Science.gov

Sample records for earth microbiome project

  1. The Earth Microbiome Project and Global Systems Biology

    SciT

    Gilbert, Jack A.; Jansson, Janet K.; Knight, Rob

    Recently, we published the first large-scale analysis of data from the Earth Microbiome Project (1, 2), a truly multidisciplinary research program involving more than 500 scientists and 27,751 samples acquired from 43 countries. These samples represent myriad specimen types and span a wide range of biotic and abiotic factors, geographic locations, and physicochemical properties. The database (https://qiita.ucsd.edu/emp/) is still growing, with over 90,000 amplicon datasets, >500 metagenomic runs, and metabolomics datasets from a similar number of samples. Importantly, the techniques, data and analytical tools are all standardized and publicly accessible, providing a framework to support research at a scale ofmore » integration that just 7 years ago seemed impossible.« less

  2. Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project

    PubMed Central

    Gilbert, Jack A.; Meyer, Folker; Antonopoulos, Dion; Balaji, Pavan; Brown, C. Titus; Brown, Christopher T.; Desai, Narayan; Eisen, Jonathan A; Evers, Dirk; Field, Dawn; Feng, Wu; Huson, Daniel; Jansson, Janet; Knight, Rob; Knight, James; Kolker, Eugene; Konstantindis, Kostas; Kostka, Joel; Kyrpides, Nikos; Mackelprang, Rachel; McHardy, Alice; Quince, Christopher; Raes, Jeroen; Sczyrba, Alexander; Shade, Ashley; Stevens, Rick

    2010-01-01

    Between July 18th and 24th 2010, 26 leading microbial ecology, computation, bioinformatics and statistics researchers came together in Snowbird, Utah (USA) to discuss the challenge of how to best characterize the microbial world using next-generation sequencing technologies. The meeting was entitled “Terabase Metagenomics” and was sponsored by the Institute for Computing in Science (ICiS) summer 2010 workshop program. The aim of the workshop was to explore the fundamental questions relating to microbial ecology that could be addressed using advances in sequencing potential. Technological advances in next-generation sequencing platforms such as the Illumina HiSeq 2000 can generate in excess of 250 billion base pairs of genetic information in 8 days. Thus, the generation of a trillion base pairs of genetic information is becoming a routine matter. The main outcome from this meeting was the birth of a concept and practical approach to exploring microbial life on earth, the Earth Microbiome Project (EMP). Here we briefly describe the highlights of this meeting and provide an overview of the EMP concept and how it can be applied to exploration of the microbiome of each ecosystem on this planet. PMID:21304727

  3. The Earth Microbiome Project and modeling the planets microbial potential (Invited)

    NASA Astrophysics Data System (ADS)

    Gilbert, J. A.

    2013-12-01

    The understanding of Earth's climate and ecology requires multiscale observations of the biosphere, of which microbial life are a major component. However, to acquire and process physical samples of soil, water and air that comprise the appropriate spatial and temporal resolution to capture the immense variation in microbial dynamics, would require a herculean effort and immense financial resources dwarfing even the most ambitious projects to date. To overcome this hurdle we created the Earth Microbiome Project, a crowd-sourced effort to acquire physical samples from researchers around the world that are, importantly, contextualized with physical, chemical and biological data detailing the environmental properties of that sample in the location and time it was acquired. The EMP leverages these existing efforts to target a systematic analysis of microbial taxonomic and functional dynamics across a vast array of environmental parameter gradients. The EMP captures the environmental gradients, location, time and sampling protocol information about every sample donated by our valued collaborators. Physical samples are then processed using a standardized DNA extraction, PCR, and shotgun sequencing protocol to generate comparable data regarding the microbial community structure and function in each sample. To date we have processed >17,000 samples from 40 different biomes. One of the key goals of the EMP is to map the spatiotemporal variability of microbial communities to capture the changes in important functional processes that need to be appropriately expressed in models to provide reliable forecasts of ecosystem phenotype across our changing planet. This is essential if we are to develop economically sound strategies to be good stewards of our Earth. The EMP recognizes that environments are comprised of complex sets of interdependent parameters and that the development of useful predictive computational models of both terrestrial and atmospheric systems requires

  4. The Home Microbiome Project

    Gilbert, Jack

    2018-02-13

    The Home Microbiome Project is an initiative aimed at uncovering the dynamic co-associations between people's bacteria and the bacteria found in their homes.The hope is that the data and project will show that routine monitoring of the microbial diversity of your body and of the environment in which you live is possible.

  5. The Home Microbiome Project

    SciT

    Gilbert, Jack

    2014-08-25

    The Home Microbiome Project is an initiative aimed at uncovering the dynamic co-associations between people's bacteria and the bacteria found in their homes.The hope is that the data and project will show that routine monitoring of the microbial diversity of your body and of the environment in which you live is possible.

  6. The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010.

    PubMed

    Gilbert, Jack A; Meyer, Folker; Jansson, Janet; Gordon, Jeff; Pace, Norman; Tiedje, James; Ley, Ruth; Fierer, Noah; Field, Dawn; Kyrpides, Nikos; Glöckner, Frank-Oliver; Klenk, Hans-Peter; Wommack, K Eric; Glass, Elizabeth; Docherty, Kathryn; Gallery, Rachel; Stevens, Rick; Knight, Rob

    2010-12-25

    This report details the outcome the first meeting of the Earth Microbiome Project to discuss sample selection and acquisition. The meeting, held at the Argonne National Laboratory on Wednesday October 6(th) 2010, focused on discussion of how to prioritize environmental samples for sequencing and metagenomic analysis as part of the global effort of the EMP to systematically determine the functional and phylogenetic diversity of microbial communities across the world.

  7. The sponge microbiome project.

    PubMed

    Moitinho-Silva, Lucas; Nielsen, Shaun; Amir, Amnon; Gonzalez, Antonio; Ackermann, Gail L; Cerrano, Carlo; Astudillo-Garcia, Carmen; Easson, Cole; Sipkema, Detmer; Liu, Fang; Steinert, Georg; Kotoulas, Giorgos; McCormack, Grace P; Feng, Guofang; Bell, James J; Vicente, Jan; Björk, Johannes R; Montoya, Jose M; Olson, Julie B; Reveillaud, Julie; Steindler, Laura; Pineda, Mari-Carmen; Marra, Maria V; Ilan, Micha; Taylor, Michael W; Polymenakou, Paraskevi; Erwin, Patrick M; Schupp, Peter J; Simister, Rachel L; Knight, Rob; Thacker, Robert W; Costa, Rodrigo; Hill, Russell T; Lopez-Legentil, Susanna; Dailianis, Thanos; Ravasi, Timothy; Hentschel, Ute; Li, Zhiyong; Webster, Nicole S; Thomas, Torsten

    2017-10-01

    Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other environments (n = 29) were collected from different locations across the globe. This dataset incorporates at least 268 different sponge species, including several yet unidentified taxa. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA using standardised procedures. Raw sequences (total of 1.1 billion sequences) were processed and clustered with (i) a standard protocol using QIIME closed-reference picking resulting in 39 543 operational taxonomic units (OTU) at 97% sequence identity, (ii) a de novo clustering using Mothur resulting in 518 246 OTUs, and (iii) a new high-resolution Deblur protocol resulting in 83 908 unique bacterial sequences. Abundance tables, representative sequences, taxonomic classifications, and metadata are provided. This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host specificity, convergent evolution, environmental drivers of microbiome structure, and the sponge-associated rare biosphere. © The Authors 2017. Published by Oxford University Press.

  8. Parasite Microbiome Project: Systematic Investigation of Microbiome Dynamics within and across Parasite-Host Interactions.

    PubMed

    Dheilly, Nolwenn M; Bolnick, Daniel; Bordenstein, Seth; Brindley, Paul J; Figuères, Cédric; Holmes, Edward C; Martínez Martínez, Joaquín; Phillips, Anna J; Poulin, Robert; Rosario, Karyna

    2017-01-01

    Understanding how microbiomes affect host resistance, parasite virulence, and parasite-associated diseases requires a collaborative effort between parasitologists, microbial ecologists, virologists, and immunologists. We hereby propose the Parasite Microbiome Project to bring together researchers with complementary expertise and to study the role of microbes in host-parasite interactions. Data from the Parasite Microbiome Project will help identify the mechanisms driving microbiome variation in parasites and infected hosts and how that variation is associated with the ecology and evolution of parasites and their disease outcomes. This is a call to arms to prevent fragmented research endeavors, encourage best practices in experimental approaches, and allow reliable comparative analyses across model systems. It is also an invitation to foundations and national funding agencies to propel the field of parasitology into the microbiome/metagenomic era.

  9. Earth System Science Project

    ERIC Educational Resources Information Center

    Rutherford, Sandra; Coffman, Margaret

    2004-01-01

    For several decades, science teachers have used bottles for classroom projects designed to teach students about biology. Bottle projects do not have to just focus on biology, however. These projects can also be used to engage students in Earth science topics. This article describes the Earth System Science Project, which was adapted and developed…

  10. The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters

    PubMed Central

    Aagaard, Kjersti; Petrosino, Joseph; Keitel, Wendy; Watson, Mark; Katancik, James; Garcia, Nathalia; Patel, Shital; Cutting, Mary; Madden, Tessa; Hamilton, Holli; Harris, Emily; Gevers, Dirk; Simone, Gina; McInnes, Pamela; Versalovic, James

    2013-01-01

    The Human Microbiome Project used rigorous good clinical practice standards to complete comprehensive body site sampling in healthy 18- to 40-yr-old adults, creating an unparalleled reference set of microbiome specimens. To ensure that specimens represented minimally perturbed microbiomes, we first screened potential participants using exclusion criteria based on health history, including the presence of systemic diseases (e.g., hypertension, cancer, or immunodeficiency or autoimmune disorders), use of potential immunomodulators, and recent use of antibiotics or probiotics. Subsequent physical examinations excluded individuals based on body mass index (BMI), cutaneous lesions, and oral health. We screened 554 individuals to enroll 300 (149 men and 151 women, mean age 26 yr, mean BMI 24 kg/m2, 20.0% racial minority, and 10.7% Hispanic). We obtained specimens from the oral cavity, nares, skin, gastrointestinal tract, and vagina (15 specimens from men and 18 from women). The study evaluated longitudinal changes in an individual's microbiome by sampling 279 participants twice (mean 212 d after the first sampling; range 30-359 d) and 100 individuals 3 times (mean 72 d after the second sampling; range 30-224 d). This sampling strategy yielded 11,174 primary specimens, from which 12,479 DNA samples were submitted to 4 centers for metagenomic sequencing. Our clinical design and well-defined reference cohort has laid a foundation for microbiome research.—Aagaard, K., Petrosino, J., Keitel, W., Watson, M., Katancik, J., Garcia, N., Patel, S., Cutting, M., Madden, T., Hamilton, H., Harris, E., Gevers, D., Simone, G., McInnes, P., Versalovic, J. The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters. PMID:23165986

  11. Spaceship Earth Curriculum Project.

    ERIC Educational Resources Information Center

    McInnis, Noel; And Others

    Three separate papers from the Project are included in this document. One of these, by the Center staff, is entitled "Potentials of the Spaceship Earth Metaphor". It discusses static, dynamic, and analogic representations of spaceship earth and their educational value. A second paper, "Some Resources for Introducing Environmental…

  12. Strains, functions, and dynamics in the expanded Human Microbiome Project

    PubMed Central

    Lloyd-Price, Jason; Mahurkar, Anup; Rahnavard, Gholamali; Crabtree, Jonathan; Orvis, Joshua; Hall, A. Brantley; Brady, Arthur; Creasy, Heather H.; McCracken, Carrie; Giglio, Michelle G.; McDonald, Daniel; Franzosa, Eric A.; Knight, Rob; White, Owen; Huttenhower, Curtis

