2025
Targeted inhibition of pathobiont virulence factor mitigates alcohol-associated liver disease
Yang Y, Duan Y, Lang S, Fondevila M, Schöler D, Harberts A, Cabré N, Chen S, Shao Y, Vervier K, Miyamoto Y, Zhang X, Chu H, Yang L, Tan C, Eckmann L, Bosques-Padilla F, Verna E, Abraldes J, Brown R, Vargas V, Altamirano J, Caballería J, Shawcross D, Louvet A, Lucey M, Mathurin P, Garcia-Tsao G, Bataller R, Stärkel P, Lawley T, Schnabl B. Targeted inhibition of pathobiont virulence factor mitigates alcohol-associated liver disease. Cell Host & Microbe 2025, 33: 957-972.e6. PMID: 40441146, PMCID: PMC12162233, DOI: 10.1016/j.chom.2025.05.003.Peer-Reviewed Original ResearchConceptsEthanol-induced liver diseaseAlcohol-associated liver diseaseAlcohol-associated hepatitisLiver diseaseGenome of Escherichia coliE. coliMetagenomic sequencing of fecal samplesInternational cohort of patientsGenetic manipulation of bacteriaGnotobiotic mouse modelOutcomes of patientsManipulation of bacteriaCohort of patientsScavenger receptor MARCOGlobal health burdenVirulence factorsMetagenomic sequencingGut microbiotaGenetic manipulationDisease progressionMouse modelKupffer cellsKpsMBacterial spreadInternational cohortOptical Photothermal Infrared Imaging Using Metabolic Probes in Biological Systems
Shuster S, Curtis A, Davis C. Optical Photothermal Infrared Imaging Using Metabolic Probes in Biological Systems. Analytical Chemistry 2025, 97: 8202-8212. PMID: 40207400, DOI: 10.1021/acs.analchem.4c03752.Peer-Reviewed Original ResearchMeSH Keywords3T3-L1 CellsAnimalsEscherichia coliGlucoseHumansInfrared RaysMiceOptical ImagingSpectrophotometry, InfraredZebrafishConceptsLive imaging of cellsSpectrally resolved imagesLiving cellsImaging of living cellsBiological systemsMultifrequency imagesAmino acid probesDynamic imaging of live cellsProbes of proteinsLive imagingConformational changes of biomoleculesConformational changesSpatial resolutionCell linesWater backgroundIdentifying biomoleculesImaging of cellsIR probeFat cellsInfrared spectraReaction mechanismCellsIn-cellInfrared spectroscopyBiological samplesWild Florida mottled ducks demonstrate strong heterogeneity in their humoral innate immune response.
Ayala A, Cheng M, Hellinger T, McBride K, Webb J, Fanning A, Snyder P, Ferragamo M, Garcia S, Sterner N, Bischoff K, Almagro-Moreno S, Ogbunugafor C. Wild Florida mottled ducks demonstrate strong heterogeneity in their humoral innate immune response. PLOS ONE 2025, 20: e0312653. PMID: 40096078, PMCID: PMC11913296, DOI: 10.1371/journal.pone.0312653.Peer-Reviewed Original ResearchConceptsFlorida mottled ducksAmerican Type Culture CollectionMottled ducksHumoral innate immune responseType Culture CollectionInnate immune responseVibrio sppEndemic subspeciesHabitat conversionInnate immune systemEco-immunologyCulture CollectionE. coliAnas platyrhynchosSubspeciesPeninsular FloridaConservation needsEffects of climate changeEcological covariatesHumoral innate immune systemBactericidal assayDucksResponse to agingWaterborne pathogensPathogensNongenetic adaptation by collective migration
Vo L, Avgidis F, Mattingly H, Edmonds K, Burger I, Balasubramanian R, Shimizu T, Kazmierczak B, Emonet T. Nongenetic adaptation by collective migration. Proceedings Of The National Academy Of Sciences Of The United States Of America 2025, 122: e2423774122. PMID: 39970001, PMCID: PMC11874451, DOI: 10.1073/pnas.2423774122.Peer-Reviewed Original ResearchMeSH KeywordsAdaptation, PhysiologicalChemotaxisEscherichia coliEscherichia coli ProteinsGene Expression Regulation, BacterialPhenotypeConceptsGene regulationCollective migrationPhenotype distributionPhenotypic compositionStress response pathwaysSwimming phenotypeCell populationsBacterial populationsStress responseAbundance distributionMultidimensional phenotypesGenetic mutationsPhenotypeDiverse environmentsEnvironmental conditionsGenesMutationsSwimming behaviorChanging environmentDoubling timeMigrating populationCellsRegulationMigrationAdaptationCharacterization of sulopenem antimicrobial activity using in vitro time-kill kinetics, synergy, post-antibiotic effect, and sub-inhibitory MIC effect methods against Escherichia coli and Klebsiella pneumoniae isolates
