2023
Salvage of ribose from uridine or RNA supports glycolysis in nutrient-limited conditions
Skinner O, Blanco-Fernández J, Goodman R, Kawakami A, Shen H, Kemény L, Joesch-Cohen L, Rees M, Roth J, Fisher D, Mootha V, Jourdain A. Salvage of ribose from uridine or RNA supports glycolysis in nutrient-limited conditions. Nature Metabolism 2023, 5: 765-776. PMID: 37198474, PMCID: PMC10229423, DOI: 10.1038/s42255-023-00774-2.Peer-Reviewed Original ResearchConceptsUpper glycolysisGenome-wide genetic screenNutrient-limited conditionsNon-oxidative branchGenetic screenCancer lineagesContext of diseaseRegulated stepGrowth of cellsATP productionGlyceraldehyde 3Cancer cell linesGlucose transportPrimary macrophagesGlycolysisCell linesComplete lossPyrimidine synthesisPathwayRNACarbon building blocksAlternative nutrientsRibose moietyUridineComplete absence
2018
IRF2BPL Is Associated with Neurological Phenotypes
Marcogliese P, Shashi V, Spillmann R, Stong N, Rosenfeld J, Koenig M, Martínez-Agosto J, Herzog M, Chen A, Dickson P, Lin H, Vera M, Salamon N, Graham J, Ortiz D, Infante E, Steyaert W, Dermaut B, Poppe B, Chung H, Zuo Z, Lee P, Kanca O, Xia F, Yang Y, Smith E, Jasien J, Kansagra S, Spiridigliozzi G, El-Dairi M, Lark R, Riley K, Koeberl D, Golden-Grant K, Diseases P, Callens S, Coucke P, Dermaut B, Hemelsoet D, Poppe B, Steyaert W, Terryn W, Van Coster R, Network U, Adams D, Alejandro M, Allard P, Azamian M, Bacino C, Balasubramanyam A, Barseghyan H, Batzli G, Beggs A, Behnam B, Bican A, Bick D, Birch C, Bonner D, Boone B, Bostwick B, Briere L, Brown D, Brush M, Burke E, Burrage L, Chen S, Clark G, Coakley T, Cogan J, Cooper C, Cope H, Craigen W, D’Souza P, Davids M, Dayal J, Dell’Angelica E, Dhar S, Dillon A, Dipple K, Donnell-Fink L, Dorrani N, Dorset D, Douine E, Draper D, Eckstein D, Emrick L, Eng C, Eskin A, Esteves C, Estwick T, Ferreira C, Fogel B, Friedman N, Gahl W, Glanton E, Godfrey R, Goldstein D, Gould S, Gourdine J, Groden C, Gropman A, Haendel M, Hamid R, Hanchard N, Handley L, Herzog M, Holm I, Hom J, Howerton E, Huang Y, Jacob H, Jain M, Jiang Y, Johnston J, Jones A, Kohane I, Krasnewich D, Krieg E, Krier J, Lalani S, Lau C, Lazar J, Lee B, Lee H, Levy S, Lewis R, Lincoln S, Lipson A, Loo S, Loscalzo J, Maas R, Macnamara E, MacRae C, Maduro V, Majcherska M, Malicdan M, Mamounas L, Manolio T, Markello T, Marom R, Martínez-Agosto J, Marwaha S, May T, McConkie-Rosell A, McCormack C, McCray A, Might M, Moretti P, Morimoto M, Mulvihill J, Murphy J, Muzny D, Nehrebecky M, Nelson S, Newberry J, Newman J, Nicholas S, Novacic D, Orange J, Pallais J, Palmer C, Papp J, Parker N, Pena L, Phillips J, Posey J, Postlethwait J, Potocki L, Pusey B, Reuter C, Robertson A, Rodan L, Rosenfeld J, Sampson J, Samson S, Schoch K, Schroeder M, Scott D, Sharma P, Shashi V, Signer R, Silverman E, Sinsheimer J, Smith K, Spillmann R, Splinter K, Stoler J, Stong N, Sullivan J, Sweetser D, Tifft C, Toro C, Tran A, Urv T, Valivullah Z, Vilain E, Vogel T, Wahl C, Walley N, Walsh C, Ward P, Waters K, Westerfield M, Wise A, Wolfe L, Worthey E, Yamamoto S, Yang Y, Yu G, Zastrow D, Zheng A, Yamamoto S, Wangler M, Mirzaa G, Hemelsoet D, Lee B, Nelson S, Goldstein D, Bellen H, Pena L. IRF2BPL Is Associated with Neurological Phenotypes. American Journal Of Human Genetics 2018, 103: 245-260. PMID: 30057031, PMCID: PMC6081494, DOI: 10.1016/j.ajhg.2018.07.006.Peer-Reviewed Original ResearchMissense variantsRange of phenotypesNeurological phenotypeProper neuronal functionNonsense variantPopulation genomicsModel organismsTranscriptional regulatorsFunction allelesPartial knockdownEctopic expressionRNA interferenceNonsense allelesBiological functionsMendelian diseasesDamaging heterozygous variantsGenesIRF2BPLNeuronal functionPhenotypeAdditional individualsComplete lossNervous systemMild phenotypeAlleles
