2025
Reduced DJ-1-F1Fo ATP synthase association correlates with midbrain dopaminergic neuron vulnerability in idiopathic Parkinson’s disease
Abulimiti A, Bae H, Ali A, Balakrishnan S, Tsujishita M, Gveric D, Tierney T, Jonas E, Smith P, Gentleman S, Alavian K. Reduced DJ-1-F1Fo ATP synthase association correlates with midbrain dopaminergic neuron vulnerability in idiopathic Parkinson’s disease. Science Advances 2025, 11: eads3051. PMID: 40479058, PMCID: PMC12143374, DOI: 10.1126/sciadv.ads3051.Peer-Reviewed Original ResearchConceptsProximity ligation assayVentral tegmental areaF1Fo-ATP synthaseProximity ligation assay signalsMetabolic efficiencyVentral tegmental area neuronsMitochondrial metabolic efficiencyProtein productionLigation assayMitochondrial activityMetabolic homeostasisIntracellular compartmentsMitochondrial efficiencyDistal neuritesParkinson's diseaseControl postmortem brainsImpaired mitochondrial efficiencySubstantia nigra pars compactaDopaminergic neuron vulnerabilityMesDA neuronsMesencephalic dopaminergicNeuronal vulnerabilityTegmental areaNeuronal subpopulationsIdiopathic Parkinson's diseasePhysiologic 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
Emerging and re-emerging themes in co-transcriptional pre-mRNA splicing
Carrocci T, Neugebauer K. Emerging and re-emerging themes in co-transcriptional pre-mRNA splicing. Molecular Cell 2024, 84: 3656-3666. PMID: 39366353, PMCID: PMC11463726, DOI: 10.1016/j.molcel.2024.08.036.Peer-Reviewed Original ResearchConceptsPre-mRNA splicingCo-transcriptional pre-mRNA splicingCo-transcriptional RNA foldingCo-transcriptional processesRNA polymerase IIPre-messenger RNAFunctional messenger RNAsCapping enzymePolymerase IIDelayed splicingPolyadenylation machinerySplicing eventsPre-mRNAGene regulationMacromolecular machinesRNA foldingRNA synthesisMRNA isoformsProtein productionGene expressionSplicingRNARegulatory importanceCross-regulationMessenger RNA
2023
Production and Purification of Cysteine-Rich Leptospiral Virulence-Modifying Proteins with or Without mCherry Fusion
Chaurasia R, Liang C, How K, Vieira D, Vinetz J. Production and Purification of Cysteine-Rich Leptospiral Virulence-Modifying Proteins with or Without mCherry Fusion. The Protein Journal 2023, 42: 792-801. PMID: 37653175, DOI: 10.1007/s10930-023-10152-2.Peer-Reviewed Original ResearchMCherry fusion proteinsFusion proteinMCherry tagGene familyMCherry fusionsProtein productionFluorescent fusion proteinsRecombinant protein expressionRecombinant protein productionVM proteinsSuch proteinsFunctional proteinsCell biologyLike domainFast protein liquid chromatographyLeptospiral virulenceSoluble proteinUnique memberPink coloniesProtein scienceStructural predictionsProtein liquid chromatographyRicin BFunctional studiesProteinScalable production of tissue-like vascularized liver organoids from human PSCs
Harrison S, Siller R, Tanaka Y, Chollet M, de la Morena-Barrio M, Xiang Y, Patterson B, Andersen E, Bravo-Pérez C, Kempf H, Åsrud K, Lunov O, Dejneka A, Mowinckel M, Stavik B, Sandset P, Melum E, Baumgarten S, Bonanini F, Kurek D, Mathapati S, Almaas R, Sharma K, Wilson S, Skottvoll F, Boger I, Bogen I, Nyman T, Wu J, Bezrouk A, Cizkova D, Corral J, Mokry J, Zweigerdt R, Park I, Sullivan G. Scalable production of tissue-like vascularized liver organoids from human PSCs. Experimental & Molecular Medicine 2023, 55: 2005-2024. PMID: 37653039, PMCID: PMC10545717, DOI: 10.1038/s12276-023-01074-1.Peer-Reviewed Original ResearchConceptsExtracellular matrixSingle-cell RNA sequencingBasic developmental biologyEmbryonic liver developmentPost-translational modificationsLiver-like functionsCostly growth factorsOrganoid modelsKey liver functionsCellular diversityCellular repertoireDevelopmental biologyCellular complexityN-glycosylationRNA sequencingDe novo vascularizationNumber of tissuesProtein productionSerum protein productionLiver developmentHuman PSCsDrug toxicity assessmentOrganoidsSmall moleculesGrowth factorViral Evolution Shaped by Host Proteostasis Networks
