2025
Matrix-producing neutrophils populate and shield the skin
Vicanolo T, Özcan A, Li J, Huerta-López C, Ballesteros I, Rubio-Ponce A, Dumitru A, Nicolás-Ávila J, Molina-Moreno M, Reyes-Gutierrez P, Johnston A, Martone C, Greto E, Quílez-Alvarez A, Calvo E, Bonzon-Kulichenko E, Álvarez-Velez R, Chooi M, Kwok I, González-Bermúdez B, Malleret B, Espinosa F, Zhang M, Wang Y, Sun D, Zhen Chong S, El-Armouche A, Kim K, Udalova I, Greco V, Garcia R, Vázquez J, Dopazo A, Plaza G, Alegre-Cebollada J, Uderhardt S, Ng L, Hidalgo A. Matrix-producing neutrophils populate and shield the skin. Nature 2025, 1-9. PMID: 40108463, DOI: 10.1038/s41586-025-08741-5.Peer-Reviewed Original ResearchRepertoire of proteinsExtracellular matrixInnate immune systemPopulation of neutrophilsImmune diversityPromote barrier functionBacterial invasionInnate immune cellsTGFB signalingForeign moleculesPhysical barrierRing formationBarrier functionImmune systemEnvironmental threatsDefenceDiverse strategiesToxic chemicalsNaive skinTGFBImmune cellsBacteriaNeutrophilsEnzymeProtein
2024
Microbial metabolism of host-derived antioxidants
Zhou Z, Hatzios S. Microbial metabolism of host-derived antioxidants. Current Opinion In Chemical Biology 2024, 84: 102565. PMID: 39721219, PMCID: PMC11863140, DOI: 10.1016/j.cbpa.2024.102565.Peer-Reviewed Original ResearchVibrio cholerae RbmB is an α-1,4-polysaccharide lyase with biofilm-disrupting activity against Vibrio polysaccharide (VPS)
Weerasekera R, Moreau A, Huang X, Nam K, Hinbest A, Huynh Y, Liu X, Ashwood C, Pepi L, Paulson E, Cegelski L, Yan J, Olson R. Vibrio cholerae RbmB is an α-1,4-polysaccharide lyase with biofilm-disrupting activity against Vibrio polysaccharide (VPS). PLOS Pathogens 2024, 20: e1012750. PMID: 39621768, PMCID: PMC11637428, DOI: 10.1371/journal.ppat.1012750.Peer-Reviewed Original ResearchVibrio polysaccharideBiofilm dispersalHuman pathogen Vibrio choleraeV. cholerae biofilmsPathogen Vibrio choleraeBiofilm disruption activityFormation of biofilmsVibrio coralliilyticusPolysaccharide lyasesLyase mechanismV. choleraeVibrio choleraeBiofilm matrixPathogenic bacteriaRbmBAntibacterial enzymesSecreted macromoleculesSolid-state NMRGlycolytic enzymesFluorescence-based biochemical assayBiofilmBiochemical assaysEnzymeSecreted glycosidasesDouble bondEpigenetics-targeted drugs: current paradigms and future challenges
Dai W, Qiao X, Fang Y, Guo R, Bai P, Liu S, Li T, Jiang Y, Wei S, Na Z, Xiao X, Li D. Epigenetics-targeted drugs: current paradigms and future challenges. Signal Transduction And Targeted Therapy 2024, 9: 332. PMID: 39592582, PMCID: PMC11627502, DOI: 10.1038/s41392-024-02039-0.Peer-Reviewed Original ResearchConceptsNon-coding RNA regulationDNA base sequenceRNA modificationsRNA regulationChromatin remodelingHistone modificationsEnhancer of zeste homolog 2Epigenetic landscapeGenetic informationOrganismal developmentDNA methyltransferasesEpigenetic enzymesDNA modificationsBase sequenceHomolog 2Zeste homolog 2Histone deacetylasesHuman diseasesIsocitrate dehydrogenaseDNAPathological contextsRegulatory systemChromatinEnzymeHistoneExploring Molecular and Phenotypic Characteristics of NAGLU Arg234Gly and Asp312Asn Variants
Celebiler H, Barak T, K. D, Kaya I, Erbilgin S, Uytun M, Oztop D, Gumus H, Per H, Ceylaner S, Bozkurt I, Kontaridis M, Bilguvar K, Akhun N, Kilincaslan A, Caglayan A, Erson-Omay E, Gunel M, Ercan-Sencicek A. Exploring Molecular and Phenotypic Characteristics of NAGLU Arg234Gly and Asp312Asn Variants. Molecular Syndromology 2024, 1-12. DOI: 10.1159/000542367.Peer-Reviewed Original ResearchWhole-exome sequencingStandard Sanger sequencingMucopolysaccharidosis type IIIBExome sequencingProgressive neurodegenerative disorderConsanguineous familySanger sequencingNAGLU genePhenotypic characteristicsMagnetic resonance imagingEnzymatic assayNeurodegenerative disordersAffected individualsLoss of activityNeurodegenerative symptomsAutosomal recessive lysosomal disorderCellular mechanismsVariantsLysosomal disorderEnzymeNormal MRI findingsSequenceMPS IIIBMRI findingsType IIIBAll the sites we cannot see: Sources and mitigation of false negatives in RNA modification studies
