2025
Elevation of hepatic de novo lipogenesis in mice with overnutrition is dependent on multiple substrates
Strober J, Siebel S, Murray S, Rodríguez M, Rodriguez-Navas Gonzalez C, Vatner D. Elevation of hepatic de novo lipogenesis in mice with overnutrition is dependent on multiple substrates. Journal Of Lipid Research 2025, 66: 100838. PMID: 40499904, DOI: 10.1016/j.jlr.2025.100838.Peer-Reviewed Original ResearchCarbon entryAntisense oligonucleotidesIncreased hepatic TG contentGlutamic-pyruvic transaminase 2Amino acidsChronic overnutritionDevelopment of novel therapiesDecreased hepatic triglyceride contentTCA cycle metabolitesInsulin-resistant subjectsIncreased de novo lipogenesisMultiple amino acidsAntisense oligonucleotide treatmentPrevention of dyslipidemiaHepatic triglyceride contentOverfed miceTG contentHepatic de novo lipogenesisHepatic TG contentC57BL6/J miceLactate dehydrogenase ANovel therapiesMultiple substratesMetabolic syndromeCarbon sourceCytoplasmic Mg2+ supersedes carbon source preference to dictate Salmonella metabolism
Pokorzynski N, Jones K, Campagna S, Groisman E. Cytoplasmic Mg2+ supersedes carbon source preference to dictate Salmonella metabolism. Proceedings Of The National Academy Of Sciences Of The United States Of America 2025, 122: e2424337122. PMID: 40131949, PMCID: PMC12002343, DOI: 10.1073/pnas.2424337122.Peer-Reviewed Original ResearchConceptsCAMP receptor proteinCarbon source preferenceUptake genesCarbon sourceCyclic adenosine monophosphateCyclic adenosine monophosphate receptor proteinCytoplasmic MgCarbon source uptakeSynthesis of cyclic adenosine monophosphateSalmonella metabolismUtilization genesCRP-cAMPCarbon utilizationMaster regulatorsAllosteric activationDecreased transcriptionIncreased transcriptionGenesTranscriptionMetabolic restrictionsReceptor proteinTyphimuriumCyclic adenosine monophosphate concentrationsMurine macrophagesReduced synthesisSynthetic Genetic Elements Enable Rapid Characterization of Inorganic Carbon Uptake Systems in Cupriavidus necator H16
Nakamura A, Fulk E, Johnson C, Isaacs F. Synthetic Genetic Elements Enable Rapid Characterization of Inorganic Carbon Uptake Systems in Cupriavidus necator H16. ACS Synthetic Biology 2025, 14: 943-953. PMID: 40048245, PMCID: PMC11934965, DOI: 10.1021/acssynbio.4c00869.Peer-Reviewed Original ResearchConceptsSynthetic genetic elementsExpression of heterologous pathwaysUptake systemCupriavidus necator H16Genome engineering technologiesHeterologous pathwaysHeterotrophic conditionsGenetic elementsChromosomal expressionTunable expressionInducible promoterGenetic engineering technologyModel microbesCarbon sourceGene expressionFacultative chemolithotrophsUptake pathwayH16PathwayLanding padExpressionGenomeGenesMicrobesChemolithotrophs
2024
Disruption of the bacterial OLE RNP complex impairs growth on alternative carbon sources
Lyon S, Wencker F, Fernando C, Harris K, Breaker R. Disruption of the bacterial OLE RNP complex impairs growth on alternative carbon sources. PNAS Nexus 2024, 3: pgae075. PMID: 38415217, PMCID: PMC10898510, DOI: 10.1093/pnasnexus/pgae075.Peer-Reviewed Original ResearchRNP complexesMinimal mediumWild-type cellsAlternative carbon sourcesUnfavorable growth conditionsOLE RNASuppressor selectionDiverse stressesCarbon/energy sourceProtein secretionCarbon sourceGenetic disruptionCellular adaptationNoncoding RNAsFunctional linkRNAGrowth conditionsRibonucleoproteinImpaired growthPhosphate homeostasisFundamental processesHomeostasisShort-chain alcoholsElevated MgCarbon/energy