Yoon J, Patrick J, Ogbunugafor C, Shoulders M. Viral Evolution Shaped by Host Proteostasis Networks. Annual Review Of Virology 2023, 10: 77-98. PMID: 37071930, PMCID: PMC10543606, DOI: 10.1146/annurev-virology-100220-112120.Peer-Reviewed Original ResearchConceptsProteostasis networkViral evolutionProtein foldingViral proteinsRegulate protein foldingViral protein productionEffective antiviral strategiesProteostasis factorsShape viral evolutionHost machineryAdaptive mutationsProtein biophysicsProtein productionFolding defectsAntiviral strategiesSequence spaceProteostasisProteinHostFoldingQuality control processChaperoneBiophysical defectsMutationsSequenceDesigning and developing a sensitive and specific SARS-CoV-2 RBD IgG detection kit for identifying positive human samples
Raoufi E, Hosseini F, Onagh B, Salehi-Shadkami M, Mehrali M, Mohsenzadegan M, Ho J, Bigdelou B, Sepand M, Webster T, Zanganeh S, Farajollahi M. Designing and developing a sensitive and specific SARS-CoV-2 RBD IgG detection kit for identifying positive human samples. Clinica Chimica Acta 2023, 542: 117279. PMID: 36871661, PMCID: PMC9985519, DOI: 10.1016/j.cca.2023.117279.Peer-Reviewed Original ResearchConceptsReceptor-binding domainPichia pastorisIon-exchange chromatographyShake flask cultivationRecombinant receptor-binding domainSARS-CoV-2 spike proteinBioreactor cultivationsIndirect enzyme-linked immunoassayBinding domainSARS-CoV-2Target proteinsProtein productionTarget genesAntigenic regionsEnzyme-linked immunoassaySpike proteinProteinReceptor binding domain antigensDetection kitEpitope analysisHuman samplesEnzyme-linked immunoassay testImmunological developmentCultivationHuman serum
2022
tRNA-m1A modification promotes T cell expansion via efficient MYC protein synthesis
Liu Y, Zhou J, Li X, Zhang X, Shi J, Wang X, Li H, Miao S, Chen H, He X, Dong L, Lee GR, Zheng J, Liu RJ, Su B, Ye Y, Flavell RA, Yi C, Wu Y, Li HB. tRNA-m1A modification promotes T cell expansion via efficient MYC protein synthesis. Nature Immunology 2022, 23: 1433-1444. PMID: 36138184, DOI: 10.1038/s41590-022-01301-3.Peer-Reviewed Original ResearchConceptsCell expansionKey functional proteinsVivo physiological roleDe novo protein productionCell cycle arrestTranslational controlRNA modificationsMyc proteinFunctional proteinsTranslation efficiencyKey proteinsCell homeostasisProtein productionPhysiological roleProtein synthesisProliferative stateCycle arrestConditional deletionT cell homeostasisNaive T cellsProteinQuiescent stateSpecific subsetT cellsCellsStructure–function analysis of cysteine residues in the plasmodium falciparum chitinase, PfCHT1
Kaur H, Garber L, Murphy JW, Vinetz JM. Structure–function analysis of cysteine residues in the plasmodium falciparum chitinase, PfCHT1. Protein Science 2022, 31: e4289. PMID: 35481637, PMCID: PMC8994504, DOI: 10.1002/pro.4289.Peer-Reviewed Original ResearchConceptsPutative chitin-binding domainChitin-binding domainPlasmodium ookinetesProtein-protein interactionsRecombinant protein productionIntermolecular protein-protein interactionsMosquito midgut invasionStructure-function analysisEnzymatic activityIntramolecular disulfide linkagesIntermolecular disulfide bondingChitin-containing peritrophic matrixParasite cladesMidgut invasionPeritrophic matrixCysteine residuesProtein productionChitinase activityBiochemical studiesDisulfide bondingUnpaired cysteineChitinaseMalaria parasitesE. coliMutants
