2024
The Current and Future State of Vaccines for Lyme Disease
Plotkin S, Shapiro E. The Current and Future State of Vaccines for Lyme Disease. Clinical Infectious Diseases 2024, ciae639. PMID: 39711074, DOI: 10.1093/cid/ciae639.Peer-Reviewed Original Research
2023
Squalene Biosynthesis in Engineered Escherichia Coli
Zhang W, Li Y, Xie L, Hu Y. Squalene Biosynthesis in Engineered Escherichia Coli. Pharmaceutical Fronts 2023, 05: e321-e329. DOI: 10.1055/s-0043-1776291.Peer-Reviewed Original ResearchMevalonate pathwaySqualene productionProduction of squaleneEngineered Escherichia coliSqualene synthasesChassis cellsMVA pathwayDimethylallyl diphosphateEscherichia coli strainsExpression strengthMetabolic fluxExtinct animalsXL1-BlueDifferent speciesSqualene biosynthesisEscherichia coliColi strainsGenesPathwayNatural triterpenoidIspH
2022
In vivo CRISPR‐Cas9‐mediated DNA chop identifies a cochlear outer hair cell‐specific enhancer
Sun Y, Zhang Y, Zhang D, Wang G, Song L, Liu Z. In vivo CRISPR‐Cas9‐mediated DNA chop identifies a cochlear outer hair cell‐specific enhancer. The FASEB Journal 2022, 36: e22233. PMID: 35225354, DOI: 10.1096/fj.202100421rr.Peer-Reviewed Original ResearchConceptsDNA fragment deletionKbp fragmentKbp segmentFragment deletionCell-specific enhancerOuter hair cellsLarge DNA fragment deletionGreen fluorescent proteinCRISPR/Motor proteinsIntron regionsGene therapeutic applicationsFluorescent proteinDifferent speciesCochlear outer hair cellsBp fragmentEnhancerSLC26A5Hair cellsEGFPProteinTransgenic miceDeletionKbpPrestin expressionTracing the cis-regulatory changes underlying the endometrial control of placental invasion
Suhail Y, Maziarz JD, Novin A, Dighe A, Afzal J, Wagner G, Kshitiz. Tracing the cis-regulatory changes underlying the endometrial control of placental invasion. Proceedings Of The National Academy Of Sciences Of The United States Of America 2022, 119: e2111256119. PMID: 35110402, PMCID: PMC8832988, DOI: 10.1073/pnas.2111256119.Peer-Reviewed Original ResearchConceptsCis-regulatory changesComparative genomic investigationCis-regulatory elementsTranscription factor GATA2Placental invasionCancer cell invasionEutherian mammalsTranscription factorsGenomic investigationsInvasibilityGene knockoutGenomic mechanismsDifferent speciesCell invasionEndometrial controlCancer malignancyDegree of invasionSpecies differencesCancer disseminationMaternal endometriumInterspecies differencesPlacental trophoblastsStromal cellsStromal characteristicsInvasionChapter 11 Role of AMP-activated protein kinase and sirtuins as antiaging proteins
Ramu M, Vishal S, Gogia N. Chapter 11 Role of AMP-activated protein kinase and sirtuins as antiaging proteins. 2022, 241-278. DOI: 10.1016/b978-0-323-90235-9.00015-x.ChaptersProtein kinaseAMP/ATP ratioDifferent cellular compartmentsCommon cellular targetActivity of AMPKFuel-sensing enzymeAge-associated disordersChapter 11 RoleSirtuin isoformsCellular compartmentsAge-related disordersSirtuin modulatorsSirtuin activityDifferent speciesAMPKCellular targetsAMPK pathwayContext of agingMitochondrial functionMitochondrial disordersPotential therapeutic targetATP ratioAge-related processesKinaseSIRT1
2019
Cellular and synaptic adaptations of neural circuits processing skylight polarization in the fly
Sancer G, Kind E, Uhlhorn J, Volkmann J, Hammacher J, Pham T, Plazaola-Sasieta H, Wernet M. Cellular and synaptic adaptations of neural circuits processing skylight polarization in the fly. Journal Of Comparative Physiology A 2019, 206: 233-246. PMID: 31811399, DOI: 10.1007/s00359-019-01389-3.Peer-Reviewed Original ResearchConceptsPolarization-sensitive photoreceptorsDorsal rim areaCell typesCentral brainCertain cell typesDrosophila melanogasterMedulla columnsLarge insectsSynaptic adaptationPhotoreceptors R7Downstream elementsDifferent speciesPost-synaptic membraneDRA regionFunctional roleComplex circuit architecturesInsectsPolarization visionDistal medullaLobula complexMedulla neuropilNeuronal elementsSpecialized ommatidiaOptic lobePhotoreceptorsMolecular and taxonomic analyses in troglobiotic Alpioniscus (Illyrionethes) species from the Dinaric Karst (Isopoda: Trichoniscidae)
Bedek J, Taiti S, Bilandžija H, Ristori E, Baratti M. Molecular and taxonomic analyses in troglobiotic Alpioniscus (Illyrionethes) species from the Dinaric Karst (Isopoda: Trichoniscidae). Zoological Journal Of The Linnean Society 2019, 187: 539-584. DOI: 10.1093/zoolinnean/zlz056.Peer-Reviewed Original ResearchNominal speciesNuclear gene fragmentsFuture species identificationDinaric karstMost nominal speciesNew morphological charactersSpecies richnessDetailed morphological analysisWidespread taxaDistinct lineagesPhylogenetic methodsMorphological charactersTerrestrial isopodsGene fragmentsTaxonomic analysisDNA fragmentsSpecies identificationDifferent speciesBody part ratiosTaxaMolecular analysisSpeciesMorphological analysisTroglobiontsFragmentsPiezo2 integrates mechanical and thermal cues in vertebrate mechanoreceptors
Zheng W, Nikolaev YA, Gracheva EO, Bagriantsev SN. Piezo2 integrates mechanical and thermal cues in vertebrate mechanoreceptors. Proceedings Of The National Academy Of Sciences Of The United States Of America 2019, 116: 17547-17555. PMID: 31413193, PMCID: PMC6717272, DOI: 10.1073/pnas.1910213116.Peer-Reviewed Original ResearchConceptsMechanotransduction apparatusVertebrate mechanoreceptorsHeterologous systemsPlasma membraneDifferent species
2017
Disruption of the gaa Gene in Zebrafish Fails to Generate the Phenotype of Classical Pompe Disease
Wu J, Yang Y, Sun C, Sun S, Li Q, Yao Y, Fei F, Lu L, Chang Z, Zhang W, Wang X, Luo F. Disruption of the gaa Gene in Zebrafish Fails to Generate the Phenotype of Classical Pompe Disease. DNA And Cell Biology 2017, 36: 10-17. PMID: 28045567, DOI: 10.1089/dna.2016.3459.Peer-Reviewed Original ResearchConceptsGAA mRNAFrameshift mutationEnzymatic activityGene expression changesGAA geneSpecies-specific differencesPresence of autophagosomesGlycogen accumulationMutant zebrafishGAA enzymatic activityWT zebrafishZebrafish modelDays postfertilizationExpression changesZebrafishDifferent speciesPhenotypic changesAdult stageLysosomal glycogen accumulationGlycogen storage disease type IIStorage disease type IIGenesProtein levelsProtein expressionMutants
2014
Analysis of Multiple Tsetse Fly Populations in Uganda Reveals Limited Diversity and Species-Specific Gut Microbiota
Aksoy E, Telleria EL, Echodu R, Wu Y, Okedi LM, Weiss BL, Aksoy S, Caccone A. Analysis of Multiple Tsetse Fly Populations in Uganda Reveals Limited Diversity and Species-Specific Gut Microbiota. Applied And Environmental Microbiology 2014, 80: 4301-4312. PMID: 24814785, PMCID: PMC4068677, DOI: 10.1128/aem.00079-14.Peer-Reviewed Original ResearchConceptsDifferent tsetse speciesRRNA gene clone librariesDifferent sympatric speciesGene clone librariesTsetse speciesLimited diversityQuantitative PCRV4 hypervariable regionGut microbiotaGut microbial abundanceSympatric speciesGut microbial diversityClone librariesMicrobial diversityMicrobial abundanceField fliesRRNA geneHost physiologyTsetse fly populationsDeep sequencingReduced diversityDifferent speciesFly populationsSpeciesWigglesworthia
2012
Genetics of germ cell development
Lesch BJ, Page DC. Genetics of germ cell development. Nature Reviews Genetics 2012, 13: 781-794. PMID: 23044825, DOI: 10.1038/nrg3294.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsGerm cell developmentGerm cellsHaploid genomeMultiple speciesCell developmentPluripotent stem cell systemsRepressive chromatin configurationGerm cell identityRNA polymerase IIGerm cell biologyStem cell systemEarly germ cellsPolymerase IICell identityDiploid genomeChromatin configurationIndividual organismsCell biologyMitotic proliferationGenomeSame speciesDifferent speciesGermline precursorsLater stepsMeiosis
2011
Luciferase inhibition by a novel naphthoquinone
Bedford R, LePage D, Hoffmann R, Kennedy S, Gutschenritter T, Bull L, Sujijantarat N, DiCesare J, Sheaff R. Luciferase inhibition by a novel naphthoquinone. Journal Of Photochemistry And Photobiology B Biology 2011, 107: 55-64. PMID: 22197716, DOI: 10.1016/j.jphotobiol.2011.11.008.Peer-Reviewed Original ResearchConceptsNovel naphthoquinoneImportant new reagentsDihydro-N-methylRenilla reniformisTU100Potential chemotherapeutic agentDifferent speciesPhotinus pyralisLuciferase inhibitionFirefly luciferaseLuciferaseCancer cellsEnzyme thiolsTopoisomerasesUnique mechanismPre-incubation experimentsPotent inhibitorBioluminescent enzymesATPIrreversible inhibitorLuciferinDixon plot analysisInhibitorsReniformisType IAncestral Genes Can Control the Ability of Horizontally Acquired Loci to Confer New Traits
Chen HD, Jewett MW, Groisman EA. Ancestral Genes Can Control the Ability of Horizontally Acquired Loci to Confer New Traits. PLOS Genetics 2011, 7: e1002184. PMID: 21811415, PMCID: PMC3140997, DOI: 10.1371/journal.pgen.1002184.Peer-Reviewed Original ResearchMeSH KeywordsAnti-Bacterial AgentsBacterial ProteinsDNA, BacterialDrug Resistance, BacterialEscherichia coliEscherichia coli ProteinsGene Expression Regulation, BacterialGene Transfer, HorizontalKineticsMagnesiumMolecular Sequence DataPhosphorylationPolymyxin BReverse Transcriptase Polymerase Chain ReactionSalmonella typhimuriumSequence Analysis, DNATranscription FactorsTransformation, BacterialConceptsGene productsPmrD proteinPmrA/PmrB systemSpecies-specific traitsPmrA/PmrBE. coliHigh phosphatase activityBacterium Escherichia coliTwo-component systemPmrA proteinPolymyxin B resistanceAncestral locusAncestral proteinAncestral geneAncestral pathwayNew traitsBiochemical activityDifferent speciesGenesPmrB proteinEscherichia coliPhosphatase activityB resistanceProteinSalmonella entericaLineage Identification and Genealogical Relationships Among Captive Galápagos Tortoises
Benavides E, Russello M, Boyer D, Wiese R, Kajdacsi B, Marquez L, Garrick R, Caccone A. Lineage Identification and Genealogical Relationships Among Captive Galápagos Tortoises. Zoo Biology 2011, 31: 107-120. PMID: 21674601, DOI: 10.1002/zoo.20397.Peer-Reviewed Original ResearchConceptsGenealogical relationshipsGalápagos tortoisesEx situ conservation programsMicrosatellite genotypic dataSan Diego ZooGalápagos giant tortoisesWild-born individualsSitu conservation programsLevels of relatednessDetailed management recommendationsSanta Cruz IslandEvolutionary lineagesAssignment testsGenetic toolsSpecies designationRelated foundersGiant tortoisesGenotypic dataUnknown ancestryHaplotypic dataPedigree relationshipsDifferent speciesLineage identificationIsabela IslandConservation programs
2008
Expanding the Substrate Tolerance of Biotin Ligase through Exploration of Enzymes from Diverse Species
Slavoff SA, Chen I, Choi YA, Ting AY. Expanding the Substrate Tolerance of Biotin Ligase through Exploration of Enzymes from Diverse Species. Journal Of The American Chemical Society 2008, 130: 1160-1162. PMID: 18171066, PMCID: PMC3501195, DOI: 10.1021/ja076655i.Peer-Reviewed Original ResearchConceptsLigation reactionProtein labeling applicationsDifferential substrate specificitySite-specific conjugationBiotin acceptor domainPhosphine probesStaudinger ligationDiverse speciesBiotin ligaseChemical probesDifferent organismsMass spectrometry assayPyrococcus horikoshiiSubstrate specificityCell biologyUnnatural analoguesLabeling applicationsAcceptor domainsSubstrate toleranceLigasesDifferent speciesSpectrometry assayReactionSpeciesBiotin
2007
Recurrent DNA copy number variation in the laboratory mouse
Egan CM, Sridhar S, Wigler M, Hall IM. Recurrent DNA copy number variation in the laboratory mouse. Nature Genetics 2007, 39: 1384-1389. PMID: 17965714, DOI: 10.1038/ng.2007.19.Peer-Reviewed Original ResearchConceptsCopy number variationsCopy numberNumber variationsGenome-wide analysisDNA copy number variationsRecent common ancestryGenerations of inbreedingRecurrent copy number variationsHigh-resolution microarraysCommon ancestryNatural variationGenetic differencesDifferent speciesDifferent lociGenerational timeLaboratory miceNonrandom processGenomeRecurrent mutationsLociAdditional strainsInbreedingLineagesGenesDiscrete segments
2005
Proton sensitivity of ASIC1 appeared with the rise of fishes by changes of residues in the region that follows TM1 in the ectodomain of the channel