    2018-01-01

    Summary The characterization of baseline microbial and functional diversity in the human microbiome has enabled studies of microbiome-related disease, microbial population diversity, biogeography, and molecular function. The NIH Human Microbiome Project (HMP) has provided one of the broadest such characterizations to date. Here, we introduce an expanded second phase of the study, abbreviated HMP1-II, comprising 1,631 new metagenomic samples (2,355 total) targeting diverse body sites with multiple time points in 265 individuals. We applied updated profiling and assembly methods to these data to provide new characterizations of microbiome personalization. Strain identification revealed distinct subspecies clades specific to body sites; it also quantified species with phylogenetic diversity under-represented in isolate genomes. Body-wide functional profiling classified pathways into universal, human-enriched, and body site-enriched subsets. Finally, temporal analysis decomposed microbial variation into rapidly variable, moderately variable, and stable subsets. This study furthers our knowledge of baseline human microbial diversity, thus enabling an understanding of personalized microbiome function and dynamics. PMID:28953883

  13. The gut mycobiome of the Human Microbiome Project healthy cohort.

    PubMed

    Nash, Andrea K; Auchtung, Thomas A; Wong, Matthew C; Smith, Daniel P; Gesell, Jonathan R; Ross, Matthew C; Stewart, Christopher J; Metcalf, Ginger A; Muzny, Donna M; Gibbs, Richard A; Ajami, Nadim J; Petrosino, Joseph F

    2017-11-25

    Most studies describing the human gut microbiome in healthy and diseased states have emphasized the bacterial component, but the fungal microbiome (i.e., the mycobiome) is beginning to gain recognition as a fundamental part of our microbiome. To date, human gut mycobiome studies have primarily been disease centric or in small cohorts of healthy individuals. To contribute to existing knowledge of the human mycobiome, we investigated the gut mycobiome of the Human Microbiome Project (HMP) cohort by sequencing the Internal Transcribed Spacer 2 (ITS2) region as well as the 18S rRNA gene. Three hundred seventeen HMP stool samples were analyzed by ITS2 sequencing. Fecal fungal diversity was significantly lower in comparison to bacterial diversity. Yeast dominated the samples, comprising eight of the top 15 most abundant genera. Specifically, fungal communities were characterized by a high prevalence of Saccharomyces, Malassezia, and Candida, with S. cerevisiae, M. restricta, and C. albicans operational taxonomic units (OTUs) present in 96.8, 88.3, and 80.8% of samples, respectively. There was a high degree of inter- and intra-volunteer variability in fungal communities. However, S. cerevisiae, M. restricta, and C. albicans OTUs were found in 92.2, 78.3, and 63.6% of volunteers, respectively, in all samples donated over an approximately 1-year period. Metagenomic and 18S rRNA gene sequencing data agreed with ITS2 results; however, ITS2 sequencing provided greater resolution of the relatively low abundance mycobiome constituents. Compared to bacterial communities, the human gut mycobiome is low in diversity and dominated by yeast including Saccharomyces, Malassezia, and Candida. Both inter- and intra-volunteer variability in the HMP cohort were high, revealing that unlike bacterial communities, an individual's mycobiome is no more similar to itself over time than to another person's. Nonetheless, several fungal species persisted across a majority of samples, evidence that

  14. A Stoichioproteomic Analysis of Samples from the Human Microbiome Project

    PubMed Central

    Vecchio-Pagan, Briana; Bewick, Sharon; Mainali, Kumar; Karig, David K.; Fagan, William F.

    2017-01-01

    Ecological stoichiometry (ES) uses organism-specific elemental content to explain differences in species life histories, species interactions, community organization, environmental constraints and even ecosystem function. Although ES has been successfully applied to a range of different organisms, most emphasis on microbial ecological stoichiometry focuses on lake, ocean, and soil communities. With the recent advances in human microbiome research, however, large amounts of data are being generated that describe differences in community composition across body sites and individuals. We suggest that ES may provide a framework for beginning to understand the structure, organization, and function of human microbial communities, including why certain organisms exist at certain locations, and how they interact with both the other microbes in their environment and their human host. As a first step, we undertake a stoichioproteomic analysis of microbial communities from different body sites. Specifically, we compare and contrast the elemental composition of microbial protein samples using annotated sequencing data from 690 gut, vaginal, oral, nares, and skin samples currently available through the Human Microbiome Project. Our results suggest significant differences in both the median and variance of the carbon, oxygen, nitrogen, and sulfur contents of microbial protein samples from different locations. For example, whereas proteins from vaginal sites are high in carbon, proteins from skin and nasal sites are high in nitrogen and oxygen. Meanwhile, proteins from stool (the gut) are particularly high in sulfur content. We interpret these differences in terms of the local environments at different human body sites, including atmospheric exposure and food intake rates. PMID:28769875

  15. Project Earth Lover

    SciT

    Slobotski, Stephanie,

    2011-09-01

    Under this project, the Ponca Tribe of Nebraska (PTN) will conduct An Energy Options Analysis (EOA) to empower Tribal Leadership with critical information to allow them to effectively screen energy options that will further develop the Tribe's long-term strategic plan and energy vision. The PTN will also provide community workshops to enhance Tribal Members' capabilities, skills and awareness of energy efficiency and conservation technology and practices. A 90- minute workshop will be conducted at each of the 5 sites and one-hundred tribal members will receive an erergy efficiency kit.

  16. Earth Science Capability Demonstration Project

    NASA Technical Reports Server (NTRS)

    Cobleigh, Brent

    2006-01-01

    A viewgraph presentation reviewing the Earth Science Capability Demonstration Project is shown. The contents include: 1) ESCD Project; 2) Available Flight Assets; 3) Ikhana Procurement; 4) GCS Layout; 5) Baseline Predator B Architecture; 6) Ikhana Architecture; 7) UAV Capability Assessment; 8) The Big Picture; 9) NASA/NOAA UAV Demo (5/05 to 9/05); 10) NASA/USFS Western States Fire Mission (8/06); and 11) Suborbital Telepresence.

  17. The Earth Resources Data Project

    NASA Technical Reports Server (NTRS)

    Harwood, P.

    1981-01-01

    The Council of State Planning Agencies, in consultation with the National Governor's Association and NASA, initiated the Earth Resources Data Project to encourage the appropriate application of cost-effective science and technology to state natural resources issues and problems. This project was established to provide a focal point for identifying those issues associated with state use of remote sensing and related technology. One project goal is to elevate to the consciousness of state policy and program officials new technologies, such as LANDSAT, by association with major issues to which policy officials are attuned. The project assists the coordination between the states and NASA and promotes communication on those issues. A related project objective is to encourage technical assistance opportunities for states that will promote better use of remote sensing and natural resources data in state programs.

  18. South Polar Projection of Earth

    1997-09-10

    This view of the Earth shows a wonderfully unique but physically impossible view of the southern hemisphere and Antarctica. While a spacecraft could find itself directly over the Earth pole, roughly half of the image should be in darkness!

  19. Earth Science: 49 Science Fair Projects Series.

    ERIC Educational Resources Information Center

    Bonnet, Robert L.; Keen, G. Daniel

    This book offers a large collection of Earth science projects and project ideas for students, teachers, and parents. The projects described are complete but can also be used as spring boards to create expanded projects. Overviews, organizational direction, suggested hypotheses, materials, procedures, and controls are provided. The projects…

  20. Solar Wind Earth Exchange Project (SWEEP)

    DTIC Science & Technology

    2016-10-28

    AFRL-AFOSR-UK-TR-2016-0035 Solar Wind Earth Exchange Project 140200 Steven Sembay UNIVERSITY OF LEICESTER Final Report 10/28/2016 DISTRIBUTION A...To) 01 Sep 2014 to 31 Aug 2016 4. TITLE AND SUBTITLE Solar Wind Earth Exchange Project (SWEEP) 5a.  CONTRACT NUMBER 5b.  GRANT NUMBER FA9550-14-1...SUPPLEMENTARY NOTES 14. ABSTRACT The grant received from AFRL/AOFSR/EOARD funded the Solar Wind Earth Exchange Project (SWEEP) at Leicester University. The goal

  1. The Earth System (ES-DOC) Project

    NASA Astrophysics Data System (ADS)

    Greenslade, Mark; Murphy, Sylvia; Treshansky, Allyn; DeLuca, Cecilia; Guilyardi, Eric; Denvil, Sebastien

    2014-05-01

    ESSI1.3 New Paradigms, Modelling, and International Collaboration Strategies for Earth System Sciences Earth System Documentation (ES-DOC) is an international project supplying tools & services in support of earth system documentation creation, analysis and dissemination. It is nurturing a sustainable standards based documentation eco-system that aims to become an integral part of the next generation of exa-scale dataset archives. ES-DOC leverages open source software and places end-user narratives at the heart of all it does. ES-DOC has initially focused upon nurturing the Earth System Model (ESM) documentation eco-system. Within this context ES-DOC leverages emerging documentation standards and supports the following projects: Coupled Model Inter-comparison Project Phase 5 (CMIP5); Dynamical Core Model Inter-comparison Project (DCMIP); National Climate Predictions and Projections Platforms Quantitative Evaluation of Downscaling Workshop. This presentation will introduce the project to a wider audience and demonstrate the range of tools and services currently available for use. It will also demonstrate how international collaborative efforts are essential to the success of ES-DOC.

  2. Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges.

    PubMed

    Blaser, Martin J; Cardon, Zoe G; Cho, Mildred K; Dangl, Jeffrey L; Donohue, Timothy J; Green, Jessica L; Knight, Rob; Maxon, Mary E; Northen, Trent R; Pollard, Katherine S; Brodie, Eoin L

    2016-05-13

    Microorganisms have shaped our planet and its inhabitants for over 3.5 billion years. Humankind has had a profound influence on the biosphere, manifested as global climate and land use changes, and extensive urbanization in response to a growing population. The challenges we face to supply food, energy, and clean water while maintaining and improving the health of our population and ecosystems are significant. Given the extensive influence of microorganisms across our biosphere, we propose that a coordinated, cross-disciplinary effort is required to understand, predict, and harness microbiome function. From the parallelization of gene function testing to precision manipulation of genes, communities, and model ecosystems and development of novel analytical and simulation approaches, we outline strategies to move microbiome research into an era of causality. These efforts will improve prediction of ecosystem response and enable the development of new, responsible, microbiome-based solutions to significant challenges of our time. Copyright © 2016 Blaser et al.

  3. Project Copernicus: An Earth observing system

    NASA Technical Reports Server (NTRS)

    1991-01-01

    Hunsaker Aerospace Corporation is presenting this proposal for Project Copernicus to fulfill the need for space-based remote sensing of Earth. Concentration is on data acquisition. Copernicus is designed to be a flexible system of spacecraft in a low near-polar orbit. The goal is to acquire data so that the scientists may begin to understand many Earth processes and interactions. The mission objective of Copernicus is to provide a space-based, remote-sensing measurement data acquisition and transfer system for 15 years. A description of the design project is presented.

