike proteinAntibody-based therapeuticsFine-tuningAntibody-antigen specificitySpecific to antigensInfluenza hemagglutininVaccine designAntigen recognitionModel embeddingsImmune functionLanguage model embeddingsSARS-CoV-2AntibodiesAntigenInfluenzaVaccinePhysiologic mechanisms underlying polycystic kidney disease
Boletta A, Caplan M. Physiologic mechanisms underlying polycystic kidney disease. Physiological Reviews 2025, 105: 1553-1607. PMID: 39938884, PMCID: PMC12174308, DOI: 10.1152/physrev.00018.2024.Peer-Reviewed Original ResearchPrimary ciliaPolycystic kidney diseaseTrafficking of proteinsHuman ciliopathiesExtracellular signalsMultiple genesKidney diseaseProtein productionMolecular basisCell biologyMonogenic disordersCyst formationGenesRenal epithelial cellsProteinCiliaBiochemical informationApical surfaceEpithelial cellsFunctional expressionPhysiological propertiesWealth of informationPhysiological mechanismsCellsFibrocystin
2024
Minimal presynaptic protein machinery governing diverse kinetics of calcium-evoked neurotransmitter release
Bose D, Bera M, Norman C, Timofeeva Y, Volynski K, Krishnakumar S. Minimal presynaptic protein machinery governing diverse kinetics of calcium-evoked neurotransmitter release. Nature Communications 2024, 15: 10741. PMID: 39738049, PMCID: PMC11685451, DOI: 10.1038/s41467-024-54960-1.Peer-Reviewed Original ResearchConceptsSynaptotagmin-7Synaptotagmin-1Protein machinerySNARE complex assemblyFusion clampExocytosis processVesicle fusionVesicular fusionComplex assemblySynaptic vesiclesFusion assayMolecular basisPhysiologically relevant conditionsPresynaptic calcium influxNeurotransmitter releaseVesiclesSNAREProteinMachineryCompetitive bindingFusion dynamicsComplexinExocytosisFusionCalcium influxOMICS Sciences for Aging Studies
Gómez-Verjan J, Rincón-Heredia R, Poot-Hernández A, Martínez-Magaña J, Montalvo-Ortiz J, Estrella-Parra E, Castillo-Vázquez S, Gutiérrez-Robledo L, Rivero-Segura N. OMICS Sciences for Aging Studies. 2024, 227-237. DOI: 10.1007/978-3-031-76469-1_16.Peer-Reviewed Original ResearchStructure of a biohybrid photosystem I-platinum nanoparticle solar fuel catalyst
Gisriel C, Malavath T, Qiu T, Menzel J, Batista V, Brudvig G, Utschig L. Structure of a biohybrid photosystem I-platinum nanoparticle solar fuel catalyst. Nature Communications 2024, 15: 9519. PMID: 39496605, PMCID: PMC11535483, DOI: 10.1038/s41467-024-53476-y.Peer-Reviewed Original ResearchLight-driven H2 productionFuel catalystUnity quantum efficiencyPhotosynthetic biohybrid systemsPigment-protein complexesLight-driven enzymePlatinum nanoparticlesH2 productionQuantum efficiencyPhotosystem I complexCatalystChemical energyCryo-EM structureResolution cryo-EM structureBiohybrid systemsFuel productionStored solar energyPhotosystem IBiology platformReducing equivalentsMolecular basisI complexSolar energyBinding sitesStructureDMXL2 Is Required for Endocytosis and Recycling of Synaptic Vesicles in Auditory Hair Cells
Peng H, Wang L, Gao Y, Liu H, Lin G, Kong Y, Xu P, Liu H, Yuan Q, Liu H, Song L, Yang T, Wu H. DMXL2 Is Required for Endocytosis and Recycling of Synaptic Vesicles in Auditory Hair Cells. Journal Of Neuroscience 2024, 44: e1405232024. PMID: 39147590, PMCID: PMC11411588, DOI: 10.1523/jneurosci.1405-23.2024.Peer-Reviewed Original ResearchEndocytic membrane retrievalSynaptic vesiclesSynaptic exocytosisMembrane retrievalEndocytic compartmentsMolecular machineryRecycling of synaptic vesiclesReserve poolMembrane capacitance measurementsRibbon synapses of inner hair cellsElectron microscopy reconstructionsAuditory synaptopathyMutant miceSynaptic endocytosisCell-specific knockout miceHuman homologMembrane-proximalHair cellsAuditory hair cellsMolecular basisEndocytosisRibbon synapsesInner hair cellsHearing lossDMXL2The BICD2 dynein cargo adaptor binds to the HPV16 L2 capsid protein and promotes HPV infection
