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Genome and clonal hematopoiesis stability contrasts with immune,cfDNA,mitochondrial,and telomere length changes during short duration spaceflight

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Precision clinical Medicine 2024年第1期7卷 1-13页

作者： J.Sebastian Garcia-Medina Karolina Sienkiewicz S.Anand Narayanan eliah G.Overbey Kirill Grigorev Krista A.Ryon Marissa Burke Jacqueline Proszynski Braden Tierney caleb M.Schmidt Nuria Mencia-Trinchant Remi Klotz Veronica Ortiz Jonathan Foox c.rist.pher chin Deena Najjar Irina Matei Irenaeus chan carlos cruchaga Ashley Kleinman JangKeun Kim Alexander Lucaci conor Loy Omary Mzava Iwijn De Vlaminck Anvita Singaraju Lynn e.Taylor Julian c.Schmidt Michael A.Schmidt Kelly Blease Juan Moreno Andrew Boddicker Junhua Zhao Bryan Lajoie Andrew Altomare Semyon Kruglyak Shawn Levy Min Yu Duane c.Hassane Susan M.Bailey Kelly Bolton Jaime Mateus c.rist.pher e.mason Department of Physiology and Biophysics Weill Cornell MedicineCornell UniversityNew YorkNY 10021USA The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for computational Biomedicine Weill Cornell MedicineNew YorkNY 10021USA Department of Immunology Weill Cornell MedicineCornell UniversityNew YorkNY 10021USA Department of Stem cell Biology and Regenerative Medicine Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA 90033USA Space exploration Technologies corporation HawthomeCA 90250USA Sovaris Aerospace BoulderCO 80302USA Advanced Pattern Analysis&Human Performance Group BoulderCO 80302USA children's cancer and Blood Foundation Laboratories Departments of Pediatrics and Cell and Developmental BiologyDrukier Institute for Children's HealthMeyer Cancer CenterWeill Cornell MedicineNew YorkNY 10021USA Meyer cancer center Weill Cornell MedicineNew YorkNY 10065USA Department of Nutrition and Integrative Physiology Florida State UniversityTallahasseeFL 32306USA Department of Systems engineering Colorado State UniversityFort CollinsCO 80523USA element Biosciences San DiegoCA 10055USA Department of environmental and Radiological Health Sciences Colorado State UniversityFort CollinsCO 80523USA cell and Molecular Biology Program Colorado State UniversityFort CollinsCO 80523USA BioAstra Inc New YorkNYUSA Washington University St Louis Oncology Division St.LouisMO 63100USA Meinig School of Biomedical engineering Cornell UniversityIthacaNY 14853USA The Feil Family Brain and Mind Research Institute Weill Cornell MedicineNY 10021USA WorldQuant Initiative for Quantitative Prediction Weill Cornell MedicineNew YorkNY 10021USA

Background The Inspiration4(I4)mission,the first all-civilian orbital flight mission,investigated the physiological effects of short-duration spaceflight through a multi-omic *** advances,there remains much to learn about human adaptation to spaceflight's unique challenges,including microgravity,immune system perturbations,and radiation *** To provide a detailed genetics analysis of the mission,we collected dried blood spots pre-,during,and post-flight for DNA *** length was measured by quantitative PcR,while whole genome and cfDNA sequencing provided insight into genomic stability and immune adaptations.A robust bioinformatic pipeline was used for data analysis,including variant calling to assess mutational *** Telomere elongation occurred during spaceflight and shortened after return to ***-free DNA analysis revealed increased immune cell signatures *** significant clonal hematopoiesis of indeterminate potential(cHIP)or whole-genome instability was *** long-term gene expression changes across immune cells suggested cellular adaptations to the space environment persisting months *** Our findings provide valuable insights into the physiological consequences of short-duration spaceflight,with telomere dynamics and immune cell gene expression adapting to spaceflight and persisting after return to *** sequencing data will serve as a reference point for studying the early development of cHIP in astronauts,an understudied phenomenon as previous studies have focused on career *** study will serve as a reference point for future commercial and non-commercial spaceflight,low earth orbit(LeO)missions,and deep-space exploration.