2021
Chronic cannabis smoking-enriched oral pathobiont drives behavioral changes, macrophage infiltration, and increases β-amyloid protein production in the brain
Luo Z, Fitting S, Robinson C, Benitez A, Li M, Wu Y, Fu X, Amato D, Ning W, Funderburg N, Wang X, Zhou Z, Yu X, Wagner A, Cong X, Xu W, Maas K, Wolf B, Huang L, Yu J, Scott A, Mcrae-Clark A, Hamlett E, Jiang W. Chronic cannabis smoking-enriched oral pathobiont drives behavioral changes, macrophage infiltration, and increases β-amyloid protein production in the brain. EBioMedicine 2021, 74: 103701. PMID: 34826801, PMCID: PMC8626580, DOI: 10.1016/j.ebiom.2021.103701.Peer-Reviewed Original ResearchConceptsCannabis smokersActinomyces meyeriCannabis smokingCentral nervous systemOral pathobiontsChronic cannabis smokersMacrophage infiltrationCannabis use disorderOral microbiomeOral microbial dysbiosisSaliva microbiomeNon-smoking controlsIncreased macrophage infiltrationCannabis exposureUse disorderMicrobial 16S rRNA sequencingCannabisCNS abnormalitiesProtein productionActinomyces odontolyticusOral bacteriaBehavioral changesNon-smokersMicrobial dysbiosisNervous system
2020
Regulation and Function of RNA Pseudouridylation in Human Cells
Borchardt EK, Martinez NM, Gilbert WV. Regulation and Function of RNA Pseudouridylation in Human Cells. Annual Review Of Genetics 2020, 54: 1-28. PMID: 32870730, PMCID: PMC8007080, DOI: 10.1146/annurev-genet-112618-043830.Peer-Reviewed Original ResearchConceptsRNA pseudouridylationHuman cellsRNA-binding proteinDistinct RNA sequencesMRNA pseudouridylationPseudouridine synthasesMolecular functionsRNA metabolismPseudouridylationGene expressionRNA conformationRNA targetsProtein productionRNA sequencesMessenger RNADiverse classRNATherapeutic mRNAWidespread effectsDestabilizing interactionsCellsRecent advancesSplicingSynthasesPotential effects
2019
Disruptive mutations in TANC2 define a neurodevelopmental syndrome associated with psychiatric disorders
Guo H, Bettella E, Marcogliese P, Zhao R, Andrews J, Nowakowski T, Gillentine M, Hoekzema K, Wang T, Wu H, Jangam S, Liu C, Ni H, Willemsen M, van Bon B, Rinne T, Stevens S, Kleefstra T, Brunner H, Yntema H, Long M, Zhao W, Hu Z, Colson C, Richard N, Schwartz C, Romano C, Castiglia L, Bottitta M, Dhar S, Erwin D, Emrick L, Keren B, Afenjar A, Zhu B, Bai B, Stankiewicz P, Herman K, Mercimek-Andrews S, Juusola J, Wilfert A, Abou Jamra R, Büttner B, Mefford H, Muir A, Scheffer I, Regan B, Malone S, Gecz J, Cobben J, Weiss M, Waisfisz Q, Bijlsma E, Hoffer M, Ruivenkamp C, Sartori S, Xia F, Rosenfeld J, Bernier R, Wangler M, Yamamoto S, Xia K, Stegmann A, Bellen H, Murgia A, Eichler E. Disruptive mutations in TANC2 define a neurodevelopmental syndrome associated with psychiatric disorders. Nature Communications 2019, 10: 4679. PMID: 31616000, PMCID: PMC6794285, DOI: 10.1038/s41467-019-12435-8.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultAnimalsAutistic DisorderBehavior, AnimalBrainChildChild, PreschoolCraniofacial AbnormalitiesDevelopmental DisabilitiesDrosophila melanogasterDrosophila ProteinsEpilepsyExome SequencingFemaleHumansIntellectual DisabilityLanguage Development DisordersMaleMembrane ProteinsMental DisordersMuscle ProteinsMutationNerve Tissue ProteinsNeurodevelopmental DisordersNeurogliaNeuronsProteinsYoung AdultConceptsDisruptive mutationsPsychiatric disordersDrosophila glial cellsGene-disrupting mutationsPostsynaptic densityGlial cellsGenetic dataPostsynaptic density proteinHuman developing brainRestriction patternsProtein productionDelayed languageIntellectual disabilityCarrier parentsNeuropsychiatric disordersPsychiatric dysfunctionBehavior problemsDegree of epilepsyPediatric patientsBehavioral outcomesMutationsFacial dysmorphismExcitatory neuronsPostsynaptic functionDeveloping brainThrombospondin-2 regulates extracellular matrix production, LOX levels, and cross-linking via downregulation of miR-29
