Featured Publications
Architecture of the Flaviviral Replication Complex PROTEASE, NUCLEASE, AND DETERGENTS REVEAL ENCASEMENT WITHIN DOUBLE-LAYERED MEMBRANE COMPARTMENTS*
Uchil P, Satchidanandam V. Architecture of the Flaviviral Replication Complex PROTEASE, NUCLEASE, AND DETERGENTS REVEAL ENCASEMENT WITHIN DOUBLE-LAYERED MEMBRANE COMPARTMENTS*. Journal Of Biological Chemistry 2003, 278: 24388-24398. PMID: 12700232, DOI: 10.1074/jbc.m301717200.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell LineDetergentsEndopeptidasesFlavivirusRibonucleasesRNA, ViralVirus ReplicationConceptsViral genomic RNAVesicle packetsMembrane compartmentsGenomic RNADouble-membrane compartmentsInner membrane vesiclesViral RNA speciesHost cell membraneHeavy membrane fractionNonionic detergent extractsRNA speciesReplicative intermediate RNAViral NS3Replication complexPrior trypsin treatmentMicrococcal nucleaseComplex proteaseMembranous sitesReplicative form RNASpecialized structuresActive proteinIntermediate RNAMembrane vesiclesMembrane fractionForm RNAPhylogenetic analysis of Japanese encephalitis virus: envelope gene based analysis reveals a fifth genotype, geographic clustering, and multiple introductions of the virus into the Indian subcontinent.
Uchil P, Satchidanandam V. Phylogenetic analysis of Japanese encephalitis virus: envelope gene based analysis reveals a fifth genotype, geographic clustering, and multiple introductions of the virus into the Indian subcontinent. American Journal Of Tropical Medicine And Hygiene 2001, 65: 242-51. PMID: 11561712, DOI: 10.4269/ajtmh.2001.65.242.Peer-Reviewed Original ResearchMeSH KeywordsAedesAmino Acid SequenceAnimalsBase SequenceCell LineCluster AnalysisDNA, ComplementaryEncephalitis Virus, JapaneseEncephalitis, JapaneseEvolution, MolecularGenes, envGenetic VariationGenotypeHumansIndiaMolecular Sequence DataPhylogenyReverse Transcriptase Polymerase Chain ReactionRNA, ViralSequence Homology, Amino AcidSequence Homology, Nucleic AcidSwineTRIM5 is an innate immune sensor for the retrovirus capsid lattice
Pertel T, Hausmann S, Morger D, Züger S, Guerra J, Lascano J, Reinhard C, Santoni FA, Uchil PD, Chatel L, Bisiaux A, Albert ML, Strambio-De-Castillia C, Mothes W, Pizzato M, Grütter MG, Luban J. TRIM5 is an innate immune sensor for the retrovirus capsid lattice. Nature 2011, 472: 361-365. PMID: 21512573, PMCID: PMC3081621, DOI: 10.1038/nature09976.Peer-Reviewed Original ResearchMeSH KeywordsAntiviral Restriction FactorsCapsidCarrier ProteinsCell LineEnzyme ActivationHEK293 CellsHIV-1HumansImmunity, InnateLipopolysaccharidesMAP Kinase Kinase KinasesNF-kappa BProtein BindingReceptors, Pattern RecognitionRetroviridaeSignal TransductionTranscription Factor AP-1Transcription FactorsTripartite Motif ProteinsUbiquitinUbiquitin-Conjugating EnzymesUbiquitin-Protein Ligases
2019
Calcium Phosphate-Mediated Transfection of Adherent Cells or Cells Growing in Suspension: Variations on the Basic Method
Kumar P, Nagarajan A, Uchil PD. Calcium Phosphate-Mediated Transfection of Adherent Cells or Cells Growing in Suspension: Variations on the Basic Method. Cold Spring Harbor Protocols 2019, 2019: pdb.prot095455. PMID: 31575795, DOI: 10.1101/pdb.prot095455.Peer-Reviewed Original ResearchTransfection of Mammalian Cells with Calcium Phosphate-DNA Coprecipitates.
Kumar P, Nagarajan A, Uchil PD. Transfection of Mammalian Cells with Calcium Phosphate-DNA Coprecipitates. Cold Spring Harbor Protocols 2019, 2019: pdb.top096255. PMID: 31575800, DOI: 10.1101/pdb.top096255.Peer-Reviewed Original ResearchCalcium Phosphate-Mediated Transfection of Eukaryotic Cells with Plasmid DNAs.
Kumar P, Nagarajan A, Uchil PD. Calcium Phosphate-Mediated Transfection of Eukaryotic Cells with Plasmid DNAs. Cold Spring Harbor Protocols 2019, 2019: pdb.prot095430. PMID: 31575793, DOI: 10.1101/pdb.prot095430.Peer-Reviewed Original Research
2018
Selective Agents for Stable Transfection.
Kumar P, Nagarajan A, Uchil PD. Selective Agents for Stable Transfection. Cold Spring Harbor Protocols 2018, 2018: pdb.top096230. PMID: 30181228, DOI: 10.1101/pdb.top096230.Peer-Reviewed Original ResearchTransfection Mediated by DEAE-Dextran.
