2018
Marker chromosome genomic structure and temporal origin implicate a chromoanasynthesis event in a family with pleiotropic psychiatric phenotypes
Grochowski CM, Gu S, Yuan B, Julia T, Brennand KJ, Sebat J, Malhotra D, McCarthy S, Rudolph U, Lindstrand A, Chong Z, Levy DL, Lupski JR, Carvalho CMB. Marker chromosome genomic structure and temporal origin implicate a chromoanasynthesis event in a family with pleiotropic psychiatric phenotypes. Human Mutation 2018, 39: 939-946. PMID: 29696747, PMCID: PMC5995661, DOI: 10.1002/humu.23537.Peer-Reviewed Original ResearchConceptsWhole-genome sequencingSmall supernumerary marker chromosomeChromosomal fragmentsMarker chromosomesGenomic structureComparative genomic hybridization analysisSupernumerary marker chromosomeGenomic hybridization analysisTemporal originHybridization analysisArray comparative genomic hybridization analysisChromosome 9Short armRepair mechanismsMarker genotypesChromosomesPrecise architectureProband's maternal grandmotherStructural variationsPsychiatric phenotypesFurther complexityFragmentsDuplicationSequencingPhenotype
2017
Catching RNAs on chromatin using hybridization capture methods
Machyna M, Simon MD. Catching RNAs on chromatin using hybridization capture methods. Briefings In Functional Genomics 2017, 17: 96-103. PMID: 29126220, PMCID: PMC5888980, DOI: 10.1093/bfgp/elx038.Peer-Reviewed Original ResearchConceptsRNA affinity purificationHybridization capture methodsCross-linked chromatin extractsGenome-wide scaleEnrichment of RNAInteraction of lncRNAsLncRNA localizationChromatin isolationChromatin extractsSite of interactionCapture methodAffinity purificationBiological roleRNA targetsHybridization analysisRNARNA purificationChromatinLncRNAsOligonucleotide hybridizationPurificationDevelopment of methodsProteinCapture experimentsHybridization
2016
Spectrum of Cytogenomic Abnormalities Revealed by Array Comparative Genomic Hybridization on Products of Conception Culture Failure and Normal Karyotype Samples
Zhou Q, Wu SY, Amato K, DiAdamo A, Li P. Spectrum of Cytogenomic Abnormalities Revealed by Array Comparative Genomic Hybridization on Products of Conception Culture Failure and Normal Karyotype Samples. Journal Of Genetics And Genomics 2016, 43: 121-131. PMID: 27020032, DOI: 10.1016/j.jgg.2016.02.002.Peer-Reviewed Original ResearchConceptsCopy number variantsIngenuity Pathway AnalysisPathogenic copy number variantsDosage-sensitive genesCell proliferation pathwaysGenomic copy number variantsArray comparative genomic hybridizationGene networksComparative genomic hybridization analysisComparative genomic hybridizationPathway analysisGenomic hybridization analysisChromosomal abnormalitiesHybridization analysisProliferation pathwaysArray comparative genomic hybridization analysisNumber variantsGenomic hybridizationSitu hybridizationGenesHybridizationCytogenomic abnormalitiesCulture successPolyploidySensitive mechanism
2015
Copy number changes and methylation patterns in an isodicentric and a ring chromosome of 15q11-q13: report of two cases and review of literature
Wang Q, Wu W, Xu Z, Luo F, Zhou Q, Li P, Xie J. Copy number changes and methylation patterns in an isodicentric and a ring chromosome of 15q11-q13: report of two cases and review of literature. Molecular Cytogenetics 2015, 8: 97. PMID: 26697114, PMCID: PMC4687147, DOI: 10.1186/s13039-015-0198-4.Peer-Reviewed Original ResearchMethylation patternsCopy number changesLow-copy repeatsNumber changesChromosome 15Further gene expressionRing chromosomesSmall ring chromosomeGenomic structureEpigenetic patternsComparative genomic hybridization analysisPhenotypic consequencesGene expressionMb regionGenomic hybridization analysisChromosomesIntrachromosomal deletionsHybridization analysisMb segmentArray comparative genomic hybridization analysisMethylation-specific multiplex ligation-dependent probe amplificationCopy repeatsMS-MLPA analysisSitu hybridizationPhenotype correlationMG-112 Ten new cases further delineate the syndromic intellectual disability phenotype caused by mutations in DYRK1A