关键词： genomes clonal hematopoiesis stability immune mitochondria ribosomes spaceflight

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Translating current biomedical therapies for long duration,deep space missions

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Precision clinical Medicine 2019年第4期2卷 259-269页

作者： Sonia Iosim Matthew MacKay craig Westover c.rist.pher e.mason Department of Physiology and Biophysics Weill Cornell MedicineNew YorkNY 10021USA The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for computational Biomedicine Weill Cornell MedicineNew YorkNY 10021USA The Feil Family Brain and Mind Research Institute Weill Cornell MedicineNew YorkNY 10021USA The WorldQuant Initiative for Quantitative Prediction Weill Cornell MedicineNew YorkNY 10021USA

It is been shown that spaceflight-induced molecular,cellular,and physiologic changes cause alterations across many modalities of the human body,including cardiovascular,musculoskeletal,hematological,immunological,ocular,and neurological *** Twin Study,a multi-year,multi-omic study of human response to spaceflight,provided detailed and comprehensive molecular and cellular maps of the human response to radiation,microgravity,isolation,and *** rich data identified epigenetic,gene expression,inflammatory,and metabolic responses to spaceflight,facilitating a better biomedical roadmap of features that should be monitored and safe-guarded in upcoming ***,by exploring new developments in pre-clinical models and clinical trials,we can begin to design potential cellular interventions for exploration-class missions to Mars and potentially *** paper will discuss the overall risks astronauts face during spaceflight,what is currently known about human response to these risks,what pharmaceutical interventions exist for use in space,and which tools of precision medicine and cellular engineering could be applied to aerospace and astronaut medicine.

关键词： NASA spaceflight International Space Station NASA Twin Study multi-scale omics

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Long-term spaceflight and the cardiovascular system

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Precision clinical Medicine 2020年第4期3卷 284-291页

作者： Nicholas A.Vernice cem Meydan ebrahim Afshinnekoo c.rist.pher e.mason The Bin Talal Bin Abdulaziz Alsaud Institute for computational Biomedicine Weill Cornell Medicine1305 York AvenueNew YorkNY 10021USA Department of Physiology and Biophysics Weill Cornell Medicine1300 York AvenueNew YorkNY 10021USA The WordQuant Initiative for Quantitative Prediction Weill Cornell Medicine1300 York AvenueNew YorkNY 10021USA The Feil Family Brain and Mind Research Institute Weill Cornell Medicine1300 York Avenue New YorkNY 10021USA

While early investigations into the physiological effects of spaceflight suggest the body’s ability to reversibly adapt,the corresponding effects of long-term spaceflight(>6months)aremuch less *** exposure to microgravity and radiation yields profound effects on the cardiovascular system,including a massive cephalad fluid translocation and altered arterial pressure,which attenuate blood pressure regulatory mechanisms and increase cardiac ***,central venous pressure decreases as a result of the loss of venous *** stimulation of baroreceptors by the cephalad shift results in an approximately 10%–15%reduction in plasma volume,with fluid translocating from the vascular lumen to the *** possible increases in cardiac workload,myocyte atrophy and notable,yet unexplained,alterations in hematocrit have been *** is postulated to result from shunting of protein synthesis from the endoplasmic reticulum to the mitochondria via mortalin-mediated *** data are scarce regarding their causative agents,arrhythmias have been frequently reported,albeit sublethal,during both Russian and American expeditions,with QT interval prolongation observed in long,but not short duration,*** of the heart to the proton and heavy ion radiation of deep space has also been shown to result in coronary artery degeneration,aortic stiffness,carotid intima thickening via collagen-mediated action,accelerated atherosclerosis,and induction of a pro-inflammatory *** return,long-term spaceflight frequently results in orthostatic intolerance and altered sympathetic responses,which can prove hazardous should any rapidmobilization or evacuation be required,and indicates that these cardiac risks should be especially monitored for future missions.

关键词： microgravity cardiovascular system spaceflight aerospace medicine

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Landscape of global urban environmental resistome and its association with local socioeconomic and medical status

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Science china(Life Sciences) 2024年第6期67卷 1292-1301页