2013
Recessive loss of function of the neuronal ubiquitin hydrolase UCHL1 leads to early-onset progressive neurodegeneration
Bilguvar K, Tyagi NK, Ozkara C, Tuysuz B, Bakircioglu M, Choi M, Delil S, Caglayan AO, Baranoski JF, Erturk O, Yalcinkaya C, Karacorlu M, Dincer A, Johnson MH, Mane S, Chandra SS, Louvi A, Boggon TJ, Lifton RP, Horwich AL, Gunel M. Recessive loss of function of the neuronal ubiquitin hydrolase UCHL1 leads to early-onset progressive neurodegeneration. Proceedings Of The National Academy Of Sciences Of The United States Of America 2013, 110: 3489-3494. PMID: 23359680, PMCID: PMC3587195, DOI: 10.1073/pnas.1222732110.Peer-Reviewed Original ResearchMeSH KeywordsAdultAge of OnsetAmino Acid SequenceBase SequenceChild, PreschoolExomeFemaleGenes, RecessiveHomozygoteHumansHydrolysisMaleModels, MolecularMolecular Sequence DataMutation, MissenseNerve DegenerationNeuronsPedigreeProtein BindingSequence Analysis, DNASubstrate SpecificitySyndromeThermodynamicsUbiquitinUbiquitin ThiolesteraseConceptsUbiquitin C-terminal hydrolase L1Upper motor neuron dysfunctionMotor neuron dysfunctionProgressive neurodegenerative syndromeEarly-onset progressive neurodegenerationChildhood-onset blindnessWhole-exome sequencingNeuron dysfunctionHomozygous missense mutationIndex caseNervous systemProgressive neurodegenerationNeurodegenerative syndromeCerebellar ataxiaHydrolase activityNear complete lossComplete lossAffected individualsConsanguineous unionsMissense mutationsRecessive lossHomozygosity mappingProper positioningReduced affinitySpasticity
2011
Mass spectrometric identification of an intramolecular disulfide bond in thermally inactivated triosephosphate isomerase from a thermophilic organism Methanocaldococcus jannaschii
Banerjee M, Gupta K, Balaram H, Balaram P. Mass spectrometric identification of an intramolecular disulfide bond in thermally inactivated triosephosphate isomerase from a thermophilic organism Methanocaldococcus jannaschii. Rapid Communications In Mass Spectrometry 2011, 25: 1915-1923. PMID: 21698673, DOI: 10.1002/rcm.5058.Peer-Reviewed Original ResearchConceptsMethanocaldococcus jannaschiiTriosephosphate isomeraseDisulfide bond formationIntramolecular disulfide bondsCysteine thiol groupsMonomer molecular massThree-dimensional structureThermophilic enzymesMass spectrometric identificationMS/MS analysisTetrameric enzymeTertiary structureMolecular massDisulfide bridgesDisulfide-bonded moleculesDisulfide bondsMonomeric massJannaschiiCircular dichroismComplete lossSpectrometric identificationIsomeraseEnzymeTryptic digestDa difference
2008
Disruption of the Plasmodium falciparum PfPMT Gene Results in a Complete Loss of Phosphatidylcholine Biosynthesis via the Serine-Decarboxylase-Phosphoethanolamine-Methyltransferase Pathway and Severe Growth and Survival Defects*