Speckhart K, Choi J, DiMaio D, Tsai B. The BICD2 dynein cargo adaptor binds to the HPV16 L2 capsid protein and promotes HPV infection. PLOS Pathogens 2024, 20: e1012289. PMID: 38829892, PMCID: PMC11230635, DOI: 10.1371/journal.ppat.1012289.Peer-Reviewed Original ResearchTrans Golgi networkL2 capsid proteinPromote infectionCapsid proteinIn vitro binding studiesDynein adaptorsGolgi networkCargo adaptorsBICD2 functionDynein motorsC-terminusDyneinSupport infectionMolecular basisBICD2EndosomesAdaptorProteinBinding studiesCell-basedVirusShort segmentHuman papillomavirusGolgiInfectionEmerging therapeutic options for follicular-derived thyroid cancer in the era of immunotherapy
Turner N, Hamidi S, Ouni R, Rico R, Henderson Y, Puche M, Alekseev S, Colunga-Minutti J, Zafereo M, Lai S, Kim S, Cabanillas M, Nurieva R. Emerging therapeutic options for follicular-derived thyroid cancer in the era of immunotherapy. Frontiers In Immunology 2024, 15: 1369780. PMID: 38868771, PMCID: PMC11167082, DOI: 10.3389/fimmu.2024.1369780.Peer-Reviewed Original ResearchConceptsAnaplastic thyroid cancerFollicular-derived thyroid cancersAdvanced thyroid cancerThyroid cancerFood and Drug AdministrationManagement of advanced thyroid cancerEra of immunotherapyTargeted kinase inhibitorsU.S Food and Drug AdministrationImmune milieuRefractory diseaseExcellent prognosisTherapeutic optionsTreatment optionsKinase inhibitorsDrug AdministrationGenetic driversTherapeutic avenuesCancerImmunotherapyGenetic landscapeRadioiodineTreatmentMolecular basisOptionsCrystal Structure of Bimekizumab Fab Fragment in Complex with IL-17F Provides Molecular Basis for Dual IL-17A and IL-17F Inhibition
Adams R, Bunick C, Lawson A, Gomez B, Shaw S. Crystal Structure of Bimekizumab Fab Fragment in Complex with IL-17F Provides Molecular Basis for Dual IL-17A and IL-17F Inhibition. Journal Of Investigative Dermatology 2024, 144: 2581-2583.e2. PMID: 38631666, DOI: 10.1016/j.jid.2024.03.037.Peer-Reviewed Original ResearchCrystal structureMolecular basisHeterozygous ZNHIT3 variants within the 17q12 recurrent deletion region are associated with Mayer-Rokitansky-Kuster Hauser (MRKH) syndrome
Brakta S, Du Q, Chorich L, Hawkins Z, Sullivan M, Ko E, Kim H, Knight J, Taylor H, Friez M, Phillips J, Layman L. Heterozygous ZNHIT3 variants within the 17q12 recurrent deletion region are associated with Mayer-Rokitansky-Kuster Hauser (MRKH) syndrome. Molecular And Cellular Endocrinology 2024, 589: 112237. PMID: 38599276, DOI: 10.1016/j.mce.2024.112237.Peer-Reviewed Original ResearchCNV regionsDetect intragenic deletionsSingle nucleotide variantsRecurrent deletion regionsC-terminal regionSequencing of familiesGenome sequenceNucleotide variantsProtein expression in vitroLXXLL sequenceMissense variantsDeleted regionChromosome 17q12Exome sequencingGenetic approachesIntragenic deletionsTruncating variantsSanger sequencingSplice variantsMolecular basisHeterozygous variantsStopgain variantsZNHIT3Steroid hormone bindingExpression in vitroA host–microbiota interactome reveals extensive transkingdom connectivity
