2022
miRNA‐encapsulated abiotic materials and biovectors for cutaneous and oral wound healing: Biogenesis, mechanisms, and delivery nanocarriers
Dey A, Yousefiasl S, Kumar A, Moghaddam F, Rahimmanesh I, Samandari M, Jamwal S, Maleki A, Mohammadi A, Rabiee N, Paiva‐Santos A, Tamayol A, Sharifi E, Makvandi P. miRNA‐encapsulated abiotic materials and biovectors for cutaneous and oral wound healing: Biogenesis, mechanisms, and delivery nanocarriers. Bioengineering & Translational Medicine 2022, 8: e10343. PMID: 36684081, PMCID: PMC9842058, DOI: 10.1002/btm2.10343.Peer-Reviewed Original Research
2016
Modulation of VEGF receptor 2 signaling by protein phosphatases
Corti F, Simons M. Modulation of VEGF receptor 2 signaling by protein phosphatases. Pharmacological Research 2016, 115: 107-123. PMID: 27888154, PMCID: PMC5205541, DOI: 10.1016/j.phrs.2016.11.022.Peer-Reviewed Original ResearchConceptsProtein phosphatasePhosphorylation of serineVascular endothelial growth factor receptor 2 signalingSignal transduction cascadePrecise biological roleSpecific signaling pathwaysKinase biologyEukaryotic cellsSignal terminatorRegulatory subunitPositive regulatorTransduction cascadePhosphorylation stateBiological roleContext of cancerParticular proteinDifferent proteinsGenome sequencingSignaling pathwaysVEGF receptor 2Receptor 2 signalingVEGF signalsProteinPhosphataseGenetic models
2015
Formation of Giant Unilamellar Proteo-Liposomes by Osmotic Shock
Motta I, Gohlke A, Adrien V, Li F, Gardavot H, Rothman JE, Pincet F. Formation of Giant Unilamellar Proteo-Liposomes by Osmotic Shock. Langmuir 2015, 31: 7091-7099. PMID: 26038815, PMCID: PMC4950989, DOI: 10.1021/acs.langmuir.5b01173.Peer-Reviewed Original ResearchConceptsGiant unilamellar vesiclesLipid-anchored proteinsOsmotic shockTrans-membrane proteinsSingle giant unilamellar vesiclesProtein substratesPeripheral proteinsSpecific lipidsDifferent proteinsPhotobleaching experimentsFluorescence recoveryCell membraneProteinLarge vesiclesPhysiological conditionsModel systemUnilamellar vesiclesPhospholipid bilayersVesiclesSimple generic methodPrevious dataMembraneHigh concentrationsLipidsBilayersQuantitative variability of 342 plasma proteins in a human twin population
Liu Y, Buil A, Collins BC, Gillet L, Blum LC, Cheng LY, Vitek O, Mouritsen J, Lachance G, Spector TD, Dermitzakis ET, Aebersold R. Quantitative variability of 342 plasma proteins in a human twin population. Molecular Systems Biology 2015, 11: msb145728. PMID: 25652787, PMCID: PMC4358658, DOI: 10.15252/msb.20145728.Peer-Reviewed Original ResearchConceptsQuantitative variabilityUnique plasma proteinsBlood-based biomarker studiesGenetic controlBiological processesDifferent proteinsDifferent traitsPlasma proteinsProteinAbundance variabilityProtein levelsHuman populationMass spectrometry techniquesSpecific plasma proteinsHuman plasma proteinsGenesRelative contributionTraitsHeritabilitySpectrometry techniquesTwin study designDifferent patternsPopulationClinical biomarkersVariability
2014
Discovering the pre‐60S ribosome biogenesis factor interactome (560.7)
McCann K, Charette J, Vincent N, Baserga S. Discovering the pre‐60S ribosome biogenesis factor interactome (560.7). The FASEB Journal 2014, 28 DOI: 10.1096/fasebj.28.1_supplement.560.7.Peer-Reviewed Original ResearchRibosome assemblyGlycerol gradient sedimentation analysisTwo-hybrid analysisHigh-throughput yeastHigh-confidence interactionsPotential regulatory mechanismsGradient sedimentation analysisRNA helicasesBiogenesis factorsSmaller subcomplexesMDa complexNucleolar proteinsRibosomal subunitRegulatory mechanismsDifferent proteinsSubcomplexHelicasesGlycerol gradientsIndependent validation experimentsInteractomeSedimentation analysisYeastCurrent knowledgeProteinAssembly
2013
Expanding Horizons: Ciliary Proteins Reach Beyond Cilia
