2024
PTMoreR-enabled cross-species PTM mapping and comparative phosphoproteomics across mammals
Wang S, Di Y, Yang Y, Salovska B, Li W, Hu L, Yin J, Shao W, Zhou D, Cheng J, Liu D, Yang H, Liu Y. PTMoreR-enabled cross-species PTM mapping and comparative phosphoproteomics across mammals. Cell Reports Methods 2024, 4: 100859. PMID: 39255793, PMCID: PMC11440062, DOI: 10.1016/j.crmeth.2024.100859.Peer-Reviewed Original ResearchConceptsP-siteSurrounding amino acid sequenceKinase-substrate networkQuantitative phosphoproteomic analysisFunctional enrichment analysisPhosphoproteomic resultsKinase motifsComparative phosphoproteomicsPTM sitesPhosphorylation eventsPhosphoproteomic analysisProteomic analysisEnrichment analysisMammalian speciesSpeciesEvolutionary anglePhosphoproteomeMotifEnvironmental factorsNon-human speciesPTMProteomicsKinaseMammalsProteinA mammalian tripartite enhancer cluster controls hypothalamic Pomc expression, food intake, and body weight
Rojo D, Hael C, Soria A, de Souza F, Low M, Franchini L, Rubinstein M. A mammalian tripartite enhancer cluster controls hypothalamic Pomc expression, food intake, and body weight. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2322692121. PMID: 38652744, PMCID: PMC11067048, DOI: 10.1073/pnas.2322692121.Peer-Reviewed Original ResearchConceptsFood intakeControl of food intakeHypothalamic POMC expressionBody weight homeostasisHypothalamic arcuate neuronsConvergent evolutionary processesReporter gene expressionPurifying selectionArcuate neuronsDeletion eventsMouse genomeMolecular evolutionWeight homeostasisFemale miceAdult micePOMC expressionTranscriptional enhancersMutant miceEnhancer mutantsTranscription factorsPlacental mammalsMammalian ordersGene expressionMiceEvolutionary processAn evolutionarily conserved ubiquitin ligase drives infection and transmission of flaviviruses
Wu L, Zhang L, Feng S, Chen L, Lin C, Wang G, Zhu Y, Wang P, Cheng G. An evolutionarily conserved ubiquitin ligase drives infection and transmission of flaviviruses. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2317978121. PMID: 38593069, PMCID: PMC11032495, DOI: 10.1073/pnas.2317978121.Peer-Reviewed Original ResearchConceptsNonstructural proteinsSingle-stranded RNA genomeER-associated degradationE3 ligase HRD1Individual functional proteinsFlavivirus infectionCellular fitnessRNA genomeUbiquitin systemFlavivirus NS4AFunctional proteinsFlavivirus proteinsLysine residuesMammalian hostsMosquito-borne flavivirusSmall molecule inhibitorsStructural proteinsHrd1Viral proteinsProgeny virionsUbiquitinPotential therapeutic targetDENV2 infectionProteinNS4AStructure, Self-Assembly, and Phase Behavior of Neuroactive N‑Acyl GABAs: Doxorubicin Encapsulation in NPGABA/DPPC Liposomes and Release Studies
Chinapaka R, Sivaramakrishna D, Choudhury S, Manasa K, Cheppali S, Swamy M. Structure, Self-Assembly, and Phase Behavior of Neuroactive N‑Acyl GABAs: Doxorubicin Encapsulation in NPGABA/DPPC Liposomes and Release Studies. Langmuir 2024, 40: 7883-7895. PMID: 38587263, DOI: 10.1021/acs.langmuir.3c03615.Peer-Reviewed Original ResearchConceptsHydrogen bondsSelf-assemblyPowder X-ray diffraction studiesX-ray diffraction studiesOdd-even alternationN-acyl amino acidsDifferential scanning calorimetric studiesPhase behaviorAmide moietyAdjacent moleculesPhysiologically relevant pH.Molecular packingDiffraction studiesStable unilamellar vesiclesCrystal structureChain compoundsDimeric structureCarboxyl groupsHomologous seriesSupramolecular organizationThermotropic phase behaviorEquimolar mixtureRelevant pH.Calorimetric studiesChain lengthThe role of epigenetic mechanisms in the long‐term effects of early‐life adversity and mother–infant relationship on physiology and behavior of offspring in laboratory rats and mice
Burenkova O, Grigorenko E. The role of epigenetic mechanisms in the long‐term effects of early‐life adversity and mother–infant relationship on physiology and behavior of offspring in laboratory rats and mice. Developmental Psychobiology 2024, 66: e22479. PMID: 38470450, PMCID: PMC10959231, DOI: 10.1002/dev.22479.Peer-Reviewed Original ResearchConceptsEarly-life adversityEffects of early-life adversityBehavior of offspringMother-infant relationshipRegulation of hypothalamic-pituitary-adrenal axisHypothalamic-pituitary-adrenal axisBrain-derived neurotrophic factorLaboratory ratsMaternity careBehavioral profileEpigenetic mechanismsNeurotrophic factorExperimental manipulationEarly postnatal periodPharmacological interventionsLong-term effectsAdversityLong-term influenceRatsAdaptation of offspringOffspringEpigenetic editingTranslational potentialNatural variationMiceUnraveling cellular complexity with transient adapters in highly multiplexed super-resolution imaging
Schueder F, Rivera-Molina F, Su M, Marin Z, Kidd P, Rothman J, Toomre D, Bewersdorf J. Unraveling cellular complexity with transient adapters in highly multiplexed super-resolution imaging. Cell 2024, 187: 1769-1784.e18. PMID: 38552613, DOI: 10.1016/j.cell.2024.02.033.Peer-Reviewed Original ResearchConceptsInter-organelle contactsSuper-resolutionMultiplexed super-resolution microscopyIntricate spatial relationshipsGolgi stacksMammalian cellsCellular functionsSuper-resolution microscopyPrimary ciliaSuper-resolution fluorescence microscopyCellular complexityTransient adaptationFluorescence microscopyDNA-PAINTFluorogenic labelingMolecular targetsSpatial relationshipsImagesThroughputEpithelial zonation along the mouse and human small intestine defines five discrete metabolic domains
Zwick R, Kasparek P, Palikuqi B, Viragova S, Weichselbaum L, McGinnis C, McKinley K, Rathnayake A, Vaka D, Nguyen V, Trentesaux C, Reyes E, Gupta A, Gartner Z, Locksley R, Gardner J, Itzkovitz S, Boffelli D, Klein O. Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains. Nature Cell Biology 2024, 26: 250-262. PMID: 38321203, PMCID: PMC11654995, DOI: 10.1038/s41556-023-01337-z.Peer-Reviewed Original ResearchConceptsDomain identityLipid metabolism-associated genesMetabolism-associated genesNutrient absorptionHuman small intestineResponse to dietary changesTranscription patternsMammalian small intestineMetabolic domainsSmall intestineStem cell populationCell populationsDistal positionIndefinite bordersZonationLow-input lipidomics reveals lipid metabolism remodelling during early mammalian embryo development