  4. The Hospital Microbiome Project: Meeting Report for the 1st Hospital Microbiome Project Workshop on sampling design and building science measurements, Chicago, USA, June 7th-8th 2012

    PubMed Central

    Smith, Daniel; Alverdy, John; An, Gary; Coleman, Maureen; Garcia-Houchins, Sylvia; Green, Jessica; Keegan, Kevin; Kelley, Scott T.; Kirkup, Benjamin C.; Kociolek, Larry; Levin, Hal; Landon, Emily; Olsiewski, Paula; Knight, Rob; Siegel, Jeffrey; Weber, Stephen; Gilbert, Jack

    2013-01-01

    This report details the outcome of the 1st Hospital Microbiome Project workshop held on June 7th-8th, 2012 at the University of Chicago, USA. The workshop was arranged to determine the most appropriate sampling strategy and approach to building science measurement to characterize the development of a microbial community within a new hospital pavilion being built at the University of Chicago Medical Center. The workshop made several recommendations and led to the development of a full proposal to the Alfred P. Sloan Foundation as well as to the creation of the Hospital Microbiome Consortium. PMID:23961316

  5. The UK Earth System Model project

    NASA Astrophysics Data System (ADS)

    Tang, Yongming

    2016-04-01

    In this talk we will describe the development and current status of the UK Earth System Model (UKESM). This project is a NERC/Met Office collaboration and has two objectives; to develop and apply a world-leading Earth System Model, and to grow a community of UK Earth System Model scientists. We are building numerical models that include all the key components of the global climate system, and contain the important process interactions between global biogeochemistry, atmospheric chemistry and the physical climate system. UKESM will be used to make key CMIP6 simulations as well as long-time (e.g. millennium) simulations, large ensemble experiments and investigating a range of future carbon emission scenarios.

  6. Motivations of participants in the citizen science of microbiomics: data from the British Gut Project.

    PubMed

    Del Savio, Lorenzo; Prainsack, Barbara; Buyx, Alena

    2017-08-01

    The establishment of databases for research in human microbiomics is dependent on the recruitment of sufficient numbers and diversity of participants. Factors that support or impede participant recruitment in studies of this type have not yet been studied. We report the results of a survey aimed at establishing the motivations of participants in the British Gut Project, a research project that relies on volunteers to provide samples and to help fund the project. The two most frequently reported motivations for participation were altruism and solidarity. Low education levels appeared to be a recruitment obstacle. More than half of our 151 respondents said they would participate in further citizen-science projects; 38% said they would not participate in a similar project if it was for-profit or in a project that did not release data sets in repositories accessible to scientists (30%). The desire to take part in research was reported as a key motivation for participation in the British Gut Project (BGP). Such prosocial motivations can be mobilized for the establishment of large data sets for research.Genet Med advance online publication 26 January 2017.

  7. COVER Project and Earth resources research transition

    NASA Technical Reports Server (NTRS)

    Botkin, D. B.; Estes, J. E. (Principal Investigator)

    1986-01-01

    Results of research in the remote sensing of natural boreal forest vegetation (the COVER project) are summarized. The study objectives were to establish a baseline forest test site; develop transforms of LANDSAT MSS and TM data for forest composition, biomass, leaf area index, and net primary productivity; and perform tasks required for testing hypotheses regarding observed spectral responses to changes in leaf area index in aspen. In addition, the transfer and documentation of data collected in the COVER project (removed from the Johnson Space Center following the discontinuation of Earth resources research at that facility) is described.

  8. IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project.

    PubMed

    Markowitz, Victor M; Chen, I-Min A; Chu, Ken; Szeto, Ernest; Palaniappan, Krishna; Jacob, Biju; Ratner, Anna; Liolios, Konstantinos; Pagani, Ioanna; Huntemann, Marcel; Mavromatis, Konstantinos; Ivanova, Natalia N; Kyrpides, Nikos C

    2012-01-01

    The Integrated Microbial Genomes and Metagenomes (IMG/M) resource is a data management system that supports the analysis of sequence data from microbial communities in the integrated context of all publicly available draft and complete genomes from the three domains of life as well as a large number of plasmids and viruses. IMG/M currently contains thousands of genomes and metagenome samples with billions of genes. IMG/M-HMP is an IMG/M data mart serving the US National Institutes of Health (NIH) Human Microbiome Project (HMP), focussed on HMP generated metagenome datasets, and is one of the central resources provided from the HMP Data Analysis and Coordination Center (DACC). IMG/M-HMP is available at http://www.hmpdacc-resources.org/imgm_hmp/.

  9. [Earth Science Technology Office's Computational Technologies Project

    NASA Technical Reports Server (NTRS)

    Fischer, James (Technical Monitor); Merkey, Phillip

    2005-01-01

    This grant supported the effort to characterize the problem domain of the Earth Science Technology Office's Computational Technologies Project, to engage the Beowulf Cluster Computing Community as well as the High Performance Computing Research Community so that we can predict the applicability of said technologies to the scientific community represented by the CT project and formulate long term strategies to provide the computational resources necessary to attain the anticipated scientific objectives of the CT project. Specifically, the goal of the evaluation effort is to use the information gathered over the course of the Round-3 investigations to quantify the trends in scientific expectations, the algorithmic requirements and capabilities of high-performance computers to satisfy this anticipated need.

  10. The Geostationary Earth Radiation Budget Project.

    NASA Astrophysics Data System (ADS)

    Harries, J. E.; Russell, J. E.; Hanafin, J. A.; Brindley, H.; Futyan, J.; Rufus, J.; Kellock, S.; Matthews, G.; Wrigley, R.; Last, A.; Mueller, J.; Mossavati, R.; Ashmall, J.; Sawyer, E.; Parker, D.; Caldwell, M.; Allan, P. M.; Smith, A.; Bates, M. J.; Coan, B.; Stewart, B. C.; Lepine, D. R.; Cornwall, L. A.; Corney, D. R.; Ricketts, M. J.; Drummond, D.; Smart, D.; Cutler, R.; Dewitte, S.; Clerbaux, N.; Gonzalez, L.; Ipe, A.; Bertrand, C.; Joukoff, A.; Crommelynck, D.; Nelms, N.; Llewellyn-Jones, D. T.; Butcher, G.; Smith, G. L.; Szewczyk, Z. P.; Mlynczak, P. E.; Slingo, A.; Allan, R. P.; Ringer, M. A.

    2005-07-01

    This paper reports on a new satellite sensor, the Geostationary Earth Radiation Budget (GERB) experiment. GERB is designed to make the first measurements of the Earth's radiation budget from geostationary orbit. Measurements at high absolute accuracy of the reflected sunlight from the Earth, and the thermal radiation emitted by the Earth are made every 15 min, with a spatial resolution at the subsatellite point of 44.6 km (north south) by 39.3 km (east west). With knowledge of the incoming solar constant, this gives the primary forcing and response components of the top-of-atmosphere radiation. The first GERB instrument is an instrument of opportunity on Meteosat-8, a new spin-stabilized spacecraft platform also carrying the Spinning Enhanced Visible and Infrared (SEVIRI) sensor, which is currently positioned over the equator at 3.5°W. This overview of the project includes a description of the instrument design and its preflight and in-flight calibration. An evaluation of the instrument performance after its first year in orbit, including comparisons with data from the Clouds and the Earth's Radiant Energy System (CERES) satellite sensors and with output from numerical models, are also presented. After a brief summary of the data processing system and data products, some of the scientific studies that are being undertaken using these early data are described. This marks the beginning of a decade or more of observations from GERB, as subsequent models will fly on each of the four Meteosat Second Generation satellites.


  11. The Denali Earth Science Education Project

    NASA Astrophysics Data System (ADS)

    Hansen, R. A.; Stachnik, J. C.; Roush, J. J.; Siemann, K.; Nixon, I.

    2004-12-01

    In partnership with Denali National Park and Preserve and the Denali Institute, the Alaska Earthquake Information Center (AEIC) will capitalize upon an extraordinary opportunity to raise public interest in the earth sciences. A coincidence of events has made this an ideal time for outreach to raise awareness of the solid earth processes that affect all of our lives. On November 3, 2002, a M 7.9 earthquake occurred on the Denali Fault in central Alaska, raising public consciousness of seismic activity in this state to a level unmatched since the M 9.2 "Good Friday" earthquake of 1964. Shortly after the M 7.9 event, a new public facility for scientific research and education in Alaska's national parks, the Murie Science and Learning Center, was constructed at the entrance to Denali National Park and Preserve only 43 miles from the epicenter of the Denali Fault Earthquake. The AEIC and its partners believe that these events can be combined to form a synergy for the creation of unprecedented opportunities for learning about solid earth geophysics among all segments of the public. This cooperative project will undertake the planning and development of education outreach mechanisms and products for the Murie Science and Learning Center that will serve to educate Alaska's residents and visitors about seismology, tectonics, crustal deformation, and volcanism. Through partnerships with Denali National Park and Preserve, this cooperative project will include the Denali Institute (a non-profit organization that assists the National Park Service in operating the Murie Science and Learning Center) and Alaska's Denali Borough Public School District. The AEIC will also draw upon the resources of long standing state partners; the Alaska Division of Geological & Geophysical Surveys and the Alaska Division of Homeland Security and Emergency Services. The objectives of this project are to increase public awareness and understanding of the solid earth processes that affect life in

  12. Turning Participatory Microbiome Research into Usable Data: Lessons from the American Gut Project

    PubMed Central

    Debelius, Justine W.; Vázquez-Baeza, Yoshiki; McDonald, Daniel; Xu, Zhenjiang; Wolfe, Elaine; Knight, Rob

    2016-01-01

    The role of the human microbiome is the subject of continued investigation resulting in increased understanding. However, current microbiome research has only scratched the surface of the variety of healthy microbiomes. Public participation in science through crowdsourcing and crowdfunding microbiome research provides a novel opportunity for both participants and investigators. However, turning participatory science into publishable data can be challenging. Clear communication with the participant base and among researchers can ameliorate some challenges. Three major aspects need to be considered: recruitment and ongoing interaction, sample collection, and data analysis. Usable data can be maximized through diligent participant interaction, careful survey design, and maintaining an open source pipeline. While participatory science will complement rather than replace traditional avenues, it presents new opportunities for studies in the microbiome and beyond. PMID:27047589

  13. Turning Participatory Microbiome Research into Usable Data: Lessons from the American Gut Project.

    PubMed

    Debelius, Justine W; Vázquez-Baeza, Yoshiki; McDonald, Daniel; Xu, Zhenjiang; Wolfe, Elaine; Knight, Rob

    2016-03-01

    The role of the human microbiome is the subject of continued investigation resulting in increased understanding. However, current microbiome research has only scratched the surface of the variety of healthy microbiomes. Public participation in science through crowdsourcing and crowdfunding microbiome research provides a novel opportunity for both participants and investigators. However, turning participatory science into publishable data can be challenging. Clear communication with the participant base and among researchers can ameliorate some challenges. Three major aspects need to be considered: recruitment and ongoing interaction, sample collection, and data analysis. Usable data can be maximized through diligent participant interaction, careful survey design, and maintaining an open source pipeline. While participatory science will complement rather than replace traditional avenues, it presents new opportunities for studies in the microbiome and beyond.

  14. The Earth System Grid Federation (ESGF) Project

    NASA Astrophysics Data System (ADS)

    Carenton-Madiec, Nicolas; Denvil, Sébastien; Greenslade, Mark

    2015-04-01

    The Earth System Grid Federation (ESGF) Peer-to-Peer (P2P) enterprise system is a collaboration that develops, deploys and maintains software infrastructure for the management, dissemination, and analysis of model output and observational data. ESGF's primary goal is to facilitate advancements in Earth System Science. It is an interagency and international effort led by the US Department of Energy (DOE), and co-funded by National Aeronautics and Space Administration (NASA), National Oceanic and Atmospheric Administration (NOAA), National Science Foundation (NSF), Infrastructure for the European Network of Earth System Modelling (IS-ENES) and international laboratories such as the Max Planck Institute for Meteorology (MPI-M) german Climate Computing Centre (DKRZ), the Australian National University (ANU) National Computational Infrastructure (NCI), Institut Pierre-Simon Laplace (IPSL), and the British Atmospheric Data Center (BADC). Its main mission is to support current CMIP5 activities and prepare for future assesments. The ESGF architecture is based on a system of autonomous and distributed nodes, which interoperate through common acceptance of federation protocols and trust agreements. Data is stored at multiple nodes around the world, and served through local data and metadata services. Nodes exchange information about their data holdings and services, trust each other for registering users and establishing access control decisions. The net result is that a user can use a web browser, connect to any node, and seamlessly find and access data throughout the federation. This type of collaborative working organization and distributed architecture context en-lighted the need of integration and testing processes definition to ensure the quality of software releases and interoperability. This presentation will introduce the ESGF project and demonstrate the range of tools and processes that have been set up to support release management activities.