Maher J, Huband M, Lindley J, Rhomberg P, Aronin S, Puttagunta S, Castanheira M. Characterization of sulopenem antimicrobial activity using in vitro time-kill kinetics, synergy, post-antibiotic effect, and sub-inhibitory MIC effect methods against Escherichia coli and Klebsiella pneumoniae isolates. Microbiology Spectrum 2025, 13: e01898-24. PMID: 39907459, PMCID: PMC11878024, DOI: 10.1128/spectrum.01898-24.Peer-Reviewed Original ResearchConceptsUncomplicated urinary tract infectionsPost-antibiotic effectIntra-abdominal infectionsTreatment of urinary tractTime-kill testsMultidrug-resistant pathogensBaseline MICPenem antibioticUrinary tractPAE effectsClinical developmentBroth microdilution susceptibility testingPhase 3 clinical trialsKlebsiella pneumoniae isolatesOral dosing regimenUrinary tract infectionMicrodilution susceptibility testingPAE-SMETime-kill assayTime-kill kineticsStudy evaluated <i>inMg/500 mgAmoxicillin-clavulanateTract infectionsSusceptibility testingEngineering a genomically recoded organism with one stop codon
Grome M, Nguyen M, Moonan D, Mohler K, Gurara K, Wang S, Hemez C, Stenton B, Cao Y, Radford F, Kornaj M, Patel J, Prome M, Rogulina S, Sozanski D, Tordoff J, Rinehart J, Isaacs F. Engineering a genomically recoded organism with one stop codon. Nature 2025, 639: 512-521. PMID: 39910296, PMCID: PMC11903333, DOI: 10.1038/s41586-024-08501-x.Peer-Reviewed Original Research
2024
Microscopic phage adsorption assay: High-throughput quantification of virus particle attachment to host bacterial cells
Antani J, Ward T, Emonet T, Turner P. Microscopic phage adsorption assay: High-throughput quantification of virus particle attachment to host bacterial cells. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2410905121. PMID: 39700139, PMCID: PMC11670125, DOI: 10.1073/pnas.2410905121.Peer-Reviewed Original ResearchMeSH KeywordsAdsorptionBacteriaBacteriophagesEscherichia coliHigh-Throughput Screening AssaysMicroscopy, FluorescenceVirionVirus AttachmentConceptsBacterial cellsViruses of bacteriaHost bacterial cellsTarget bacterial strainsEnumeration of bacteriaPhage biologyPhage attachmentHigh-throughput quantificationPhage libraryBacterial pathogensHigh-throughput screeningPhageBacterial strainsSingle-virusVirus particlesIndividual virus particlesFluorescence microscopyBacteriaEarth's biosphereParticle trackingCellsLow throughputBacteriumRate constantsPathogensDiverse phage communities are maintained stably on a clonal bacterial host
Pyenson N, Leeks A, Nweke O, Goldford J, Schluter J, Turner P, Foster K, Sanchez A. Diverse phage communities are maintained stably on a clonal bacterial host. Science 2024, 386: 1294-1300. PMID: 39666794, PMCID: PMC7617280, DOI: 10.1126/science.adk1183.Peer-Reviewed Original ResearchConceptsPhage communitiesBacterial hostsPhage speciesEcology of bacteriophagesDiverse biological entitiesPhage diversityGrowth phenotypeCommunity ecologyEcological mechanismsPhageBacterial cellsPhenotypic heterogeneityHost populationsBacteriophageBiological entitiesDiversityHostSpeciesPhylogeneticallyNichePhenotypeStrainCellsCommunityRluA is the major mRNA pseudouridine synthase in Escherichia coli
Schaening-Burgos C, LeBlanc H, Fagre C, Li G, Gilbert W. RluA is the major mRNA pseudouridine synthase in Escherichia coli. PLOS Genetics 2024, 20: e1011100. PMID: 39241085, PMCID: PMC11421799, DOI: 10.1371/journal.pgen.1011100.Peer-Reviewed Original ResearchConceptsPseudouridine synthasesHigh-confidence sitesMRNA-modifying enzymesE. coli mRNAsStructure probing dataIdentified target sitesTarget siteDiverse eukaryotesBacterial mRNAsRNA modificationsRluAEscherichia coliSecondary structureE. coliTRNAPseudouridineRRNAStructural motifsMRNAModification capacityRecognition elementsSynthaseRNASequenceEukaryotesCorrigendum: Identification of genes influencing the evolution of Escherichia coli ST372 in dogs and humans.