Calabro NE, Barrett A, Chamorro-Jorganes A, Tam S, Kristofik NJ, Xing H, Loye AM, Sessa WC, Hansen K, Kyriakides TR. Thrombospondin-2 regulates extracellular matrix production, LOX levels, and cross-linking via downregulation of miR-29. Matrix Biology 2019, 82: 71-85. PMID: 30876926, PMCID: PMC6710120, DOI: 10.1016/j.matbio.2019.03.002.Peer-Reviewed Original ResearchConceptsECM protein productionProtein productionLysyl oxidaseThrombospondin-2MiR-29Matricellular proteinQuantitative proteomics approachLevels of LOXExtracellular matrix productionProteomic approachECM proteinsMajor regulatorECM homeostasisExtracellular matrixMatrix productionProteinCollagen fibrillogenesisMiR-29 expressionFibrillar collagenImportant modulatorDependent processesLOX levelsRegulatorProductionHomeostasisConvergent Identification and Interrogation of Tumor-Intrinsic Factors that Modulate Cancer Immunity In Vivo
Codina A, Renauer PA, Wang G, Chow RD, Park JJ, Ye H, Zhang K, Dong MB, Gassaway B, Ye L, Errami Y, Shen L, Chang A, Jain D, Herbst RS, Bosenberg M, Rinehart J, Fan R, Chen S. Convergent Identification and Interrogation of Tumor-Intrinsic Factors that Modulate Cancer Immunity In Vivo. Cell Systems 2019, 8: 136-151.e7. PMID: 30797773, PMCID: PMC6592847, DOI: 10.1016/j.cels.2019.01.004.Peer-Reviewed Original ResearchConceptsSingle-cell transcriptomic profilingExtracellular protein productionCancer cellsMutant cellsFunctional interrogationGenetic programCRISPR screensTranscriptomic profilingTumor-intrinsic mutationsTranscriptomic alterationsTumor microenvironmentProtein productionPRKAR1A lossGenetic makeupHost myeloid cellsTumor-intrinsic factorsDrastic alterationsCytometry analysisConvergent identificationMyeloid cellsCellsImmunocompetent hostsCancer immunityMutant tumorsHost
2018
An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer
Li J, Choi P, Chaffer C, Labella K, Hwang J, Giacomelli A, Kim J, Ilic N, Doench J, Ly S, Dai C, Hagel K, Hong A, Gjoerup O, Goel S, Ge J, Root D, Zhao J, Brooks A, Weinberg R, Hahn W. An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer. ELife 2018, 7: e37184. PMID: 30059005, PMCID: PMC6103745, DOI: 10.7554/elife.37184.Peer-Reviewed Original ResearchMeSH KeywordsAlternative SplicingAnimalsBase SequenceBreast NeoplasmsCell Line, TumorEpithelial-Mesenchymal TransitionExonsFemaleFilaminsGene Expression Regulation, NeoplasticGenome, HumanHumansHyaluronan ReceptorsMesenchymal Stem CellsMice, NudeNeoplasm ProteinsOpen Reading FramesProtein IsoformsReproducibility of ResultsRNA-Binding ProteinsRNA, MessengerConceptsEpithelial-to-mesenchymal transitionAlternative splicing of mRNA precursorsMesenchymal cell stateSplicing of mRNA precursorsCell statesRNA-binding proteinsAlternative splicing switchDysregulation of splicingBreast cancer patient samplesEMT gene signatureRegulation of epithelial-to-mesenchymal transitionCancer patient samplesInduce epithelial-to-mesenchymal transitionFOXC1 transcription factorRNA-seqAlternative splicingExpression screeningMRNA precursorsRegulating tumor cell plasticityRegulatory stepTranscription factorsSplicing switchProtein productionDiverse functionsIncreased tumorigenicity
2016
Expression of ribosomopathy genes during Xenopus tropicalis embryogenesis