  15. American Gut: an Open Platform for Citizen Science Microbiome Research

    PubMed Central

    2018-01-01

    ABSTRACT Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown. Using standardized protocols from the Earth Microbiome Project and sample contributions from over 10,000 citizen-scientists, together with an open research network, we compare human microbiome specimens primarily from the United States, United Kingdom, and Australia to one another and to environmental samples. Our results show an unexpected range of beta-diversity in human stool microbiomes compared to environmental samples; demonstrate the utility of procedures for removing the effects of overgrowth during room-temperature shipping for revealing phenotype correlations; uncover new molecules and kinds of molecular communities in the human stool metabolome; and examine emergent associations among the microbiome, metabolome, and the diversity of plants that are consumed (rather than relying on reductive categorical variables such as veganism, which have little or no explanatory power). We also demonstrate the utility of the living data resource and cross-cohort comparison to confirm existing associations between the microbiome and psychiatric illness and to reveal the extent of microbiome change within one individual during surgery, providing a paradigm for open microbiome research and education. IMPORTANCE We show that a citizen science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n = 1 study data with the population data, showing that the extent of microbiome change after events such as surgery can exceed differences between distinct environmental biomes, and the effect of diverse plants in the diet, which we confirm with untargeted metabolomics on

  16. American Gut: an Open Platform for Citizen Science Microbiome Research.

    PubMed

    McDonald, Daniel; Hyde, Embriette; Debelius, Justine W; Morton, James T; Gonzalez, Antonio; Ackermann, Gail; Aksenov, Alexander A; Behsaz, Bahar; Brennan, Caitriona; Chen, Yingfeng; DeRight Goldasich, Lindsay; Dorrestein, Pieter C; Dunn, Robert R; Fahimipour, Ashkaan K; Gaffney, James; Gilbert, Jack A; Gogul, Grant; Green, Jessica L; Hugenholtz, Philip; Humphrey, Greg; Huttenhower, Curtis; Jackson, Matthew A; Janssen, Stefan; Jeste, Dilip V; Jiang, Lingjing; Kelley, Scott T; Knights, Dan; Kosciolek, Tomasz; Ladau, Joshua; Leach, Jeff; Marotz, Clarisse; Meleshko, Dmitry; Melnik, Alexey V; Metcalf, Jessica L; Mohimani, Hosein; Montassier, Emmanuel; Navas-Molina, Jose; Nguyen, Tanya T; Peddada, Shyamal; Pevzner, Pavel; Pollard, Katherine S; Rahnavard, Gholamali; Robbins-Pianka, Adam; Sangwan, Naseer; Shorenstein, Joshua; Smarr, Larry; Song, Se Jin; Spector, Timothy; Swafford, Austin D; Thackray, Varykina G; Thompson, Luke R; Tripathi, Anupriya; Vázquez-Baeza, Yoshiki; Vrbanac, Alison; Wischmeyer, Paul; Wolfe, Elaine; Zhu, Qiyun; Knight, Rob

    2018-01-01

    Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown. Using standardized protocols from the Earth Microbiome Project and sample contributions from over 10,000 citizen-scientists, together with an open research network, we compare human microbiome specimens primarily from the United States, United Kingdom, and Australia to one another and to environmental samples. Our results show an unexpected range of beta-diversity in human stool microbiomes compared to environmental samples; demonstrate the utility of procedures for removing the effects of overgrowth during room-temperature shipping for revealing phenotype correlations; uncover new molecules and kinds of molecular communities in the human stool metabolome; and examine emergent associations among the microbiome, metabolome, and the diversity of plants that are consumed (rather than relying on reductive categorical variables such as veganism, which have little or no explanatory power). We also demonstrate the utility of the living data resource and cross-cohort comparison to confirm existing associations between the microbiome and psychiatric illness and to reveal the extent of microbiome change within one individual during surgery, providing a paradigm for open microbiome research and education. IMPORTANCE We show that a citizen science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n = 1 study data with the population data, showing that the extent of microbiome change after events such as surgery can exceed differences between distinct environmental biomes, and the effect of diverse plants in the diet, which we confirm with untargeted metabolomics on hundreds of

  17. Low Earth Orbit (LEO) Commercial Market Projections

    DOT National Transportation Integrated Search

    1995-05-16

    This study assesses the possible number of small commercial satellites to be : launched to Low Earth Orbit (LEO) in the period 1995-2005. The information : provided reflects an Office of Commercial Space Transportation (OCST) : assessment of overall ...

  18. Assessment of Variation in Microbial Community Amplicon Sequencing by the Microbiome Quality Control (MBQC) Project Consortium

    EPA Science Inventory

    Precision medicine has been made possible by the translation of ‘omics to the clinic, and human microbiome studies must likewise transition to applications in public health. This will require especially robust measurements and assimilation of data from multiple population-scale c...

  19. The Collaborative Seismic Earth Model Project

    NASA Astrophysics Data System (ADS)

    Fichtner, A.; van Herwaarden, D. P.; Afanasiev, M.

    2017-12-01

    We present the first generation of the Collaborative Seismic Earth Model (CSEM). This effort is intended to address grand challenges in tomography that currently inhibit imaging the Earth's interior across the seismically accessible scales: [1] For decades to come, computational resources will remain insufficient for the exploitation of the full observable seismic bandwidth. [2] With the man power of individual research groups, only small fractions of available waveform data can be incorporated into seismic tomographies. [3] The limited incorporation of prior knowledge on 3D structure leads to slow progress and inefficient use of resources. The CSEM is a multi-scale model of global 3D Earth structure that evolves continuously through successive regional refinements. Taking the current state of the CSEM as initial model, these refinements are contributed by external collaborators, and used to advance the CSEM to the next state. This mode of operation allows the CSEM to [1] harness the distributed man and computing power of the community, [2] to make consistent use of prior knowledge, and [3] to combine different tomographic techniques, needed to cover the seismic data bandwidth. Furthermore, the CSEM has the potential to serve as a unified and accessible representation of tomographic Earth models. Generation 1 comprises around 15 regional tomographic refinements, computed with full-waveform inversion. These include continental-scale mantle models of North America, Australasia, Europe and the South Atlantic, as well as detailed regional models of the crust beneath the Iberian Peninsula and western Turkey. A global-scale full-waveform inversion ensures that regional refinements are consistent with whole-Earth structure. This first generation will serve as the basis for further automation and methodological improvements concerning validation and uncertainty quantification.

  20. EOS ART: Six Artistic Projects Inspired by Earth Science

    NASA Astrophysics Data System (ADS)

    Kerlow, Isaac

    2015-04-01

    The six projects produced under the artists' residencies at the Earth Observatory of Singapore (EOS) were inspired by Earth science and by the human experience in naturally hazardous regions. These contemporary artworks were created within an interdisciplinary framework that fostered collaborations between artists and scientists. EOS ART was a pilot program that also facilitated the active engagement of regional artists with issues related to Earth science, sustainable societies, and innovative methods for science outreach. An interdisciplinary jury of art critics, curators and Earth scientists selected art projects proposed by regional artists, and funds were awarded to develop and realize the projects. The artworks-including installations, photographs, and video art-were showcased in the "Unearthed" public exhibit at the Singapore Art Museum from March to July of 2014. A 92-page catalog accompanied the show and public seminars about interdisciplinary connections complemented the event. This was a unique example of collaboration between scientific and artistic institutions in Southeast Asia. The paper provides an overview of the motivations, process and accomplished results. The art projects include "Coastline" by Zhang Xiao (China), "Lupang" by Clara Balaguer and Carlos Casas (Philippines and Spain), "Sound of the Earth" by Chen Sai Hua Kuan (Singapore), "Sudden Nature" by Isaac Kerlow (Mexico/USA), "The Possibility of Knowing" by Robert Zhao Renhui (Singapore), and "When Need Moves the Earth" by Sutthirat Supaparinya (Thailand).

  1. The Earth System Documentation (ES-DOC) project

    NASA Astrophysics Data System (ADS)

    Murphy, S.; Greenslade, M. A.; Treshansky, A.; DeLuca, C.; Guilyardi, E.; Denvil, S.

    2013-12-01

    Earth System Documentation (ES-DOC) is an international project supplying high quality tools and services in support of Earth system documentation creation, analysis and dissemination. It is nurturing a sustainable standards based documentation ecosystem that aims to become an integral part of the next generation of exa-scale dataset archives. ES-DOC leverages open source software, and applies a software development methodology that places end-user narratives at the heart of all it does. ES-DOC has initially focused upon nurturing the Earth System Model (ESM) documentation eco-system. Within this context ES-DOC leverages the emerging Common Information Model (CIM) metadata standard, which has supported the following projects: ** Coupled Model Inter-comparison Project Phase 5 (CMIP5); ** Dynamical Core Model Inter-comparison Project (DCMIP-2012); ** National Climate Predictions and Projections Platforms (NCPP) Quantitative Evaluation of Downscaling Workshop (QED-2013). This presentation will introduce the project to a wider audience and will demonstrate the current production level capabilities of the eco-system: ** An ESM documentation Viewer embeddable into any website; ** An ESM Questionnaire configurable on a project by project basis; ** An ESM comparison tool reusable across projects; ** An ESM visualization tool reusable across projects; ** A search engine for speedily accessing published documentation; ** Libraries for streamlining document creation, validation and publishing pipelines.

  2. Magnetic Earth Ionosphere Resonant Frequencies (MEIRF) project

    NASA Technical Reports Server (NTRS)

    Spaniol, Craig

    1993-01-01

    The West Virginia State College Community College Division NASA Magnetic Earth Ionosphere Resonant Frequencies (MEIRF) study is described. During this contract period, the two most significant and professionally rewarding events were the presentation of the research activity at the Sir Isaac Newton Conference in St. Petersburg, Russia, and the second Day of Discovery Conference, focusing on economic recovery in West Virginia. An active antenna concept utilizing a signal feedback principle similar to regenerative receivers used in early radio was studied. The device has potential for ELF research and other commercial applications for improved signal reception. Finally, work continues to progress on the development of a prototype monitoring station. Signal monitoring, data display, and data storage are major areas of activity. In addition, we plan to continue our dissemination of research activity through presentations at seminars and other universities.

  3. Energy Exascale Earth System Model (E3SM) Project Strategy

    SciT

    Bader, D.

    The E3SM project will assert and maintain an international scientific leadership position in the development of Earth system and climate models at the leading edge of scientific knowledge and computational capabilities. With its collaborators, it will demonstrate its leadership by using these models to achieve the goal of designing, executing, and analyzing climate and Earth system simulations that address the most critical scientific questions for the nation and DOE.

  4. Earth Science Enterprise Scientific Data Purchase Project: Verification and Validation

    NASA Technical Reports Server (NTRS)

    Jenner, Jeff; Policelli, Fritz; Fletcher, Rosea; Holecamp, Kara; Owen, Carolyn; Nicholson, Lamar; Dartez, Deanna

    2000-01-01

    This paper presents viewgraphs on the Earth Science Enterprise Scientific Data Purchase Project's verification,and validation process. The topics include: 1) What is Verification and Validation? 2) Why Verification and Validation? 3) Background; 4) ESE Data Purchas Validation Process; 5) Data Validation System and Ingest Queue; 6) Shipment Verification; 7) Tracking and Metrics; 8) Validation of Contract Specifications; 9) Earth Watch Data Validation; 10) Validation of Vertical Accuracy; and 11) Results of Vertical Accuracy Assessment.