Zhang L, Zhao J, Lam S, Chen L, Gao Y, Wang W, Xu Y, Tan T, Yu H, Zhang M, Liao X, Wu M, Zhang T, Huang J, Li B, Zhou Q, Shen N, Lee H, Ye C, Li D, Shui G, Zhang J. Low-input lipidomics reveals lipid metabolism remodelling during early mammalian embryo development. Nature Cell Biology 2024, 26: 278-293. PMID: 38302721, DOI: 10.1038/s41556-023-01341-3.Peer-Reviewed Original ResearchConceptsMammalian preimplantation embryo developmentEmbryo developmentIn vitro blastocyst developmentPreimplantation embryo developmentEight-cell embryosMammalian early embryonic developmentMammalian embryo developmentDegree of phospholipid unsaturationEarly embryo developmentApical-basal polarityBlastocyst developmentBlastocyst stageLipid metabolism remodelingHuman early embryo developmentBlastocyst implantationRegulation of embryogenesisEarly embryonic developmentBlastocystLipid landscapeApical proteinsLipid desaturasesMetabolic remodelingCell signalingPlasma membraneLipid signaturesReaction hijacking inhibition of Plasmodium falciparum asparagine tRNA synthetase
Xie S, Wang Y, Morton C, Metcalfe R, Dogovski C, Pasaje C, Dunn E, Luth M, Kumpornsin K, Istvan E, Park J, Fairhurst K, Ketprasit N, Yeo T, Yildirim O, Bhebhe M, Klug D, Rutledge P, Godoy L, Dey S, De Souza M, Siqueira-Neto J, Du Y, Puhalovich T, Amini M, Shami G, Loesbanluechai D, Nie S, Williamson N, Jana G, Maity B, Thomson P, Foley T, Tan D, Niles J, Han B, Goldberg D, Burrows J, Fidock D, Lee M, Winzeler E, Griffin M, Todd M, Tilley L. Reaction hijacking inhibition of Plasmodium falciparum asparagine tRNA synthetase. Nature Communications 2024, 15: 937. PMID: 38297033, PMCID: PMC10831071, DOI: 10.1038/s41467-024-45224-z.Peer-Reviewed Original ResearchConceptsX-ray crystallographic studiesStructure-activity relationshipSynthetically accessible scaffoldMass spectrometryTargeted mass spectrometryAccessible scaffoldInhibitor adductX-rayMechanism of actionAmino acid starvation responseMammalian cell toxicityPro inhibitorsAdductsLow mammalian cell toxicityParasite culturesDeploying drugsInhibitor classCell toxicityReactionPlasmodiumResistance developmentLow propensityIncreased resistanceInhibitionSpectrometryNon-mutational neoantigens in disease
Stern L, Clement C, Galluzzi L, Santambrogio L. Non-mutational neoantigens in disease. Nature Immunology 2024, 25: 29-40. PMID: 38168954, PMCID: PMC11075006, DOI: 10.1038/s41590-023-01664-1.Peer-Reviewed Original ResearchConceptsNon-canonical initiation codonsPost-translational protein modificationMature T cellsRibosomal RNA processingAlternative RNA splicingProtein-coding regionsNon-mutational mechanismsAbility of mammalsRNA processingRNA splicingInitiation codonProtein modificationHuman diseasesMature T cell repertoireAntigenic peptidesImmune recognitionAdaptive immune responsesT cellsAntigenic determinantsMHC class ICellsSplicingNovel antigenic determinantsMammalsCodon
2023
Autoregulation of the LIM kinases by their PDZ domain
Casanova-Sepúlveda G, Sexton J, Turk B, Boggon T. Autoregulation of the LIM kinases by their PDZ domain. Nature Communications 2023, 14: 8441. PMID: 38114480, PMCID: PMC10730565, DOI: 10.1038/s41467-023-44148-4.Peer-Reviewed Original ResearchLRRC23 truncation impairs radial spoke 3 head assembly and sperm motility underlying male infertility
Hwang J, Chai P, Nawaz S, Choi J, Lopez-Giraldez F, Hussain S, Bilguvar K, Mane S, Lifton R, Ahmad W, Zhang K, Chung J. LRRC23 truncation impairs radial spoke 3 head assembly and sperm motility underlying male infertility. ELife 2023, 12: rp90095. PMID: 38091523, PMCID: PMC10721216, DOI: 10.7554/elife.90095.Peer-Reviewed Original ResearchSialylated Glycan Bindings from SARS-CoV-2 Spike Protein to Blood and Endothelial Cells Govern the Severe Morbidities of COVID-19