Witola WH, El Bissati K, Pessi G, Xie C, Roepe PD, Mamoun CB. Disruption of the Plasmodium falciparum PfPMT Gene Results in a Complete Loss of Phosphatidylcholine Biosynthesis via the Serine-Decarboxylase-Phosphoethanolamine-Methyltransferase Pathway and Severe Growth and Survival Defects*. Journal Of Biological Chemistry 2008, 283: 27636-27643. PMID: 18694927, PMCID: PMC2562060, DOI: 10.1074/jbc.m804360200.Peer-Reviewed Original ResearchConceptsSDPM pathwayBiosynthesis of phosphatidylcholinePhosphatidylcholine biosynthesisParasite growthMajor membrane phospholipidsHuman malaria parasiteHost serineSerine decarboxylaseGenetic evidenceMethyltransferase enzymeSurvival defectGene resultsYeast cellsMethylation of phosphatidylethanolamineBiosynthesisSynthesis of phosphatidylcholineBiochemical studiesMembrane phospholipidsMalaria parasitesPlasmodium parasitesSevere growthPathwaySignificant defectsParasitesComplete lossA novel missense mutation in SLC34A3 that causes hereditary hypophosphatemic rickets with hypercalciuria in humans identifies threonine 137 as an important determinant of sodium-phosphate cotransport in NaPi-IIc
Jaureguiberry G, Carpenter TO, Forman S, Jüppner H, Bergwitz C. A novel missense mutation in SLC34A3 that causes hereditary hypophosphatemic rickets with hypercalciuria in humans identifies threonine 137 as an important determinant of sodium-phosphate cotransport in NaPi-IIc. American Journal Of Physiology. Renal Physiology 2008, 295: f371-f379. PMID: 18480181, PMCID: PMC2519180, DOI: 10.1152/ajprenal.00090.2008.Peer-Reviewed Original ResearchMeSH KeywordsAdultAllelesAnimalsBase SequenceExocytosisFamilial Hypophosphatemic RicketsFemaleHaplotypesHumansHypercalciuriaKidneyMaleMolecular Sequence DataMutation, MissenseOocytesOpossumsPhosphatesPolymorphism, Single NucleotideSodiumSodium-Phosphate Cotransporter ProteinsSodium-Phosphate Cotransporter Proteins, Type IIcThreonineXenopus laevisConceptsEncoding enhanced green fluorescent proteinHereditary hypophosphatemic ricketsNaPi-IIcSodium-phosphate cotransporterLoss of expressionAmino acid residuesSodium-phosphate cotransportGreen fluorescence proteinImportant functional roleComplete lossOpossum kidneyHypophosphatemic ricketsXenopus laevis oocytesNovel missense mutationPaternal alleleWild-typeFunctional analysisFluorescence proteinNH2 terminusAcid residuesApical patchesCompound heterozygous mutationsExpression plasmidFunctional roleRecurrent kidney stones
2006
Identification and functional analysis of Human FMO3 Genetic Variants
Hines R, Koukouritaki S, Poch M, Henderson M, Siddens L, Krueger S, VanDyke J, Romero A, Williams D. Identification and functional analysis of Human FMO3 Genetic Variants. The FASEB Journal 2006, 20: a264-a264. DOI: 10.1096/fasebj.20.4.a264-a.Peer-Reviewed Original ResearchPromoter activityFunctional analysisTransient expression analysisHaplotype AComplete lossHigher promoter activityNear complete lossTranscript splicingExpression analysisSynonymous SNPsReporter constructsIntron SNPSNP frequenciesStructural variantsObserved haplotypesMultiple substratesHaplotype DGenetic variantsExpression levelsSNPsEnzyme activityDNA samplesHaplotypesPromoter variantsVivo impact
2005
Integrinα5 and Delta/Notch Signaling Have Complementary Spatiotemporal Requirements during Zebrafish Somitogenesis
Ju¨lich D, Geisler R, Consortium T, Holley S. Integrinα5 and Delta/Notch Signaling Have Complementary Spatiotemporal Requirements during Zebrafish Somitogenesis. Developmental Cell 2005, 8: 575-586. PMID: 15809039, DOI: 10.1016/j.devcel.2005.01.016.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsAnimals, Genetically ModifiedBody PatterningCell PolarityExtracellular MatrixFibronectinsGene Expression Regulation, DevelopmentalIn Situ HybridizationIntegrin alpha5Intracellular Signaling Peptides and ProteinsMembrane ProteinsMolecular Sequence DataMorphogenesisPhenotypePoint MutationReceptors, NotchRecombinant Fusion ProteinsSignal TransductionSomitesZebrafishZebrafish ProteinsConceptsFibronectin matrix assemblyDelta/Notch signalingMatrix assemblyNotch pathway mutantsEntire body axisZebrafish somitogenesisVertebrate embryogenesisPathway mutantsDouble mutantSomite defectsSomite formationPosterior somitesGenetic controlSomitogenesisNotch signalingNotch pathwayEpithelial transitionSpatiotemporal requirementsBody axisCell polarizationSegmentation defectsPoint mutationsMutantsComplete lossSkeletal muscle6 The Conduction Properties of Demyelinated and Remyelinated Axons