  5. The Human Microbiome Project (HMP) and the Data Analysis and Coordination Center (DAAC) Portal to the HMP (GSC8 Meeting)

    SciT

    Weinstock, George; Wortman, Jennifer

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. George Weinstock from Washington University School of Medicine talks about the Human Microbiome Project (HMP) followed briefly by Jennifer Wortman from the University ofmore » Maryland School of Medicine on the Data Analysis and Coordination Center (DACC) portal to the HMP at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.« less

  6. The Human Microbiome Project (HMP) and the Data Analysis and Coordination Center (DAAC) Portal to the HMP (GSC8 Meeting)

    Weinstock, George; Wortman, Jennifer

    2018-01-22

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. George Weinstock from Washington University School of Medicine talks about the Human Microbiome Project (HMP) followed briefly by Jennifer Wortman from the University of Maryland School of Medicine on the Data Analysis and Coordination Center (DACC) portal to the HMP at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.

  7. Natural Hazards in Earth Science education projects

    NASA Astrophysics Data System (ADS)

    Ferrero, Elena; Magagna, Alessandra

    2013-04-01

    reconstructing situations recognizable only by clues and following events widely spread in geologic times. These examples will illustrate how methodologies and strategies have been applied to achieve the following purposes: (i) to act according to the principles of geoethics in the formation of professionals of Geosciences education and communication; (ii) to increase individual and collective awareness of the interference of mankind on natural systems, especially on geological heritage. All the mentioned activities have been designed following these common strategies: - to respect and to value the great emotional impact of the issues proposed; - to lighten the irrational aspects of an approximate communication carried out by some media; - to place the impulsive events between the effects of "normal" terrestrial dynamical processes; - to train to a constant and curious attention towards "common" situations, in order to be able to interpret them with awareness; - to highlight the complexity of the phenomena and the richness of the relations between abiotic and living world, despite of convenient simplifications; - to highlight the role of mankind in the system of relationships, as "victim" or "creator" of the changes; - to encourage the awareness of individual responsibility, to enhance the development of a respectful and careful attitude towards other living beings and the Earth system, attitude mindful of the values and the need to protect them. The importance of taking care of the communication approach has been evaluated and tested, giving constant attention to the interlocutors participation, creating informal moments of dialogue, valuing the contributions of their previous knowledge and experience, integrating other contributions of knowledge, relevant to the humanities and the arts.

  8. Endometrial microbiome.

    PubMed

    Franasiak, Jason M; Scott, Richard T

    2017-06-01

    There have been great improvements in assisted reproduction in the recent decade; however, there are still a significant number of chromosomally normal blastocysts that fail to produce live births. The human microbiome is the totality of the microbes and their genomes that exist in and on the host. The understanding of its impact on health and human disease, particularly in human reproduction, is evolving. New technologies have empowered metagenomic sample analysis that allows for more fully characterizing the reproductive tract microbiome. With these technologies, we have determined not only that sites previously thought to be sterile in fact have robust microbiomes, but also have better characterized the normal and abnormal vaginal and endometrial microbiome. The understanding of the microbiome in health and human disease, in particular in relation to human reproduction, is in its infancy. As the reproductive tract dysbiosis are better characterized and understood, we may be better equipped to manipulate it more expertly.

  9. THE EOS ART Projects: Six Art Projects Inspired by Earth Science

    NASA Astrophysics Data System (ADS)

    Kerlow, I.

    2015-12-01

    The six projects produced under the artists' residencies at the Earth Observatory of Singapore (EOS) were inspired by Earth science and by the human experience in naturally hazardous regions. These contemporary artworks were created within an interdisciplinary framework that fostered collaborations between artists and scientists. The EOS ART 2010-2013 was a pilot program that also facilitated the active engagement of regional artists with issues related to Earth science, sustainable societies, and innovative methods for science outreach. An interdisciplinary jury of art critics, curators and Earth scientists selected art projects proposed by regional artists, and funds were awarded to develop and realize the projects.The artworks-including installations, photographs, and video art-were showcased in the "Unearthed" public exhibit at the Singapore Art Museum from March to July of 2014. A 92-page catalog accompanied the show and public seminars about interdisciplinary connections complemented the event. This was a unique example of collaboration between scientific and artistic institutions in Southeast Asia.The presentation provides an overview of the motivations, process and accomplished results. The art projects include "Coastline" by Zhang Xiao (China), "Lupang" by Clara Balaguer and Carlos Casas (Philippines and Spain), "Sound of the Earth" by Chen Sai Hua Kuan (Singapore), "Sudden Nature" by Isaac Kerlow (Mexico/USA), "The Possibility of Knowing" by Robert Zhao Renhui (Singapore), and "When Need Moves the Earth" by Sutthirat Supaparinya (Thailand). http://art-science-media.com/the-eos-art-projects/

  10. Projections of leaf area index in earth system models

    NASA Astrophysics Data System (ADS)

    Mahowald, Natalie; Lo, Fiona; Zheng, Yun; Harrison, Laura; Funk, Chris; Lombardozzi, Danica; Goodale, Christine

    2016-03-01

    The area of leaves in the plant canopy, measured as leaf area index (LAI), modulates key land-atmosphere interactions, including the exchange of energy, moisture, carbon dioxide (CO2), and other trace gases and aerosols, and is therefore an essential variable in predicting terrestrial carbon, water, and energy fluxes. Here our goal is to characterize the LAI projections from the latest generation of earth system models (ESMs) for the Representative Concentration Pathway (RCP) 8.5 and RCP4.5 scenarios. On average, the models project increases in LAI in both RCP8.5 and RCP4.5 over most of the globe, but also show decreases in some parts of the tropics. Because of projected increases in variability, there are also more frequent periods of low LAI across broad regions of the tropics. Projections of LAI changes varied greatly among models: some models project very modest changes, while others project large changes, usually increases. Modeled LAI typically increases with modeled warming in the high latitudes, but often decreases with increasing local warming in the tropics. The models with the most skill in simulating current LAI in the tropics relative to satellite observations tend to project smaller increases in LAI in the tropics in the future compared to the average of all the models. Using LAI projections to identify regions that may be vulnerable to climate change presents a slightly different picture than using precipitation projections, suggesting LAI may be an additional useful tool for understanding climate change impacts. Going forward, users of LAI projections from the CMIP5 ESMs evaluated here should be aware that model outputs do not exhibit clear-cut relationships to vegetation carbon and precipitation. Our findings underscore the need for more attention to LAI projections, in terms of understanding the drivers of projected changes and improvements to model skill.

  11. Projections of leaf area index in earth system models

    DOE PAGES

    Mahowald, Natalie; Lo, Fiona; Zheng, Yun; ...

    2016-03-09

    The area of leaves in the plant canopy, measured as leaf area index (LAI), modulates key land–atmosphere interactions, including the exchange of energy, moisture, carbon dioxide (CO 2), and other trace gases and aerosols, and is therefore an essential variable in predicting terrestrial carbon, water, and energy fluxes. Here our goal is to characterize the LAI projections from the latest generation of earth system models (ESMs) for the Representative Concentration Pathway (RCP) 8.5 and RCP4.5 scenarios. On average, the models project increases in LAI in both RCP8.5 and RCP4.5 over most of the globe, but also show decreases in somemore » parts of the tropics. Because of projected increases in variability, there are also more frequent periods of low LAI across broad regions of the tropics. Projections of LAI changes varied greatly among models: some models project very modest changes, while others project large changes, usually increases. Modeled LAI typically increases with modeled warming in the high latitudes, but often decreases with increasing local warming in the tropics. The models with the most skill in simulating current LAI in the tropics relative to satellite observations tend to project smaller increases in LAI in the tropics in the future compared to the average of all the models. Using LAI projections to identify regions that may be vulnerable to climate change presents a slightly different picture than using precipitation projections, suggesting LAI may be an additional useful tool for understanding climate change impacts. Going forward, users of LAI projections from the CMIP5 ESMs evaluated here should be aware that model outputs do not exhibit clear-cut relationships to vegetation carbon and precipitation. Lastly, our findings underscore the need for more attention to LAI projections, in terms of understanding the drivers of projected changes and improvements to model skill.« less

  12. [Earth and Space Sciences Project Services for NASA HPCC

    NASA Technical Reports Server (NTRS)

    Merkey, Phillip

    2002-01-01

    This grant supported the effort to characterize the problem domain of the Earth Science Technology Office's Computational Technologies Project, to engage the Beowulf Cluster Computing Community as well as the High Performance Computing Research Community so that we can predict the applicability of said technologies to the scientific community represented by the CT project and formulate long term strategies to provide the computational resources necessary to attain the anticipated scientific objectives of the CT project. Specifically, the goal of the evaluation effort is to use the information gathered over the course of the Round-3 investigations to quantify the trends in scientific expectations, the algorithmic requirements and capabilities of high-performance computers to satisfy this anticipated need.

  13. Human Papillomavirus Community in Healthy Persons, Defined by Metagenomics Analysis of Human Microbiome Project Shotgun Sequencing Data Sets

    PubMed Central

    Ma, Yingfei; Madupu, Ramana; Karaoz, Ulas; Nossa, Carlos W.; Yang, Liying; Yooseph, Shibu; Yachimski, Patrick S.; Brodie, Eoin L.; Nelson, Karen E.

    2014-01-01

    ABSTRACT Human papillomavirus (HPV) causes a number of neoplastic diseases in humans. Here, we show a complex normal HPV community in a cohort of 103 healthy human subjects, by metagenomics analysis of the shotgun sequencing data generated from the NIH Human Microbiome Project. The overall HPV prevalence was 68.9% and was highest in the skin (61.3%), followed by the vagina (41.5%), mouth (30%), and gut (17.3%). Of the 109 HPV types as well as additional unclassified types detected, most were undetectable by the widely used commercial kits targeting the vaginal/cervical HPV types. These HPVs likely represent true HPV infections rather than transitory exposure because of strong organ tropism and persistence of the same HPV types in repeat samples. Coexistence of multiple HPV types was found in 48.1% of the HPV-positive samples. Networking between HPV types, cooccurrence or exclusion, was detected in vaginal and skin samples. Large contigs assembled from short HPV reads were obtained from several samples, confirming their genuine HPV origin. This first large-scale survey of HPV using a shotgun sequencing approach yielded a comprehensive map of HPV infections among different body sites of healthy human subjects. IMPORTANCE This nonbiased survey indicates that the HPV community in healthy humans is much more complex than previously defined by widely used kits that are target selective for only a few high- and low-risk HPV types for cervical cancer. The importance of nononcogenic viruses in a mixed HPV infection could be for stimulating or inhibiting a coexisting oncogenic virus via viral interference or immune cross-reaction. Knowledge gained from this study will be helpful to guide the designing of epidemiological and clinical studies in the future to determine the impact of nononcogenic HPV types on the outcome of HPV infections. PMID:24522917

  14. Earth Science community support in the EGI-Inspire Project

    NASA Astrophysics Data System (ADS)

    Schwichtenberg, H.