Oberdoerffer S, Gilbert W. All the sites we cannot see: Sources and mitigation of false negatives in RNA modification studies. Nature Reviews Molecular Cell Biology 2024, 26: 237-248. PMID: 39433914, DOI: 10.1038/s41580-024-00784-2.Peer-Reviewed Original ResearchRNA modificationsRNA-modifying enzymesTranscriptome-wide mappingRNA modification mappingPost-transcriptional controlModified sitesSequencing depthRNA functionRNA targetsModification mappingRNAModification studiesProfiling studiesEnzymeModification sequenceNeurodevelopmental disordersTechnical artifactsFalse negativesSitesSequenceHuman healthFalse positivesTransparent reportingRegulation and signaling of the LIM domain kinases
Casanova‐Sepúlveda G, Boggon T. Regulation and signaling of the LIM domain kinases. BioEssays 2024, 47: e2400184. PMID: 39361252, PMCID: PMC11663136, DOI: 10.1002/bies.202400184.Peer-Reviewed Original ResearchLIM domain kinaseDownstream of Rho GTPasesCofilin/actin depolymerizing factorActin cytoskeleton regulationIntra-molecular mechanismFilament severingDepolymerizing factorRho GTPasesActin depolymerizationCytoskeleton regulationRegulation mechanismKinaseLIMProteinRegulationGTPaseLIMK2LIMK1ActinEnzymeHuman healthSignalDepolymerizationCascadeMechanismA fluorescence-based assay for measuring polyamine biosynthesis aminopropyl transferase–mediated catalysis
Singh P, Choi J, Wang W, Lam T, Lechner P, Vanderwal C, Pou S, Nilsen A, Mamoun C. A fluorescence-based assay for measuring polyamine biosynthesis aminopropyl transferase–mediated catalysis. Journal Of Biological Chemistry 2024, 300: 107832. PMID: 39342998, PMCID: PMC11541840, DOI: 10.1016/j.jbc.2024.107832.Peer-Reviewed Original ResearchAminopropyl transferaseFluorescence-based assayLack of high-throughput assaysHigh-throughput screeningCarbon chain lengthChemical librariesMass spectrometryChain lengthHigh-throughput assayDrug discoveryMass spectrometry analysisSaccharomyces cerevisiaeThin-layer chromatographyFluorescence intensityCellular functionsSpectrometry analysisPolycationic moleculesFluorescent conjugatesIsoindoleAPT activityCatalysisAssayBenzeneAdductsEnzymeMicrobial transformation of dietary xenobiotics shapes gut microbiome composition
Culp E, Nelson N, Verdegaal A, Goodman A. Microbial transformation of dietary xenobiotics shapes gut microbiome composition. Cell 2024, 187: 6327-6345.e20. PMID: 39321800, PMCID: PMC11531382, DOI: 10.1016/j.cell.2024.08.038.Peer-Reviewed Original ResearchGut microbiomeHuman gut microbesGut microbiome compositionDiet-microbiome interactionsGut microbesCommunity compositionMicrobiome compositionMicrobial metabolismResponse to dietInterindividual variationMicrobiomeDietary xenobioticsMap interactionsGutMetabolic activityEnzymeXenobioticsDetoxificationGenesMicrobesResveratrolRemodelingTraitsInteractionVariationMetabolic model guided CRISPRi identifies a central role for phosphoglycerate mutase in Chlamydia trachomatis persistence
Chowdhury N, Pokorzynski N, Rucks E, Ouellette S, Carabeo R, Saha R. Metabolic model guided CRISPRi identifies a central role for phosphoglycerate mutase in Chlamydia trachomatis persistence. MSystems 2024, 9: e00717-24. PMID: 38940523, PMCID: PMC11323709, DOI: 10.1128/msystems.00717-24.Peer-Reviewed Original ResearchTranscriptome dataEnzyme costNutrient starvationMetabolic modelsPhosphoglycerate mutaseGenome-scale metabolic modelsResponse to nutrient starvationIron starvation conditionsNutrient-starved conditionsSerovar L2Absence of tryptophanTranscriptional regulationBacterial phenomenonStarvation conditionsNutrient-repleteTranscriptome rewiringCRISPRi knockdownEnzymatic costCRISPRiStress responseTranscriptomeAdaptive response mechanismsNon-replicating formStress conditionsEnzymeA dual-acting DNASE1/DNASE1L3 biologic prevents autoimmunity and death in genetic and induced lupus models
