2025
DSP-1, the major fibronectin type-II protein of donkey seminal plasma is a small heat-shock protein and exhibits chaperone-like activity against thermal and oxidative stress
Alim S, Cheppali S, Pawar S, Swamy M. DSP-1, the major fibronectin type-II protein of donkey seminal plasma is a small heat-shock protein and exhibits chaperone-like activity against thermal and oxidative stress. Biochimica Et Biophysica Acta (BBA) - Proteins And Proteomics 2025, 1873: 141064. PMID: 39956303, DOI: 10.1016/j.bbapap.2025.141064.Peer-Reviewed Original ResearchConceptsChaperone-like activitySeminal plasmaFibronectin type IITetramer to monomersSperm capacitationSurface hydrophobicityMolecular chaperonesClient proteinsHeat shock proteinsBiophysical studiesAlcohol dehydrogenaseOxidative stressPhysiological ligandsShock proteinsProteinHead group moietySHspsBinding of phosphorylcholineCholine phospholipidsBindingFibronectinDehydrogenaseChaperoneSpermMammals
2024
Ectopic reconstitution of a spine-apparatus-like structure provides insight into mechanisms underlying its formation
Falahati H, Wu Y, Fang M, De Camilli P. Ectopic reconstitution of a spine-apparatus-like structure provides insight into mechanisms underlying its formation. Current Biology 2024, 35: 265-276.e4. PMID: 39626668, PMCID: PMC11753949, DOI: 10.1016/j.cub.2024.11.010.Peer-Reviewed Original ResearchEndoplasmic reticulumSpine apparatusActin bundlesEndomembrane networkER sheetsConserved regionProtein synaptopodinCisternal organelleNon-neuronal cellsER cisternsOrganellesSynaptopodinProteinNeuronal dendritesNeuronal spinesAxon initial segmentFindings shed lightBiogenesisActinProtein matrixNarrow lumenReticulumMammalsInitial segmentMechanismEvolutionary innovations in germline biology of placental mammals identified by transcriptomics of first-wave spermatogenesis in opossum
Marshall K, Stadtmauer D, Maziarz J, Wagner G, Lesch B. Evolutionary innovations in germline biology of placental mammals identified by transcriptomics of first-wave spermatogenesis in opossum. Developmental Cell 2024, 60: 646-664.e8. PMID: 39536760, PMCID: PMC11859772, DOI: 10.1016/j.devcel.2024.10.013.Peer-Reviewed Original ResearchPlacental mammalsLevel of transcriptionSingle-cell dataGene expression patternsMammalian spermatogenesisGene expression programsEpigenomic dataAdult testisEvolutionary innovationSpermatogenic cellsGene setsSpermatogenic developmentModel marsupialOpossum Monodelphis domesticaGene expressionExpression patternsGenesDevelopmental processesExpression programsSpermatogenesisMonodelphis domesticaMammalsDevelopmental timeCombination of featuresExpressionEvolutionary Innovations in Conserved Regulatory Elements Associate With Developmental Genes in Mammals
Uebbing S, Kocher A, Baumgartner M, Ji Y, Bai S, Xing X, Nottoli T, Noonan J. Evolutionary Innovations in Conserved Regulatory Elements Associate With Developmental Genes in Mammals. Molecular Biology And Evolution 2024, 41: msae199. PMID: 39302728, PMCID: PMC11465374, DOI: 10.1093/molbev/msae199.Peer-Reviewed Original ResearchSequence evolutionRegulatory evolutionDevelopmental signaling genesEnhanced evolutionEvolutionary innovationMammalian phylogenyTranscriptional enhancersGenetic variationPhenotypic variationPleiotropic genesDevelopmental genesEnhancer elementsHoofed mammalsEnhancer sequencesActivation domainSignaling genesEvolutionary adaptationDiverse organismsGenesHuman diseasesRegulatory functionsDevelopmental processesDeveloping limbCell typesMammalsA comparative roadmap of PIWI-interacting RNAs across seven species reveals insights into de novo piRNA-precursor formation in mammals
Konstantinidou P, Loubalova Z, Ahrend F, Friman A, Almeida M, Poulet A, Horvat F, Wang Y, Losert W, Lorenzi H, Svoboda P, Miska E, van Wolfswinkel J, Haase A. A comparative roadmap of PIWI-interacting RNAs across seven species reveals insights into de novo piRNA-precursor formation in mammals. Cell Reports 2024, 43: 114777. PMID: 39302833, PMCID: PMC11615739, DOI: 10.1016/j.celrep.2024.114777.Peer-Reviewed Original ResearchPIWI-interacting RNAsPiwi-interacting RNA clustersPiRNA clustersPiRNA biologySilencing mobile genetic elementsGenomic piRNA clustersSingle-stranded precursorsMobile genetic elementsSafeguarding genome integrityGerm cell biologySpecies-specific variationGenome invadersTranscriptional readthroughTransposon insertionGenetic elementsGenome integrityRetroviral invasionMolecular mechanismsCell biologyRNAMammalsSpeciesBiologyTransposonReadthroughPTMoreR-enabled cross-species PTM mapping and comparative phosphoproteomics across mammals
Wang S, Di Y, Yang Y, Salovska B, Li W, Hu L, Yin J, Shao W, Zhou D, Cheng J, Liu D, Yang H, Liu Y. PTMoreR-enabled cross-species PTM mapping and comparative phosphoproteomics across mammals. Cell Reports Methods 2024, 4: 100859. PMID: 39255793, PMCID: PMC11440062, DOI: 10.1016/j.crmeth.2024.100859.Peer-Reviewed Original ResearchConceptsP-siteSurrounding amino acid sequenceKinase-substrate networkQuantitative phosphoproteomic analysisFunctional enrichment analysisPhosphoproteomic resultsKinase motifsComparative phosphoproteomicsPTM sitesPhosphorylation eventsPhosphoproteomic analysisProteomic analysisEnrichment analysisMammalian speciesSpeciesEvolutionary anglePhosphoproteomeMotifEnvironmental factorsNon-human speciesPTMProteomicsKinaseMammalsProteinThe mammary hair of Monodelphis domestica and homology of the mammary pilosebacous unit
Stadtmauer D, Wagner G. The mammary hair of Monodelphis domestica and homology of the mammary pilosebacous unit. Journal Of Morphology 2024, 285: e21769. PMID: 39188032, DOI: 10.1002/jmor.21769.Peer-Reviewed Original ResearchInbreeding avoidance, competition and natal dispersal in a pair-living, genetically monogamous mammal, Azara’s owl monkey (Aotus azarae)
Corley M, de la Chica A, van der Heide G, Rotundo M, Caccone A, Fernandez-Duque E. Inbreeding avoidance, competition and natal dispersal in a pair-living, genetically monogamous mammal, Azara’s owl monkey (Aotus azarae). Royal Society Open Science 2024, 11: 240379. PMID: 39113772, PMCID: PMC11305132, DOI: 10.1098/rsos.240379.Peer-Reviewed Original ResearchAzara's owl monkeysNatal dispersalInbreeding avoidanceMating systemPair-livingPotential matesNatal groupMaintenance of social organizationTiming of natal dispersalLife history stagesPopulation structureGenetic dataMonogamous mammalsWild populationsParental careIndividual fitnessEcological factorsRegulating dispersalAotus azaraeDispersal patternsInbreedingStep-parentsAgonistic conflictsMatingMammalsNon-mutational neoantigens in disease
Stern L, Clement C, Galluzzi L, Santambrogio L. Non-mutational neoantigens in disease. Nature Immunology 2024, 25: 29-40. PMID: 38168954, PMCID: PMC11075006, DOI: 10.1038/s41590-023-01664-1.Peer-Reviewed Original ResearchConceptsNon-canonical initiation codonsPost-translational protein modificationMature T cellsRibosomal RNA processingAlternative RNA splicingProtein-coding regionsNon-mutational mechanismsAbility of mammalsRNA processingRNA splicingInitiation codonProtein modificationHuman diseasesMature T cell repertoireAntigenic peptidesImmune recognitionAdaptive immune responsesT cellsAntigenic determinantsMHC class ICellsSplicingNovel antigenic determinantsMammalsCodon
2023
Reproductive inequality in humans and other mammals
Ross C, Hooper P, Smith J, Jaeggi A, Smith E, Gavrilets S, Zohora F, Ziker J, Xygalatas D, Wroblewski E, Wood B, Winterhalder B, Willführ K, Willard A, Walker K, von Rueden C, Voland E, Valeggia C, Vaitla B, Urlacher S, Towner M, Sum C, Sugiyama L, Strier K, Starkweather K, Major-Smith D, Shenk M, Sear R, Seabright E, Schacht R, Scelza B, Scaggs S, Salerno J, Revilla-Minaya C, Redhead D, Pusey A, Purzycki B, Power E, Pisor A, Pettay J, Perry S, Page A, Pacheco-Cobos L, Oths K, Oh S, Nolin D, Nettle D, Moya C, Migliano A, Mertens K, McNamara R, McElreath R, Mattison S, Massengill E, Marlowe F, Madimenos F, Macfarlan S, Lummaa V, Lizarralde R, Liu R, Liebert M, Lew-Levy S, Leslie P, Lanning J, Kramer K, Koster J, Kaplan H, Jamsranjav B, Hurtado A, Hill K, Hewlett B, Helle S, Headland T, Headland J, Gurven M, Grimalda G, Greaves R, Golden C, Godoy I, Gibson M, Mouden C, Dyble M, Draper P, Downey S, DeMarco A, Davis H, Crabtree S, Cortez C, Colleran H, Cohen E, Clark G, Clark J, Caudell M, Carminito C, Bunce J, Boyette A, Bowles S, Blumenfield T, Beheim B, Beckerman S, Atkinson Q, Apicella C, Alam N, Mulder M. Reproductive inequality in humans and other mammals. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2220124120. PMID: 37216525, PMCID: PMC10235947, DOI: 10.1073/pnas.2220124120.Peer-Reviewed Original ResearchLeveraging base-pair mammalian constraint to understand genetic variation and human disease
Sullivan P, Meadows J, Gazal S, Phan B, Li X, Genereux D, Dong M, Bianchi M, Andrews G, Sakthikumar S, Nordin J, Roy A, Christmas M, Marinescu V, Wang C, Wallerman O, Xue J, Yao S, Sun Q, Szatkiewicz J, Wen J, Huckins L, Lawler A, Keough K, Zheng Z, Zeng J, Wray N, Li Y, Johnson J, Chen J, Paten B, Reilly S, Hughes G, Weng Z, Pollard K, Pfenning A, Forsberg-Nilsson K, Karlsson E, Lindblad-Toh K, Andrews G, Armstrong J, Bianchi M, Birren B, Bredemeyer K, Breit A, Christmas M, Clawson H, Damas J, Di Palma F, Diekhans M, Dong M, Eizirik E, Fan K, Fanter C, Foley N, Forsberg-Nilsson K, Garcia C, Gatesy J, Gazal S, Genereux D, Goodman L, Grimshaw J, Halsey M, Harris A, Hickey G, Hiller M, Hindle A, Hubley R, Hughes G, Johnson J, Juan D, Kaplow I, Karlsson E, Keough K, Kirilenko B, Koepfli K, Korstian J, Kowalczyk A, Kozyrev S, Lawler A, Lawless C, Lehmann T, Levesque D, Lewin H, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu V, Marques-Bonet T, Mason V, Meadows J, Meyer W, Moore J, Moreira L, Moreno-Santillan D, Morrill K, Muntané G, Murphy W, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat N, Pfenning A, Phan B, Pollard K, Pratt H, Ray D, Reilly S, Rosen