Bronicki L, Redin C, Drunat S, Piton A, Lyons M, Passemard S, Baumann C, Faivre L, Thevenon J, Rivière J, Isidor B, Gan G, Francannet C, Gunel M, Jones J, Gleeson J, Willems M, Mandel J, Stevenson R, Friez M, Aylsworth A. MG-112 Ten new cases further delineate the syndromic intellectual disability phenotype caused by mutations in DYRK1A. Journal Of Medical Genetics 2015, 52: a2. DOI: 10.1136/jmedgenet-2015-103577.6.Peer-Reviewed Original ResearchDual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) geneDNA sequence variationExome next-generation sequencingLarge chromosomal deletionsDown syndrome critical regionIntellectual disability phenotypeIdentification of mutationsWhole-exome next-generation sequencingIntellectual disabilitySyndrome critical regionComparative genomic hybridization analysisNext-generation sequencingSyndromic intellectual disabilityChromosomal rearrangementsMultiple genesSequence variationGenomic hybridization analysisRecurrent clinical featuresTypes of mutationsDYRK1AHybridization analysisArray comparative genomic hybridization analysisChromosomal deletionsPoor weight gainDisability phenotype
2012
A molecular characterization of the choroid plexus and stress-induced gene regulation
Sathyanesan M, Girgenti MJ, Banasr M, Stone K, Bruce C, Guilchicek E, Wilczak-Havill K, Nairn A, Williams K, Sass S, Duman JG, Newton SS. A molecular characterization of the choroid plexus and stress-induced gene regulation. Translational Psychiatry 2012, 2: e139-e139. PMID: 22781172, PMCID: PMC3410626, DOI: 10.1038/tp.2012.64.Peer-Reviewed Original ResearchConceptsStress-induced gene regulationGene expression changesGene expression analysisCP gene expressionGlial fibrillary acidic proteinChoroid plexusMolecular functionsGene regulationSitu hybridization analysisTranscriptomic characterizationHigh-resolution tandem mass spectrometryTarget genesExpression analysisGene expressionExpression changesTarget proteinsCP proteinsMolecular characterizationAdult choroid plexusHybridization analysisCP functionGene profilesProteinBlood-cerebrospinal fluid barrierResolution tandem mass spectrometry
2011
A balanced t(10;15) translocation in a male patient with developmental language disorder
Ercan-Sencicek AG, Wright N, Sanders SJ, Oakman N, Valdes L, Bakkaloglu B, Doyle N, Yrigollen CM, Morgan TM, Grigorenko EL. A balanced t(10;15) translocation in a male patient with developmental language disorder. European Journal Of Medical Genetics 2011, 55: 128-131. PMID: 22266071, PMCID: PMC3322462, DOI: 10.1016/j.ejmg.2011.12.005.Peer-Reviewed Case Reports and Technical NotesConceptsLanguage disordersDevelopmental language disorderMale patientsMale childrenCytogenetic findingsPhysical abnormalitiesDisordersChildren's parentsSitu hybridization analysisSample of individualsFurther evidenceDe novoClone mappingPatientsHybridization analysisTranslocationENTPD1AbnormalitiesBreakpointsThe genomic binding sites of a noncoding RNA
Simon MD, Wang CI, Kharchenko PV, West JA, Chapman BA, Alekseyenko AA, Borowsky ML, Kuroda MI, Kingston RE. The genomic binding sites of a noncoding RNA. Proceedings Of The National Academy Of Sciences Of The United States Of America 2011, 108: 20497-20502. PMID: 22143764, PMCID: PMC3251105, DOI: 10.1073/pnas.1113536108.Peer-Reviewed Original ResearchConceptsDosage compensationCross-linked chromatin extractsMale-specific lethal (MSL) complexLevel of chromatinSpecific genomic sitesImportant regulatory roleHybridization-based techniquesLethal complexLncRNAs bindWide mappingSites of proteinsGenomic sitesChromatin extractsGenomic targetsEndogenous RNAEndogenous lncRNARNA targetsProtein targetsRegulatory roleHybridization analysisRoX2RNAChromatinProteinBinds
2007
A novel syndrome of cerebral cavernous malformation and Greig cephalopolysyndactyly. Laboratory investigation.