Stabach P, Sims D, Gomez-Bañuelos E, Zehentmeier S, Dammen-Brower K, Bernhisel A, Kujawski S, Lopez S, Petri M, Goldman D, Lester E, Le Q, Ishaq T, Kim H, Srivastava S, Kumar D, Pereira J, Yarema K, Koumpouras F, Andrade F, Braddock D. A dual-acting DNASE1/DNASE1L3 biologic prevents autoimmunity and death in genetic and induced lupus models. JCI Insight 2024, 9: e177003. PMID: 38888971, PMCID: PMC11383374, DOI: 10.1172/jci.insight.177003.Peer-Reviewed Original ResearchSystemic lupus erythematosusDNASE1L3 deficiencySporadic systemic lupus erythematosusAssociated with systemic lupus erythematosusChromatin degradationDNA accumulationDevelopment of lupusPristane-induced lupusSelf-DNACell free DNAHuman isoformsSystemic lupus erythematosus plasmasDouble knockout miceDNASE1L3Pathogenic effectsFree DNALupus modelEnzymeInducible lupus modelAdult patientsLupus erythematosusKnockout micePediatric populationAutoimmune diseasesDNAQuantitative correlation of ENPP1 pathogenic variants with disease phenotype
Ansh A, Stabach P, Ciccone C, Cao W, De La Cruz E, Sabbagh Y, Carpenter T, Ferreira C, Braddock D. Quantitative correlation of ENPP1 pathogenic variants with disease phenotype. Bone 2024, 186: 117136. PMID: 38806089, PMCID: PMC11227391, DOI: 10.1016/j.bone.2024.117136.Peer-Reviewed Original ResearchEctonucleotide pyrophosphatase/phosphodiesterase 1Pathogenic variantsDisease phenotypeEnzyme velocityCompound heterozygotesEnzyme activityVariable enzyme activityAutosomal dominant phenotypeHigh-throughput assayAutosomal recessive formInnate immune responseENPP1 variantsDamaging variantsENPP1 deficiencyCole diseaseDominant phenotypeAutosomal dominant diseaseCatalytic velocityRecessive formEnzymePhenotypeWT levelsBio-active moleculesClinical phenotypeDominant diseaseThe Importance of PET Imaging to Understanding Whole-Body Cortisol Metabolism in Alzheimer’s Disease
Bini J. The Importance of PET Imaging to Understanding Whole-Body Cortisol Metabolism in Alzheimer’s Disease. Journal Of Alzheimer's Disease 2024, 99: 113-115. PMID: 38607759, DOI: 10.3233/jad-231463.Peer-Reviewed Original ResearchDivergent role of Mitochondrial Amidoxime Reducing Component 1 (MARC1) in human and mouse
Smagris E, Shihanian L, Mintah I, Bigdelou P, Livson Y, Brown H, Verweij N, Hunt C, Johnson R, Greer T, Hartford S, Hindy G, Sun L, Nielsen J, Halasz G, Lotta L, Murphy A, Sleeman M, Gusarova V. Divergent role of Mitochondrial Amidoxime Reducing Component 1 (MARC1) in human and mouse. PLOS Genetics 2024, 20: e1011179. PMID: 38437227, PMCID: PMC10939284, DOI: 10.1371/journal.pgen.1011179.Peer-Reviewed Original ResearchConceptsAssociation studiesExome-wide association studyHuman genome-wide association studiesGenome-wide association studiesLoss of function variantsFamily enzymesMissense variantsObserved phenotypesFunctional variantsAberrant localizationProtein instabilityAncestry groupsHepatic triglyceride accumulationDivergent rolesLiver phenotypePhysiological functionsTriglyceride accumulationPhenotypeDeletionMouse liverIn vitro studiesHepatic cellsProteinEnzymeKnockout micePlain language summary of a study looking at the long-term benefits of enzyme replacement therapy in children and teenagers with Gaucher disease type 3