J, Ruf I, Ryan L, Ryder O, Sabeti P, Schäffer D, Serres A, Shapiro B, Smit A, Springer M, Srinivasan C, Steiner C, Storer J, Sullivan K, Sullivan P, Sundström E, Supple M, Swofford R, Talbot J, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder A, Wirthlin M, Xue J, Zhang X. Leveraging base-pair mammalian constraint to understand genetic variation and human disease. Science 2023, 380: eabn2937. PMID: 37104612, PMCID: PMC10259825, DOI: 10.1126/science.abn2937.Peer-Reviewed Original ResearchConceptsHuman genomeHuman diseasesCopy-number variationsHeritable human diseasesGenome annotationVariant annotationGenomic positionsGenomic regionsDisease heritabilityFunctional annotationEvolutionary constraintsAssociation studiesCopy-numberGenetic variationGenetic findingsGenomeCell typesRegulatory landscapeDisease mechanismsAnnotationBiological mechanismsCancer dataMammalsPredictor of functionHeritabilityEvolutionary constraint and innovation across hundreds of placental mammals
Christmas M, Kaplow I, Genereux D, Dong M, Hughes G, Li X, Sullivan P, Hindle A, Andrews G, Armstrong J, Bianchi M, Breit A, Diekhans M, Fanter C, Foley N, Goodman D, Goodman L, Keough K, Kirilenko B, Kowalczyk A, Lawless C, Lind A, Meadows J, Moreira L, Redlich R, Ryan L, Swofford R, Valenzuela A, Wagner F, Wallerman O, Brown A, Damas J, Fan K, Gatesy J, Grimshaw J, Johnson J, Kozyrev S, Lawler A, Marinescu V, Morrill K, Osmanski A, Paulat N, Phan B, Reilly S, Schäffer D, Steiner C, Supple M, Wilder A, Wirthlin M, Xue J, Birren B, Gazal S, Hubley R, Koepfli K, Marques-Bonet T, Meyer W, Nweeia M, Sabeti P, Shapiro B, Smit A, Springer M, Teeling E, Weng Z, Hiller M, Levesque D, Lewin H, Murphy W, Navarro A, Paten B, Pollard K, Ray D, Ruf I, Ryder O, Pfenning A, Lindblad-Toh K, Karlsson E, Andrews G, Armstrong J, Bianchi M, Birren B, Bredemeyer K, Breit A, Christmas M, Clawson H, Damas J, Di Palma F, Diekhans M, Dong M, Eizirik E, Fan K, Fanter C, Foley N, Forsberg-Nilsson K, Garcia C, Gatesy J, Gazal S, Genereux D, Goodman L, Grimshaw J, Halsey M, Harris A, Hickey G, Hiller M, Hindle A, Hubley R, Hughes G, Johnson J, Juan D, Kaplow I, Karlsson E, Keough K, Kirilenko B, Koepfli K, Korstian J, Kowalczyk A, Kozyrev S, Lawler A, Lawless C, Lehmann T, Levesque D, Lewin H, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu V, Marques-Bonet T, Mason V, Meadows J, Meyer W, Moore J, Moreira L, Moreno-Santillan D, Morrill K, Muntané G, Murphy W, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat N, Pfenning A, Phan B, Pollard K, Pratt H, Ray D, Reilly S, Rosen J, Ruf I, Ryan L, Ryder O, Sabeti P, Schäffer D, Serres A, Shapiro B, Smit A, Springer M, Srinivasan C, Steiner C, Storer J, Sullivan K, Sullivan P, Sundström E, Supple M, Swofford R, Talbot J, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder A, Wirthlin M, Xue J, Zhang X. Evolutionary constraint and innovation across hundreds of placental mammals. Science 2023, 380: eabn3943. PMID: 37104599, PMCID: PMC10250106, DOI: 10.1126/science.abn3943.Peer-Reviewed Original ResearchConceptsEncyclopedia of DNA ElementsProtein-coding exonsUltraconserved elementsGenome functionGenomic resourcesOrganismal phenotypesDNA elementsFunctional annotationEvolutionary constraintsHuman genomeRegulatory elementsMammalian traitsGenomeGenetic variantsPlacental mammalsTherapeutic developmentMammalsSpeciesDisease riskExonGenesBiodiversityPhenotypeTraitsRepeatsMegahertz Sampling of Prestin (SLC26a5) Voltage-Sensor Charge Movements in Outer Hair Cell Membranes Reveals Ultrasonic Activity that May Support Electromotility and Cochlear Amplification