Scheim D, Vottero P, Santin A, Hirsh A. Sialylated Glycan Bindings from SARS-CoV-2 Spike Protein to Blood and Endothelial Cells Govern the Severe Morbidities of COVID-19. International Journal Of Molecular Sciences 2023, 24: 17039. PMID: 38069362, PMCID: PMC10871123, DOI: 10.3390/ijms242317039.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 spike proteinRed blood cellsCOVID-19Severe COVID-19 patientsSpike proteinSevere COVID-19COVID-19 correlatesCOVID-19 patientsCommon cold infectionsCOVID-19 morbidityLong-COVID patientsFuture therapeutic strategiesSARS-CoV-2Key risk factorsKey morbiditiesSurface of plateletsSevere morbidityClinical efficacyVascular damageViral loadMicrovascular occlusionRisk factorsCOVID patientsClinical studiesClinical susceptibilityPlant MDL proteins synergize with the cytokine MIF at CXCR2 and CXCR4 receptors in human cells
Spiller L, Manjula R, Leissing F, Basquin J, Bourilhon P, Sinitski D, Brandhofer M, Levecque S, Gerra S, Sabelleck B, Zhang L, Feederle R, Flatley A, Hoffmann A, Panstruga R, Bernhagen J, Lolis E. Plant MDL proteins synergize with the cytokine MIF at CXCR2 and CXCR4 receptors in human cells. Science Signaling 2023, 16: eadg2621. PMID: 37988455, DOI: 10.1126/scisignal.adg2621.Peer-Reviewed Original ResearchConceptsMammalian macrophage migration inhibitory factorHetero-oligomeric complexesHigh structural similarityMultifunctional inflammatory cytokineHuman lung epithelial cellsYeast reporter systemReporter systemLung epithelial cellsPlant leavesFunctional similarityCellular responsesHuman cellsPharmacological inhibitorsDopachrome tautomeraseFunctional implicationsX-ray crystallographyMacrophage migration inhibitory factorStructural similarityEpithelial cellsMigration inhibitory factorCXCR4 receptorProteinTautomerase activityCellsMIF receptorHOXC6 drives a therapeutically targetable pancreatic cancer growth and metastasis pathway by regulating MSK1 and PPP2R2B
Malvi P, Chava S, Cai G, Hu K, Zhu L, Edwards Y, Green M, Gupta R, Wajapeyee N. HOXC6 drives a therapeutically targetable pancreatic cancer growth and metastasis pathway by regulating MSK1 and PPP2R2B. Cell Reports Medicine 2023, 4: 101285. PMID: 37951219, PMCID: PMC10694669, DOI: 10.1016/j.xcrm.2023.101285.Peer-Reviewed Original ResearchConceptsPancreatic ductal adenocarcinomaHomeobox C6PDAC growthInsulin-like growth factor 1 receptorGrowth factor 1 receptorKinase MSK1Factor 1 receptorTranscription factorsPancreatic cancer growthMSK1Tumor growthPDAC tumor growthMost pancreatic ductal adenocarcinomasMammalian targetIGF1R inhibitorsTherapeutic vulnerabilitiesRapamycin (mTOR) pathway activationMEK inhibitor trametinibMetastasis pathwaysPDAC mouse modelPDAC cellsMTOR inhibitionPharmacological inhibitionPathway activationInhibition blocksChromosome instability and aneuploidy in the mammalian brain
Albert O, Sun S, Huttner A, Zhang Z, Suh Y, Campisi J, Vijg J, Montagna C. Chromosome instability and aneuploidy in the mammalian brain. Chromosome Research 2023, 31: 32. PMID: 37910282, PMCID: PMC10833588, DOI: 10.1007/s10577-023-09740-w.Peer-Reviewed Original ResearchConceptsChromosome instabilityExcess of chromosomesRole of aneuploidyNon-transformed cellsSomatic tissuesDiploid setChromosomal countsAneuploid cellsChromosomal alterationsMammalian brainCancer cellsAneuploidyCellsAging processChromosomesDevelopmental disordersPresent understandingSpecific consequencesDNAValuable insightsFuture research effortsBroad rangeHallmarkStructural modificationsEvidence for an ancient aquatic origin of the RNA viral order Articulavirales