El-Beshlawy A, Tylki-Szymanska A, Belmatoug N, Mistry P. Plain language summary of a study looking at the long-term benefits of enzyme replacement therapy in children and teenagers with Gaucher disease type 3. Future Rare Diseases 2024, 4: frd52. DOI: 10.2217/frd-2023-0015.Peer-Reviewed Original ResearchBeta-glucosidase enzymePlain Language SummaryGaucher diseaseSlow growthBeta-glucosidaseEnzyme replacement therapyLanguage SummaryQuality of life of peopleLife-prolonging treatmentInternational Collaborative Gaucher GroupQuality of lifeGenetic conditionsEnzymeType 3Year of treatmentImproved most symptomsLong-term symptomsLocal and dynamic regulation of neuronal glycolysis in vivo
Wolfe A, Koberstein J, Smith C, Stewart M, Gonzalez I, Hammarlund M, Hyman A, Stork P, Goodman R, Colón-Ramos D. Local and dynamic regulation of neuronal glycolysis in vivo. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2314699121. PMID: 38198527, PMCID: PMC10801914, DOI: 10.1073/pnas.2314699121.Peer-Reviewed Original ResearchConceptsGlycolytic stateEnergy stressEnergy metabolismConditions of energy stressDynamic regulationNeuronal functionIndividual cell typesMitochondrial localizationGenetic analysisSubcellular regionsRegulatory enzymeCell-autonomousNeuronal identityGlycolysisCell typesMetabolic stateImaging dynamic changesMetabolismLiving organismsIn vivoCellsEnergy landscapeIndividual neuronsEnzymeDynamic changesNeuroendocrine Properties of the Ciliary Epithelium
Coca-Prados M. Neuroendocrine Properties of the Ciliary Epithelium. 2024 DOI: 10.1016/b978-0-443-13820-1.00083-9.Peer-Reviewed Original ResearchGene expressionExpression of bioactive peptidesIdentity of genesGene expression of enzymesMicroarray-based analysisExpression of enzymesSensor proteinsRegulate metabolismGenesPhysiological processesCiliary epitheliumPhysiological functionsT4 to T3Neuronal Ca2Neuroendocrine propertiesVasoconstrictive functionVasoactive aminesPeptide receptorBioactive peptidesIon channelsMetabolismPeptideEyesEnzymeProtein“Dark” Pathways of Protein Transnitrosylation Injure Synapses in Alzheimer’s Disease: Mechanism and Potential Treatment
LIPTON S. “Dark” Pathways of Protein Transnitrosylation Injure Synapses in Alzheimer’s Disease: Mechanism and Potential Treatment. 2024, pl. DOI: 10.14869/toxpt.51.1.0_pl.Peer-Reviewed Original ResearchAlzheimer's diseaseDisruption of protein functionUbiquitin-protein hydrolaseS-nitrosylationS-nitrosylation reactionLoss of synapsesCorrelated to cognitive declineGuanosine triphosphataseMitochondrial fragmentationAD brainProtein functionAmyloid-betaAggregated proteinsProtein hydrolaseSynapse lossSynaptic lossBioenergetic compromiseSynaptic damageTransnitrosylation reactionsProteinUCH-L1Environmental factorsEnzymeAlzheimerCascade
2023
Discovery of the first unconventional myosin: Acanthamoeba myosin-I
Pollard T, Korn E. Discovery of the first unconventional myosin: Acanthamoeba myosin-I. Frontiers In Physiology 2023, 14: 1324623. PMID: 38046947, PMCID: PMC10693453, DOI: 10.3389/fphys.2023.1324623.Peer-Reviewed Original ResearchUnconventional myosinActin filamentsMyosin heavy chain kinaseFirst unconventional myosinsEvolution of eukaryotesClass I MyosinHeavy chain kinaseNovel unconventional myosinPhylogenetic analysisSlime moldMembrane lipidsChain kinaseProteolytic fragmentsHeavy chainMuscle myosinMyosinCofactorEnzymeMg-ATPaseMg-ATPase activityEukaryotesFilamentsCrude enzymeKinaseActinEpistasis 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 ResearchConceptsProtein spaceAmino acid sequenceAmino acid substitutionsGenotype-phenotype mapAcid sequenceProtein variantsBacterial enzymesAcid substitutionsProtein phenotypesEngineered proteinsDHFR enzymeProteinEpistasisDrug resistanceMutationsAminoProcess of evolutionEnzymePhenotypeTraitsPleiotropySequenceVariantsBiophysical components
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