Elankumaran P, Browning G, Marenda M, Kidsley A, Osman M, Haenni M, Johnson J, Trott D, Reid C, Djordjevic S. Corrigendum: Identification of genes influencing the evolution of Escherichia coli ST372 in dogs and humans. Microbial Genomics 2024, 10 PMID: 39166982, PMCID: PMC11561579, DOI: 10.1099/mgen.0.001286.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsDog DiseasesDogsEscherichia coliEscherichia coli InfectionsEvolution, MolecularHumansConceptsIdentification of genesDual function of LapB (YciM) in regulating Escherichia coli lipopolysaccharide synthesis
Shu S, Tsutsui Y, Nathawat R, Mi W. Dual function of LapB (YciM) in regulating Escherichia coli lipopolysaccharide synthesis. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2321510121. PMID: 38635633, PMCID: PMC11046580, DOI: 10.1073/pnas.2321510121.Peer-Reviewed Original ResearchMeSH KeywordsAmidohydrolasesEscherichia coliEscherichia coli ProteinsLipopolysaccharidesMembrane ProteinsMutationRubredoxinsConceptsLPS synthesisTetratricopeptide repeatCytoplasmic domainLevels of lipopolysaccharideCryo-EM structureGram-negative bacteriaLipopolysaccharide synthesisProtease FtsHRubredoxin domainLpxC activityTransmembrane helicesIn vivo analysisLpxCPseudomonas aeruginosaEnzymatic activityLapBFtsHAllosteric effectsYciMDual functionIn vitroTetratricopeptideAdaptorMotifDeacetylaseChaperone Hsp70 helps Salmonella survive infection-relevant stress by reducing protein synthesis
Chan C, Groisman E. Chaperone Hsp70 helps Salmonella survive infection-relevant stress by reducing protein synthesis. PLOS Biology 2024, 22: e3002560. PMID: 38574172, PMCID: PMC10994381, DOI: 10.1371/journal.pbio.3002560.Peer-Reviewed Original ResearchMeSH KeywordsBacteriaEscherichia coliEscherichia coli ProteinsHSP70 Heat-Shock ProteinsMagnesiumMolecular ChaperonesProtein FoldingSalmonellaConceptsRibosome associationProtein synthesisProtein homeostasisS. typhimuriumProtein folding capacityPreventing protein aggregationC-terminal amino acidsDomains of lifeProtein synthesis in vitroInhibit protein synthesisFolding capacityHsp70 chaperonesJ-domainSynthesis in vitroProtein foldingReduction of protein synthesisChaperone Hsp70DnaKRibosomeProtein aggregationChaperoneAmino acidsProteinStarvationHSP70Engineered mRNA–ribosome fusions for facile biosynthesis of selenoproteins
Thaenert A, Sevostyanova A, Chung C, Vargas-Rodriguez O, Melnikov S, Söll D. Engineered mRNA–ribosome fusions for facile biosynthesis of selenoproteins. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2321700121. PMID: 38442159, PMCID: PMC10945757, DOI: 10.1073/pnas.2321700121.Peer-Reviewed Original ResearchMeSH KeywordsCodon, TerminatorEscherichia coliMagnoliopsidaRibosomesRNA, MessengerRNA, Ribosomal, 16SSelenocysteineSelenoproteinsConceptsSelenocysteine insertion sequenceRibosomal RNARibosome engineeringMessenger RNARegulatory RNA elementsMachinery of protein synthesisInsertion of SecSec-containing proteinsSite-specific insertionBiosynthesis of selenoproteinsNatural messenger RNALive bacterial cellsRNA elementsUAG codonInsertion sequenceRibosome structureUGA codonSec codonInsert SecStop codonSynthetic biologyDesigning proteinsRibosomePolypeptide chainBacterial cells
