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Marine mammal noise-exposure criteria: Initial scientific recommendations

Bioacoustics 2008年第1-3期17卷 273-275页

作者： Southall, Brandon L. Bowles, Ann E. Ellison, William T. Finneran, James J. Gentry, Roger L. Greene, Charles R. Kastak, David Ketten, Darlene R. Miller, James H. Nachtigall, Paul E. Richardson, W. John Thomas, Jeanette A. Tyack, Peter L. Marine Ecosystems Division Ocean Acoustics Program National Oceanic and Atmospheric Administration (NOAA) National Marine Fisheries Service Office of Science and Technology Silver Spring MD 20910-6233 1315 East-West Highway United States Long Marine Laboratory University of California Santa Cruz Santa Cruz CA 95060 100 Shaffer Road United States Hubbs-Sea World Research Institute San Diego CA 92109 2595 Ingraham Street United States Marine Acoustics Inc. Middletown RI 02842 809 Aquidneck Avenue United States U. S. Navy Marine Mammal Program Space and Naval Warfare Systems Center San Diego San Diego CA 92152-5000 53560 Hull Street United States ProScience Consulting LLC Dickerson MD 20842-0177 22331 Mt. Ephraim Road United States Greeneridge Sciences Inc. Santa Barbara CA 93110 4512 Via Huerto United States Woods Hole Oceanographic Institution Woods Hole MA 02543 United States Department of Otology and Laryngology Harvard Medical School Boston MA 02114 United States Department of Ocean Engineering University of Rhode Island Narragansett RI 02882 South Ferry Road United States Hawaii Institute of Marine Biology Kane'ohe HI 96744 P.O. Box 1346 United States LGL Ltd. Environmental Research Associates King City ON L7B 1A6 P.O. Box 280 22 Fisher Street Canada Department of Biological Sciences Western Illinois University Quad Cities Moline IL 61265 3561 60th Street United States

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关键词： MARINE animals

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The impact of climate change on global wheat production

The impact of climate change on global wheat production

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第七届国际作物科学大会

作者： S.Asseng P.Martre A.Maiorano R.P.Rtter G.O'Leary G.Fitzgerald C.Girousse M.A.Baber M.P.Reynolds A.M.S.Kheir P.J.Thorburn K.Waha A.C.Ruane P.K.Aggarwal M.Ahmed J.Balkovic B.Basso A.Berger C.Biernath M.Bindi D.Cammarano A.J.Challinor G.De Sanctis J.Doltra B.Dumont E.Eyshi Rezaei E.Fereres R.Ferrise M.Garcia-Vila S.Gayler G.Hoogenboom R.C.Izaurralde M.Jabloun C.D.Jones B.T.Kassie K.C.Kersebaum C.Klein A.K.Koehler B.Liu S.Minoli M.Montesino San Martin C.Muller S.Naresh Kumar C.Nendel J.E.Olesen T.Palosuo J.R.Porter E.Priesack D.Ripoche M.A.Semenov C.Stockle P.Stratonovitch T.Streck I.Supit F.Tao M.Van der Velde D.Wallach E.Wang H.Webber J.Wolf P.Woli Z.Zhang Y.Zhu F.Ewert Agricultural & Biological Engineering Department University of Florida UMR GDEC INRAUniversite Blaise Pascal World Food Crops Breeding(wheat & oat) 3105 McCarty Hall BDepartment of AgronomyIFASUniversity of Florida CIMMYT Int.Adpo D.F.Mexico CSIRO Agriculture Flagship CSIRO Queensland Biosci Precinct St Lucia CGIAR Research Program on Climate Change Agriculture and Food SecurityInternational Water Management Institute Biological Systems Engineering Washington State University Department of agronomy PMAS Arid Agriculture University Comenius University Faculty of Natural ScienceDepartment of Soil Science Department of Geological Sciences Michigan State University W.K.Kellogg Biological Station Michigan State University Department of Agri-food Production and Environmental Sciences(DISPAA) University of Florence Institute for Climate and Atmospheric Science School of Earth and EnvironmentUniversity of Leeds CGIAR-ESSP Program on Climate Change Agriculture and Food SecurityInternational Centre for Tropical Agriculture(CIAT) Institute of Crop Science and Resource Conservation INRES University of Bonn IAS-CSIC and University of Cordoba Institute of Soil Science and Land Evaluation University of Hohenheim Department of Geographical Sciences University of Maryland Texas A&M AgriLife Research and Extension Center Texas A&M University Department of Agroecology Aarhus University Institute of Biochemical Plant Pathology Helmholtz Zentrum Munchen-German Research Center for Environmental Health College of Agriculture Nanjing Agricultural University Potsdam Institute for Climate Impact Research University of Copenhagen Department of Plant & Environmental Science Centre for Environment Science and Climate Resilient Agriculture Indian Agricultural Research InstituteIARI PUSA University of Greenwich Natural Resources Institute INRA US1116 AgroClim Computational and Systems Biology Department Rothamsted Research Plant Production Systems & Earth System Science Wageningen University Institute of Geographical Sciences and Natu

The Agricultural Model Intercomparison and Improvement Project has shown that many wheat crop models can simulate grain yields and growth dynamics under a range of growing conditions,but simulation results often *** model uncertainties increase with higher temperatures and with combined increased temperature and CO,however,multi-model ensemble medians have proven with field observations to be a good predictor of observed data under various growing *** multi-model ensemble median simulations showed that global wheat production declines by 6% for each degree of global temperature *** simulated impact is similar to temperature impact assessments using statistical regression methods with aggregated farm *** on the temperature impact study,new simulations of increased temperature were combined with elevated CO and rainfall changes to assess their impact on yield and protein and included the possible role of genetic adaptations to climate change at local,regional and global scales.

关键词： Global foods security Climate change Adaptation Wheat

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Measuring 60-pc-scale Star Formation Rate of the Nearby Seyfert Galaxy NGC 1068 with ALMA, HST, VLT/MUSE, and VLA

arXiv

引用

arXiv 2024年

作者： Nagashima, Yuzuki Saito, Toshiki Ikarashi, Soh Takano, Shuro Nakanishi, Kouichiro Harada, Nanase Nakajima, Taku Taniguchi, Akio Tosaki, Tomoka Bamba, Kazuharu Physics and Mechatronics Course Major in Symbiotic Systems Science and Technology Graduate School of Symbiotic Systems Science and Technology Fukushima University 1 Kanayagawa Fukushima Fukushima960-1296 Japan National Astronomical Observatory of Japan 2-21-1 Osawa Mitaka Tokyo181-8588 Japan Faculty of Global Interdisciplinary Science and Innovation Shizuoka University 836 Ohya Suruga-ku Shizuoka422-8529 Japan Department of Physics General Studies College of Engineering Nihon University Tamura-machi Fukushima Koriyama963-8642 Japan Astronomical Science Program Graduate Institute for Advanced Studies SOKENDAI 2-21-1 Osawa Mitaka Tokyo181-1855 Japan Institute for Space-Earth Environmental Research Nagoya University Furo-cho Chikusa-ku Aichi Nagoya464-8601 Japan Department of Physics Graduate School of Science Nagoya University Furo-cho Chikusa-ku Aichi Nagoya464-8602 Japan Department of Geoscience Joetsu University of Education Yamayashiki-machi Niigata Joetsu943-8512 Japan

Star formation rate (SFR) is a fundamental parameter for describing galaxies and inferring their evolutionary course. H II regions yield the best measure of instantaneous SFR in galaxies, although the derived SFR can have large uncertainties depending on tracers and assumptions. We present an SFR calibration for the entire molecular gas disk of the nearby Seyfert galaxy NGC 1068, based on our new high-sensitivity ALMA 100 GHz continuum data at 55 pc (= 0′′ . 8) resolution in combination with the HST Paα line data. In this calibration, we account for the spatial variations of dust extinction, electron temperature of H II regions, AGN contamination, and diffuse ionized gas (DIG) based on publicly available multi-wavelength data. Especially, given the extended nature and the possible non-negligible contribution to the total SFR, a careful consideration of DIG is essential. With a cross-calibration between two corrected ionized gas tracers (free-free continuum and Paα), the total SFR of the NGC 1068 disk is estimated to be 3.2 ± 0.5 M☉ yr−1, one-third of the SFR without accounting for DIG (9.1 ± 1.4 M☉ yr−1). We confirmed high SFR around the southern bar-end and the corotation radius, which is consistent with the previous SFR measurements. In addition, our total SFR exceeds the total SFR based on 8 µm dust emission by a factor of 1.5. We attribute this discrepancy to the differences in the young stars at different stages of evolution traced by each tracer and their respective timescales. This study provides an example to address the various uncertainties in conventional SFR measurements and their potential to lead to significant SFR miscalculations. © 2024, CC0.