作者： Jun Wu Yige Hu Michael H Perlin David Danko Jun Lu Manuela Oliveira Johannes Werner Maria M Zambrano Maria A Sierra Olayinka O Osuolale Paweł Łabaj Nicolás Rascovan Nur Hazlin Hazrin-chong Soojin Jang Haruo Suzuki Marina Nieto-caballero Bharath Prithiviraj Patrick K H Lee Agnieszka chmielarczyk Anna Różańska Yongxiang Zhao Lan Wang c.rist.pher e.mason Tieliu Shi center for Bioinformatics and computational Biology and the Institute of Biomedical SciencesSchool of Life SciencesEast China Normal UniversityShanghai 200241China Department of Biology Program on Disease EvolutionUniversity of LouisvilleLouisville 40292USA Weill cornell Medicine New York 10065USA The Bin Talal Bin Abdulaziz Alsaud Institute for computational Biomedicine New York 10065USA Department of Pulmonary Medicine Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghai 200025China i3S-Instituto de Investiga玢o e Inova玢o em Saúde Universidade do PortoPorto 4050-290Portugal Ipatimup-Instituto de Patologia e Imunologia Molecular da Universidade do Porto Porto 4200-465Portugal Departamento de Biologia Faculdade de CiênciasUniversidade do PortoPorto 4050-290Portugal High Performance and cloud computing Group Zentrum für Datenverarbeitung(ZDV)Eberhard Karls University of TübingenW鋍hterstra遝7672074TübingenGermany corporación corpogen Research center Bogotá110311Colombia Applied environmental Metagenomics and Infectious Diseases Research(AeMIDR) Department of Biological SciencesElizade UniversityIlara-Mokin 340271Nigeria Maopolska centre of Biotechnology Jagiellonian UniversityKraków 30-005Poland Aix-Marseille Université Mediterranean Institute of OceanologyUniversitéde ToulonCNRSIRDUM 110Marseille 83041France Department of Biological Sciences and Biotechnology Faculty of Science and TechnologyUniversiti Kebangsaan Malaysia43600 UKM BangiSelangor Institut Pasteur Korea Seoul 13488Republic of Korea Faculty of environment and Information Studies Keio UniversityFujisawaKanagawa 252-0882Japan University of colorado at Boulder CivilEnvironmental and Architectural DepartmentBoulder 80303USA Brooklyn college of the city University of New York Brooklyn 11210USA School of energy and environment City University of Hong KongHong Kong 999077China Department of Microbiology Faculty of MedicineJagiellonian UniversityKraków 30-005Poland Biological Targeting Diagnosis and The

Antimicrobial resistance(AMR)poses a critical threat to global health and development,with environmental factors—particularly in urban areas—contributing significantly to the spread of antibiotic resistance genes(ARGs).However,most research to date has been conducted at a local level,leaving significant gaps in our understanding of the global status of antibiotic resistance in urban *** address this issue,we thoroughly analyzed a total of 86,213 ARGs detected within 4,728 metagenome samples,which were collected by the Meta SUB International consortium involving diverse urban environments in 60 cities of 27 countries,utilizing a deep-learning based *** findings demonstrated the strong geographical specificity of urban environmental resistome,and their correlation with various local socioeconomic and medical *** also identified distinctive evolutionary patterns of ARG-related biosynthetic gene clusters(BGcs)across different countries,and discovered that the urban environment represents a rich source of novel *** study provides a comprehensive overview of the global urban environmental resistome,and fills a significant gap in our knowledge of large-scale urban antibiotic resistome analysis.

关键词： urban environment metagenome antibiotic resistance resistance diversity biosynthetic gene clusters

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Improved gastrointestinal health for irritable bowel syndrome with metagenome-guided interventions

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Precision clinical Medicine 2020年第2期3卷 136-146页

作者： cem Meydan ebrahim Afshinnekoo Nate Rickard Guy Daniels Laura Kunces Theresa Hardy Loukia Lili Sarah Pesce Paul Jacobson c.rist.pher e.mason Joel Dudley Bodi Zhang Onegevity Health 152 W 57thNew YorkNY 10019USA Thorne Research 152 W 57thNew YorkNY 10019USA

Irritable bowel syndrome(IBS)is the most prevalent functional gastrointestinal disorder worldwide,and the most common reason for referral to gastroenterology ***,the pathophysiology is still not fully understood and consequently current management guidelines are very symptom-specific,leading to mixed *** we present a study of 88 individuals with IBS who had baseline sequencing of their gut microbiome(stool samples),received targeted interventions that included dietary,supplement,prebiotic/probiotic,and lifestyle recommendations for a 30-day period,and a follow-up sequencing of their gut *** study’s objectives were to demonstrate unique metagenomic signatures across the IBS phenotypes and to validate whether metagenomic-guided interventions could lead to improvement of symptom scores in individuals with *** subjects also completed a baseline and post-intervention questionnaire that assessed their symptom *** average symptom score of an individual with IBS at baseline was 160 and at the endpoint of the study the average symptom score of the cohort was *** mixed IBS subtype showed the most significant reduction in symptom scores across the different subtypes(average decrease by 102 points,P=0.005).The metagenomics analysis reveals shifts in the microbiome post-intervention that have been cross-validated with the literature as being associated with improvement of IBS *** the complex nature of IBS,further studies with larger sample sizes,more targeted analyses,and a broader population cohort are needed to explore these results further.