2023
Ice nucleation proteins self-assemble into large fibres to trigger freezing at near 0 °C
Hansen T, Lee J, Reicher N, Ovadia G, Guo S, Guo W, Liu J, Braslavsky I, Rudich Y, Davies P. Ice nucleation proteins self-assemble into large fibres to trigger freezing at near 0 °C. ELife 2023, 12: rp91976. PMID: 38109272, PMCID: PMC10727499, DOI: 10.7554/elife.91976.Peer-Reviewed Original ResearchThe emergence of carbapenemase-producing Enterobacterales in hospitals: a major challenge for a debilitated healthcare system in Lebanon
Daaboul D, Oueslati S, Rima M, Kassem I, Mallat H, Birer A, Girlich D, Hamze M, Dabboussi F, Osman M, Naas T. The emergence of carbapenemase-producing Enterobacterales in hospitals: a major challenge for a debilitated healthcare system in Lebanon. Frontiers In Public Health 2023, 11: 1290912. PMID: 38074718, PMCID: PMC10699444, DOI: 10.3389/fpubh.2023.1290912.Peer-Reviewed Original ResearchMeSH KeywordsAnti-Bacterial AgentsCarbapenemsEscherichia coliHospitalsKlebsiella pneumoniaeLebanonMultilocus Sequence TypingConceptsKirby-Bauer disk diffusionDifferent Lebanese hospitalsSelf-medication practicesDisk diffusionPublic health systemCarbapenemase-producing EnterobacteralesConventional diagnostic methodsESBL producersHospital settingAntibiotic susceptibilityLebanese hospitalsClinical settingHospitalHealth systemSusceptibility profilesAntimicrobial resistanceHealthcare systemPlasmid typesHealthcare challengesDiagnostic methodsNDMCarbapenemsAMR awarenessIsolatesLebanese communityEpistasis and pleiotropy shape biophysical protein subspaces associated with drug resistance
Ogbunugafor C, Guerrero R, Miller-Dickson M, Shakhnovich E, Shoulders M. Epistasis and pleiotropy shape biophysical protein subspaces associated with drug resistance. Physical Review E 2023, 108: 054408. PMID: 38115433, PMCID: PMC10935598, DOI: 10.1103/physreve.108.054408.Peer-Reviewed Original ResearchMeSH KeywordsDrug ResistanceEpistasis, GeneticEscherichia coliMutationPhenotypeTetrahydrofolate DehydrogenaseConceptsProtein spaceAmino acid sequenceAmino acid substitutionsGenotype-phenotype mapAcid sequenceProtein variantsBacterial enzymesAcid substitutionsProtein phenotypesEngineered proteinsDHFR enzymeProteinEpistasisDrug resistanceMutationsAminoProcess of evolutionEnzymePhenotypeTraitsPleiotropySequenceVariantsBiophysical componentsBacterial production of recombinant contraceptive vaccine antigen from CatSper displayed on a human papilloma virus-like particle
Nand K, Jordan T, Yuan X, Basore D, Zagorevski D, Clarke C, Werner G, Hwang J, Wang H, Chung J, McKenna A, Jarvis M, Singh G, Bystroff C. Bacterial production of recombinant contraceptive vaccine antigen from CatSper displayed on a human papilloma virus-like particle. Vaccine 2023, 41: 6791-6801. PMID: 37833124, DOI: 10.1016/j.vaccine.2023.09.044.Peer-Reviewed Original ResearchConceptsVirus-like particlesSperm hyperactivated motilityHuman papilloma virusInclusion bodiesLong-acting protectionCalcium ion channelsNon-hormonal interventionsContraceptive efficacyHyperactivated motilityPapilloma virusPrincipal pieceSperm tailContraceptive vaccineBALB/c miceHypervariable regionCatSperVaccine antigensBacterial productionVaccine candidatesIon channelsIn vitroVaccinePregnancyRecombinant vaccineExtracellular loopStructure of the native chemotaxis core signaling unit from phage E-protein lysed E. coli cells
