2025
The multilayered transcriptional architecture of glioblastoma ecosystems
Nomura M, Spitzer A, Johnson K, Garofano L, Nehar-belaid D, Galili Darnell N, Greenwald A, Bussema L, Oh Y, Varn F, D’Angelo F, Gritsch S, Anderson K, Migliozzi S, Gonzalez Castro L, ChowdhFury T, Robine N, Reeves C, Park J, Lipsa A, Hertel F, Golebiewska A, Niclou S, Nusrat L, Kellet S, Das S, Moon H, Paek S, Bielle F, Laurenge A, Di Stefano A, Mathon B, Picca A, Sanson M, Tanaka S, Saito N, Ashley D, Keir S, Ligon K, Huse J, Yung W, Lasorella A, Verhaak R, Iavarone A, Suvà M, Tirosh I. The multilayered transcriptional architecture of glioblastoma ecosystems. Nature Genetics 2025, 57: 1155-1167. PMID: 40346361, PMCID: PMC12081307, DOI: 10.1038/s41588-025-02167-5.Peer-Reviewed Original ResearchConceptsCell typesSingle-nucleus RNA sequencingDiversity of cellular statesMalignant cell statesGene expression programsTumor DNA sequencingDNA sequencesTranscriptional architectureCellular statesTranscriptional heterogeneityRNA sequencingCell statesCellular heterogeneityExpression programsGenetic aberrationsRecurrent GBM samplesPathway activationLayer of heterogeneityNeuronal-likeNonmalignant cell typesGBM samplesTherapeutic resistanceSequenceEcosystemCell-likeDeciphering the longitudinal trajectories of glioblastoma ecosystems by integrative single-cell genomics
Spitzer A, Johnson K, Nomura M, Garofano L, Nehar-belaid D, Darnell N, Greenwald A, Bussema L, Oh Y, Varn F, D’Angelo F, Gritsch S, Anderson K, Migliozzi S, Gonzalez Castro L, Chowdhury T, Robine N, Reeves C, Park J, Lipsa A, Hertel F, Golebiewska A, Niclou S, Nusrat L, Kellet S, Das S, Moon H, Paek S, Bielle F, Laurenge A, Di Stefano A, Mathon B, Picca A, Sanson M, Tanaka S, Saito N, Ashley D, Keir S, Ligon K, Huse J, Yung W, Lasorella A, Iavarone A, Verhaak R, Tirosh I, Suvà M. Deciphering the longitudinal trajectories of glioblastoma ecosystems by integrative single-cell genomics. Nature Genetics 2025, 57: 1168-1178. PMID: 40346362, PMCID: PMC12081298, DOI: 10.1038/s41588-025-02168-4.Peer-Reviewed Original ResearchConceptsSingle-cell genomicsSingle-nucleus RNA sequencingMalignant cell statesDNA sequencesNeuronal cell typesTumor microenvironmentRNA sequencingMalignant cell fractionCell statesCell typesCell fractionIsocitrate dehydrogenase (IDH)-wildtype glioblastomaStandard-of-care therapyCo-evolutionMolecular heterogeneityTumor microenvironment modifierEcosystemTumor microenvironment compositionSubsets of patientsSequenceRecurrent glioblastomaOrganic carbon dry deposition outpaces atmospheric processing with unaccounted implications for air quality and freshwater ecosystems
Liggio J, Makar P, Li S, Hayden K, Darlington A, Moussa S, Wren S, Staebler R, Wentzell J, Wheeler M, Leithead A, Mittermeier R, Narayan J, Wolde M, Blanchard D, Aherne J, Kirk J, Lee C, Stroud C, Zhang J, Akingunola A, Katal A, Cheung P, Ghahreman R, Majdzadeh M, He M, Ditto J, Gentner D. Organic carbon dry deposition outpaces atmospheric processing with unaccounted implications for air quality and freshwater ecosystems. Science Advances 2025, 11: eadr0259. PMID: 39752507, PMCID: PMC11698116, DOI: 10.1126/sciadv.adr0259.Peer-Reviewed Original ResearchDry depositionFreshwater ecosystemsOrganic carbonInclusion of dry depositionRegional air quality modelAir quality modelsOrganic carbon deposition rateReactive organic carbonReactive carbonLarge-scale estimatesChemical oxidation processAir qualityAtmospheric processesTerrestrial sourcesQuality modelEnvironmental systemsCarbon balanceDeposition algorithmEcosystemDepositionFluxOxidation processCarbonCarbon deposition rateDeposition ratePathogens and planetary change