2023
Lineage-specific genes are clustered with HET-domain genes and respond to environmental and genetic manipulations regulating reproduction in Neurospora
Wang Z, Wang Y, Kasuga T, Lopez-Giraldez F, Zhang Y, Zhang Z, Wang Y, Dong C, Sil A, Trail F, Yarden O, Townsend J. Lineage-specific genes are clustered with HET-domain genes and respond to environmental and genetic manipulations regulating reproduction in Neurospora. PLOS Genetics 2023, 19: e1011019. PMID: 37934795, PMCID: PMC10684091, DOI: 10.1371/journal.pgen.1011019.Peer-Reviewed Original ResearchConceptsLineage-specific genesHET domain genesSexual reproductionFunctional roleUnusual carbon sourcesPotential functional roleMating lociAsexual growthGenetic mutantsNeurospora crassaPossible functional roleSexual phaseGenetic manipulationTranscriptomic profilingReproduction regulationGene knockoutPP-1ADV-1Environmental alterationsGenesSexual developmentNeurosporaReproductionCarbon sourceGenetic barrierEvidence that OLE RNA is a component of a major stress‐responsive ribonucleoprotein particle in extremophilic bacteria
Breaker R, Harris K, Lyon S, Wencker F, Fernando C. Evidence that OLE RNA is a component of a major stress‐responsive ribonucleoprotein particle in extremophilic bacteria. Molecular Microbiology 2023, 120: 324-340. PMID: 37469248, DOI: 10.1111/mmi.15129.Peer-Reviewed Original ResearchConceptsOLE RNAPrecise biochemical functionFundamental cellular processesCell growthTOR complexesProtein partnersRibonucleoprotein complexesCellular processesRNP complexesBiochemical functionsGram-positive bacteriaNoncoding RNAsRibonucleoprotein particleExtremophilic bacteriaBacterial speciesGenetic disruptionStress conditionsDiverse pathwaysRNAMetabolic adaptationCell membraneExtreme environmentsCarbon sourceBacteriaComplexes
2019
Bioinformatics applied to biotechnology: A review towards bioenergy research
de Carvalho L, Borelli G, Camargo A, de Assis M, de Ferraz S, Fiamenghi M, José J, Mofatto L, Nagamatsu S, Persinoti G, Silva N, Vasconcelos A, Pereira G, Carazzolle M. Bioinformatics applied to biotechnology: A review towards bioenergy research. Biomass And Bioenergy 2019, 123: 195-224. DOI: 10.1016/j.biombioe.2019.02.016.Peer-Reviewed Original ResearchSecond-generation ethanol technologyGenetic engineering toolsLignocellulosic biomassMicroorganism fermentationBioethanol productionEthanol technologyBiotechnological researchInteresting phenotypesPromising technologyMass spectrometry technologyNon-renewable originBiological systemsGenetic modificationNew organismsNew industrial processesMetabolic processesMolecular biologyDNA sequencingBioinformatics workflowsBioenergy researchHigh-performance computingIndustrial applicationsSpectrometry technologyCarbon sourceBiotechnology
2017
Optimality and sub-optimality in a bacterial growth law
Towbin B, Korem Y, Bren A, Doron S, Sorek R, Alon U. Optimality and sub-optimality in a bacterial growth law. Nature Communications 2017, 8: 14123. PMID: 28102224, PMCID: PMC5253639, DOI: 10.1038/ncomms14123.Peer-Reviewed Original Research
2015
Vitamin D Regulates Fatty Acid Composition in Subcutaneous Adipose Tissue Through Elovl3
