2023
Experimental Evolution of the TolC-Receptor Phage U136B Functionally Identifies a Tail Fiber Protein Involved in Adsorption through Strong Parallel Adaptation
Burmeister A, Tzintzun-Tapia E, Roush C, Mangal I, Barahman R, Bjornson R, Turner P. Experimental Evolution of the TolC-Receptor Phage U136B Functionally Identifies a Tail Fiber Protein Involved in Adsorption through Strong Parallel Adaptation. Applied And Environmental Microbiology 2023, 89: e00079-23. PMID: 37191555, PMCID: PMC10304864, DOI: 10.1128/aem.00079-23.Peer-Reviewed Original ResearchConceptsExperimental evolutionPhage populationsParallel molecular evolutionWhole-population sequencingAntibiotic resistance proteinsTail fiber proteinE. coli hostPhage evolutionEvolutionary potentialMolecular evolutionPhage genotypesTolC proteinParallel adaptationProtein geneAntibiotic resistanceExperimental populationsBacterial diversitySelection pressureBacterial hostsColi hostFiber proteinBacterial populationsBacterial cellsPhage resistancePhage dynamicsExcluding Digenic Inheritance of PGAP2 and PGAP3 Variants in Mabry Syndrome (OMIM 239300) Patient: Phenotypic Spectrum Associated with PGAP2 Gene Variants in Hyperphosphatasia with Mental Retardation Syndrome-3 (HPMRS3)
Thompson M, Li X, Spencer-Manzon M, Andrade D, Murakami Y, Kinoshita T, Carpenter T. Excluding Digenic Inheritance of PGAP2 and PGAP3 Variants in Mabry Syndrome (OMIM 239300) Patient: Phenotypic Spectrum Associated with PGAP2 Gene Variants in Hyperphosphatasia with Mental Retardation Syndrome-3 (HPMRS3). Genes 2023, 14: 359. PMID: 36833286, PMCID: PMC9957281, DOI: 10.3390/genes14020359.Peer-Reviewed Original ResearchConceptsDigenic inheritanceDeficient CHO cell lineCell linesGPI deficiency disordersDeficient cell linesCHO cell linesBiosynthesis genesGPI attachmentMabry syndromeProtein geneStrong promoterCHO cellsUnknown significanceGenesInheritanceGene variantsAutosomal recessive inheritanceHomozygous variantNeurologic deficitsVariantsCase reportRecessive inheritanceSyndrome patientsCD55 expressionPGAP2
2019
Targeting Unique Synthetic Lethal Interactions between PI3K and MYC in B-ALL
Xiao G, Kume K, Geng H, Han T, Klemm L, Müschen M. Targeting Unique Synthetic Lethal Interactions between PI3K and MYC in B-ALL. Blood 2019, 134: 3785. DOI: 10.1182/blood-2019-128719.Peer-Reviewed Original ResearchMYC protein levelsPI3KCell deathMYC overexpressionPTEN deletionRescue effectProtein levelsPI3K hyperactivationMYC protein stabilityTranscription factor Pax5Wild-type MycDegradation of MycSynthetic lethal interactionsGlutamine consumptionGene expression profilesCellular ATP levelsInhibition of glutaminolysisATP levelsPTEN inhibitor SF1670Deletion of PTENMyc mutantsPI3K pathwayPI3K subunitsMyc proteinProtein geneUpdate on the human and mouse lipocalin (LCN) gene family, including evidence the mouse Mup cluster is result of an “evolutionary bloom”
Charkoftaki G, Wang Y, McAndrews M, Bruford EA, Thompson DC, Vasiliou V, Nebert DW. Update on the human and mouse lipocalin (LCN) gene family, including evidence the mouse Mup cluster is result of an “evolutionary bloom”. Human Genomics 2019, 13: 11. PMID: 30782214, PMCID: PMC6381713, DOI: 10.1186/s40246-019-0191-9.Peer-Reviewed Original ResearchConceptsMajor urinary protein genesKingdoms of lifeLipocalin gene familyGene familyMUP genesMouse genomeHuman genomeProtein geneChromosome 4Regulation of glucoseBarrel structurePhysiological processesΒ-strandsPhysiological functionsSecretory tissueGenesScent marksPseudogenesGenomeLipid metabolismBloomsEvidence pointsSyntenicImportant roleSteroid hormones
2018
Intrinsic cooperativity potentiates parallel cis-regulatory evolution
Sorrells T, Johnson A, Howard C, Britton C, Fowler K, Feigerle J, Weil P, Johnson A. Intrinsic cooperativity potentiates parallel cis-regulatory evolution. ELife 2018, 7: e37563. PMID: 30198843, PMCID: PMC6173580, DOI: 10.7554/elife.37563.Peer-Reviewed Original ResearchConceptsRegulatory sequencesGeneral transcription factor TFIIDCis-regulatory evolutionRibosomal protein genesTranscription factor TFIIDCommon interaction partnersFungal lineagesAncestral regulatorFactor TFIIDIndependent lineagesEvolutionary eventsGenomic scaleTranscription regulatorsTranscriptional activationParallel evolutionProtein geneRegulatory proteinsSecond regulatorInteraction partnersRandom mutationsFunctional sitesIntrinsic cooperativityMcm1Rap1Regulator
2016
Almendravirus: A Proposed New Genus of Rhabdoviruses Isolated from Mosquitoes in Tropical Regions of the Americas.