Carlson C, Brookson C, Becker D, Cummings C, Gibb R, Halliday F, Heckley A, Huang Z, Lavelle T, Robertson H, Vicente-Santos A, Weets C, Poisot T. Pathogens and planetary change. Nature Reviews Biodiversity 2025, 1: 32-49. DOI: 10.1038/s44358-024-00005-w.Peer-Reviewed Original ResearchBiodiversity lossAnthropogenic environmental changesLand-use changeBiodiversity conservationWildlife healthLand-useEcological costsDie-offGlobal changeBiodiversityEnvironmental changesEcological interventionsLive animal marketsInfectious disease riskPathogen surveillanceHuman-animal contactPathogensVector-borne diseasesSpeciesEvolutionary principlesWildlifeHigh-risk virusesEcosystemGlobal gapConservation
2024
Beautoide A, an Anti‐Osteoclastogenic Sterol from Beauveria sp. NBUF147 Associated with an Irciniidae Sponge from the Marine Mesophotic Zone
Ran G, Wang P, Wang H, Wei T, Liu Y, Jin H, Wang T, He S. Beautoide A, an Anti‐Osteoclastogenic Sterol from Beauveria sp. NBUF147 Associated with an Irciniidae Sponge from the Marine Mesophotic Zone. Chemistry & Biodiversity 2024, 21: e202401689. PMID: 39136520, DOI: 10.1002/cbdv.202401689.Peer-Reviewed Original ResearchMesophotic coral ecosystemsMesophotic zoneCoral ecosystemsBeauveria sp.Prednisolone-induced osteoporotic zebrafishMarine bioresourcesMarineEvaluation of biological activityIrciniidaeSterolsBeauveriaBiological activityEcosystemAnti-osteoclastogenicX-ray crystallographyAnalysis of spectroscopic dataSpongeBioactive moleculesDepthZoneZebrafishBioresourcesChemical investigationX-rayThe Progression of Microbiome Therapeutics for the Management of Gastrointestinal Diseases and Beyond
Allegretti J, Khanna S, Mullish B, Feuerstadt P. The Progression of Microbiome Therapeutics for the Management of Gastrointestinal Diseases and Beyond. Gastroenterology 2024, 167: 885-902. PMID: 38754739, DOI: 10.1053/j.gastro.2024.05.004.Peer-Reviewed Original ResearchFecal microbiota transplantationMicrobiome therapeuticsNext generation sequencingIntestinal ecosystemHuman microbiotaMicrobiota restorationGeneration sequencingGastrointestinal microbiomeMicrobiota transplantationMicrobiotaExtraintestinal conditionsMitigate diseaseIncreased abilityEcosystemMicrobiomeTherapeuticsGastrointestinal diseasesSequenceA method for sampling the living wood microbiome
Arnold W, Gewirtzman J, Raymond P, Bradford M, Butler C, Peccia J. A method for sampling the living wood microbiome. Methods In Ecology And Evolution 2024, 15: 1084-1096. DOI: 10.1111/2041-210x.14311.Peer-Reviewed Original ResearchGlobal microbial ecologyExtraction of nucleic acidsGlobal biogeochemical cyclesTree microbiomeUnique taxaEndophytic microbiomeDiverse taxaDownstream analysisTree speciesMicrobiomeBiogeochemical cyclesMicrobial lifeTaxaDiverse environmentsNucleic acidsMicrobial analysisEcosystem healthSpeciesMethane cycleTreesEndophytesWoodNicheLeavesEcosystemA guideline on the molecular ecosystem regulating ferroptosis
Dai E, Chen X, Linkermann A, Jiang X, Kang R, Kagan V, Bayir H, Yang W, Garcia-Saez A, Ioannou M, Janowitz T, Ran Q, Gu W, Gan B, Krysko D, Zhu X, Wang J, Krautwald S, Toyokuni S, Xie Y, Greten F, Yi Q, Schick J, Liu J, Gabrilovich D, Liu J, Zeh H, Zhang D, Yang M, Iovanna J, Kopf M, Adolph T, Chi J, Li C, Ichijo H, Karin M, Sankaran V, Zou W, Galluzzi L, Bush A, Li B, Melino G, Baehrecke E, Lotze M, Klionsky D, Stockwell B, Kroemer G, Tang D. A guideline on the molecular ecosystem regulating ferroptosis. Nature Cell Biology 2024, 26: 1447-1457. PMID: 38424270, PMCID: PMC11650678, DOI: 10.1038/s41556-024-01360-8.Peer-Reviewed Original Research
2022
Trait-based approaches to global change ecology: moving from description to prediction