Ji L, Gupta M, Feldman B. Vitamin D Regulates Fatty Acid Composition in Subcutaneous Adipose Tissue Through Elovl3. Endocrinology 2015, 157: 91-97. PMID: 26488808, PMCID: PMC4701879, DOI: 10.1210/en.2015-1674.Peer-Reviewed Original ResearchMeSH KeywordsAcetyltransferasesAnimalsCalcitriolCells, CulturedChromatin ImmunoprecipitationFatty Acid ElongasesFatty AcidsGene Expression Regulation, EnzymologicGenes, ReporterInjections, IntraperitonealIntra-Abdominal FatIsoenzymesLigandsMaleMice, Inbred C57BLMice, KnockoutOrgan SpecificityReceptors, CalcitriolSignal TransductionSubcutaneous FatVitamin D Response ElementConceptsWhite adipose tissueElovl3 expressionBrown fat biologyPromoter proximal regionFatty acidsVDRKO miceIncreased levels of expressionSc white adipose tissueFA compositionElovl3 geneFat biologyLevel of expressionVitamin D/VDRElongase enzymesCarbon sourceVitamin D in vivoWAT depotsElovl3Proximal regionAdipose tissueAcid compositionFatty acid compositionAdipose depotsVDRKOHormone receptors
2002
Conflicting needs for a Salmonella hypervirulence gene in host and non‐host environments
Mouslim C, Hilbert F, Huang H, Groisman EA. Conflicting needs for a Salmonella hypervirulence gene in host and non‐host environments. Molecular Microbiology 2002, 45: 1019-1027. PMID: 12180921, DOI: 10.1046/j.1365-2958.2002.03070.x.Peer-Reviewed Original ResearchConceptsSole carbon sourceD-Ala-D-Ala dipeptidaseNon-host environmentsNutrient-poor conditionsPathogen Salmonella entericaCarbon sourceWild-type SalmonellaPathogen fitnessFaster growth rateGenesInfected hostHypervirulence genesMutantsInnate immunitySalmonella entericaDipeptidase activityGrowth rateHostInactivationPhenotypeFitnessDipeptidasePathogensSalmonellaEnterica
1999
A Periplasmicd-Alanyl-d-Alanine Dipeptidase in the Gram-Negative Bacterium Salmonella enterica
Hilbert F, del Portillo F, Groisman E. A Periplasmicd-Alanyl-d-Alanine Dipeptidase in the Gram-Negative Bacterium Salmonella enterica. Journal Of Bacteriology 1999, 181: 2158-2165. PMID: 10094694, PMCID: PMC93629, DOI: 10.1128/jb.181.7.2158-2165.1999.Peer-Reviewed Original ResearchConceptsD-alanyl-D-alanine dipeptidaseD-Ala-D-Ala dipeptidaseHorizontal gene transferRelated bacterial speciesSpecies Salmonella entericaEscherichia coli KSimilar substrate specificityBacterium Salmonella entericaSalmonella entericaDipeptidase geneWild-type SalmonellaPeptidoglycan metabolismSole carbon sourcePeriplasmic spaceSalmonella chromosomeSubstrate specificityD-AlaColi KBacterial speciesSalmonella enzymeVanX proteinGene transferEnzymatic activityGlycopeptide antibiotic vancomycinCarbon source
1998
Seeking the genetic basis of phenotypic differences among bacterial species
Ochman H, Groisman E. Seeking the genetic basis of phenotypic differences among bacterial species. 1998, 221-235. DOI: 10.1007/978-3-0348-8948-3_12.Peer-Reviewed Original ResearchEnteric bacteria Escherichia coliBacterial speciesSpecies-specific genesSpecies-specific charactersGene complementSole carbon sourceDNA regionsPhenotypic charactersGenetic basisAllelic variationBacteria Escherichia coliPhenotypic differencesEscherichia coliSpeciesSalmonella entericaCarbon sourceGenesMicrobesCertain compoundsColiObserved differencesPhysiologySequenceEntericaCharacter
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