Cassidy C, Qin Z, Frosio T, Gosink K, Yang Z, Sansom M, Stansfeld P, Parkinson J, Zhang P. Structure of the native chemotaxis core signaling unit from phage E-protein lysed E. coli cells. MBio 2023, 14: e00793-23. PMID: 37772839, PMCID: PMC10653900, DOI: 10.1128/mbio.00793-23.Peer-Reviewed Original ResearchMeSH KeywordsBacterial ProteinsChemotaxisEscherichia coliEscherichia coli ProteinsMethyl-Accepting Chemotaxis ProteinsSignal TransductionConceptsCore signalling unitChemosensory arraysLyse E. coli cellsCryo-electron tomographyBacterial chemotaxisSignal transductionCell movementEscherichia coli</i>.Sensing machinerySensory signal transductionSignaling unitStructural basisMolecular mechanismsMechanistic hypothesesDesign new experimentsChemotaxisCellsComplete structurePhageMotilityTransductionMachineryUbiquitous behaviorFirst report of the mobile colistin resistance gene, mcr-1.26, in multidrug-resistant Escherichia coli isolated from retail chicken meat
Kassem I, Osman M, Hassan J, Sulaiman A, Mann D, Esseili M, Naas T, Deng X. First report of the mobile colistin resistance gene, mcr-1.26, in multidrug-resistant Escherichia coli isolated from retail chicken meat. Journal Of Global Antimicrobial Resistance 2023, 34: 176-178. PMID: 37429544, DOI: 10.1016/j.jgar.2023.07.005.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnti-Bacterial AgentsChickensColistinEscherichia coliEscherichia coli ProteinsHumansMeatConceptsMinimum inhibitory concentrationColistin resistanceColistin-resistant Escherichia coliKirby-Bauer disk diffusionMultidrug-resistant Escherichia coliMDR E. coliPlasmid replicon typesWhole-genome sequencingSequence typesColistin resistance geneRetail chicken meatBroth microdilution methodMobile colistin resistance geneReplicon typesSusceptibility testingIncX4 plasmidsFirst reportMultidrug resistanceWhole-genome sequencing analysisDepth phenotypicInhibitory concentrationDisk diffusionMicrodilution methodGenomic epidemiologyAntimicrobial resistance genesMistranslation of the genetic code by a new family of bacterial transfer RNAs
Schuntermann D, Fischer J, Bile J, Gaier S, Shelley B, Awawdeh A, Jahn M, Hoffman K, Westhof E, Söll D, Clarke C, Vargas-Rodriguez O. Mistranslation of the genetic code by a new family of bacterial transfer RNAs. Journal Of Biological Chemistry 2023, 299: 104852. PMID: 37224963, PMCID: PMC10404621, DOI: 10.1016/j.jbc.2023.104852.Peer-Reviewed Original ResearchConceptsTransfer RNAsAmino acidsBacterial transfer RNAsUnfavorable environmental conditionsProlyl-tRNA synthetaseWrong amino acidPoor substrate specificitySubstrate discriminationGrowth defectTransfer RNAGenetic codePosttranslational modificationsProtein reporterTranslation factorsEnvironmental stressFunctional proteinsSubstrate specificityThreonine codonGenetic informationDistinct isoformsPro mutationAntibiotic carbenicillinEscherichia coliNovel familyEnvironmental conditions
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