Bilguvar K, Bydon M, Bayrakli F, Ercan-Sencicek AG, Bayri Y, Mason C, DiLuna ML, Seashore M, Bronen R, Lifton RP, State M, Gunel M. A novel syndrome of cerebral cavernous malformation and Greig cephalopolysyndactyly. Laboratory investigation. Journal Of Neurosurgery 2007, 107: 495-9. PMID: 18154020, DOI: 10.3171/ped-07/12/495.Peer-Reviewed Original ResearchMeSH KeywordsAbnormalities, MultipleCarrier ProteinsChild, PreschoolChromosome DeletionChromosomes, Human, Pair 7Craniofacial AbnormalitiesDNAFemaleGene DosageHemangioma, Cavernous, Central Nervous SystemHeterozygoteHumansKruppel-Like Transcription FactorsNerve Tissue ProteinsOligonucleotide Array Sequence AnalysisReverse Transcriptase Polymerase Chain ReactionSyndromeZinc Finger Protein Gli3ConceptsGreig cephalopolysyndactyly syndromeCerebral cavernous malformationsDeleterious genetic variantsComparative genome hybridization analysisChromosome 7pArray-based CGHGene GLI3Distinct genesMultiple genesGenetic analysisGenomic DNANovel syndromeGenomic lesionsChromosome 7Contiguous gene syndromeQuantitative real-time polymerase chain reactionQuantitative RT-PCRGli3Hybridization analysis
1998
A substrate of the centisome 63 type III protein secretion system of Salmonella typhimurium is encoded by a cryptic bacteriophage
Hardt W, Urlaub H, Galán J. A substrate of the centisome 63 type III protein secretion system of Salmonella typhimurium is encoded by a cryptic bacteriophage. Proceedings Of The National Academy Of Sciences Of The United States Of America 1998, 95: 2574-2579. PMID: 9482928, PMCID: PMC19418, DOI: 10.1073/pnas.95.5.2574.Peer-Reviewed Original ResearchConceptsType III protein secretion systemType III secretion systemProtein secretion systemSecretion systemEffector proteinsInvasion-associated type III secretion systemCluster of genesTail fiber proteinHost cell cytoplasmSouthern hybridization analysisMobile genetic elementsCultured epithelial cellsInduction of apoptosisSopE proteinEnterica serovar TyphimuriumBacteriophage genesBacterial entryCytoskeletal rearrangementsS. enterica serovar TyphimuriumGenetic elementsPathogenicity islandFiber proteinHybridization analysisCell cytoplasmEffector molecules
1997
Developmental expression of the murine spliceosome‐associated protein mSAP49
Ruiz‐Lozano P, Doevendans P, Brown A, Gruber P, Chien K. Developmental expression of the murine spliceosome‐associated protein mSAP49. Developmental Dynamics 1997, 208: 482-490. PMID: 9097020, DOI: 10.1002/(sici)1097-0177(199704)208:4<482::aid-aja4>3.0.co;2-e.Peer-Reviewed Original ResearchConceptsRNA recognition motifTissue-specific splicingBasic C-terminusAmino acid sequencePeak of expressionHuman spliceosomeSpliceosome componentsSitu hybridization analysisMouse homologueRecognition motifRNA stabilizationAcid sequenceCardiac developmentC-terminusMouse embryosN-terminusNorthern analysisEmbryonic tissuesDevelopmental expressionHybridization analysisDay 11.5Optic vesicleMRNA distributionDay 13.5Spliceosome
1995
An orphan nuclear receptor, mROR α, and its spatial expression in adult mouse brain
Matsui T, Sashihara S, Oh Y, Waxman S. An orphan nuclear receptor, mROR α, and its spatial expression in adult mouse brain. Brain Research 1995, 33: 217-226. PMID: 8750880, DOI: 10.1016/0169-328x(95)00126-d.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBase SequenceBinding SitesBlotting, NorthernBrainCell DifferentiationCell LineGene ExpressionHumansIn Situ HybridizationMiceMolecular Sequence DataNeuronsNuclear Receptor Subfamily 1, Group F, Member 1Olfactory BulbOrgan SpecificityReceptors, Cytoplasmic and NuclearReceptors, Retinoic AcidSequence Homology, Amino AcidThalamusTrans-ActivatorsTransfectionTumor Cells, CulturedConceptsResponsive elementActivation of transcriptionThyroid hormone responsive elementRetinoic acid responsive elementNeural cell lineagesAcid-responsive elementLaminin B1 geneOrphan nuclear receptorHormone-responsive elementsRAR beta geneSitu hybridization analysisRetinoic acid receptor-related orphan receptorTranscription factorsAdult mouse brainCotransfection experimentsP19 cellsCell lineagesReceptor-related orphan receptorNorthern hybridizationAcid receptor-related orphan receptorHybridization analysisSpatial expressionOrphan receptorBeta geneNuclear receptors
1993