Smith K, Waxman S. 6 The Conduction Properties of Demyelinated and Remyelinated Axons. 2005, 85-100. DOI: 10.1016/b978-012738761-1/50007-9.Peer-Reviewed Original ResearchRestoration of conductionConduction blockDemyelination-induced conduction blockExperimental demyelinating lesionsDemyelinating lesionsSegmental demyelinationMyelin thinningDemyelinated axonsElectrophysiological featuresConduction failureAxonal functionElectrophysiological propertiesDemyelinationAxonsMyelinLesionsIon channel populationsDemyelinated membraneChannel populationsAdaptive responseComplete loss
2003
Role of the DPC4 Tumor Suppressor Gene in Adenocarcinoma of the Ampulla of Vater: Analysis of 140 Cases
McCarthy D, Hruban R, Argani P, Howe J, Conlon K, Brennan M, Zahurak M, Wilentz R, Cameron J, Yeo C, Kern S, Klimstra D. Role of the DPC4 Tumor Suppressor Gene in Adenocarcinoma of the Ampulla of Vater: Analysis of 140 Cases. Modern Pathology 2003, 16: 272-278. PMID: 12640108, DOI: 10.1097/01.mp.0000057246.03448.26.Peer-Reviewed Original ResearchConceptsLoss of Dpc4 expressionDpc4 expressionK-ras gene mutationAmpulla of VaterK-ras oncogeneK-rasPancreatic adenocarcinomaAreas of high-grade dysplasiaGene mutationsDPC4 tumor suppressor genesAssociated with shorter survivalDPC4 gene productLoss of DPC4Resected ampullary adenocarcinomaHigh-grade dysplasiaPredictor of prognosisDevelopment of adenocarcinomaLymph node metastasisActivating point mutationsIntestinal-type tumorsTumor suppressor geneK-ras geneComplete lossInvasive carcinomaAmpullary adenocarcinoma
2000
The Roles of Carbohydrate Chains of the β-Subunit on the Functional Expression of Gastric H+,K+-ATPase*
Asano S, Kawada K, Kimura T, Grishin A, Caplan M, Takeguchi N. The Roles of Carbohydrate Chains of the β-Subunit on the Functional Expression of Gastric H+,K+-ATPase*. Journal Of Biological Chemistry 2000, 275: 8324-8330. PMID: 10722662, DOI: 10.1074/jbc.275.12.8324.Peer-Reviewed Original ResearchConceptsAlpha/beta assemblyN-glycosylation sitesATPase activityBeta assemblyPutative N-glycosylation sitesCarbohydrate chainsAlpha/beta complexSingle carbohydrate chainCatalytic subunitSurface deliveryFunctional enzymeAsparagine residuesAlpha subunitΒ-subunitBeta complexDelivery mechanismFunctional expressionComplete lossATPaseAssemblyExpressionSubunits
1998
Loss of p120ctn in human colorectal cancer predicts metastasis and poor survival
Gold J, Reynolds A, Rimm D. Loss of p120ctn in human colorectal cancer predicts metastasis and poor survival. Cancer Letters 1998, 132: 193-201. PMID: 10397474, DOI: 10.1016/s0304-3835(98)00190-6.Peer-Reviewed Original ResearchConceptsColorectal cancerPrimary human colorectal adenocarcinomasHigher stage diseasePoor clinical outcomeHuman colorectal cancerHuman colorectal adenocarcinomaStage diseaseClinical outcomesNodal metastasisColorectal adenocarcinomaPoor survivalColorectal tumorsColon cancerImmunohistochemical methodsMetastasisReduced expressionCancerE-cadherinP120ctn expressionLoss of p120ctnFamily membersSurvivalPreliminary studyExpressionComplete lossThe expression of p120ctn protein in breast cancer is independent of alpha- and beta-catenin and E-cadherin.