Contreras MA, Eastwood G, Guzman H, Popov V, Savit C, Uribe S, Kramer LD, Wood TG, Widen SG, Fish D, Tesh RB, Vasilakis N, Walker PJ. Almendravirus: A Proposed New Genus of Rhabdoviruses Isolated from Mosquitoes in Tropical Regions of the Americas. American Journal Of Tropical Medicine And Hygiene 2016, 96: 100-109. PMID: 27799634, PMCID: PMC5239673, DOI: 10.4269/ajtmh.16-0403.Peer-Reviewed Original ResearchConceptsL protein sequencesSimilar genome organizationStructural protein genesAnimal rhabdovirusesGenome organizationUnique cladePhylogenetic analysisEverglades National ParkArthropod populationsProtein geneProtein sequencesL geneVertebrate hostsNew genusSequence analysisDiverse familyHematophagous arthropodsRNA virusesAnopheles quadrimaculatus mosquitoesGenesNational ParkCladeArthropodsNovel virusRhabdovirusGenetic Relationship between Schizophrenia and Nicotine Dependence
Chen J, Bacanu SA, Yu H, Zhao Z, Jia P, Kendler KS, Kranzler HR, Gelernter J, Farrer L, Minica C, Pool R, Milaneschi Y, Boomsma DI, Penninx BW, Tyndale RF, Ware JJ, Vink JM, Kaprio J, Munafò M, Chen X. Genetic Relationship between Schizophrenia and Nicotine Dependence. Scientific Reports 2016, 6: 25671. PMID: 27164557, PMCID: PMC4862382, DOI: 10.1038/srep25671.Peer-Reviewed Original ResearchConceptsNeuroactive ligand-receptor interaction pathwayGenetic relationshipsEnergy production genesProtein modification genesLong non-coding RNAsNon-coding RNAsMultiple long non-coding RNAsProduction genesModification genesProtein geneInteraction pathwayGenesCalcium signalingP-value thresholdCritical roleRNANeuronal plasticityDifferent hypothesesFurther analysisLong-term potentiationSummary statisticsSignalingTraitsPathwayPlasticityThe poly(A)-binding protein genes, EPAB, PABPC1, and PABPC3 are differentially expressed in infertile men with non-obstructive azoospermia
Ozturk S, Sozen B, Uysal F, Bassorgun I, Usta M, Akkoyunlu G, Demir N. The poly(A)-binding protein genes, EPAB, PABPC1, and PABPC3 are differentially expressed in infertile men with non-obstructive azoospermia. Journal Of Assisted Reproduction And Genetics 2016, 33: 335-348. PMID: 26843391, PMCID: PMC4785164, DOI: 10.1007/s10815-016-0654-z.Peer-Reviewed Original ResearchConceptsPoly(A)-binding proteinNon-obstructive azoospermiaPoly(A)-binding protein geneSertoli cell-only syndromeTesticular biopsy samplesRound spermatidsPABP expressionExpression levelsIsolated spermatocytesTranslational controlProtein geneInfertile menPABPC1Male infertilitySpermatocytesPABPC3MRNA expressionArrest groupEPABSco groupBiopsy samplesMolecular backgroundProteinAzoospermiaEvaluate expression levels
2015
Atypical hemolytic uremic syndrome: Korean pediatric series
Lee J, Park Y, Lee J, Park S, Shin J, Park Y, Yoo K, Cho M, Kim S, Kim S, Namgoong M, Lee S, Lee J, Cho H, Han K, Kang H, Ha I, Bae J, Kim N, Park W, Cheong H. Atypical hemolytic uremic syndrome: Korean pediatric series. Pediatrics International 2015, 57: 431-438. PMID: 25443527, DOI: 10.1111/ped.12549.Peer-Reviewed Original ResearchConceptsAtypical hemolytic uremic syndromeAnti-CFHMultiplex ligation-dependent probe amplification assayTargeted exome sequencingGroup BGroup AGroup B + CHemolytic uremic syndromeHealthy Korean controlsProtein geneDetect deletionsKorean childrenExome sequencingHigher onset ageMann-Whitney U testGene frequenciesRelated genesCombined mutationsChi-square testRenal outcomesUremic syndromePediatric cohortGenesMulticenter cohortClinical characteristics
2013
Epidemiological mechanisms of genetic resistance to kuru