    2012-04-01

    The Earth Science Grid community is following its strategy of propagating Grid technology to the ES disciplines, setting up interactive collaboration among the members of the community and stimulating the interest of stakeholders on the political level since ten years already. This strategy was described in a roadmap published in an Earth Science Informatics journal. It was applied through different European Grid projects and led to a large Grid Earth Science VRC that covers a variety of ES disciplines; in the end, all of them were facing the same kind of ICT problems. .. The penetration of Grid in the ES community is indicated by the variety of applications, the number of countries in which ES applications are ported, the number of papers in international journals and the number of related PhDs. Among the six virtual organisations belonging to ES, one, ESR, is generic. Three others -env.see-grid-sci.eu, meteo.see-grid-sci.eu and seismo.see-grid-sci.eu- are thematic and regional (South Eastern Europe) for environment, meteorology and seismology. The sixth VO, EGEODE, is for the users of the Geocluster software. There are also ES users in national VOs or VOs related to projects. The services for the ES task in EGI-Inspire concerns the data that are a key part of any ES application. The ES community requires several interfaces to access data and metadata outside of the EGI infrastructure, e.g. by using grid-enabled database interfaces. The data centres have also developed service tools for basic research activities such as searching, browsing and downloading these datasets, but these are not accessible from applications executed on the Grid. The ES task in EGI-Inspire aims to make these tools accessible from the Grid. In collaboration with GENESI-DR (Ground European Network for Earth Science Interoperations - Digital Repositories) this task is maintaining and evolving an interface in response to new requirements that will allow data in the GENESI-DR infrastructure to

  15. Dream project: Applications of earth observations to disaster risk management

    NASA Astrophysics Data System (ADS)

    Dyke, G.; Gill, S.; Davies, R.; Betorz, F.; Andalsvik, Y.; Cackler, J.; Dos Santos, W.; Dunlop, K.; Ferreira, I.; Kebe, F.; Lamboglia, E.; Matsubara, Y.; Nikolaidis, V.; Ostoja-Starzewski, S.; Sakita, M.; Verstappen, N.

    2011-01-01

    The field of disaster risk management is relatively new and takes a structured approach to managing uncertainty related to the threat of natural and man-made disasters. Disaster risk management consists primarily of risk assessment and the development of strategies to mitigate disaster risk. This paper will discuss how increasing both Earth observation data and information technology capabilities can contribute to disaster risk management, particularly in Belize. The paper presents the results and recommendations of a project conducted by an international and interdisciplinary team of experts at the 2009 session of the International Space University in NASA Ames Research Center (California, USA). The aim is to explore the combination of current, planned and potential space-aided, airborne, and ground-based Earth observation tools, the emergence of powerful new web-based and mobile data management tools, and how this combination can support and improve the emerging field of disaster risk management. The starting point of the project was the World Bank's Comprehensive Approach to Probabilistic Risk Assessment (CAPRA) program, focused in Central America. This program was used as a test bed to analyze current space technologies used in risk management and develop new strategies and tools to be applied in other regions around the world.

  16. BioChar Amendments for Improved Plant Microbiome and Crop Health Project

    NASA Technical Reports Server (NTRS)

    Zeitlin, Nancy; Smith, David; Catechis, John; Khodadad, Christina; Koss, Lawrence; Mejia, Oscar Monje; Spencer, Lashelle

    2015-01-01

    Plant-based Environmental Control and Life Support Systems (ECLSS) enable human existence beyond Low Earth Orbit (LEO) by providing oxygen, water and food. The root modules are key to success of sustainable plant-based ECLSS. In microgravity, hydroponics is not viable as gases separate from fluids, thus plants are grown in soil substrates, which are bulky and must be maintained for optimal plant growth. Soil substrate selection also impacts ECLSS self-sufficiency. Savings in resupply mass and volume are possible if soil is developed in-situ from regolith found on moons or planets. Biochar, a soil amendment used by ancient civilizations to improve soil fertility that promotes plant health and root zone microbes, can be produced by pyrolysis of plant biomass. The goal is to study the effect of biochar on sequential crop plantings in a single root module. The objectives are: 1) follow changes in root-microbe interactions using metagenomic techniques, 2) measure changes in microbial populations during sequential cropping in a single root module, and 3) examine effect of biochar amendments.

  17. Satellite Emission Range Inferred Earth Survey (SERIES) project

    NASA Technical Reports Server (NTRS)

    Buennagel, L. A.; Macdoran, P. F.; Neilan, R. E.; Spitzmesser, D. J.; Young, L. E.

    1984-01-01

    The Global Positioning System (GPS) was developed by the Department of Defense primarily for navigation use by the United States Armed Forces. The system will consist of a constellation of 18 operational Navigation Satellite Timing and Ranging (NAVSTAR) satellites by the late 1980's. During the last four years, the Satellite Emission Range Inferred Earth Surveying (SERIES) team at the Jet Propulsion Laboratory (JPL) has developed a novel receiver which is the heart of the SERIES geodetic system designed to use signals broadcast from the GPS. This receiver does not require knowledge of the exact code sequence being transmitted. In addition, when two SERIES receivers are used differentially to determine a baseline, few cm accuracies can be obtained. The initial engineering test phase has been completed for the SERIES Project. Baseline lengths, ranging from 150 meters to 171 kilometers, have been measured with 0.3 cm to 7 cm accuracies. This technology, which is sponsored by the NASA Geodynamics Program, has been developed at JPL to meet the challenge for high precision, cost-effective geodesy, and to complement the mobile Very Long Baseline Interferometry (VLBI) system for Earth surveying.

  18. Project Centaur. [for earth dayside magnetic cleft investigation

    NASA Technical Reports Server (NTRS)

    Brence, W. A.; Hardin, J. W.; Crook, E. D.; Roberts, H.

    1982-01-01

    The National Aeronautics and Space Administration (NASA) and the Canada Centre for Space Science, National Research Council of Canada (NRCC), conducted a cooperative sounding rocket campaign in the Canadian Arctic during November/December 1981. The objective of the campaign was to investigate the earth's dayside magnetic cleft region. The project was named CENTAUR for Cleft Energetics Transport and Ultraviolet Radiation. Remote launch support facilities were established at Cape Parry, NWT, Canada (70 deg 10 min N latitude, 124 deg 40 min W longitude). The cleft region is accessible from this location when launched poleward during reasonably quiet magnetic activity. Five large sounding rockets were launched (3 NASA, 2 NRCC). About 30 scientific experiments were launched, and an extensive array of ground based experiments was established at Cape Parry and at Sachs Harbour, Banks Island, 130 miles poleward. This paper discusses the unique organization, planning, facilities, instrumentation, and operation required to support the campaign, and looks briefly at the results.

  19. Spacecraft design project: Low Earth orbit communications satellite

    NASA Technical Reports Server (NTRS)

    Moroney, Dave; Lashbrook, Dave; Mckibben, Barry; Gardener, Nigel; Rivers, Thane; Nottingham, Greg; Golden, Bill; Barfield, Bill; Bruening, Joe; Wood, Dave

    1991-01-01

    This is the final product of the spacecraft design project completed to fulfill the academic requirements of the Spacecraft Design and Integration 2 course (AE-4871) taught at the U.S. Naval Postgraduate School. The Spacecraft Design and Integration 2 course is intended to provide students detailed design experience in selection and design of both satellite system and subsystem components, and their location and integration into a final spacecraft configuration. The design team pursued a design to support a Low Earth Orbiting (LEO) communications system (GLOBALSTAR) currently under development by the Loral Cellular Systems Corporation. Each of the 14 team members was assigned both primary and secondary duties in program management or system design. Hardware selection, spacecraft component design, analysis, and integration were accomplished within the constraints imposed by the 11 week academic schedule and the available design facilities.

  20. COMUNICA Project: a commitment for strategic communication on Earth Sciences

    NASA Astrophysics Data System (ADS)

    Cortes-Picas, Jordi; Diaz, Jordi; Fernandez-Turiel, Jose-Luis

    2016-04-01

    The Institute of Earth Sciences Jaume Almera (ICTJA-CSIC) has just celebrated its 50-year anniversary last year. It is a reference research center on Earth Sciences both national and international level. The Institute includes 4 research groups which focus their scientific activity on the structure and dynamics of the Earth, the environmental changes in the geological record, geophysical and geochemical modelling and crystallography and optical properties. Only when large geological disasters happens, mainly earthquakes and volcanic eruptions, some interaction between ICTJA-CSIC researchers and traditional media occurs, which is limited by the fact that the aim of the Institute is the scientific research and it has no responsibilities in the area of civil protection. This relationship reduces the knowledge of our activity to the general public. To overcome this situation, the ICTJA-CSIC has decided to take an active role in the social dissemination of geological and geophysical knowledge. Thus, the ICTJA-CSIC has launched the COMUNICA Project. The project is aimed to increase the social visibility of the ICTJA-CSIC and to promote the outreach of researchers. Therefore ICTJA-CSIC has created the Communication Unit, which is in charge of designing communication strategies to give to different audiences (media, students of secondary and higher education, general public) an overview of the scientific and institutional activity of the ICTJA-CSIC. A global communication plan is being designed to define the strategic actions, both internal and external. An important role has been reserved for digital channels, to promote ICTJA-CSIC activity on social networks such as Twitter, Facebook or Youtube, besides making a major effort in the renovation and maintenance of the corporate website. A strong effort will be done to collect and spread through press releases the major scientific milestones achieved by the researchers, to promote the interest of mass media. Communication

  1. KLENOT Project - Near Earth Objects Follow-up Program

    NASA Astrophysics Data System (ADS)

    Tichy, Milos; Ticha, Jana; Kocer, Michal; Tichy, Milos

    2015-08-01

    Near Earth Object (NEO) research is important not only as a great challenge for science but also as an important challenge for planetary defense. Therefore NEO discoveries, astrometric follow-up, orbit computations as well as physical studies are of high interest both to science community and humankind.The KLENOT Project of the Klet Observatory, South Bohemia, Czech Republic pursued the confirmation, early follow-up, long-arc follow-up and recovery of NEOs since 2002. Tens of thousands astrometric measurements helped to make inventory of NEOs as well as to understand the NEO distribution. It ranked among the world most prolific professional NEO follow-up programmes during its first phase from 2002 to 2008.The fundamental improvement of the 1.06-m KLENOT Telescope was started in autumn 2008. The new computer controlled paralactic mount was built to substantially increase telescope-time efficiency, the number of observations, their accuracy and limiting magnitude. The testing observations of the KLENOT Telescope Next Generation were started in October 2011. The new more efficient CCD camera FLI ProLine 230 was installed in summer 2013.The original Klet Software Package has been continually upgraded over the past two decades of operation.Both the system and strategy for the NEO follow-up observation used in the framework of the KLENOT Project are described here, including methods for selecting useful and important targets for NEO follow-up astrometry.The modernized KLENOT System was put into full operation in September 2013. More than 8000 of minor planet and comet astrometric positions including NEA measurements were published from September 2013 to February 2015.The 1.06-m KLENOT telescope is still the largest telescope in continental Europe used exclusively for observations of asteroids and comets. Full observing time is dedicated to the KLENOT team. Considering our results and long-time experience obtained at the Klet Observatory, we have the large potential to

  2. Earth

    2012-01-30

    Behold one of the more detailed images of the Earth yet created. This Blue Marble Earth montage shown above -- created from photographs taken by the Visible/Infrared Imager Radiometer Suite (VIIRS) instrument on board the new Suomi NPP satellite -- shows many stunning details of our home planet. The Suomi NPP satellite was launched last October and renamed last week after Verner Suomi, commonly deemed the father of satellite meteorology. The composite was created from the data collected during four orbits of the robotic satellite taken earlier this month and digitally projected onto the globe. Many features of North America and the Western Hemisphere are particularly visible on a high resolution version of the image. http://photojournal.jpl.nasa.gov/catalog/PIA18033

  3. Klenot Project - Near Earth Objects Follow-Up Program

    NASA Astrophysics Data System (ADS)