关键词： Galaxies

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Effect of adoption of electric vehicles on public health and air pollution in China: a modelling study

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The Lancet Planetary Health 2021年 5卷 S8-S8页

作者： Daniel E Horton Jordan L Schnell Daniel R Peters David C Wong Xi Lu Hao Gao Hongliang Zhang Patrick L Kinney Department of Earth and Planetary Sciences and Institute for Sustainability and Energy Northwestern University Evanston IL USA Cooperative Institute for Research in Environmental Sciences at the University of Colorado Boulder National Oceanic and Atmospheric Administration Global Systems Laboratory Boulder CO USA Program in Environmental Sciences Northwestern University Evanston IL USA Environmental Defense Fund Austin TX USA US Environmental Protection Agency Research Triangle Park NC USA School of Environment State Key Joint Laboratory of Environment Simulation and Pollution Control Tsinghua University Beijing China Beijing China Department of Earth System Science University of California Irvine Irvine CA USA Department of Environmental Science and Engineering Fudan University Shanghai China Department of Environmental Health Boston University School of Public Health Boston MA USA

Background Adoption of electric vehicles has the potential to reduce air pollutant and greenhouse gas emissions, hence China has implemented policies incentivising use of electric vehicles. However, much is unknown about the potential air quality and public health benefits of electric vehicles, including optimal vehicle type prioritisation and the vehicles' ability to reduce acute health impacts due to extreme air quality events. We aimed to assess the potential climate and acute public health benefits of use of electric vehicles during an extreme winter air pollution event. Methods In this modelling study, we used the Weather Research Forecast and Community Multiscale Air Quality Modeling System air quality model to simulate the interplay between weather and atmospheric chemistry. We used this model to examine potential co-benefits of electric vehicle adoption during an extreme pollution episode in China. We simulated heavy-duty and light-duty electric vehicle adoption scenarios, in which 40% of the population adopted a heavy-duty or light-duty passenger electric vehicle, re-mapped battery power needs to energy generation facilities, and characterised differences in public health outcomes using China-specific concentration-response functions. Findings We found that widespread adoption of heavy-duty electric vehicles would reduces nitric oxide and fine particulate matter resulting in 562 (95% CI 410–723) fewer premature acute deaths than the non-electrified baseline scenario. However, widespread adoption of heavy-duty electric vehicles does not reduce carbon dioxide emissions without the addition of emission-free electricity generation. By contrast, widespread adoption of light-duty electric vehicles robustly reduces greenhouse gas emissions, but results in lesser air quality improvements and fewer premature deaths avoided (145 [95% CI 38–333]) than the heavy-duty scenario. Economic effects of human health endpoints and carbon dioxide reductions for adoption of ligh

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THE NAVYS TECHNOLOGICAL PROGRESS IN WATER POLLUTION ABATEMENT

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Naval Engineers Journal 1968年第5期80卷 795-801页

作者： SINGERMAN, HAROLD H. KINNEY, EDWARD T. Mr. H. H. Singerman is Head of the Fluid Processes Branch of the Annapolis Division of the Naval Ship Research and Development Center. A native of Massachusetts he has been at the Center since 1951. He has a B.S. in Chemical Engineering from Northeastern University and is a degree candidate for Master of Public Administration (Technology of Management) at the American University. His group is responsible for Research and Development in such diverse fields as life support in nuclear submarines analytical chemistry water treatment and control and shipboard sewage systems. He is a member of the American Institute of Chemical Engineers. Mr. E. T. Kinney a native of Grand Rapids Michigan earned his Bachelor of Science degree with honors in Civil Engineering from Michigan State University in 1952. After a brief stint as an assistant county engineer in Michigan he began his career with the Bureau of Ships as a Naval Architect in the Hull Design Training Program in September 1952. Mr. Kinney is currently a Project Coordinator in the Propulsion Power and Auxiliary Systems Division (SEC 6151) of NAVSEC where he is responsible for auxiliary and landing ships deep submersible vehicles and the NAVSEC Environmental Pollution Control Program. He is a member of the board of directors of the Federal Conference of Sanitary Engineers Panel M-17 of SNAME and Tau Beta Pi Engineering Honor Society.

