2024
Adverse Food Reactions: Physiological and Ecological Perspectives
Korn L, Kutyavin V, Bachtel N, Medzhitov R. Adverse Food Reactions: Physiological and Ecological Perspectives. Annual Review Of Nutrition 2024, 44: 155-178. PMID: 38724028, DOI: 10.1146/annurev-nutr-061021-022909.Peer-Reviewed Original ResearchLeveraging a large language model to predict protein phase transition: A physical, multiscale, and interpretable approach
Frank M, Ni P, Jensen M, Gerstein M. Leveraging a large language model to predict protein phase transition: A physical, multiscale, and interpretable approach. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2320510121. PMID: 39110734, PMCID: PMC11331094, DOI: 10.1073/pnas.2320510121.Peer-Reviewed Original ResearchConceptsProtein phase transitionsAssociated with reduced gene expressionProtein structure predictionAlzheimer's disease-related proteinsDisease-related proteinsAlzheimer's diseaseProtein sequencesSequence variantsStructure predictionAmyloid aggregatesProtein designGene expressionAge-related diseasesNatural defense mechanismsSoluble stateProteinDefense mechanismsBiophysical featuresAlzheimerSequenceAmyloidVariantsExpressionLanguage modelComputational frameworkA kidney-hypothalamus axis promotes compensatory glucose production in response to glycosuria
Faniyan T, Zhang X, Morgan D, Robles J, Bathina S, Brookes P, Rahmouni K, Perry R, Chhabra K. A kidney-hypothalamus axis promotes compensatory glucose production in response to glycosuria. ELife 2024, 12 DOI: 10.7554/elife.91540.4.Peer-Reviewed Original ResearchGlucose productionEndogenous glucose productionReabsorption of nutrientsLoss of glucoseHypothalamic-pituitary-adrenal axisNormal energy supplyProteomic analysisCompensatory increaseAfferent renal nervesAfferent renal denervationPlasma proteomic analysisDefense mechanismsAcute phase proteinsRenal denervationKO miceSGLT2 inhibitorsKnockout miceRenal nervesAfferent nervesEfficiency of drugsBody's defense mechanismsGlycosuriaGlucosePhase proteinsTreat hyperglycemia
2023
Parkinson’s disease kinase LRRK2 coordinates a cell-intrinsic itaconate-dependent defence pathway against intracellular Salmonella
Lian H, Park D, Chen M, Schueder F, Lara-Tejero M, Liu J, Galán J. Parkinson’s disease kinase LRRK2 coordinates a cell-intrinsic itaconate-dependent defence pathway against intracellular Salmonella. Nature Microbiology 2023, 8: 1880-1895. PMID: 37640963, PMCID: PMC10962312, DOI: 10.1038/s41564-023-01459-y.Peer-Reviewed Original ResearchConceptsLeucine-rich repeat kinase 2Loss of LRRK2Host defense mechanismsKinase leucine-rich repeat kinase 2Parkinson's disease-associated leucine-rich repeat kinase 2Host defense pathwaysBacterial pathogen SalmonellaRepeat kinase 2Salmonella infectionSalmonella-containing vacuolesCell-intrinsic defenseIntracellular pathogensIntracellular SalmonellaFirst lineSalmonella replicationSalmonella mutantsKinase 2Pathogen SalmonellaDefense mechanismsSalmonellaHost mitochondriaDefense pathwaysDeliveryDefense responsesCellsSyntaxin 11 Contributes to the Interferon-Inducible Restriction of Coxiella burnetii Intracellular Infection
Ganesan S, Alvarez N, Steiner S, Fowler K, Corona A, Roy C. Syntaxin 11 Contributes to the Interferon-Inducible Restriction of Coxiella burnetii Intracellular Infection. MBio 2023, 14: e03545-22. PMID: 36728431, PMCID: PMC9972978, DOI: 10.1128/mbio.03545-22.Peer-Reviewed Original ResearchConceptsC. burnetii replicationSNARE proteinsHost cellsSyntaxin-11Cell-autonomous responsesIntracellular pathogensMembrane fusion eventsLysosome-derived organellesDefense mechanismsModel bacterial pathogenMultiple cell typesEukaryotic cellsDefense pathwaysDelivery of cargoReplication of pathogensHuman proteinsFusion eventsDissemination of pathogensFusion pathwayHost proteinsIntrinsic defense mechanismsHost vesiclesHost restriction factorsStable expressionSubcellular organelles
2020
Immature defense mechanisms mediate the relationship between childhood trauma and onset of bipolar disorder