Petrone M, Parry R, Mifsud J, Van Brussel K, Voorhees I, Richards Z, Holmes E. Evidence for an ancient aquatic origin of the RNA viral order Articulavirales. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2310529120. PMID: 37906647, PMCID: PMC10636315, DOI: 10.1073/pnas.2310529120.Peer-Reviewed Original ResearchConceptsEvolutionary historyAquatic-terrestrial transitionsDeep phylogenetic historiesVirus-host codivergenceMajor evolutionary transitionsLong-term evolutionary processesTotal RNA sequencingClose phylogenetic relationshipTranscriptome data miningPhylogenetic diversityEvolutionary transitionsPhylogenetic historyPhylogenetic relationshipsInfluenza virus lineagesPhylum CnidariaDivergent familiesPutative familiesRNA sequencingAquatic animalsEvolutionary processesNew hostAquatic originDisease-causing virusesEmergence of virusesVirus lineagesAdiponectin in the mammalian host influences ticks’ acquisition of the Lyme disease pathogen Borrelia
Tang X, Cao Y, Booth C, Arora G, Cui Y, Matias J, Fikrig E. Adiponectin in the mammalian host influences ticks’ acquisition of the Lyme disease pathogen Borrelia. PLOS Biology 2023, 21: e3002331. PMID: 37862360, PMCID: PMC10619873, DOI: 10.1371/journal.pbio.3002331.Peer-Reviewed Original ResearchConceptsAdipocyte-derived hormoneBite siteAdiponectin-deficient miceInfiltration of neutrophilsTick bite sitePro-inflammatory responseWild-type animalsIxodes scapularis ticksIL-1βVascular leakageHistamine releaseTick biteAdiponectinInfectious diseasesLyme disease agentBlood feeding arthropodsBorrelia burgdorferiScapularis ticksAnimal infectious diseasesBlood feedingB. burgdorferi survivalHuman bloodHormonePathogen acquisitionMammalian hostsEverglades virus: an underrecognized disease-causing subtype of Venezuelan equine encephalitis virus endemic to Florida, USA
Burkett-Cadena N, Fish D, Weaver S, Vittor A. Everglades virus: an underrecognized disease-causing subtype of Venezuelan equine encephalitis virus endemic to Florida, USA. Journal Of Medical Entomology 2023, 60: 1149-1164. PMID: 37862065, PMCID: PMC10645373, DOI: 10.1093/jme/tjad070.Peer-Reviewed Original ResearchConceptsEverglades virusEncephalitis virusCases of meningitisCotton rat Sigmodon hispidusHigh natural infection rateEpidemic strainsNatural infection rateInfection rateWidespread transmissionAbundance of AedesNatural infectionSubtype IISubtypesFrequent feedingFrequency of contactCertain mosquitoesVector competenceVirusHuman diseasesRodentsVertebrate hostsProgress on the Endometrium
Frankfurter D, Kliman H. Progress on the Endometrium. Obstetrics And Gynecology Clinics Of North America 2023, 50: 677-694. PMID: 37914487, DOI: 10.1016/j.ogc.2023.09.002.Peer-Reviewed Original ResearchConceptsAbsence of pregnancyEvidence-based approachEndometrial assessmentStromal maturationEndometrial proliferationEndometrial pathologyInflammatory mediatorsOvarian steroidsImplantation failureBlastocyst implantationEndometrial sloughingDiagnostic measuresEndometriumOffer hopeDynamic tissueDevelopmental markersSingle testTissueInternal reproductionMaturationEndometriosisPregnancyDecidualizationInfertilityUterus
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