Yuan S, Sun Z. Expanding Horizons: Ciliary Proteins Reach Beyond Cilia. Annual Review Of Genetics 2013, 47: 353-376. PMID: 24016188, PMCID: PMC5703194, DOI: 10.1146/annurev-genet-111212-133243.Peer-Reviewed Original ResearchMeSH KeywordsAbnormalities, MultipleAnimalsBardet-Biedl SyndromeCell MovementCerebellar DiseasesCerebellumCiliaCiliary Motility DisordersDisease Models, AnimalDNA DamageDNA RepairEncephaloceleEye AbnormalitiesFlagellaHeterotaxy SyndromeHomeostasisHumansKidney Diseases, CysticMolecular Motor ProteinsNervous SystemPolycystic Kidney DiseasesPolycystic Kidney, Autosomal DominantPolycystic Kidney, Autosomal RecessiveRetinaRetinitis Pigmentosa
2010
Construction and maintenance of randomized retroviral expression libraries for transmembrane protein engineering
Marlatt SA, Kong Y, Cammett TJ, Korbel G, Noonan JP, DiMaio D. Construction and maintenance of randomized retroviral expression libraries for transmembrane protein engineering. Protein Engineering Design And Selection 2010, 24: 311-320. PMID: 21149273, PMCID: PMC3038463, DOI: 10.1093/protein/gzq112.Peer-Reviewed Original ResearchConceptsSignificant genetic bottleneckRetroviral expression libraryDeep DNA sequencingAmino acid segmentNovel biological activitiesGenetic bottleneckTransmembrane domainMammalian cellsLibrary sequencesRandom mutagenesisProtein engineeringExpression libraryDeep sequencingDifferent proteinsSmall proteinsGenetic selectionAcid segmentRetroviral libraryDNA sequencingSequencing resultsRandomized libraryProteinPowerful approachSequencingDiversity
2009
Multistrip Western Blotting to Increase Quantitative Data Output
Kiyatkin A, Aksamitiene E. Multistrip Western Blotting to Increase Quantitative Data Output. Methods In Molecular Biology 2009, 536: 149-161. PMID: 19378054, PMCID: PMC2923389, DOI: 10.1007/978-1-59745-542-8_17.Peer-Reviewed Original ResearchConceptsCell signaling researchDiverse cellular processesWestern blottingHigh-throughput technologiesQuantitative data outputModification statesCellular processesProtein abundanceSystems biologyDifferent proteinsSingle membrane sheetMembrane sheetsPolyacrylamide gelsBlottingProteinElectrophoretic transferImmunoblotting procedureBiologyAbundance
2008
Analyzing Protein-Protein Spatial-Temporal Dependencies from Image Sequences Using Fuzzy Temporal Random Sets
Daz M, Ayala G, Len T, Zoncu R, Toomre D. Analyzing Protein-Protein Spatial-Temporal Dependencies from Image Sequences Using Fuzzy Temporal Random Sets. Journal Of Computational Biology 2008, 15: 1221-1236. PMID: 18973437, DOI: 10.1089/cmb.2008.0055.Peer-Reviewed Original ResearchConceptsTotal internal reflection fluorescence microscopyFluorescent-tagged proteinsReflection fluorescence microscopyEndocytic proteinsBiological questionsPlasma membraneDifferent proteinsFluorescence microscopyProteinSequenceK-functionArea of fluorescenceEndocytosisFree tuning parametersGFPBiologistsColocalizationHigh spatial-temporal resolutionMembraneSpatial-temporal resolutionPoisson cluster modelCellsFluorescence
2006
Global Analysis of Protein Phosphorylation in Yeast
Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A, Sopko R, McCartney R, Schmidt M, Rachidi N, Lee S, Mah A, Meng L, Stark M, Stern D, De Virgilio C, Tyers M, Andrews B, Gerstein M, Schweitzer B, Predki P, Snyder M. Global Analysis of Protein Phosphorylation in Yeast. The FASEB Journal 2006, 20: a1308-a1308. DOI: 10.1096/fasebj.20.5.a1308.Peer-Reviewed Original ResearchProtein phosphorylationProtein kinaseNovel regulatory moduleDifferent biochemical functionsNumber of kinasesMajor regulatory mechanismSame cellular compartmentSame functional categoryYeast kinasesCellular rolesCyclin subunitPhosphorylation eventsRegulatory modulesYeast proteinsVivo substratePhosphorylation resultsBiochemical functionsRelated kinasesTranscription factorsCellular compartmentsFunctional categoriesBiochemical understandingRegulatory mechanismsDifferent proteinsKinase
2002
MEN1 tumor‐suppressor protein localizes to telomeres during meiosis