关键词： irritable bowel syndrome microbiome metagenomics

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The influence of stocking levels,clone,fertilization,and weed control on surface cO_(2)efflux in a mid-rotation Pinus radiata *** plantation in canterbury,New Zealand

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Journal of Forestry Research 2021年第6期32卷 2567-2575页

作者： Mohan Kc euan G.mason Horacio e.Bown School of Forestry University of CanterburyPrivate Bag 4800ChristchurchNew Zealand Ministry of Industry TourismForests and EnvironmentHetaudaBagmati ProvinceNepal Faculty of Forestry University of ChileP.O.Box 9206SantiagoChile

Silvicultural practices applied in managed forest plantations may help counteract the effects of climate change by influencing soil surface cO_(2)efflux(Fs).Understanding the effects of silvicultural practices on Fs will provide unbiased estimates of carbon fluxes and allow better silvicultural decisions for carbon ***,we assessed how Fs differed seasonally across silvicultural practices(i.e.,stocking levels,clone,fertilization and weed control treatments)and evaluated the effects of soil temperature(Ts)and soil volumetric water content(θv)on Fs across these practices for a mid-rotation(14 year-old)Pinus radiata plantation in the canterbury region of New *** were significant differences in Fs(per the four seasons,three levels of stocking,and five *** effects of fertilization and weed control applied 12 years previously on Fs were *** estimate of Fs(mean±1 standard deviation)from the study site was 22.7±7.1 t ha^(-1)a^(-1)in the form of cO_(2)(6.2±2.1 t ha^(-1)a^(-1)in the form of c).Fs values were consistently higher in plots with 1250 stems ha^(-1)compared to 2500 stems ha^(-1),which may be related to a strong soil resource limitation because of the close spacing in the latter *** differences in Fs across clones suggest that variations in carbon partitioning might explain their growth *** treatments influenced Fs response to soil temperature(pesulting in models explaining 28-49%of the total variance in *** findings provide insights into how silvicultural management decisions may impact Fs in mid-rotation radiata pine plantations,contributing towards developing more precise and unbiased plantation carbon budgets.

关键词： clone Silvicultural practices Soil cO_(2)efflux Stocking Weed control

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Impact of patch size on woody tree species richness and abundance in a tropical montane evergreen forest patches of south India

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Journal of Forestry Research 2018年第6期29卷 1675-1687页

作者： Dharmalingam Mohandass mason J.campbell Priya Davidar Root and Soil Biology Laboratory Department of BotanyBharathiar UniversityCoimbatoreTaminadu 641046India centre for Tropical environmental and Sustainability Science(T.e.S.S.) College of Science and EngineeringJames Cook UniversityCairnsQLD 4870Australia Department of ecology and environmental Sciences Pondicherry UniversityKalapetPondicherry 605014India

We examined the effects of forest patch size on woody tree species richness and abundance in tropical montane evergreen forest patches of the Nilgiri region,south India. We sampled woody trees(>1 cm dbh) from 21 forest patches in the upper Nilgiri hills(> 2000 m elevation) and recorded a total of 35,146 individuals of 61 species, 45 genera and 30 families. Species richness and abundance of sapling/shrubs(≥ 1 to cm dbh)increased significantly with increasing patch size, but the species richness and abundance of small, medium and larger trees(≥ 10 to cm dbh,respectively) did not. Overall, forest interior species richness and abundance increased significantly with increasing patch size but edge species richness did not. Species richness and abundance of shade-tolerant and shade-demanding tree species also increased with increasing patch size. The abundance of zoochory dispersed tree species was significantly related to increasing patch size, but those dispersed by autochory did not display any clear relationship between patch size and species richness or *** findings suggest that with increasing forest patch area,tree compositional patterns may be driven by species specific shade-tolerance adaptations and dispersal *** responses in these traits by the plant community within the individual habitat zones of forest edge and interiors likely plays a major role in determining the inherent plant community and thus the subsequent ecological processes of forest patches, including their responses to increasing patch area.