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Ecology: Protect the deep seaAssociated Content

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Nature 2014年第7484期505卷 475-477页

作者： Edward B. Barbier David Moreno-Mateos Alex D. Rogers James Aronson Linwood Pendleton Roberto Danovaro Lea-Anne Henry Telmo Morato Jeff Ardron Cindy L. Van Dover Edward B. Barbier is professor of economics at the University of Wyoming Laramie. David Moreno-Mateos is at the CNRS Centre of Evolutionary and Functional Ecology Montpellier France. Alex D. Rogers is in the Department of Zoology University of Oxford UK. James Aronson is at the CNRS Centre of Evolutionary and Functional Ecology Montpellier France and at the Missouri Botanical Garden St Louis Missouri. Linwood Pendleton is senior fellow in the Ocean and Coastal Policy Program Nicholas Institute for Environmental Policy Solutions Duke University Durham North Carolina. Roberto Danovaro is in the Department of Life and Environmental Sciences Polytechnic University of Marche Ancona Italy and at the Anton Dohrn Zoological Station Naples Italy. Lea-Anne Henry is at the Centre for Marine Biodiversity and Biotechnology School of Life Sciences Heriot-Watt University Edinburgh UK. Telmo Morato is at the Institute of Marine Research in the Department of Oceanography and Fisheries University of the Azores Horta Portugal and at the Laboratory for Robotics and Systems in Engineering and Science Portugal. Jeff Ardron is at the Institute for Advanced Sustainability Studies Potsdam Germany. Cindy L. Van Dover is in the Division of Marine Science and Conservation Nicholas School of the Environment Duke University Beaufort North Carolina.

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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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BioTIME 2.0: Expanding and Improving a Database of Biodiversity Time Series

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Global Ecology and Biogeography 2025年第5期34卷