Suphapeetiporn K, Greally JM, Walpita D, Ashley T, Bale AE. MEN1 tumor‐suppressor protein localizes to telomeres during meiosis. Genes Chromosomes And Cancer 2002, 35: 81-85. PMID: 12203793, DOI: 10.1002/gcc.10113.Peer-Reviewed Original ResearchConceptsSomatic cellsTelomerase activityAbsence of meninTumor suppressor gene MEN1Normal cell physiologyTelomeric protein TRF2Normal telomerase activityTumor suppressor proteinRole of meninMeiotic telomeresTelomere functionProtein TRF2Meiotic cellsTranscriptional activationNuclear proteinsCell physiologyFunctional motifsDifferent proteinsTumor suppressorTelomeresMeninElevated telomerase activityDifferent tissuesJunDCancer predisposition syndrome
1996
Molecular basis of the magnesium deprivation response in Salmonella typhimurium: identification of PhoP-regulated genes
Soncini FC, Véscovi E, Solomon F, Groisman EA. Molecular basis of the magnesium deprivation response in Salmonella typhimurium: identification of PhoP-regulated genes. Journal Of Bacteriology 1996, 178: 5092-5099. PMID: 8752324, PMCID: PMC178303, DOI: 10.1128/jb.178.17.5092-5099.1996.Peer-Reviewed Original ResearchConceptsTranscription of PhoPPhoP-dependent mannerOpen reading frameLac gene fusionsWild-type strainPhoP-PhoQ systemTwo-component systemUDP-glucose dehydrogenaseSequence similarityPhoP-PhoQPhoPQ operonReading frameDeprivation responseFusion strainMolecular basisSalmonella typhimuriumPhoPDifferent proteinsSolid mediumGene fusionsUptake systemGenesNormal growthMgtASuch fusionExpression of Additional Genes in a Vector Derived from a Minimal RNA Virus
ROLLS M, HAGLUND K, ROSE J. Expression of Additional Genes in a Vector Derived from a Minimal RNA Virus. Virology 1996, 218: 406-411. PMID: 8610469, DOI: 10.1006/viro.1996.0211.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceCapsidCD4 AntigensCell LineChloramphenicol O-AcetyltransferaseCloning, MolecularCricetinaeGene ExpressionGenetic VectorsMembrane GlycoproteinsMolecular Sequence DataPromoter Regions, GeneticRecombinant Fusion ProteinsRNA, ViralSemliki forest virusVesicular stomatitis Indiana virusViral Core ProteinsViral Envelope ProteinsConceptsVSV G proteinG proteinsVSV G geneVesicular stomatitis virus glycoproteinTotal cell proteinMembrane fusion activityViral structural proteinsHost protein synthesisTissue culture cellsUnselected genesMultiple cloning siteInfectious particlesAdditional genesForeign genesPlasma membraneG RNADifferent proteinsStructural proteinsMajor proteinsRNA repliconsCell proteinsFusion activityRNA virusesProtein synthesisGenes
1995
Mapping of ribosomal protein S3 and internally nested snoRNA U15A gene to human chromosome 11q13.3–q13.5
Polakiewicz R, Munroe D, Sait S, Tycowski K, Nowak N, Shows T, Housman D, Page D. Mapping of ribosomal protein S3 and internally nested snoRNA U15A gene to human chromosome 11q13.3–q13.5. Genomics 1995, 25: 577-580. PMID: 7789996, DOI: 10.1016/0888-7543(95)80063-r.Peer-Reviewed Original ResearchConceptsRibosomal proteinsHuman chromosomesSomatic cell hybrid analysisCell hybrid analysisRibosomal protein S3Small nucleolar RNAsUV-induced DNA damageSTS content mappingMammalian ribosomesProtein S3RNA speciesHuman genomeNucleolar RNAsFirst intronDifferent proteinsDNA damageSitu hybridizationProteinChromosomesHybrid analysisGenesContent mappingIntronsGenomeRibosomes
1989
Flagellar Membrane and Paraxial Rod Proteins of Leishmania: Characterization Employing Monoclonal Antibodies
ISMACH R, CIANCI C, CAULFIELD J, LANGER P, HEIN A, McMAHON‐PRATT D. Flagellar Membrane and Paraxial Rod Proteins of Leishmania: Characterization Employing Monoclonal Antibodies. Journal Of Eukaryotic Microbiology 1989, 36: 617-624. PMID: 2689639, DOI: 10.1111/j.1550-7408.1989.tb01105.x.Peer-Reviewed Original ResearchConceptsDoublet of proteinsImmunocytochemical electron microscopic studyIndirect immunofluorescence experimentsRod proteinsMonoclonal antibody fFlagellar membraneSingle proteinDifferent proteinsFlagellar tipImmunofluorescence experimentsFlagellaParaxial rodProteinMonoclonal antibodiesAntibody FElectron microscopic experimentsMembraneLeishmaniaElectron microscopic studyMoleculesDAMicroscopic experimentsMicroscopic studyMonoclonal antibody techniqueLocalized patches
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