关键词： Dispersal mode Forest fragments Shade-tolerance Species–area relationships Western Ghats

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QuaPra: efficient transcript assembly and quantification using quadratic programming with Apriori algorithm

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Science china(Life Sciences) 2019年第7期62卷 937-946页

作者： Xiangjun Ji Weida Tong Baitang Ning c.rist.pher e. mason David P. Kreil Pawel P. Labaj Geng chen Tieliu Shi The center for Bioinformatics and computational Biology Shanghai Key Laboratory of Regulatory BiologyInstitute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China National center for Toxicological Research U.S. Food and Drug Administration3900 NCTR RDJefferson AR 72079USA Department of Physiology and Biophysics Weill Cornell MedicineNew York 10065USA The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for computational Biomedicine New York 10021USA Feil Family Brain & Mind Research Institute New York 10065USA chair of Bioinformatics Research Group Boku UniversityVienna A-1190Austria Malopolska centre of Biotechnology Jagiellonian UniversityKrakow 30-387Poland APART Fellow Austrian Academy of ScienceVienna A-1190Austria National center for International Research of Biological Targeting Diagnosis and Therapy Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy ResearchCollaborative Innovation Center for Targeting Tumor Diagnosis and TherapyGuangxi Medical UniversityNanning 530021China

RNA sequencing(RNA-seq) has greatly facilitated the exploring of transcriptome landscape for diverse ***,transcriptome reconstruction is still challenging due to various limitations of current tools and sequencing ***,we introduce an efficient tool,QuaPra(Quadratic Programming combined with Apriori),for accurate transcriptome assembly and *** could detect at least 26.5% more low abundance(0.1–1 FPKM) transcripts with over 2.7% increase of sensitivity and precision on simulated data compared to other currently popular ***,around one-quarter more known transcripts were correctly assembled by QuaPra than other assemblers on real sequencing *** is freely available at http://***/QuaPra/.

关键词： RNA-Seq transcriptome reconstruction transcript assembly transcript quantification

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The effect of active sitting on trunk motion

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Journal of Sport and Health Science 2014年第4期3卷 333-337页

作者： Henry Wang Kaitlyn J.Weiss mason c.Haggerty Jacqueline e.Heath School of Physical education Sportand Exercise ScienceBall State UniversityMuncieIN 47306USA

Background： Prolonged sitting is a risk factor for low-back pain. The primary purpose of this study is to determine if prolonged active sitting will result in increased trunk motion. Methods： Fifteen healthy female participants volunteered to sit for 30 vain on each of three surfaces including an air-cushion, a stability ball, and a hard surface. Trunk motion was monitored using a Vicon motion capture system, and foot center of pressure was collected with two AMTI force plates. Results： Our findings indicated that the average speed of the trunk center of mass significantly increased with seating surface compliance. There were significant differences in fight and left foot centers of pressure in the antero-posterior direction between the ball and air-cushion conditions and the ball and chair conditions. conclusion： Active sitting results in increased trunk motion and could have a positive effect on low-back health.

关键词： Active sitting Air-cushion center of pressure Low-back pain Stability ball Trunk motion

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Vertical stratification of ichneumonid wasp communities： the effects of forest structure and life-history traits

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Insect Science 2015年第5期22卷 688-699页

作者： Filippo Di Giovanni Pierfilippo cerretti Franco mason emma Minari Lorenzo Marini Dipartimento di Biologia e Biotecnologie 'charles Darwin' Universita di Roma 'La Sapienza' Piazzale A. Moro 5 00185 Rome Italy centro Nazionale per lo Studio e la conservazione della Biodiversita Forestale Corpo Forestale dello Stato via Carlo Ederle 161A 37100 Verona Italy and DAFNAe Universit& di Padova viale dell'Universita 16 35020 Legnaro Padua Italy

Parasitoid wasp communities of the canopy of temperate forests are still largely unexplored. Very little is known about the community composition ofparasitoids between canopy and understory and how much of this difference is related to forest structure or parasitoid biological strategies. In this study we investigated upon the difference in the community composition of the parasitic wasps Ichneumonidae between canopy and understory in a lowland temperate forest in northern Italy. We used general linear models to test whether parasitic strategy modifies species vertical stratification and the effect of forest structure. We also tested differences in β-diversity between canopy and understory traps and over time within single forest layers. We found that stand basal area was positively related to species richness, suggesting that the presence of mature trees can influence local wasp diversity, providing a higher number of microhabitats and hosts. The ichneumonid community of the canopy was different from that of the understory, and theβ-diversity analysis showed higher values for the canopy, due to a higher degree of species turnover between traps. In our analyses, the vertical stratification was different between groups of ichneumonids sharing different parasitic strategies. Idiobiont parasitoids of weakly or deeply concealed hosts were more diverse in the understory than in the canopy while parasitoids of spiders were equally distributed between the two layers. even though the ichneumonid community was not particularly species-rich in the canopy of the temperate forests, the extension of sampling to that habitat significantly increased the number of species recorded.

关键词： β-diversity biological traits canopy forest structure Ichneumonidae vertical stratification

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