作者： Maria Dornelas Laura H. Antão Amanda E. Bates Viviana Brambilla Jonathan M. Chase Cher F. Y. Chow Ada Fontrodona-Eslava Anne E. Magurran Inês S. Martins Faye Moyes Alban Sagouis Samuel Adu-Acheampong Daniel Acquah-Lamptey Dušan Adam Penelope A. Ajani Aitor Albaina Pablo Almaraz Jeongseop An Roger Sigismund Anderson Madelaine Jean Robertson Anderson Alexsander Z. Antunes Ivan Arismendi Linda Armbrecht Pedro Aros-Mardones Sreejith Kalpuzha Ashtamoorthy Narayanan Ayyappan Gal Badihi Joseph J. Bailey Andrew H. Baird Mark Edward Baird Sreekumar Vadakkethil Balakrishnan José António L. Barão-Nóbrega Adi Barash Miguel Barbosa Jos Barlow Claus Bässler Matthieu Beaumont Natalie Beenaerts Tiago Octavio Begot Wallace Beiroz Ricardo Beldade David M. Bell Alecia Bellgrove Jonathan Belmaker Lisandro Benedetti-Cecchi Cassandra E. Benkwitt Pamela Medina-van Berkum Brandon T. Bestelmeyer Matthew G. Betts Maxwell Kelvin Billah Anne D. Bjorkman Magdalena Błażewicz Christopher P. Bloch Shane A. Blowes Antonio Bode Juliano A. Bogoni Thomas Bolger Timothy C. Bonebrake Erik Bonsdorff Roberta Bottarin Luke N. Brokensha Rob W. Brooker Andrew J. Brooks Helge Bruelheide Thiago Almeida Bueno Claire Laguionie Mariana Lopes Campagnoli James Cant Erica Pellegrini Caramaschi Alexandre Caron Tadhg Carroll Tancredi Caruso Juan Carvajal-Quintero Giuseppe Castaldelli Edward Castañeda-Moya Pedro V. Castilho Sonia Zanini Cechin Shahar Chaikin Uchangi Manjunatha Chandrashekara Tory J. Chase Chaolun Allen Chen Jorge José Cherem Sei-Woong Choi Erica M. Christensen Alexander V. Christianini Jackson Wing Four Chu Peter Coad Carl Van Colen Lise Comte Elisabeth J. Cooper J. Hans C. Cornelissen Eddy Cosson Unai Cotano Luc Crevecoeur Shannan Kyle Crow Graeme S. Cumming Vanessa S. Daga Gabriella Damasceno Gergana N. Daskalova Claire H. Davies Robert A. Davis Frank P. Day Sussy De-La-Zerda Amy Elizabeth Deacon Indradatta de Castro-Arrazola Steven Degraer Kharran Deonarinesingh Juan C. Diaz-Ricaurte Christopher R. Dickman Tara Dirilgen Ciaran John Dolan J. Emmet Centre for Biological Diversity School of Biology University of St Andrews Fife UK MARE—Centro de Ciências do Mar e do Ambiente Faculdade de Ciências Universidade de Lisboa Lisboa Portugal Research Centre for Ecological Change Organismal and Evolutionary Biology Research Programme Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland Department of Biology University of Victoria Victoria British Columbia Canada German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany Department of Computer Science Martin Luther University Halle-Wittenberg Halle (Saale) Germany Leverhulme Centre for Anthropocene Biodiversity Department of Biology University of York York UK Department of Animal Biology and Conservation Science University of Ghana Accra Ghana Philipps Universität Marburg Marburg Germany Department of Forest Ecology Silva Tarouca Research Institute Brno Czech Republic School of Life Sciences University of Technology Sydney Sydney New South Wales Australia Zoology and Animal Cell Biology Department University of the Basque Country (UPV/EHU) Leioa Spain Grupo de Oceanografía de Ecosistemas Instituto de Ciencias Marinas de Andalucía CSIC Campus Universitario de Puerto Real Puerto Real Spain National Institute of Ecology Seocheon Republic of Korea African Regional Postgraduate Programme in Insect Science University of Ghana Accra Ghana Département de Biologie Université de Sherbrooke Sherbrooke Quebec Canada Núcleo de Conservação da Biodiversidade Instituto de Pesquisas Ambientais Secretaria de Meio Ambiente Infraestrutura e Logística do Estado de São Paulo São Paulo Brazil Department of Fisheries Wildlife and Conservation Sciences Oregon State University Corvallis Oregon USA Institute for Marine and Antarctic Studies Ecology & Biodiversity Centre University of Tasmania Hobart Tasmania Australia Graduate Program in Oceanography Department of Oceanography Faculty of Natural Scienc

Motivation Here, we make available a second version of the BioTIME database, which compiles records of abundance estimates for species in sample events of ecological assemblages through time. The updated version expands version 1.0 of the database by doubling the number of studies and includes substantial additional curation to the taxonomic accuracy of the records, as well as the metadata. Moreover, we now provide an R package (BioTIMEr) to facilitate use of the database. Main Types of Variables Included The database is composed of one main data table containing the abundance records and 11 metadata tables. The data are organised in a hierarchy of scales where 11,989,233 records are nested in 1,603,067 sample events, from 553,253 sampling locations, which are nested in 708 studies. A study is defined as a sampling methodology applied to an assemblage for a minimum of 2 years. Spatial Location and Grain Sampling locations in BioTIME are distributed across the planet, including marine, terrestrial and freshwater realms. Spatial grain size and extent vary across studies depending on sampling methodology. We recommend gridding of sampling locations into areas of consistent size. Time Period and Grain The earliest time series in BioTIME start in 1874, and the most recent records are from 2023. Temporal grain and duration vary across studies. We recommend doing sample-level rarefaction to ensure consistent sampling effort through time before calculating any diversity metric. Major Taxa and Level of Measurement The database includes any eukaryotic taxa, with a combined total of 56,400 taxa. Software Format csv and. SQL.