Atkins KE, Townsend JP, Medlock J, Galvani AP. Epidemiological mechanisms of genetic resistance to kuru. Journal Of The Royal Society Interface 2013, 10: 20130331. PMID: 23740487, PMCID: PMC4043168, DOI: 10.1098/rsif.2013.0331.Peer-Reviewed Original ResearchConceptsTransmissible spongiform encephalopathiesGenotype frequency dataPopulation geneticsProtein geneGenetic resistanceEpidemiological mechanismsPrion protein geneMechanistic basisPrion proteinHost resistanceFatal neurodegenerative conditionHuman populationHuman resistancePapua New GuineaNew GuineaSpongiform encephalopathiesIncubation periodCodon 129Neurodegenerative conditionsIncidence dataReduced susceptibilityLong incubation periodKuruGenesMechanismMicroRNA 33 Regulates Glucose Metabolism
Ramírez CM, Goedeke L, Rotllan N, Yoon JH, Cirera-Salinas D, Mattison JA, Suárez Y, de Cabo R, Gorospe M, Fernández-Hernando C. MicroRNA 33 Regulates Glucose Metabolism. Molecular And Cellular Biology 2013, 33: 2891-2902. PMID: 23716591, PMCID: PMC3719675, DOI: 10.1128/mcb.00016-13.Peer-Reviewed Original ResearchConceptsHost genesSterol regulatory element-binding protein (SREBP) genesSmall noncoding RNAsKey regulatory enzymeMiR-33bIntronic miRNAsHuman hepatic cellsMiR-33a/bPosttranscriptional regulationRegulatory genesExpression of PCK1Regulation of lipidNoncoding RNAsProtein geneG6pc expressionGene expressionBiological processesRegulatory enzymeMicroRNA-33GenesSpecific pathwaysMetabolic diseasesNovel therapeutic targetPhosphoenolpyruvate carboxykinaseRecent discoveryCompeting E3 Ubiquitin Ligases Govern Circadian Periodicity by Degradation of CRY in Nucleus and Cytoplasm
Yoo S, Mohawk J, Siepka S, Shan Y, Huh S, Hong H, Kornblum I, Kumar V, Koike N, Xu M, Nussbaum J, Liu X, Chen Z, Chen Z, Green C, Takahashi J. Competing E3 Ubiquitin Ligases Govern Circadian Periodicity by Degradation of CRY in Nucleus and Cytoplasm. Cell 2013, 152: 1091-1105. PMID: 23452855, PMCID: PMC3694781, DOI: 10.1016/j.cell.2013.01.055.Peer-Reviewed Original ResearchConceptsE3 ligase complexLigase complexSCF E3 ligase complexF-box protein genesCircadian periodE3 ligase activityMammalian circadian clockCry proteinsUbiquitin ligasesE3 ligasesCRY degradationLoss of functionCircadian mutantsLigase activityProtein geneCellular compartmentalizationCircadian clockFBXL21FBXL3Missense mutationsLigasesCytoplasmDual roleMutationsTurnover rate
2012
MicroRNAs regulating lipid metabolism in atherogenesis
Rayner K, Fernandez-Hernando C, Moore K. MicroRNAs regulating lipid metabolism in atherogenesis. Thrombosis And Haemostasis 2012, 107: 642-647. PMID: 22274626, PMCID: PMC3618663, DOI: 10.1160/th11-10-0694.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAtherosclerosisATP Binding Cassette Transporter 1ATP-Binding Cassette TransportersCholesterolDisease Models, AnimalFatty AcidsGene Expression RegulationHumansLipid MetabolismLipoproteins, HDLLipoproteins, VLDLLiverMiceMicroRNAsModels, BiologicalSterol Regulatory Element Binding Protein 1Sterol Regulatory Element Binding Protein 2TriglyceridesConceptsSmall non-coding RNAsImportant post-transcriptional regulatorsCellular sterol levelsPost-transcriptional regulatorsNon-coding RNAsVariety of genesSterol response elementFatty acid homeostasisIntronic microRNAsLipid metabolismFatty acid synthesisHost genesTranscription factorsProtein geneCholesterol exportMetabolic programsKey regulatorFatty acid oxidationResponse elementHigh-density lipoproteinMicroRNAsRelated metabolic diseasesGenesABCA1 pathwayAcid homeostasis
2011