Wang L, Yin Y, Bian Q, Zhou Y, Huang J, Zhang P, Chen S, Fan H, Cui Y, Luo X, Tan S, Wang Z, Li CR, Tian B, Tian L, Hong LE, Tan Y. Immature defense mechanisms mediate the relationship between childhood trauma and onset of bipolar disorder. Journal Of Affective Disorders 2020, 278: 672-677. PMID: 33125910, DOI: 10.1016/j.jad.2020.10.029.Peer-Reviewed Original ResearchConceptsChildhood Trauma QuestionnaireDiagnosis of BDBipolar disorderBD-IIChildhood traumaTotal scoreImmature defense mechanismsImmature defense stylesImportant risk factorDefense Style QuestionnairePhysical neglectPsychosocial intervention strategiesDefense mechanismsEmotional abuseSevere childhood traumaBD patientsDefense stylesRisk factorsHealthy controlsHealthy volunteersChildhood traumatic experiencesPatientsDSM-IVTraumaTrauma QuestionnaireMulti-Omics Investigation of Innate Navitoclax Resistance in Triple-Negative Breast Cancer Cells
Marczyk M, Patwardhan GA, Zhao J, Qu R, Li X, Wali VB, Gupta AK, Pillai MM, Kluger Y, Yan Q, Hatzis C, Pusztai L, Gunasekharan V. Multi-Omics Investigation of Innate Navitoclax Resistance in Triple-Negative Breast Cancer Cells. Cancers 2020, 12: 2551. PMID: 32911681, PMCID: PMC7563413, DOI: 10.3390/cancers12092551.Peer-Reviewed Original ResearchTriple-negative breast cancer cellsCancer cellsBreast cancer cellsStress response genesMulti-omics landscapeCell population compositionDrug-induced cell deathMulti-omics investigationsCell linesBCL2 family inhibitorsSingle-cell analysisChromatin accessibilityGenome structureMDA-MB-231 triple-negative breast cancer cellsChromatin structureMethylation stateResponse genesFamily inhibitorsCell deathTNBC cell linesNumber variationsDefense mechanismsResistance mechanismsNew therapeutic strategiesGenesItaconate is an effector of a Rab GTPase cell-autonomous host defense pathway against Salmonella
Chen M, Sun H, Boot M, Shao L, Chang SJ, Wang W, Lam TT, Lara-Tejero M, Rego EH, Galán JE. Itaconate is an effector of a Rab GTPase cell-autonomous host defense pathway against Salmonella. Science 2020, 369: 450-455. PMID: 32703879, PMCID: PMC8020367, DOI: 10.1126/science.aaz1333.Peer-Reviewed Original Research
2019
Adaptive Immunity: Antigen Recognition by T and B Lymphocytes
Kavathas P, Krause P, Ruddle N. Adaptive Immunity: Antigen Recognition by T and B Lymphocytes. 2019, 55-74. DOI: 10.1007/978-3-030-25553-4_4.ChaptersB cell receptorCell receptorMajor histocompatibility complexB lymphocytesKiller T cellsEffective immune responseVariety of antigensT cell receptors (TCRs) bindCentral toleranceT cellsImmune responseHLA proteinsAntigen recognitionHistocompatibility complexIntracellular pathogensCell surfaceReceptorsHLALymphocytesCorresponding antibodiesHost cellsAntibodiesIsotypesMHC systemDefense mechanismsHepatic metabolic adaptation in a murine model of glutathione deficiency
Chen Y, Golla S, Garcia-Milian R, Thompson DC, Gonzalez FJ, Vasiliou V. Hepatic metabolic adaptation in a murine model of glutathione deficiency. Chemico-Biological Interactions 2019, 303: 1-6. PMID: 30794799, PMCID: PMC6743730, DOI: 10.1016/j.cbi.2019.02.015.Peer-Reviewed Original ResearchConceptsCellular non-protein thiolsMetabolic adaptationGlutamate-cysteine ligase modifier subunitNon-protein thiolsHepatic metabolic adaptationCellular redoxGlobal profilingGSH homeostasisModifier subunitLiver developmentBiochemical mechanismsMetabolic homeostasisAmino acidsGclm null miceDefense mechanismsEnvironmental insultsOxidative damageFatty liver developmentNull miceSpectrum of changesNucleic acidsMetabolic signaturesPivotal roleHomeostasisGlutathione deficiency
2018
Coagulopathies and inflammatory diseases: ‘…glimpse of a Snark’