Kumar P, Nagarajan A, Uchil PD. Transfection Mediated by DEAE-Dextran. Cold Spring Harbor Protocols 2018, 2018: pdb.prot095463. PMID: 29967275, DOI: 10.1101/pdb.prot095463.Peer-Reviewed Original ResearchAnalysis of Cell Viability by the Lactate Dehydrogenase Assay.
Kumar P, Nagarajan A, Uchil PD. Analysis of Cell Viability by the Lactate Dehydrogenase Assay. Cold Spring Harbor Protocols 2018, 2018: pdb.prot095497. PMID: 29858337, DOI: 10.1101/pdb.prot095497.Peer-Reviewed Original ResearchConceptsCytoplasmic enzymePlasma membraneConversion of lactateLactate dehydrogenase assayLactate dehydrogenaseCellular damageYellow tetrazolium saltCell viabilityAmount of LDHDehydrogenase assayEnzymeCellsNADHTetrazolium saltCell culture supernatantsCulture supernatantsLDH activityAmount of formazanApoptosisDehydrogenaseMembraneActivityAssays
2017
Assay for β-Galactosidase in Extracts of Mammalian Cells.
Uchil PD, Nagarajan A, Kumar P. Assay for β-Galactosidase in Extracts of Mammalian Cells. Cold Spring Harbor Protocols 2017, 2017: pdb.prot095778. PMID: 28974657, DOI: 10.1101/pdb.prot095778.Peer-Reviewed Original Research
2015
TRIM5 Retroviral Restriction Activity Correlates with the Ability To Induce Innate Immune Signaling
Lascano J, Uchil PD, Mothes W, Luban J. TRIM5 Retroviral Restriction Activity Correlates with the Ability To Induce Innate Immune Signaling. Journal Of Virology 2015, 90: 308-316. PMID: 26468522, PMCID: PMC4702541, DOI: 10.1128/jvi.02496-15.Peer-Reviewed Original ResearchConceptsInnate immune signalingImmune signalingHIV-1 transductionHIV-1 restrictionAP-1 signalingViral nucleic acidsAP-1Retroviral capsid latticeAP-1 activationRestriction activityPast infectionProtein cyclophilin ARetrovirus infectionTRIM5Cyclophilin AActivity correlatesInfectionTRIM5 geneReverse transcriptionRetroviral transductionSignalingHost cell nucleusRetroviral capsidActivationTRIM familyHIV cell-to-cell transmission: effects on pathogenesis and antiretroviral therapy
Agosto LM, Uchil PD, Mothes W. HIV cell-to-cell transmission: effects on pathogenesis and antiretroviral therapy. Trends In Microbiology 2015, 23: 289-295. PMID: 25766144, PMCID: PMC4417442, DOI: 10.1016/j.tim.2015.02.003.Peer-Reviewed Original ResearchConceptsAntiretroviral therapyVirological synapsesT-cell depletionCell transmissionHIV infectionCell depletionHIV cellMatter of debateViral replicationTherapyUninfected cellsReduced efficacyHigh MOISynapsesHIVPathogenesisRecent dataInfectionCell deathTrigger cell deathCellsVivoCell-cell contactCellular surveillanceHigher number
2014
Attachment of Cell-Binding Ligands to Arginine-Rich Cell-Penetrating Peptides Enables Cytosolic Translocation of Complexed siRNA
Zeller S, Choi CS, Uchil PD, Ban HS, Siefert A, Fahmy TM, Mothes W, Lee SK, Kumar P. Attachment of Cell-Binding Ligands to Arginine-Rich Cell-Penetrating Peptides Enables Cytosolic Translocation of Complexed siRNA. Cell Chemical Biology 2014, 22: 50-62. PMID: 25544044, PMCID: PMC4320807, DOI: 10.1016/j.chembiol.2014.11.009.Peer-Reviewed Original Research
2011
Targeted Disruption of the CCR5 Gene in Human Hematopoietic Stem Cells Stimulated by Peptide Nucleic Acids
Schleifman EB, Bindra R, Leif J, del Campo J, Rogers FA, Uchil P, Kutsch O, Shultz LD, Kumar P, Greiner DL, Glazer PM. Targeted Disruption of the CCR5 Gene in Human Hematopoietic Stem Cells Stimulated by Peptide Nucleic Acids. Cell Chemical Biology 2011, 18: 1189-1198. PMID: 21944757, PMCID: PMC3183429, DOI: 10.1016/j.chembiol.2011.07.010.Peer-Reviewed Original ResearchConceptsHematopoietic stem cellsHIV-1CCR5 geneHIV-1-infected individualsHIV-1 infectionGene modificationHIV-1 entryCCR5-Delta32 mutationImmune system functionStem cellsCCR5 knockoutMonths posttransplantationChemokine receptorsHuman hematopoietic stem cellsTherapeutic strategiesSubsequent engraftmentGenome modificationProtein levelsHuman cellsTargeted disruptionCCR5Peptide nucleic acidInfectionNucleic acidsCellsTRIM22 Inhibits HIV-1 Transcription Independently of Its E3 Ubiquitin Ligase Activity, Tat, and NF-κB-Responsive Long Terminal Repeat Elements