Dillon DA, D'Aquila T, Reynolds AB, Fearon ER, Rimm DL. The expression of p120ctn protein in breast cancer is independent of alpha- and beta-catenin and E-cadherin. American Journal Of Pathology 1998, 152: 75-82. PMID: 9422525, PMCID: PMC1858125.Peer-Reviewed Original Research
1996
Mutations of the Human Homolog of Drosophila patched in the Nevoid Basal Cell Carcinoma Syndrome
Hahn H, Wicking C, Zaphiropoulos P, Gailani M, Shanley S, Chidambaram A, Vorechovsky I, Holmberg E, Unden A, Gillies S, Negus K, Smyth I, Pressman C, Leffell D, Gerrard B, Goldstein A, Dean M, Toftgard R, Chenevix-Trench G, Wainwright B, Bale A. Mutations of the Human Homolog of Drosophila patched in the Nevoid Basal Cell Carcinoma Syndrome. Cell 1996, 85: 841-851. PMID: 8681379, DOI: 10.1016/s0092-8674(00)81268-4.Peer-Reviewed Original ResearchMeSH KeywordsAllelesAnimalsBasal Cell Nevus SyndromeBase SequenceChromosome MappingChromosomes, Human, Pair 9Cloning, MolecularDNA, ComplementaryDrosophilaDrosophila ProteinsExonsFemaleGene DeletionGene ExpressionGenes, Tumor SuppressorHumansIn Vitro TechniquesInsect HormonesIntronsMembrane ProteinsMolecular Sequence DataMutationPedigreeReceptors, Cell SurfaceSequence Homology, Nucleic AcidConceptsDrosophila segment polarity geneSegment polarity genesCertain cell typesDevelopmental abnormalitiesPolarity genesHuman homologStrong homologySporadic basal cell carcinomasHuman sequenceCosmid contigTumor suppressorLoss of heterozygosityCell typesGenesPatched geneChromosome 9q22.3Complete lossFunction contributesNevoid basal cell carcinoma syndromeMutation analysisBasal cell carcinoma syndromeAutosomal dominant disorderNBCCS patientsDrosophilaDominant disorder
1981
Identification of regulatory sequences contained in the 5'-flanking region of Drosophila lysine tRNA2 genes.
DeFranco D, Sharp S, Söll D. Identification of regulatory sequences contained in the 5'-flanking region of Drosophila lysine tRNA2 genes. Journal Of Biological Chemistry 1981, 256: 12424-12429. PMID: 6913581, DOI: 10.1016/s0021-9258(18)43290-5.Peer-Reviewed Original ResearchConceptsTRNA genesTranscriptional repressionMature tRNATemplate activityDrosophila tRNA genesLow template activityInsertion of nucleotidesPoor transcriptional activityRegulatory sequencesDeletion analysisNucleotides 23Transcriptional activityAdditional nucleotidesGenesTRNARepressionNucleotidesTranscriptionComplete lossSequenceDeletionOligonucleotideOligonucleotide sequencesRegionActivity
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