    Tichý, Miloš; Tichá, Jana; Kočer, Michal

    2016-01-01

    NEO research is a great challenge just now - for science, for exploration and for planetary defence. Therefore NEO discoveries, astrometric follow-up, orbit computations as well as physical studies are of high interest both to science community and humankind. The KLENOT Project of the Klet Observatory, South Bohemia, Czech Republic pursued the confirmation, early follow-up, long-arc follow-up and recovery of Near Earth Objects since 2002. Tens of thousands astrometric measurements helped to make inventory of NEOs as well as to understand the NEO population. It ranked among the world most prolific professional NEO follow-up programmes during its first phase from 2002 to 2008. The fundamental improvement of the 1.06-m KLENOT Telescope was started in autumn 2008. The new computer controlled paralactic mount was built to substantially increase telescope-time efficiency, the number of observations, their accuracy and limiting magnitude. The testing observations of the KLENOT Telescope Next Generation (NG) were started in October 2011. The new more efficient CCD camera FLI ProLine 230 was installed in summer 2013. The original Klet Software Package has been continually upgraded over the past two decades of operation. Along with huge hardware changes we have decided for essential changes in software and the whole KLENOT work-flow. Using the current higher computing power available, enhancing and updating our databases and astrometry program, the core of our software package, will prove highly beneficial. Moreover, the UCAC4 as the more precise astrometric star catalog was implemented. The modernized KLENOT System was put into full operation in September 2013. This step opens new possibilities for the KLENOT Project, the long-term European Contribution to Monitoring and Cataloging Near Earth Objects. KLENOT Project Goals are confirmatory observations of newly discovered fainter NEO candidates, early follow-up of newly discovered NEOs, long-arc follow-up astrometry of NEOs

  4. "From Earth to the Universe" Project Launches Around Globe

    NASA Astrophysics Data System (ADS)

    2009-02-01

    A worldwide exhibition of large-scale astronomical images has launched in the United States under the banner of the International Year of Astronomy 2009 (IYA2009). The "From Earth to the Universe" (FETTU) project is designed to bring the undeniable beauty of astronomy to the general public in a series of free showings across the country, which have begun with a traveling image exhibit now open at Tucson International Airport in Arizona. FETTU (www.fromearthtotheuniverse.org) is a major project of both the US and global efforts for IYA2009. With images taken from both ground- and space-based telescopes, FETTU showcases the incredible variety of astronomical objects that are known to exist - planets, comets, stars, nebulae, galaxies, clusters, and more. The exhibit also shows how some of these objects look different when viewed across the electromagnetic spectrum, from the ultraviolet and visible light to infrared, X-rays and gamma rays. FETTU is being shown in non-traditional public venues such as parks and gardens, shopping malls, metro stations and airports in major cities across the world. The FETTU images have been selected for their stunning beauty to engage members of the general public who might normally ignore or avoid astronomy. With short, but informative captions on each panel, the goal is introduce some basics of the science involved once an individual has been drawn to the image. In the US, FETTU is being sponsored by NASA and will appear in semi- permanent installations in Atlanta and Chicago later this spring. The traveling version of FETTU, with its first stop in Tucson, will then move to Memphis in April. More FETTU locations are being planned across the US and an enhanced schedule is being developed. People Who Read This Also Read... Galaxies Coming of Age in Cosmic Blobs Searching for Primordial Antimatter Action Replay of Powerful Stellar Explosion Jet Power and Black Hole Assortment Revealed in New Chandra Image Several editions of FETTU will

  5. The EarthKAM project: creating space imaging tools for teaching and learning

    NASA Astrophysics Data System (ADS)

    Dodson, Holly; Levin, Paula; Ride, Sally; Souviney, Randall

    2000-07-01

    The EarthKAM Project is a NASA-supported partnership of secondary and university students with Earth Science and educational researchers. This report describes an ongoing series of activities that more effectively integrate Earth images into classroom instruction. In this project, students select and analyze images of the Earth taken during Shuttle flights and use the tools of modern science (computers, data analysis tools and the Internet) to disseminate the images and results of their research. A related study, the Visualizing Earth Project, explores in greater detail the cognitive aspects of image processing and the educational potential of visualizations in science teaching and learning. The content and organization of the EarthKAM datasystem of images and metadata are also described. An associated project is linking this datasystem of images with the Getty Thesaurus of Geographic Names, which will allow users to access a wide range of geographic and political information for the regions shown in EarthKAM images. Another project will provide tools for automated feature extraction from EarthKAM images. In order to make EarthKAM resources available to a larger number of schools, the next important goal is to create an integrated datasystem that combines iterative resource validation and publication, with multimedia management of instructional materials.

  6. Coordinating Earth and Environmental Cross-disciplinary projects to promote GEOSS: the EGIDA project

    NASA Astrophysics Data System (ADS)

    Nativi, S.

    2011-12-01

    Earth Observation System of Systems' (GEOSS) is completed in 2015, it will constitute a flexible network of global content providers allowing decision makers to access an extraordinary range of information, proactively linking existing and planned observing systems around the world. Where gaps exist, GEOSS will support the development of new systems and promote common technical standards, so that information from thousands of different instruments can be combined into coherent datasets. The basic need for open access to data across disciplines is still omnipresent in Europe and beyond. Available datasets are often not easy to find, or lack proper metadata, making them virtually useless, while data interoperability continues to be a key hurdle. 'Coordinating Earth and Environmental Cross-disciplinary projects to promote GEOSS' (EGIDA) is an initiative which prepares a sustainable process promoting coordination of activities carried out by the GEO Science & Technology (S&T) Committee, the S&T national and European initiatives, and other S&T communities. The project builds on existing national initiatives and European projects, facilitating the S&T Community contributions to, and interactions with, GEOSS, and will involve developing countries by transferring the EGIDA S&T methodology to them. EGIDA has established a stakeholder network across Europe, the U.S., Brazil, South Africa, Turkey, China, Japan and Australia. The network implements the links between EGIDA and the global programmes framework, facilitating S&T community contributions to GEOSS and disseminating project results to the S&T community. Several key organisations, representing the different regions involved in GEO/GEOSS, have joined the network, which also acts as a forum for refining the EGIDA Methodology, and will help ensure it is sustainable beyond the project. By utilising new and existing groups of stakeholders throughout the network, the project aims to enhance information exchange, knowledge

  7. Functional sequencing read annotation for high precision microbiome analysis

    PubMed Central

    Zhu, Chengsheng; Miller, Maximilian; Marpaka, Srinayani; Vaysberg, Pavel; Rühlemann, Malte C; Wu, Guojun; Heinsen, Femke-Anouska; Tempel, Marie; Zhao, Liping; Lieb, Wolfgang; Franke, Andre; Bromberg, Yana

    2018-01-01

    Abstract The vast majority of microorganisms on Earth reside in often-inseparable environment-specific communities—microbiomes. Meta-genomic/-transcriptomic sequencing could reveal the otherwise inaccessible functionality of microbiomes. However, existing analytical approaches focus on attributing sequencing reads to known genes/genomes, often failing to make maximal use of available data. We created faser (functional annotation of sequencing reads), an algorithm that is optimized to map reads to molecular functions encoded by the read-correspondent genes. The mi-faser microbiome analysis pipeline, combining faser with our manually curated reference database of protein functions, accurately annotates microbiome molecular functionality. mi-faser’s minutes-per-microbiome processing speed is significantly faster than that of other methods, allowing for large scale comparisons. Microbiome function vectors can be compared between different conditions to highlight environment-specific and/or time-dependent changes in functionality. Here, we identified previously unseen oil degradation-specific functions in BP oil-spill data, as well as functional signatures of individual-specific gut microbiome responses to a dietary intervention in children with Prader–Willi syndrome. Our method also revealed variability in Crohn's Disease patient microbiomes and clearly distinguished them from those of related healthy individuals. Our analysis highlighted the microbiome role in CD pathogenicity, demonstrating enrichment of patient microbiomes in functions that promote inflammation and that help bacteria survive it. PMID:29194524

  8. An Interview with Mark Ahlness and Jean Carmody about the Earth Day Groceries Project.

    ERIC Educational Resources Information Center

    Strangman, Nicole

    2002-01-01

    Outlines an interview with Mark Ahlness, a third-grade teacher at Arbor Heights Elementary School in Seattle, Washington, and Jean Carmody, an art teacher at two elementary schools in Cranston, Rhode Island. Describes their collaborative project called the Earth Day Groceries Project. Explains that in this Internet project, students decorate…

  9. Individualized Instruction in Science, Earth-Space Project, Self-Directed Activities.

    ERIC Educational Resources Information Center

    Kuczma, R. M.

    As a supplement to Learning Activity Packages (LAP) of the earth-space project, this manual presents self-directed activities especially designed for individualized instruction. Besides an introduction to LAP characteristics, sets of instructions are given in connection with the metric system, the earth's dimensions, indirect evidence for atomic…

  10. Communicating the promise, risks, and ethics of large-scale, open space microbiome and metagenome research.

    PubMed

    Shamarina, Daria; Stoyantcheva, Iana; Mason, Christopher E; Bibby, Kyle; Elhaik, Eran

    2017-10-04

    The public commonly associates microorganisms with pathogens. This suspicion of microorganisms is understandable, as historically microorganisms have killed more humans than any other agent while remaining largely unknown until the late seventeenth century with the works of van Leeuwenhoek and Kircher. Despite our improved understanding regarding microorganisms, the general public are apt to think of diseases rather than of the majority of harmless or beneficial species that inhabit our bodies and the built and natural environment. As long as microbiome research was confined to labs, the public's exposure to microbiology was limited. The recent launch of global microbiome surveys, such as the Earth Microbiome Project and MetaSUB (Metagenomics and Metadesign of Subways and Urban Biomes) project, has raised ethical, financial, feasibility, and sustainability concerns as to the public's level of understanding and potential reaction to the findings, which, done improperly, risk negative implications for ongoing and future investigations, but done correctly, can facilitate a new vision of "smart cities." To facilitate improved future research, we describe here the major concerns that our discussions with ethics committees, community leaders, and government officials have raised, and we expound on how to address them. We further discuss ethical considerations of microbiome surveys and provide practical recommendations for public engagement.

  11. Individualized Instruction in Science, Earth Space Project, Learning Activities Package.

    ERIC Educational Resources Information Center

    Kuczma, R. M.

    Learning Activity Packages (LAP) relating to the earth and space are presented for use in sampling a new type of learning for a whole year. Eighteen topics are incorporated into five units: (1) introduction to individualized learning, (2) observation versus interpretation, (3) chemistry in the space age, (4) the space age interdisciplines, and (5)…

  12. The EarthServer project: Exploiting Identity Federations, Science Gateways and Social and Mobile Clients for Big Earth Data Analysis

    NASA Astrophysics Data System (ADS)

    Barbera, Roberto; Bruno, Riccardo; Calanducci, Antonio; Messina, Antonio; Pappalardo, Marco; Passaro, Gianluca

    2013-04-01

    The EarthServer project (www.earthserver.eu), funded by the European Commission under its Seventh Framework Program, aims at establishing open access and ad-hoc analytics on extreme-size Earth Science data, based on and extending leading-edge Array Database technology. The core idea is to use database query languages as client/server interface to achieve barrier-free "mix & match" access to multi-source, any-size, multi-dimensional space-time data -- in short: "Big Earth Data Analytics" - based on the open standards of the Open Geospatial Consortium Web Coverage Processing Service (OGC WCPS) and the W3C XQuery. EarthServer combines both, thereby achieving a tight data/metadata integration. Further, the rasdaman Array Database System (www.rasdaman.com) is extended with further space-time coverage data types. On server side, highly effective optimizations - such as parallel and distributed query processing - ensure scalability to Exabyte volumes. Six Lighthouse Applications are being established in EarthServer, each of which poses distinct challenges on Earth Data Analytics: Cryospheric Science, Airborne Science, Atmospheric Science, Geology, Oceanography, and Planetary Science. Altogether, they cover all Earth Science domains; the Planetary Science use case has been added to challenge concepts and standards in non-standard environments. In addition, EarthLook (maintained by Jacobs University) showcases use of OGC standards in 1D through 5D use cases. In this contribution we will report on the first applications integrated in the EarthServer Science Gateway and on the clients for mobile appliances developed to access them. We will also show how federated and social identity services can allow Big Earth Data Providers to expose their data in a distributed environment keeping a strict and fine-grained control on user authentication and authorisation. The degree of fulfilment of the EarthServer implementation with the recommendations made in the recent TERENA Study on

  13. The hospital microbiome project: meeting report for the UK science and innovation network UK-USA workshop ‘beating the superbugs: hospital microbiome studies for tackling antimicrobial resistance’, October 14th 2013

    PubMed Central

    2014-01-01

    The UK Science and Innovation Network UK-USA workshop ‘Beating the Superbugs: Hospital Microbiome Studies for tackling Antimicrobial Resistance’ was held on October 14th 2013 at the UK Department of Health, London. The workshop was designed to promote US-UK collaboration on hospital microbiome studies to add a new facet to our collective understanding of antimicrobial resistance. The assembled researchers debated the importance of the hospital microbial community in transmission of disease and as a reservoir for antimicrobial resistance genes, and discussed methodologies, hypotheses, and priorities. A number of complementary approaches were explored, although the importance of the built environment microbiome in disease transmission was not universally accepted. Current whole genome epidemiological methods are being pioneered in the UK and the benefits of moving to community analysis are not necessarily obvious to the pioneers; however, rapid progress in other areas of microbiology suggest to some researchers that hospital microbiome studies will be exceptionally fruitful even in the short term. Collaborative studies will recombine different strengths to tackle the international problems of antimicrobial resistance and hospital and healthcare associated infections.