Cloning and molecular characterization of a gene involved in Salmonella adherence and invasion of cultured epithelial cells
Altmeyer R, McNern J, Bossio JC, Rosenshine I, Finlay B, Galán J. Cloning and molecular characterization of a gene involved in Salmonella adherence and invasion of cultured epithelial cells. Molecular Microbiology 1993, 7: 89-98. PMID: 8382333, DOI: 10.1111/j.1365-2958.1993.tb01100.x.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBacterial AdhesionBacterial ProteinsBase SequenceCells, CulturedDNA Transposable ElementsEpithelial CellsEpitheliumGenes, BacterialMolecular Sequence DataMutagenesisPhenotypeRecombinant Fusion ProteinsSalmonellaSalmonella typhimuriumSequence Homology, Nucleic AcidVirulenceConceptsCultured epithelial cellsInvH geneT7 RNA polymerase expression systemBacterial membrane fractionsEpithelial cellsSignal sequenceExtensive homologyColony hybridization analysisNucleotide sequenceGene productsHomologous sequencesExpression systemException of strainsMolecular characterizationGenesHybridization analysisMembrane fractionCultured cellsEscherichia coliPolypeptideInsertion sequence IS3E. coliOrganismsInvHSequence
1989
Expression of Na,K‐ATPase alpha subunit isoforms in the human ciliary body and cultured ciliary epithelial cells
Martin‐Vasallo P, Ghosh S, Coca‐Prados M. Expression of Na,K‐ATPase alpha subunit isoforms in the human ciliary body and cultured ciliary epithelial cells. Journal Of Cellular Physiology 1989, 141: 243-252. PMID: 2553750, DOI: 10.1002/jcp.1041410203.Peer-Reviewed Original ResearchConceptsK-ATPase alpha subunit isoformsAlpha-subunit isoformsSubunit isoformsCultured cellsK-ATPase alpha subunitPE cellsExpression of NaBasolateral membrane domainsNorthern hybridization analysisNPE cell linesAlpha 2 mRNACell linesAlpha 3 isoformMembrane domainsAlpha 3 mRNAAlpha 1Alpha subunitCultured ciliary epithelial cellsWestern blot analysisHybridization analysisIsoformsCiliary epithelial cellsNPE layerBlot analysisK-ATPase
1987
Cultured human endothelial cells express platelet-derived growth factor A chain.
Collins T, Pober JS, Gimbrone MA, Hammacher A, Betsholtz C, Westermark B, Heldin CH. Cultured human endothelial cells express platelet-derived growth factor A chain. American Journal Of Pathology 1987, 126: 7-12. PMID: 2433948, PMCID: PMC1899550.Peer-Reviewed Original ResearchConceptsRNA speciesSame relative abundanceHuman endothelial cellsRelative abundanceB polypeptide chainsEndothelial cellsChain transcriptsC-sis geneB-chain transcriptsPlatelet-derived growth factorExtensive structural dataTranscript speciesCultured human umbilical vein endothelial cellsB-chain expressionBovine aortic endothelial cellsHuman umbilical vein endothelial cellsDimeric proteinUmbilical vein endothelial cellsCultured vascular endothelial cellsDifferent genesPrincipal cell typesHybridization analysisPolypeptide chainVein endothelial cellsCell types
1983
Tandem Arrangement of Tubulin Genes in the Protozoan Parasite Leishmania enriettii
Landfear S, McMahon-Pratt D, Wirth D. Tandem Arrangement of Tubulin Genes in the Protozoan Parasite Leishmania enriettii. Molecular And Cellular Biology 1983, 3: 1070-1076. DOI: 10.1128/mcb.3.6.1070-1076.1983.Peer-Reviewed Original ResearchTandem arrangement of tubulin genes in the protozoan parasite Leishmania enriettii.
Landfear S, McMahon-Pratt D, Wirth D. Tandem arrangement of tubulin genes in the protozoan parasite Leishmania enriettii. Molecular And Cellular Biology 1983, 3: 1070-1076. PMID: 6877238, PMCID: PMC368636, DOI: 10.1128/mcb.3.6.1070.Peer-Reviewed Original Research
1981
The initiator tRNA genes of Drosophila melanogaster: evidence for a tRNA pseudogene
Sharp S, DeFranco D, Silberklang M, Hosbach H, Schmidt T, Kubli E, Gergen J, Wensink P, Söll D. The initiator tRNA genes of Drosophila melanogaster: evidence for a tRNA pseudogene. Nucleic Acids Research 1981, 9: 5867-5882. PMID: 6273811, PMCID: PMC327570, DOI: 10.1093/nar/9.22.5867.Peer-Reviewed Original ResearchConceptsInitiator tRNA geneTRNA genesDrosophila genomeDrosophila melanogasterTRNA gene familyRNA polymerase IIIDrosophila melanogaster DNAKb DNA fragmentTRNA pseudogenesRepetitive DNAGene familyPolymerase IIISingle copyGenomic DNADNA fragmentsPseudogenesRepeat segmentsGenesHybridization analysisFourth cloneMelanogasterSitu hybridizationGenomeDNAFragments
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