Coric T, Zheng D, Gerstein M, Canessa CM. Proton sensitivity of ASIC1 appeared with the rise of fishes by changes of residues in the region that follows TM1 in the ectodomain of the channel. The Journal Of Physiology 2005, 568: 725-735. PMID: 16002453, PMCID: PMC1464184, DOI: 10.1113/jphysiol.2005.087734.Peer-Reviewed Original ResearchMeSH KeywordsAcid Sensing Ion ChannelsAmino Acid SequenceAmino AcidsAnimalsEvolution, MolecularFishesHydrogen-Ion ConcentrationIon Channel GatingMembrane ProteinsMolecular Sequence DataNerve Tissue ProteinsProtein Structure, TertiaryProtonsSequence Homology, Amino AcidSodium ChannelsSpecies SpecificityStructure-Activity RelationshipConceptsAmino acid conservationChanges of residuesProton sensitivityMammalian nervous systemChordate lineageEarly vertebratesFunctional chimerasMammalian counterpartsLower vertebratesAllosteric changesProtein sequencesExtracellular domainSequence analysisDifferent speciesRat sequenceRat channelKinetics of activationStructural determinantsDistinct kineticsVertebratesASIC1 channelsMembrane potentialChimerasSharksEctodomain
2004
Comparative cis‐regulatory analyses identify new elements of the mouse Hoxc8 early enhancer
Wang W, Anand S, Powell D, Pawashe A, Amemiya C, Shashikant C. Comparative cis‐regulatory analyses identify new elements of the mouse Hoxc8 early enhancer. Journal Of Experimental Zoology Part B Molecular And Developmental Evolution 2004, 302B: 436-445. PMID: 15384168, DOI: 10.1002/jez.b.21009.Peer-Reviewed Original ResearchConceptsHoxc8 early enhancerCis-acting elementsHoxc8 expressionEarly enhancerAdditional cis-acting elementsEnhancer sequencesNeural tubeDistinct cis-acting elementsHox expression patternsCis-regulatory regionsEarly enhancer regionMouse embryonic developmentCis-regulatory analysisTransgenic mouse embryosPosterior neural tubeEmbryonic developmentReporter expressionReporter geneMouse embryosExpression patternsEnhancer regionBp regionRemarkable plasticityDifferent speciesSignificant divergenceAn Evolutionary Perspective on Single-Nucleotide Polymorphism Screening in Molecular Cancer Epidemiology
Zhu Y, Spitz MR, Amos CI, Lin J, Schabath MB, Wu X. An Evolutionary Perspective on Single-Nucleotide Polymorphism Screening in Molecular Cancer Epidemiology. Cancer Research 2004, 64: 2251-2257. PMID: 15026370, DOI: 10.1158/0008-5472.can-03-2800.Peer-Reviewed Original ResearchConceptsSingle nucleotide polymorphismsAmino acidsConservation levelDifferent cancer-related genesHuman DNA repair genesTolerance indexMolecular evolutionary approachEntire human genomeNonsynonymous single nucleotide polymorphismsSingle nucleotide polymorphism (SNP) screeningTarget single nucleotide polymorphismsDNA repair genesAmino acid changesEvolutionary conservationHuman genomeCancer-related genesMolecular epidemiological studiesSelective pressureMolecular cancer epidemiologyDifferent speciesPhenotypic functionsAcid changesRepair genesEvolutionary perspectivePolymorphism screening
2003
Divergence of Hoxc8 early enhancer parallels diverged axial morphologies between mammals and fishes
Anand S, Wang W, Powell D, Bolanowski S, Zhang J, Ledje C, Pawashe A, Amemiya C, Shashikant C. Divergence of Hoxc8 early enhancer parallels diverged axial morphologies between mammals and fishes. Proceedings Of The National Academy Of Sciences Of The United States Of America 2003, 100: 15666-15669. PMID: 14673077, PMCID: PMC307625, DOI: 10.1073/pnas.2535667100.Peer-Reviewed Original ResearchConceptsHoxc8 early enhancerCis-regulatory elementsHox genesHox cis-regulatory elementsGene expressionEarly enhancerCis-regulatory modificationsDevelopmental regulatory genesHox gene expressionTransgenic mouse embryosReporter gene analysisReporter gene expressionGene expression correlatesRegulatory genesMorphological diversityRegulatory regionsRegulatory elementsComparative sequenceEmbryonic axisMouse embryosEnhancer elementsNucleotide substitutionsDifferent speciesGene analysisEvolutionary perspective
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