del Carmen S, Hapak SM, Ghosh S, Rothlin CV. Coagulopathies and inflammatory diseases: ‘…glimpse of a Snark’. Current Opinion In Immunology 2018, 55: 44-53. PMID: 30268838, PMCID: PMC6366937, DOI: 10.1016/j.coi.2018.09.005.BooksConceptsAnti-pathogen defenseUnderlying molecular basisInflammatory diseasesMolecular basisSelective pressureHost defense mechanismsSubset of patientsDefense mechanismsVertebratesRegulation of inflammationHuman populationThrombophilic stateTherapeutic roleDefenseDiseaseInvertebratesCoagulopathyInflammationPhysical injuryMutationsRegulationPathogensCascadeApixabanThrombophiliaInnate Immunity of the Lung: From Basic Mechanisms to Translational Medicine
Hartl D, Tirouvanziam R, Laval J, Greene CM, Habiel D, Sharma L, Yildirim AÖ, Dela Cruz CS, Hogaboam CM. Innate Immunity of the Lung: From Basic Mechanisms to Translational Medicine. Journal Of Innate Immunity 2018, 10: 487-501. PMID: 29439264, PMCID: PMC6089674, DOI: 10.1159/000487057.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsRespiratory tractImmune systemInnate immunityHumoral host defense mechanismsPulmonary immune systemPulmonary innate immunityHost defense mechanismsInnate immune proteinsInnate armBroad armamentariumAirway compartmentImmune cellsChronic diseasesImmune proteinsTranslational medicineImmunityKey pathwaysTractRecent findingsDefense mechanismsAirwayLungArmamentariumDiseaseBiomarkers
2017
Visualization and quantification of injury to the ciliated epithelium using quantitative flow imaging and speckle variance optical coherence tomography
Gamm UA, Huang BK, Mis EK, Khokha MK, Choma MA. Visualization and quantification of injury to the ciliated epithelium using quantitative flow imaging and speckle variance optical coherence tomography. Scientific Reports 2017, 7: 15115. PMID: 29118359, PMCID: PMC5678121, DOI: 10.1038/s41598-017-14670-9.Peer-Reviewed Original ResearchConceptsOptical coherence tomographyCiliated epitheliumCoherence tomographyType of injuryExtent of injuryQuantification of injuryVariance optical coherence tomographyRespiratory infectionsDiffuse injuryFocal injuryImportant defense mechanismMouse tracheaInjuryMucociliary flowEpitheliumRegeneration of ciliaTomographyMultiple factorsDefense mechanismsQuantitative flowLungInfectionTracheaDiseaseViral Replication Complexes Are Targeted by LC3-Guided Interferon-Inducible GTPases
Biering SB, Choi J, Halstrom RA, Brown HM, Beatty WL, Lee S, McCune BT, Dominici E, Williams LE, Orchard RC, Wilen CB, Yamamoto M, Coers J, Taylor GA, Hwang S. Viral Replication Complexes Are Targeted by LC3-Guided Interferon-Inducible GTPases. Cell Host & Microbe 2017, 22: 74-85.e7. PMID: 28669671, PMCID: PMC5591033, DOI: 10.1016/j.chom.2017.06.005.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAutophagyCaliciviridae InfectionsCarrier ProteinsCell LineCytosolFemaleFibroblastsGene Knockdown TechniquesGTP PhosphohydrolasesHeLa CellsHumansImmunity, InnateInterferon-gammaInterferonsMacrophagesMaleMiceMice, Inbred C57BLMicrotubule-Associated ProteinsNorovirusRAW 264.7 CellsVacuolesViral Plaque AssayVirus ReplicationConceptsViral replication complexReplication complexImmunity-related GTPasesGuanylate-binding proteinsIFN-inducible GTPasesMNV replication complexPositive-sense RNA genomeLC3 conjugation systemConjugation systemInterferon-inducible GTPasesMembranes of vacuolesAutophagy proteinsRNA genomeGTPasesDiverse pathogensMNV replicationHuman cellsAdvantageous microenvironmentImmune defense mechanismsMembranous structuresDefense mechanismsMurine norovirusHost immune systemMembrane structureProteinInflammation: A Double-Edged Sword in the Response to Pseudomonas aeruginosa Infection
Lin CK, Kazmierczak BI. Inflammation: A Double-Edged Sword in the Response to Pseudomonas aeruginosa Infection. Journal Of Innate Immunity 2017, 9: 250-261. PMID: 28222444, PMCID: PMC5469373, DOI: 10.1159/000455857.Peer-Reviewed Original ResearchConceptsP. aeruginosa pulmonary infectionInnate immune recognitionPseudomonas aeruginosa infectionInflamed airwaysPulmonary infectionAcute infectionAdjunct therapyChronic infectionBarrier defenseAeruginosa infectionAnatomic sitesPathogen clearanceBacterial productsImmune recognitionInnate immunityInfectionHost outcomesResistant pathogensP. aeruginosa adaptationInflammationP. aeruginosaPathogen persistenceDouble-Edged SwordPseudomonas aeruginosaDefense mechanisms