Santos-Sacchi J, Bai J, Navaratnam D. Megahertz Sampling of Prestin (SLC26a5) Voltage-Sensor Charge Movements in Outer Hair Cell Membranes Reveals Ultrasonic Activity that May Support Electromotility and Cochlear Amplification. Journal Of Neuroscience 2023, 43: 2460-2468. PMID: 36868859, PMCID: PMC10082455, DOI: 10.1523/jneurosci.2033-22.2023.Peer-Reviewed Original ResearchConceptsConformational switchingMammalian hearingMembrane motor proteinCochlear amplificationMotor protein prestinVoltage-sensor charge movementOuter hair cell electromotilityHair cell electromotilityProtein prestinMotor proteinsConformation switchingCharge movementPrestinPrestin activityCell membraneOHC electromotilityHair cell membraneElectromotilityTransmembrane voltageOrgan of CortiAmplificationMammalsMembrane capacitanceProteinChemiexcitation: Mammalian Photochemistry in the Dark†
Brash D, Goncalves L. Chemiexcitation: Mammalian Photochemistry in the Dark†. Photochemistry And Photobiology 2023, 99: 251-276. PMID: 36681894, PMCID: PMC10065968, DOI: 10.1111/php.13781.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsExcited statesMammalian cellsCyclobutane pyrimidine dimersEvolutionary selectionBond rearrangementUnoccupied orbitalsGround stateReaction productsPyrimidine dimersChemiexcitationRecent findingsBiologyPathogenic eventsRadicalsUltraviolet lightMoleculesDrug-induced deafnessPotential pathogenesisCellsMelaninAchilles heelMammalsBiomoleculesPhotochemistryDNAQuestioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies
Kennedy K, de Goffau M, Perez-Muñoz M, Arrieta M, Bäckhed F, Bork P, Braun T, Bushman F, Dore J, de Vos W, Earl A, Eisen J, Elovitz M, Ganal-Vonarburg S, Gänzle M, Garrett W, Hall L, Hornef M, Huttenhower C, Konnikova L, Lebeer S, Macpherson A, Massey R, McHardy A, Koren O, Lawley T, Ley R, O’Mahony L, O’Toole P, Pamer E, Parkhill J, Raes J, Rattei T, Salonen A, Segal E, Segata N, Shanahan F, Sloboda D, Smith G, Sokol H, Spector T, Surette M, Tannock G, Walker A, Yassour M, Walter J. Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 2023, 613: 639-649. PMID: 36697862, PMCID: PMC11333990, DOI: 10.1038/s41586-022-05546-8.Peer-Reviewed Original ResearchConceptsMicrobial populationsHuman immune developmentMicrobial ecologyReproductive biologyMicrobial communitiesLow biomass environmentsMicrobial signalsMicrobial studiesDNA sequencingMicrobiome studiesDNA extractionMicrobial analysisClinical microbiologyMechanistic conceptsCautionary exampleImmune developmentRecent studiesHuman fetusesFetal tissuesMammalsGnotobiologyEcologyMicrobiologyFetal microbiomeBiology
2022
Proteotype coevolution and quantitative diversity across 11 mammalian species