Green S, Brookson C, Hardy N, Crowder L. Trait-based approaches to global change ecology: moving from description to prediction. Proceedings Of The Royal Society B 2022, 289: 20220071. PMID: 35291837, PMCID: PMC8924753, DOI: 10.1098/rspb.2022.0071.Peer-Reviewed Original ResearchConceptsTrait-based approachGlobal change predictionsGlobal changeIntensifying global changesPredicting ecological effectsConservation decision-makingChange predictionsGlobal change ecologyTrait-based researchLife history traitsTraits to changesEcological effectsAbiotic limitationsEnvironmental filteringSpecies distributionSpecies rangeChange ecologyEnvironmental parametersMultivariate traitsOrgan sizePlant morphologyTraitsOrgan distributionEcosystemRe-assembly
2020
A global parasite conservation plan
Carlson C, Hopkins S, Bell K, Doña J, Godfrey S, Kwak M, Lafferty K, Moir M, Speer K, Strona G, Torchin M, Wood C. A global parasite conservation plan. Biological Conservation 2020, 250: 108596. DOI: 10.1016/j.biocon.2020.108596.Peer-Reviewed Original Research
2019
The Mathematics of Extinction Across Scales: From Populations to the Biosphere
Carlson C, Burgio K, Dallas T, Getz W. The Mathematics of Extinction Across Scales: From Populations to the Biosphere. Mathematics Of Planet Earth 2019, 5: 225-264. DOI: 10.1007/978-3-030-22044-0_9.Peer-Reviewed Original ResearchSpecies–area relationshipPopulation viability analysisOccupancy modelsSighting recordsExtinction riskConservation biologistsRare birdsViability analysisExtinction dateExtinction ratesEvolutionary rescueSpix's macawsMass extinctionExtinctionQuantitative challengesChanging environmentEcologistsEcosystemConservationBirdsAnalytical methodBiosphereSpeciesSpixPopulationCyclic Metabolism as a Mode of Microbial Existence
Dorofeev A, Nikolaev Y, Mardanov A, Pimenov N. Cyclic Metabolism as a Mode of Microbial Existence. Microbiology 2019, 88: 402-415. DOI: 10.1134/s0026261719040052.Peer-Reviewed Original ResearchType of metabolismCyclic cultivationBiomass biosynthesisMicrobial existenceContinuous cultivationDevelopment of microorganismsPhysiological groupsBiochemical modelNatural ecosystemsGeneration timeEcological aspectsMicroorganismsCyclic metabolismMetabolismCultivationBiosynthesisTraditional batchBacteriaTwo-phase growthStable ambient conditionsEcosystemOrganizationMicroplastics in the diet of nestling double-crested cormorants (Phalacrocorax auritus), an obligate piscivore in a freshwater ecosystem
Brookson C, de Solla S, Fernie K, Cepeda M, Rochman C. Microplastics in the diet of nestling double-crested cormorants (Phalacrocorax auritus), an obligate piscivore in a freshwater ecosystem. Canadian Journal Of Fisheries And Aquatic Sciences 2019, 76: 2156-2163. DOI: 10.1139/cjfas-2018-0388.Peer-Reviewed Original ResearchLaurentian Great LakesAnthropogenic debrisDouble-crested cormorantsGreat LakesPhalacrocorax auritusDiet of double-crested cormorantsObligate piscivoresCormorant chicksFreshwater ecosystemsIngested debrisAquatic ecosystemsCharacterize debrisMarine systemsAmount of debrisAnthropogenic materialsFreshwater birdsFreshwater systemsDiving birdsCormorantsLaurentianMicroplasticsFreshwaterEcosystemLakeBirds
2007
Anopheles gambiae exploits the treehole ecosystem in western Kenya: a new urban malaria risk?
Omlin F, Carlson J, Ogbunugafor C, Hassanali A. Anopheles gambiae exploits the treehole ecosystem in western Kenya: a new urban malaria risk? American Journal Of Tropical Medicine And Hygiene 2007, 77: 264-9. PMID: 18165501, DOI: 10.4269/ajtmh.2007.77.264.Peer-Reviewed Original Research
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