2016
A Bacterial Pathogen Targets a Host Rab-Family GTPase Defense Pathway with a GAP
Spanò S, Gao X, Hannemann S, Lara-Tejero M, Galán JE. A Bacterial Pathogen Targets a Host Rab-Family GTPase Defense Pathway with a GAP. Cell Host & Microbe 2016, 19: 216-226. PMID: 26867180, PMCID: PMC4854434, DOI: 10.1016/j.chom.2016.01.004.Peer-Reviewed Original ResearchConceptsAntimicrobial defenseCell-autonomous defense mechanismS. typhi infectionHuman pathogen Salmonella typhiExchange factor BLOC-3Host defense pathwaysTyphi infectionType III secretion effectorsIntracellular pathogensPotential broad roleVacuolar pathogensSalmonella typhiPotent strategySalmonella effectorsBacterial pathogensMiceS. typhimuriumDefense pathwaysDefense mechanismsPathogen targetsPathogensEffectorsPathwayBroader roleBLOC-3Autophagy Snuffs a Macrophage’s Inner Fire
Khoury-Hanold W, Iwasaki A. Autophagy Snuffs a Macrophage’s Inner Fire. Cell Host & Microbe 2016, 19: 9-11. PMID: 26764592, DOI: 10.1016/j.chom.2015.12.015.Peer-Reviewed Original Research
2013
Metallothioneins (MTs) in the human eye: a perspective article on the zinc–MT redox cycle
Gonzalez-Iglesias H, Alvarez L, García M, Petrash C, Sanz-Medel A, Coca-Prados M. Metallothioneins (MTs) in the human eye: a perspective article on the zinc–MT redox cycle. Metallomics 2013, 6: 201-208. PMID: 24419560, DOI: 10.1039/c3mt00298e.Peer-Reviewed Original ResearchConceptsCellular zinc homeostasisOxidative damageAntioxidant functionMT genesMultiple isoformsReactive oxygen speciesPotential oxidative damageDe novo synthesisZinc homeostasisAntioxidant defense mechanismsMain regulatorDefense mechanismsNovo synthesisProtein expressionOxygen speciesExogenous zincZn7-MTMetallothioneinOxidative stressMT complexZinc releaseStoichiometric transitionsZinc-MTPro-inflammatory cytokinesLevels of metallothioneinParvovirus evades interferon-dependent viral control in primary mouse embryonic fibroblasts
Mattei LM, Cotmore SF, Tattersall P, Iwasaki A. Parvovirus evades interferon-dependent viral control in primary mouse embryonic fibroblasts. Virology 2013, 442: 20-27. PMID: 23676303, PMCID: PMC3767977, DOI: 10.1016/j.virol.2013.03.020.Peer-Reviewed Original ResearchConceptsType I IFNsI IFNsI interferonIFN responseAntiviral immune mechanismsType I interferonInnate defense mechanismsMouse embryonic fibroblastsMVMp infectionViral controlImmune mechanismsInnate sensingAntiviral programViral replicationViral sensorsMurine parvovirusPoly (I:C) stimulationVirusEmbryonic fibroblastsType IMiceDefense mechanismsMinute virusMVMpPrimary mouse embryonic fibroblastsUpregulation of Cytoprotective Defense Mechanisms and Hypoxia-Responsive Proteins Imparts Tolerance to Acute Hypobaric Hypoxia
Jain K, Suryakumar G, Prasad R, Ganju L. Upregulation of Cytoprotective Defense Mechanisms and Hypoxia-Responsive Proteins Imparts Tolerance to Acute Hypobaric Hypoxia. High Altitude Medicine & Biology 2013, 14: 65-77. PMID: 23537263, DOI: 10.1089/ham.2012.1064.Peer-Reviewed Original ResearchMeSH KeywordsAltitudeAnimalsAtmospheric PressureCatalaseCreatine Kinase, MB FormDyspneaEndothelin-1ErythropoietinHeme Oxygenase-1HSP70 Heat-Shock ProteinsHSP90 Heat-Shock ProteinsHypoxiaHypoxia-Inducible Factor 1, alpha SubunitMaleMalondialdehydeMyocarditisMyocardiumNitric OxideOxidative StressProtein CarbonylationRatsRats, Sprague-DawleyReactive Oxygen SpeciesSuperoxide DismutaseTime FactorsUp-RegulationVascular Endothelial Growth Factor AConceptsEnvironmental stressHypoxia-responsive proteinsSubsequent oxidative damageReactive oxygen species levelsCellular machineryHypoxia-responsive moleculesResponsive genesOxygen species levelsSpecies levelDifferential expressionTolerant animalsDefense mechanismsOxidative damageCytoprotective chaperoneAntioxidant enzymesHypobaric hypoxiaHigh expressionHIF-1αProteinAdult Sprague-Dawley ratsExpressionMyocardial antioxidant enzymesAcute hypobaric hypoxiaSprague-Dawley ratsCK-MB activity
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