Ba Q, Hei Y, Dighe A, Li W, Maziarz J, Pak I, Wang S, Wagner GP, Liu Y. Proteotype coevolution and quantitative diversity across 11 mammalian species. Science Advances 2022, 8: eabn0756. PMID: 36083897, PMCID: PMC9462687, DOI: 10.1126/sciadv.abn0756.Peer-Reviewed Original ResearchConceptsMammalian speciesRNA metabolic processesCommon mammalian speciesUbiquitin-proteasome systemEvolutionary profilingMammalian lineagesProteomic methodsProtein degradationProtein abundanceGene expressionProtein expression levelsHigh interspeciesMetabolic processesCovariation analysisFunctional roleNucleotide levelExpression levelsQuantitative diversityCoevolutionMammalsSpeciesRemarkable variationExpressionTranscriptomeBiological variabilityCellular recovery after prolonged warm ischaemia of the whole body
Andrijevic D, Vrselja Z, Lysyy T, Zhang S, Skarica M, Spajic A, Dellal D, Thorn SL, Duckrow RB, Ma S, Duy PQ, Isiktas AU, Liang D, Li M, Kim SK, Daniele SG, Banu K, Perincheri S, Menon MC, Huttner A, Sheth KN, Gobeske KT, Tietjen GT, Zaveri HP, Latham SR, Sinusas AJ, Sestan N. Cellular recovery after prolonged warm ischaemia of the whole body. Nature 2022, 608: 405-412. PMID: 35922506, PMCID: PMC9518831, DOI: 10.1038/s41586-022-05016-1.Peer-Reviewed Original ResearchConceptsSingle-nucleus transcriptomic analysesSpecific gene expression patternsCellular recoveryGene expression patternsCellular processesMammalian cellsTranscriptomic analysisLarge mammalsExpression patternsCellular repair processesCell deathComprehensive resourceUnderappreciated potentialPhysiological challengesTissue integrityRepair processSpecific changesPorcine brainMammalsOrgansMultiple organsSome thoughts about what non-mammalian jawed vertebrates are telling us about antigen processing and peptide loading of MHC molecules
Martin R, Kaufman J. Some thoughts about what non-mammalian jawed vertebrates are telling us about antigen processing and peptide loading of MHC molecules. Current Opinion In Immunology 2022, 77: 102218. PMID: 35687979, PMCID: PMC9586880, DOI: 10.1016/j.coi.2022.102218.Peer-Reviewed Original ResearchWound Healing Induced Hair Follicle Regeneration
Jiang Y, Myung P. Wound Healing Induced Hair Follicle Regeneration. Stem Cell Biology And Regenerative Medicine 2022, 72: 277-290. DOI: 10.1007/978-3-030-98331-4_13.Peer-Reviewed Original ResearchEmbryonic hair follicle developmentHair follicle developmentHair follicle regenerationHair follicle neogenesisDe novo hair folliclesComplex cellular signalingFollicle regenerationFollicle neogenesisDifferent cellular behaviorsHair follicle formationFollicle developmentLimited regeneration potentialCellular signalingExtrinsic signalsAppendage formationMore mechanistic studiesHair neogenesisCellular behaviorRegenerative woundCrucial playersHair folliclesAdult mammalsRegeneration potentialFollicle formationMammalsFossil biomolecules reveal an avian metabolism in the ancestral dinosaur
Wiemann J, Menéndez I, Crawford JM, Fabbri M, Gauthier JA, Hull PM, Norell MA, Briggs DEG. Fossil biomolecules reveal an avian metabolism in the ancestral dinosaur. Nature 2022, 606: 522-526. PMID: 35614213, DOI: 10.1038/s41586-022-04770-6.Peer-Reviewed Original ResearchConceptsHigh metabolic rateCretaceous mass extinctionTerminal Cretaceous mass extinctionLate Cretaceous taxaMetabolic rateCrown mammalsAvian lineagesAncestral stateEcological nichesGiant sauropodsCretaceous taxaMammalsMetabolic abilitiesMetabolic performanceMass extinctionBirdsPhysiological activityEndothermyAvian metabolismCostly adaptationsMetabolismVivo accumulationTheropodsOrnithischiansEctotherms
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