Update of the human secretoglobin (SCGB) gene superfamily and an example of 'evolutionary bloom' of androgen-binding protein genes within the mouse Scgb gene superfamily
Jackson BC, Thompson DC, Wright MW, McAndrews M, Bernard A, Nebert DW, Vasiliou V. Update of the human secretoglobin (SCGB) gene superfamily and an example of 'evolutionary bloom' of androgen-binding protein genes within the mouse Scgb gene superfamily. Human Genomics 2011, 5: 691. PMID: 22155607, PMCID: PMC3251818, DOI: 10.1186/1479-7364-5-6-691.Peer-Reviewed Original ResearchConceptsGene familyLarge gene familyNovel drug targetsMammalian lineagesProtein geneMammalian secretionsDrug targetsGenesMate selectionProteinSecretoglobinTissue repairBloomsBiological activityFamilyAndrogen-binding proteinPseudogenesHuman healthImportant roleModulation of inflammationLineagesSalivary glandsRoleTumorigenesisBetter understandingCrystal Structure of the E2 Domain of Amyloid Precursor Protein-like Protein 1 in Complex with Sucrose Octasulfate*
Xue Y, Lee S, Wang Y, Ha Y. Crystal Structure of the E2 Domain of Amyloid Precursor Protein-like Protein 1 in Complex with Sucrose Octasulfate*. Journal Of Biological Chemistry 2011, 286: 29748-29757. PMID: 21715329, PMCID: PMC3191016, DOI: 10.1074/jbc.m111.219659.Peer-Reviewed Original ResearchConceptsAPP-like proteinsE2 domainHEK-293 cellsSucrose OctasulfateSignal transductionProtein geneBasic residuesSOS moleculesMutational analysisE2 dimerMost residuesProcessing of APPFamilial Alzheimer's diseaseExtracellular matrixAmyloid precursor protein geneProteolysis of APPMissense mutationsProtein 1Key heparinProteinResiduesSymmetry mateAPLP1Precursor protein geneCrystal structure
2010
Molecular characterization of two novel milk proteins in the tsetse fly (Glossina morsitans morsitans)
Yang G, Attardo GM, Lohs C, Aksoy S. Molecular characterization of two novel milk proteins in the tsetse fly (Glossina morsitans morsitans). Insect Molecular Biology 2010, 19: 253-262. PMID: 20136662, PMCID: PMC2862765, DOI: 10.1111/j.1365-2583.2009.00987.x.Peer-Reviewed Original ResearchConceptsViviparous reproductionKnockdown fliesRNA interferenceMilk protein genesTranscriptional regulation mechanismPotential phosphorylation sitesIntrauterine larval developmentRNA interference treatmentSpecific gene expressionTissue-specific expressionNovel milk proteinsSpecific expression profilesTsetse fliesHydrophobic amino acidsMajor milk proteinsNorthern blot analysisIntrauterine larvaeNovel genesPhosphorylation sitesProtein functionRT-PCR analysisTranscript abundanceProtein geneCDNA libraryGland proteins
2009
Chromatin Architecture and Transcription Factor Binding Regulate Expression of Erythrocyte Membrane Protein Genes
Steiner LA, Maksimova Y, Schulz V, Wong C, Raha D, Mahajan MC, Weissman SM, Gallagher PG. Chromatin Architecture and Transcription Factor Binding Regulate Expression of Erythrocyte Membrane Protein Genes. Molecular And Cellular Biology 2009, 29: 5399-5412. PMID: 19687298, PMCID: PMC2756878, DOI: 10.1128/mcb.00777-09.Peer-Reviewed Original ResearchMeSH KeywordsBasic Helix-Loop-Helix Transcription FactorsChromatinErythrocyte MembraneErythrocytesGATA1 Transcription FactorGene Expression RegulationHeLa CellsHistone DeacetylasesHumansMembrane ProteinsNF-E2 Transcription Factor, p45 SubunitNuclear ProteinsProto-Oncogene ProteinsRepressor ProteinsT-Cell Acute Lymphocytic Leukemia Protein 1Transcription FactorsConceptsErythrocyte membrane protein genesMembrane protein geneNF-E2 bindingGATA-1Protein geneChromatin architectureFOG-1Nonerythroid cellsBinding motifDynamic chromatin architectureHistone H3 trimethylationNF-E2Numerous candidate regionsTranscription factor bindingGATA-1 bindingTranscriptional start siteComplex genetic lociParallel DNA sequencingGenomic organizationLocus structureLysine 4H3 trimethylationGene regulationChromatin immunoprecipitationStart siteThe Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits
Schoch CL, Sung GH, López-Giráldez F, Townsend JP, Miadlikowska J, Hofstetter V, Robbertse B, Matheny PB, Kauff F, Wang Z, Gueidan C, Andrie RM, Trippe K, Ciufetti LM, Wynns A, Fraker E, Hodkinson BP, Bonito G, Groenewald JZ, Arzanlou, de Hoog GS, Crous PW, Hewitt D, Pfister DH, Peterson K, Gryzenhout M, Wingfield MJ, Aptroot A, Suh SO, Blackwell M, Hillis DM, Griffith GW, Castlebury LA, Rossman AY, Lumbsch HT, Lücking R, Büdel B, Rauhut A, Diederich P, Ertz D, Geiser DM, Hosaka K, Inderbitzin P, Kohlmeyer J, Volkmann-Kohlmeyer B, Mostert L, O'Donnell K, Sipman H, Rogers JD, Shoemaker RA, Sugiyama J, Summerbell RC, Untereiner W, Johnston PR, Stenroos S, Zuccaro A, Dyer PS, Crittenden PD, Cole MS, Hansen K, Trappe JM, Yahr R, Lutzoni F, Spatafora JW. The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits. Systematic Biology 2009, 58: 224-239. PMID: 20525580, DOI: 10.1093/sysbio/syp020.Peer-Reviewed Original ResearchConceptsCharacter state reconstructionCommon ancestorAncestral character state reconstructionPhylogenetic informativeness analysesSexual reproductive structuresAscus dehiscenceMaximum likelihood phylogenyPhylogenetic informativenessEcological traitsFungal systematicsAncestral reconstructionNutritional modesRibosomal genesLargest phylumMorphological traitsRelated speciesReproductive structuresProtein geneAscomycota TreePezizomycotinaMultiple originsState reconstructionSporocarpsGene assessmentGenes
2008
Insulator Elements in Erythrocyte Membrane Genes
Steiner L, Maksimova Y, Lin J, Owen A, Schulz V, Bodine D, Gallagher P. Insulator Elements in Erythrocyte Membrane Genes. Blood 2008, 112: 3584. DOI: 10.1182/blood.v112.11.3584.3584.Peer-Reviewed Original ResearchErythrocyte membrane protein genesPosition-effect variegationMembrane protein geneProtein geneChromatin domainsAnkyrin promoterDNA sequencesErythroid cellsInsulator elementsMapping protein-DNA interactionsHeterochromatin-mediated geneGenome-wide scaleGenomic DNA microarrayBinding of CTCFStage-specific transcriptsEnhancer-blocking functionProtein-DNA interactionsCopy number-dependent expressionTissue-specific expressionProtein gene expressionCTCF occupancyRepetitive DNAInsulator functionSeparate enhancersErythroid promoterChromatin Architecture and Transcription Factor Occupancy of Erythrocyte Membrane Genes Studied by Chromatin Immunoprecipitation on Microarrays (ChIP-chip)
Steiner L, Maksimova Y, Wong C, Schulz V, Gallagher P. Chromatin Architecture and Transcription Factor Occupancy of Erythrocyte Membrane Genes Studied by Chromatin Immunoprecipitation on Microarrays (ChIP-chip). Blood 2008, 112: 2436. DOI: 10.1182/blood.v112.11.2436.2436.Peer-Reviewed Original ResearchErythrocyte membrane protein genesNF-E2 siteMembrane protein geneGATA-1 sitesTranscriptional start siteChromatin architectureTranscription factor bindingPrimary erythroid cellsGATA-1Protein geneChromatin immunoprecipitationTranscription factorsErythroid cellsH3K4me3 enrichmentFlanking DNAFactor bindingDNA sequencesK562 cellsErythroid transcription factor GATA-1Mapping protein-DNA interactionsNon-erythroid cell linesTranscription factor GATA-1Quantitative ChIP analysisTranscription factor occupancyGenome-wide scale
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