关键词： assemblage biodiversity community database ecoinformatics species taxa time

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ANTARCTICA AND THE SOUTHERN OCEAN

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BULLETIN OF THE AMERICAN METEOROLOGICAL SOCIETY 2023年第9期104卷 S322-S365页

作者： Clem, Kyle R. Raphael, Marilyn N. School of Geography Environment and Earth Sciences Victoria University of Wellington Wellington New Zealand Scripps Institution of Oceanography University of California San Diego La Jolla California Department of Atmospheric and Oceanic Sciences University of Colorado Boulder Boulder Colorado Earth Science Observation Center Cooperative Institute for Research in Environmental Sciences (ESOC/CIRES) University of Colorado Boulder Boulder Colorado Argentine Naval Hydrographic Service Buenos Aires Argentina Department of Earth and Environmental Science Temple University Philadelphia Pennsylvania Department of Meteorology University of Valparaíso Valparaíso Chile Center for Climate and Resilience Research (CR)2 Santiago Chile British Antarctic Survey Cambridge United Kingdom Science Systems and Applications Inc. Lanham Maryland NASA Goddard Space Flight Center Greenbelt Maryland Royal Netherlands Meteorological Institute (KNMI) DeBilt The Netherlands Department of Marine Sciences University of Gothenburg Gothenburg Sweden Department of Geography Ohio University Athens Ohio NASA Jet Propulsion Laboratory Pasadena California NOAA/OAR Earth System Research Laboratory Global Monitoring Division Boulder Colorado University of Colorado Boulder Boulder Colorado National Oceanography Centre Southampton United Kingdom. Antarctic Meteorological Research and Data Center Space Science and Engineering Center University of Wisconsin-Madison Madison Wisconsin Department of Physical Sciences School of Arts and Sciences Madison Area Technical College Madison Wisconsin Australian Bureau of Meteorology and Institute for Marine and Antarctic Studies (IMAS) University of Tasmania Hobart Australia Earth Science and Observation Center CIRES University of Colorado Boulder Colorado University of St. Andrews St Andrews United Kingdom Princeton University Princeton New Jersey Australian Antarctic Division Australian Antarctic Program Partnership (AAPP) and Australian Centre fo

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Computation of Microbial Ecosystems in Time and Space (COMETS): An open source collaborative platform for modeling ecosystems metabolism

arXiv

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arXiv 2020年

作者： Dukovski, Ilija Bajić, Djordje Chacón, Jeremy M. Quintin, Michael Vila, Jean C.C. Sulheim, Snorre Pacheco, Alan R. Bernstein, David B. Riehl, William J. Korolev, Kirill S. Sanchez, Alvaro Harcombe, William R. Segrè, Daniel Bioinformatics Program Boston University BostonMA United States Biological Design Center Boston University BostonMA United States Department of Ecology and Evolutionary Biology Yale University New HavenCT United States Microbial Sciences Institute Yale University West HavenCT United States Department of Ecology Evolution and Behavior University of Minnesota St. PaulMN United States BioTechnology Institute University of Minnesota St. PaulMN United States Department of Biotechnology and Food Science Norwegian University of Science and Technology Trondheim Norway Department of Biotechnology and Nanomedicine SINTEF Industry Trondheim Norway Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory BerkeleyCA United States Department of Biomedical Engineering Boston University BostonMA United States Department of Physics Boston University BostonMA United States Department of Biology Boston University BostonMA United States

Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are also emerging as a valuable avenue for predicting, understanding and designing microbial communities. COMETS (Computation Of Microbial Ecosystems in Time and Space) was initially developed as an extension of dynamic flux balance analysis, which incorporates cellular and molecular diffusion, enabling simulations of multiple microbial species in spatially structured environments. Here we describe how to best use and apply the most recent version of this platform, COMETS 2, which incorporates a more accurate biophysical model of microbial biomass expansion upon growth, as well as several new biological simulation modules, including evolutionary dynamics and extracellular enzyme activity. COMETS 2 provides user-friendly Python and MATLAB interfaces compatible with the well-established COBRA models and methods, and comprehensive documentation and tutorials, facilitating the use of COMETS for researchers at all levels of expertise with metabolic simulations. This protocol provides a detailed guideline for installing, testing and applying COMETS 2 to different scenarios, with broad applicability to microbial communities across biomes and scales. Copyright © 2020, The Authors. All rights reserved.

关键词： Microorganisms

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