Sonnert N, Rosen C, Ghazi A, Franzosa E, Duncan-Lowey B, González-Hernández J, Huck J, Yang Y, Dai Y, Rice T, Nguyen M, Song D, Cao Y, Martin A, Bielecka A, Fischer S, Guan C, Oh J, Huttenhower C, Ring A, Palm N. A host–microbiota interactome reveals extensive transkingdom connectivity. Nature 2024, 628: 171-179. PMID: 38509360, DOI: 10.1038/s41586-024-07162-0.Peer-Reviewed Original ResearchNiche colonizationHost–microorganism interactionsHost-microbiota interactionsInvade host tissuesStrain-specific interactionsHost cells in vitroConspecific strainsEffect of indigenous microorganismsHost biologyHost proteinsSecreted proteinsCommensal microorganismsExoproteinsBacterial strainsDiverse phylogenyMolecular basisMyriad microorganismsTissue of originTissue isolationCells in vitroInteractomeBinding patternsHost tissuesBiological logicHost immune system in vivoThe molecular basis of sugar detection by an insect taste receptor
Gomes J, Singh-Bhagania S, Cenci M, Chacon Cordon C, Singh M, Butterwick J. The molecular basis of sugar detection by an insect taste receptor. Nature 2024, 629: 228-234. PMID: 38447670, PMCID: PMC11062906, DOI: 10.1038/s41586-024-07255-w.Peer-Reviewed Original ResearchLigand-binding pocketGustatory receptorsD-fructoseMolecular basisStructure-guided mutagenesisSilkworm Bombyx moriPatterns of chemical groupsIon conductivitySugar selectivityAllosteric pathwaysBombyx moriExperimental binding assaysReceptor-ligand interactionsL-sorboseComputational dockingAromatic residuesActive ligandsAllosteric couplingConformational changesSugar detectionBinding assaysFunctional assaysChemical specificityChemical groupsTaste receptorsEmbracing cancer complexity: Hallmarks of systemic disease
Swanton C, Bernard E, Abbosh C, André F, Auwerx J, Balmain A, Bar-Sagi D, Bernards R, Bullman S, DeGregori J, Elliott C, Erez A, Evan G, Febbraio M, Hidalgo A, Jamal-Hanjani M, Joyce J, Kaiser M, Lamia K, Locasale J, Loi S, Malanchi I, Merad M, Musgrave K, Patel K, Quezada S, Wargo J, Weeraratna A, White E, Winkler F, Wood J, Vousden K, Hanahan D. Embracing cancer complexity: Hallmarks of systemic disease. Cell 2024, 187: 1589-1616. PMID: 38552609, PMCID: PMC12077170, DOI: 10.1016/j.cell.2024.02.009.Peer-Reviewed Original ResearchConceptsHuman genetic variationSystemic diseaseHallmarks of cancerTumor-related thrombosisGenetic variationGene-environment interactionsCancer-related deathsComplexity of cancerMolecular basisTreat human cancersNervous system interactionsMechanisms of carcinogenesisHuman cancersImprove patient qualityCancer cachexiaSystemic manifestationsTumor micro-Cancer outcomesDistant organsTumor initiationMolecular oncologyTumorPatients' qualityPrevent cancerCancer
2023
Nicotine addiction: More than just dopamine
Kim K, Picciotto M. Nicotine addiction: More than just dopamine. Current Opinion In Neurobiology 2023, 83: 102797. PMID: 37832393, PMCID: PMC10842238, DOI: 10.1016/j.conb.2023.102797.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsNicotine addictionImportant public health problemAnti-tobacco messagingNicotine-induced behaviorsPublic health problemReward-related behaviorsNovel glutamateDopaminergic mechanismsSmoking cessationNicotine reinforcementMesolimbic systemNicotine seekingRecent studiesTherapeutic targetNicotine aversionHealth problemsActive investigationAdditional pathwaysSex differencesNicotine vapingMolecular mechanismsWithdrawalAddictionPathwayMolecular basisStructural comparison of allophycocyanin variants reveals the molecular basis for their spectral differences
Gisriel C, Elias E, Shen G, Soulier N, Brudvig G, Croce R, Bryant D. Structural comparison of allophycocyanin variants reveals the molecular basis for their spectral differences. Photosynthesis Research 2023, 162: 157-170. PMID: 37773575, PMCID: PMC11614940, DOI: 10.1007/s11120-023-01048-4.Peer-Reviewed Original ResearchMolecular basisAuthor Correction: Molecular basis for integrin adhesion receptor binding to p21-activated kinase 4 (PAK4)