Robson A, Owens ND, Baserga SJ, Khokha MK, Griffin JN. Expression of ribosomopathy genes during Xenopus tropicalis embryogenesis. BMC Developmental Biology 2016, 16: 38. PMID: 27784267, PMCID: PMC5081970, DOI: 10.1186/s12861-016-0138-5.Peer-Reviewed Original ResearchConceptsRibosome biogenesis factorsBiogenesis factorsVentral blood islandsHuman congenital diseasesCranial neural crestRNA-seq dataAntisense mRNA probesBlood islandsEmbryonic developmentDistinct tissuesNeural crestProtein productionDifferential expressionTranscript numbersMachinery componentsSpecific tissuesSpecific phenotypesRibosomopathiesSitu hybridizationMRNA probesRibosomesExpressionTissue localizationPhenotypeFactor expression
2015
The Torsin Activator LULL1 Is Required for Efficient Growth of Herpes Simplex Virus 1
Turner EM, Brown RS, Laudermilch E, Tsai PL, Schlieker C. The Torsin Activator LULL1 Is Required for Efficient Growth of Herpes Simplex Virus 1. Journal Of Virology 2015, 89: 8444-8452. PMID: 26041288, PMCID: PMC4524217, DOI: 10.1128/jvi.01143-15.Peer-Reviewed Original ResearchConceptsNuclear egressDouble knockout cell linesNuclear envelope dynamicsType II transmembrane proteinHerpes simplex virus 1HSV-1 nuclear egressKnockout cell linesSimplex virus 1Viral protein productionAAA ringGenome engineeringTransmembrane proteinLULL1CRISPR/Virus 1Unexpected roleProtein productionComprehensive geneticPhenotypic analysisHost cellsViral genomeEnvelope dynamicsEfficient growthCell linesHSV-1 production
2014
Virus Meets Host MicroRNA: the Destroyer, the Booster, the Hijacker
Guo YE, Steitz JA. Virus Meets Host MicroRNA: the Destroyer, the Booster, the Hijacker. Molecular And Cellular Biology 2014, 34: 3780-3787. PMID: 25047834, PMCID: PMC4187717, DOI: 10.1128/mcb.00871-14.Peer-Reviewed Original ResearchConceptsKey regulatory stepSmall noncoding RNAsVirus-host interactionsViral life cycleNoncoding RNAsCellular miRNAsMiRNA interactionsRegulatory stepGene expressionProtein productionHost microRNAsRNA virusesRecent discoveryLife cycleMicroRNAsMiRNAsRNADNAMRNAVirusExpressionInteractionMinireviewDiscovery
2013
AMPK-Dependent Degradation of TXNIP upon Energy Stress Leads to Enhanced Glucose Uptake via GLUT1
Wu N, Zheng B, Shaywitz A, Dagon Y, Tower C, Bellinger G, Shen C, Wen J, Asara J, McGraw T, Kahn B, Cantley L. AMPK-Dependent Degradation of TXNIP upon Energy Stress Leads to Enhanced Glucose Uptake via GLUT1. Molecular Cell 2013, 49: 1167-1175. PMID: 23453806, PMCID: PMC3615143, DOI: 10.1016/j.molcel.2013.01.035.Peer-Reviewed Original ResearchConceptsThioredoxin-interacting proteinAMP-dependent protein kinaseGLUT1 messenger RNAMessenger RNAEnergy stressArrestin family proteinGlucose uptakeGlucose transporter GLUT1Negative feedback loopFamily proteinsProtein kinaseProtein productionEnhanced glucose uptakeGLUT1 functionBiochemical mechanismsLong-term adaptationTransporter GLUT1ADP ratioEnergy homeostasisGLUT1Rapid degradationProteinGlucose influxFeedback loopUptake
2012
SIRNA-MEDIATED INHIBITION OF INTERLEUKINE-13 PRODUCTION IN VITRO
Shilovskiy I, Mazurov D, Shershakova N, Khaitov M. SIRNA-MEDIATED INHIBITION OF INTERLEUKINE-13 PRODUCTION IN VITRO. Russian Journal Of Allergy 2012, 9: 24-27. DOI: 10.36691/rja683.Peer-Reviewed Original ResearchExpression of IL-13Gene expressionIL-13Gene expression changesGene expression of miceSmall interfering RNA moleculesEfficiency of siRNAIL-13 in vitroExpression of IL-13 mRNARNA moleculesExpression of mouseConA-stimulated spleen cellsPathogenesis of allergic conditionsProtein productionCo-transfectionExpression changesGene expression of IL-13IL-13 mRNASiRNA moleculesGenesTwenty-four hoursSiRNAQuantitative PCRGFP+ cellsSpleen cells
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply