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

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 christopher 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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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 christopher 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 christopher 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 christopher 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 christopher 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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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 christopher 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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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 christopher 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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Dynamics of self-hybridized exciton–polaritons in 2D halide perovskites

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Light(Science & Applications) 2024年第1期13卷 13-22页

作者： Surendra B.Anantharaman Jason Lynch christopher e.Stevens christopher Munley Chentao Li Jin Hou Hao Zhang Andrew Torma Thomas Darlington Francis Coen Kevin Li Arka Majumdar PJames Schuck Aditya Mohite Hayk Harutyunyan Joshua R.Hendrickson Deep Jariwala Department of electrical and Systems engineering University of PennsylvaniaPhiladelphiaPA19104USA KBR Inc. BeavercreekOH45431USA Air Force Research Laboratory Sensors DirectorateWright-Patterson Air Force BaseOH45433USA Department of Physics University of WashingtonSeattleWA98195USA Department of Physics Emory UniversityAtlantaGA30322USA Department of Chemical and Biomolecular engineering Rice UniversityHoustonTX77005USA Department of Materials Science and Nanoengineering Rice UniversityHoustonTX77005USA Applied Physics Program Smalley‐Curl InstituteRice UniversityHoustonTX77005USA Department of Mechanical engineering Columbia UniversityNew YorkNY10027USA Department of electrical and Computer engineering University of WashingtonSeattleWA98195USA

excitons,bound electron–hole pairs,in two-dimensional hybrid organic inorganic perovskites(2D HOIPs)are capable of forming hybrid light-matter states known as exciton-polaritons(e–Ps)when the excitonic medium is confined in an optical *** the case of 2D HOIPs,they can self-hybridize into e–Ps at specific thicknesses of the HOIP crystals that form a resonant optical cavity with the ***,the fundamental properties of these self-hybridized e–Ps in 2D HOIPs,including their role in ultrafast energy and/or charge transfer at interfaces,remain ***,we demonstrate that>0.5µm thick 2D HOIP crystals on Au substrates are capable of supporting multiple-orders of self-hybridized e–P *** e–Ps have high Q factors(>100)and modulate the optical dispersion for the crystal to enhance sub-gap absorption and *** varying excitation energy and ultrafast measurements,we also confirm energy transfer from higher energy e–Ps to lower energy e–***,we also demonstrate that e–Ps are capable of charge transport and transfer at *** findings provide new insights into charge and energy transfer in e–Ps opening new opportunities towards their manipulation for polaritonic devices.

关键词： charge polar excitation

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Ige-Mast cell mediated allergy: a sensor of food quality

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Signal Transduction and Targeted Therapy 2024年第1期9卷 8-9页

作者： christopher C.Udoye Rudolf A.Manz Institute for Systemic Inflammation Research University of LübeckLübeckGermany

In two recent studies published in Nature,Florsheim et *** Plum et *** that allergic-specific reactions induced by immunoglobulin(Ig)e mediated mast cell activation is crucial for the timely induction of antigen-avoidance behaviour.1,2 These studies prove the concept that allergic sensitization triggers the formation of avoidance behaviour and define the underlying molecular mechanism.

关键词： allergic mechanism

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Tocotrienol isoforms:The molecular mechanisms underlying their effects in cancer therapy and their implementation in clinical trials

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Journal of Integrative Medicine 2024年第1期22卷 1-11页

作者： Maria Younes Ghady Loubnane christopher Sleiman Sandra Rizk Department of Natural Sciences Lebanese American UniversityByblosLebanon

Tocotrienols are found in a variety of natural sources,like rice bran,annatto seeds and palm oil,and have been shown to have several health-promoting properties,particularly against chronic diseases such as *** incidence of cancer is rapidly increasing around the world,not only a result of continued aging and population growth,but also due to the adoption of aspects of the Western lifestyle,such as high-fat diets and low-physical *** literature provides strong evidence that tocotrienols are able to inhibit the growth of various cancers,including breast,lung,ovarian,prostate,liver,brain,colon,myeloma and pancreatic *** findings,along with the reported safety profile of tocotrienols in healthy human volunteers,encourage further research into these compounds’potential use in cancer prevention and *** current review provided detailed information about the molecular mechanisms of action of different tocotrienol isoforms in various cancer models and evaluated the potential therapeutic effects of different vitamin e analogues on important cancer hallmarks,such as cellular proliferation,apoptosis,angiogenesis and ***/PubMed and Scopus databases were used to identify recently published articles that investigated the anticancer effects of vitamin e derivatives in various types of cancer in vitro and in vivo along with clinical evidence of adjuvant chemopreventive *** an overview of pre-clinical studies,we describe several completed and ongoing clinical trials that are paving the way for the successful implementation of tocotrienols in cancer chemotherapy.

关键词： Vitamin e Tocotrienols Cancer Molecular mechanism Clinical trials

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Graphene-calcium carbonate coating to improve the degradation resistance and mechanical integrity of a biodegradable implant

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Journal of Magnesium and Alloys 2024年第1期12卷 394-404页

作者： Lokesh Choudhary Parama Chakraborty Banerjee R.K.Singh Raman Derrek e.Lobo christopher D.easton Mainak Majumder Frank Witte Jörg F.Löffler Department of Mechanical and Aerospace engineering Monash UniversityClayton CampusMelbourneVIC 3800Australia Department of Chemical and Biological engineering Monash UniversityClayton CampusMelbourneVIC 3800Australia Nanoscale Science and engineering Laboratory(NSeL) Bldg 37Monash UniversityClayton CampusMelbourneVIC 3800Australia CSIRO Materials Science and engineering Bayview AvenueClaytonVIC 3168Australia Julius Wolff Institute and Berlin Brandenburg Center for Regenerative Therapies Charité–Universitätsmedizin BerlinAugustenburger Platz 113353 BerlinGermany Laboratory of Metal Physics and Technology Department of MaterialsETH Zurich8093 ZurichSwitzerland

Biodegradable implants are critical for regenerative orthopaedic procedures,but they may suffer from too fast corrosion in human-body *** necessitates the synthesis of a suitable coating that may improve the corrosion resistance of these implants without compromising their mechanical *** this study,an AZ91 magnesium alloy,as a representative for a biodegradable Mg implant material,was modified with a thin reduced graphene oxide(RGO)-calcium carbonate(CaCO_(3))composite *** analytical and in-vitro electrochemical characterization reveals that this coating significantly improves the corrosion resistance and mechanical integrity,and thus has the potential to greatly extend the related application field.

关键词： Graphene coating Biodegradable implant Hydroxyapatite Corrosion Magnesium alloy

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