Ha B, Yigit S, Natarajan N, Morse E, Calderwood D, Boggon T. Author Correction: Molecular basis for integrin adhesion receptor binding to p21-activated kinase 4 (PAK4). Communications Biology 2023, 6: 794. PMID: 37524913, PMCID: PMC10390574, DOI: 10.1038/s42003-023-05176-4.Peer-Reviewed Original ResearchAcetate controls endothelial-to-mesenchymal transition
Zhu X, Wang Y, Soaita I, Lee H, Bae H, Boutagy N, Bostwick A, Zhang R, Bowman C, Xu Y, Trefely S, Chen Y, Qin L, Sessa W, Tellides G, Jang C, Snyder N, Yu L, Arany Z, Simons M. Acetate controls endothelial-to-mesenchymal transition. Cell Metabolism 2023, 35: 1163-1178.e10. PMID: 37327791, PMCID: PMC10529701, DOI: 10.1016/j.cmet.2023.05.010.Peer-Reviewed Original ResearchConceptsTGF-β signalingChronic vascular diseaseTGF-β receptor ALK5Mesenchymal transitionInduction of EndMTVascular diseaseMolecular basisPositive feedback loopReceptor ALK5Cellular levelSMADs 2Novel targetEndMT inductionMetabolic modulationMetabolic basisFibrotic stateSignalingPotential treatmentEndMTTGFDiseaseActivationInductionACSS2PDK4Peripheral signature of altered synaptic integrity in young onset cannabis use disorder: A proteomic study of circulating extracellular vesicles
Ganesh S, Lam T, Garcia-Milian R, D'Souza D, Nairn A, Elgert K, Eitan E, Ranganathan M. Peripheral signature of altered synaptic integrity in young onset cannabis use disorder: A proteomic study of circulating extracellular vesicles. The World Journal Of Biological Psychiatry 2023, 24: 603-613. PMID: 36994633, PMCID: PMC10471733, DOI: 10.1080/15622975.2023.2197039.Peer-Reviewed Original ResearchConceptsNeuron-derived extracellular vesiclesLabel-free quantification mass spectrometryProteomic studiesCannabis use disorderExtracellular vesiclesMass spectrometry proteomic analysisDifferential proteomic profilesAdapter proteinProteomic analysisPost-synaptic densityPeripheral signatureMolecular basisProteomic profilesProteinMarkers of neuropathologyBrain tissue samplesSynaptic pathologyVesiclesSynaptic integrityImmunoaffinity methodUse disordersFunctional integrityImportant insightsNeuropathologyPilot study
2022
Molecular basis for antiviral activity of two pediatric neutralizing antibodies targeting SARS-CoV-2 Spike RBD
Chen Y, Prévost J, Ullah I, Romero H, Lisi V, Tolbert W, Grover J, Ding S, Gong S, Beaudoin-Bussières G, Gasser R, Benlarbi M, Vézina D, Anand S, Chatterjee D, Goyette G, Grunst M, Yang Z, Bo Y, Zhou F, Béland K, Bai X, Zeher A, Huang R, Nguyen D, Sherburn R, Wu D, Piszczek G, Paré B, Matthies D, Xia D, Richard J, Kumar P, Mothes W, Côté M, Uchil P, Lavallée V, Smith M, Pazgier M, Haddad E, Finzi A. Molecular basis for antiviral activity of two pediatric neutralizing antibodies targeting SARS-CoV-2 Spike RBD. IScience 2022, 26: 105783. PMID: 36514310, PMCID: PMC9733284, DOI: 10.1016/j.isci.2022.105783.Peer-Reviewed Original ResearchReceptor-binding domainSARS-CoV-2 patientsK18-hACE2 micePlasma neutralization activitySARS-CoV-2 variantsSARS-CoV-2 spike receptor-binding domainSpike receptor-binding domainProphylactic administrationNAb responsesPediatric patientsPotent NAbsLethal challengeNeutralizing antibodiesNeutralization activityDelta VOCEffector activityAntiviral mechanismAntiviral activityClinical interventionsPatientsNAbsAntibodiesEpitopesMolecular determinantsMolecular basis
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