Kajaste-Rudnitski A, Marelli SS, Pultrone C, Pertel T, Uchil PD, Mechti N, Mothes W, Poli G, Luban J, Vicenzi E. TRIM22 Inhibits HIV-1 Transcription Independently of Its E3 Ubiquitin Ligase Activity, Tat, and NF-κB-Responsive Long Terminal Repeat Elements. Journal Of Virology 2011, 85: 5183-5196. PMID: 21345949, PMCID: PMC3126207, DOI: 10.1128/jvi.02302-10.Peer-Reviewed Original ResearchConceptsHIV-1 replicationHIV-1 transcriptionHuman immunodeficiency virus type 1 (HIV-1) replicationU937 promonocytic cell lineHIV-1 restriction factorsTumor necrosis factor alphaInhibits HIV-1 transcriptionType 1 replicationRestriction factorsHIV-1 productionNecrosis factor alphaLower peak levelsPermissive cellsHIV-1 LTRHost restriction factorsPromonocytic cell lineU937 cellsReplication-competent virusNF-κB binding siteFactor alphaT cellsHIV-1Overexpression of TRIM22NF-κBLTR transactivation
2010
Anaplasma phagocytophilum AptA modulates Erk1/2 signalling
Sukumaran B, Mastronunzio JE, Narasimhan S, Fankhauser S, Uchil PD, Levy R, Graham M, Colpitts TM, Lesser CF, Fikrig E. Anaplasma phagocytophilum AptA modulates Erk1/2 signalling. Cellular Microbiology 2010, 13: 47-61. PMID: 20716207, PMCID: PMC3005019, DOI: 10.1111/j.1462-5822.2010.01516.x.Peer-Reviewed Original ResearchConceptsA. phagocytophilum infectionPhagocytophilum infectionCommon tick-borne diseasesHuman granulocytic anaplasmosisActivation of ERK1/2ERK1/2 mitogen-activated protein kinasesA. phagocytophilum survivalPolymorphonuclear leucocytesMitogen-activated protein kinaseHuman neutrophilsObligate intracellular pathogensGranulocytic anaplasmosisIntracellular pathogensTick-borne diseasesInfectionERK1/2 activationAnaplasma phagocytophilumVimentinSurvivalActivationBacterial inclusionsHost proteinsIntermediate filament protein vimentinVirulence proteinsProtein vimentin
2008
Retroviruses Human Immunodeficiency Virus and Murine Leukemia Virus Are Enriched in Phosphoinositides
Chan R, Uchil PD, Jin J, Shui G, Ott DE, Mothes W, Wenk MR. Retroviruses Human Immunodeficiency Virus and Murine Leukemia Virus Are Enriched in Phosphoinositides. Journal Of Virology 2008, 82: 11228-11238. PMID: 18799574, PMCID: PMC2573248, DOI: 10.1128/jvi.00981-08.Peer-Reviewed Original ResearchConceptsPlasma membraneMurine leukemia virusHIV-1 buddingLipid contentLeukemia virusMass spectrometry analysisCholesterol-rich regionsOverall lipid contentCell peripheryMutant virionsLipid envelopeTotal lipid contentPhosphorylated derivativesSpectrometry analysisPhosphoinositideRetrovirusesMembraneCellsMatrix domainParticle releaseHuman immunodeficiency virus type 1Immunodeficiency virus type 1VirusVirus type 1PhosphatidylinositolEffective suppression of HIV-1 by artificial bispecific miRNA targeting conserved sequences with tolerance for wobble base-pairing
Son J, Uchil PD, Kim YB, Shankar P, Kumar P, Lee SK. Effective suppression of HIV-1 by artificial bispecific miRNA targeting conserved sequences with tolerance for wobble base-pairing. Biochemical And Biophysical Research Communications 2008, 374: 214-218. PMID: 18619945, DOI: 10.1016/j.bbrc.2008.06.125.Peer-Reviewed Original ResearchConceptsFunctional RNAiHIV-1 isolatesHigh genetic diversityAntiviral therapyHIV replicationHIV-1Vif sequencesArtificial microRNAsGenetic diversityGenome sequenceSustained inhibitionVif geneHIV sequencesVariant residuesSequence databasesLuciferase constructSimultaneous targetingNatural variantsViral sequencesRNAiSequenceInhibition
2003
Characterization of RNA synthesis, replication mechanism, and in vitro RNA-dependent RNA polymerase activity of japanese encephalitis virus
Uchil P, Satchidanandam V. Characterization of RNA synthesis, replication mechanism, and in vitro RNA-dependent RNA polymerase activity of japanese encephalitis virus. Virology 2003, 307: 358-371. PMID: 12667804, DOI: 10.1016/s0042-6822(02)00130-7.Peer-Reviewed Original Research