  14. The lung microbiome in health and disease.

    PubMed

    Moffatt, Miriam F; Cookson, William Ocm

    2017-12-01

    The Human Microbiome Project began 10 years ago, leading to a significant growth in understanding of the role the human microbiome plays in health and disease. In this article, we explain with an emphasis on the lung, the origins of microbiome research. We discuss how 16S rRNA gene sequencing became the first major molecular tool to examine the bacterial communities present within the human body. We highlight the pitfalls of molecular-based studies, such as false findings resulting from contamination, and the limitations of 16S rRNA gene sequencing. Knowledge about the lung microbiome has evolved from initial scepticism to the realisation that it might have a significant influence on many illnesses. We also discuss the lung microbiome in the context of disease by giving examples of important respiratory conditions. In addition, we draw attention to the challenges for metagenomic studies of respiratory samples and the importance of systematic bacterial isolation to enable host-microbiome interactions to be understood. We conclude by discussing how knowledge of the lung microbiome impacts current clinical diagnostics. © Royal College of Physicians 2017. All rights reserved.

  15. The Oral Microbiome Bank of China.

    PubMed

    Xian, Peng; Xuedong, Zhou; Xin, Xu; Yuqing, Li; Yan, Li; Jiyao, Li; Xiaoquan, Su; Shi, Huang; Jian, Xu; Ga, Liao

    2018-05-03

    The human microbiome project (HMP) promoted further understanding of human oral microbes. However, research on the human oral microbiota has not made as much progress as research on the gut microbiota. Currently, the causal relationship between the oral microbiota and oral diseases remains unclear, and little is known about the link between the oral microbiota and human systemic diseases. To further understand the contribution of the oral microbiota in oral diseases and systemic diseases, a Human Oral Microbiome Database (HOMD) was established in the US. The HOMD includes 619 taxa in 13 phyla, and most of the microorganisms are from American populations. Due to individual differences in the microbiome, the HOMD does not reflect the Chinese oral microbial status. Herein, we established a new oral microbiome database-the Oral Microbiome Bank of China (OMBC, http://www.sklod.org/ombc ). Currently, the OMBC includes information on 289 bacterial strains and 720 clinical samples from the Chinese population, along with lab and clinical information. The OMBC is the first curated description of a Chinese-associated microbiome; it provides tools for use in investigating the role of the oral microbiome in health and diseases, and will give the community abundant data and strain information for future oral microbial studies.

  16. Physical Oceanography: Project Earth Science. Material for Middle School Teachers in Earth Science.

    ERIC Educational Resources Information Center

    Ford, Brent A.; Smith, P. Sean

    This book is one in a series of Earth science books and contains a collection of 18 hands-on activities/demonstrations developed for the middle/junior high school level. The activities are organized around three key concepts. First, students investigate the unique properties of water and how these properties shape the ocean and the global…

  17. Principle characteristics of the National Earth Observation Satellite. Project SPOT

    NASA Technical Reports Server (NTRS)

    Cazenave, M.

    1977-01-01

    A recent meeting of the Economic and Social Committee examined the programs and means currently being implemented by France in the field in the field of space research and industry which could bring about fast results. This was prompted by man's desire to insure rational resource management of his planet and by man's awareness of the definite contribution that space observation can make to this field of research. Through discussion, the Economic and Social Committee has approved the plan for creating an earth observation satellite. A detailed discussion of the principle characteristics of this earth observation satellite include the objectives, the orbit, characteristics and operations of the platform, maintenance, attitude measurement, the power available and many other characteristics.

  18. Diatomaceous Earth Project put on standby by Texaco

    SciT

    Not Available

    1986-09-01

    Texaco has placed its Diatomite Project, located at McKittrick in California's Kern County, in a standby condition. The Project will be reactivated when conditions in the industry dictate. Texaco stressed that the Project is not being abandoned, but is being put on hold due to the current worldwide energy supply picture. The Lurgi pilot unit is being maintained in condition for future operations. Texaco estimates that the Project could yield in excess of 300 million barrels of 21 to 23 API oil from the oil-bearing diatomite deposits which lie at depths up to 1200 feet. The deposits will be recoveredmore » by open pit mining and back filling techniques.« less

  19. The "Sky on Earth" Project: A Synergy between Formal and Informal Astronomy Education

    ERIC Educational Resources Information Center

    Rossi, Sabrina; Giordano, Enrica; Lanciano, Nicoletta

    2016-01-01

    In this paper we present the "Sky on Earth" project funded in 2008 by the Italian Ministry of Instruction, Research and University, inside its annual public outreach education program. The project's goal was to realise a stable and open-access astronomical garden, where children, teachers and citizens could be engaged in investigations…

  20. New observational project for revealing natural and anthropogenic threats at the near-Earth space

    NASA Astrophysics Data System (ADS)

    Harutyunian, Haik A.; Nikoghosyan, Elena H.; Melikian, Norayr D.; Azatyan, Naira M.; Abrahamyan, Hayk V.; Paronyan, Gurgen M.; Andreasyan, Hasmik R.; Ohanian, Gabriel A.; Gevorgyan, Mkrtich H.; Mikayelyan, Gor A.

    2017-12-01

    In 2014, a new monitoring project started at the observational base Saravand of the Byurakan astrophysical observatory. This project initiated for revealing natural and artificial objects at the near-Earth space. This is a kind of continuation of earlier observational projects implemented at the observatory prior the collapse of Soviet Union. This time, near-Earth space monitoring is carried out at the request of the Russian agency ROSKOSMOS. For observations, the EOP-1 module is used, which includes small telescopes with a mirror diameter of 40cm, 25cm and 19cm.

  1. Eta-Sub-Earth Projection from Kepler Data

    NASA Technical Reports Server (NTRS)

    Traub, Wesley A.

    2012-01-01

    Outline of talk: (1) The Kepler database (2) Biases (3) The radius distribution (4) The period distribution (5) Projecting from the sam ple to the population (6) Extrapolating the period distribution (7) The Habitable Zone (8) Calculating the number of terrestrial, HZ plan ets (10) Conclusions

  2. Photovoltaic power system for satellite Earth stations in remote areas: Project status and design description

    NASA Technical Reports Server (NTRS)

    Delombard, R.

    1984-01-01

    A photovoltaic power system which will be installed at a remote location in Indonesia to provide power for a satellite Earth station and a classroom for video and audio teleconferences are described. The Earth station may also provide telephone service to a nearby village. The use of satellite communications for development assistance applications and the suitability of a hybrid photovoltaic engine generator power system for remote satellite Earth stations are demonstrated. The Indonesian rural satellite project is discussed and the photovoltaic power system is described.

  3. Project Mapping to Build Capacity and Demonstrate Impact in the Earth Sciences

    NASA Astrophysics Data System (ADS)

    Hemmings, S. N.; Searby, N. D.; Murphy, K. J.; Mataya, C. J.; Crepps, G.; Clayton, A.; Stevens, C. L.

    2017-12-01

    Diverse organizations are increasingly using project mapping to communicate location-based information about their activities. NASA's Earth Science Division (ESD), through the Earth Science Data Systems and Applied Sciences' Capacity Building Program (CBP), has created a geographic information system of all ESD projects to support internal program management for the agency. The CBP's NASA DEVELOP program has built an interactive mapping tool to support capacity building for the program's varied constituents. This presentation will explore the types of programmatic opportunities provided by a geographic approach to management, communication, and strategic planning. We will also discuss the various external benefits that mapping supports and that build capacity in the Earth sciences. These include activities such as project matching (location-focused synergies), portfolio planning, inter- and intra-organizational collaboration, science diplomacy, and basic impact analysis.

  4. Identifying personal microbiomes using metagenomic codes

    PubMed Central

    Franzosa, Eric A.; Huang, Katherine; Meadow, James F.; Gevers, Dirk; Lemon, Katherine P.; Bohannan, Brendan J. M.; Huttenhower, Curtis

    2015-01-01

    Community composition within the human microbiome varies across individuals, but it remains unknown if this variation is sufficient to uniquely identify individuals within large populations or stable enough to identify them over time. We investigated this by developing a hitting set-based coding algorithm and applying it to the Human Microbiome Project population. Our approach defined body site-specific metagenomic codes: sets of microbial taxa or genes prioritized to uniquely and stably identify individuals. Codes capturing strain variation in clade-specific marker genes were able to distinguish among 100s of individuals at an initial sampling time point. In comparisons with follow-up samples collected 30–300 d later, ∼30% of individuals could still be uniquely pinpointed using metagenomic codes from a typical body site; coincidental (false positive) matches were rare. Codes based on the gut microbiome were exceptionally stable and pinpointed >80% of individuals. The failure of a code to match its owner at a later time point was largely explained by the loss of specific microbial strains (at current limits of detection) and was only weakly associated with the length of the sampling interval. In addition to highlighting patterns of temporal variation in the ecology of the human microbiome, this work demonstrates the feasibility of microbiome-based identifiability—a result with important ethical implications for microbiome study design. The datasets and code used in this work are available for download from huttenhower.sph.harvard.edu/idability. PMID:25964341

  5. Microspacecraft and Earth observation: Electrical field (ELF) measurement project

    NASA Technical Reports Server (NTRS)

    Olsen, Tanya; Elkington, Scot; Parker, Scott; Smith, Grover; Shumway, Andrew; Christensen, Craig; Parsa, Mehrdad; Larsen, Layne; Martinez, Ranae; Powell, George

    1990-01-01

    The Utah State University space system design project for 1989 to 1990 focuses on the design of a global electrical field sensing system to be deployed in a constellation of microspacecraft. The design includes the selection of the sensor and the design of the spacecraft, the sensor support subsystems, the launch vehicle interface structure, on board data storage and communications subsystems, and associated ground receiving stations. Optimization of satellite orbits and spacecraft attitude are critical to the overall mapping of the electrical field and, thus, are also included in the project. The spacecraft design incorporates a deployable sensor array (5 m booms) into a spinning oblate platform. Data is taken every 0.1 seconds by the electrical field sensors and stored on-board. An omni-directional antenna communicates with a ground station twice per day to down link the stored data. Wrap-around solar cells cover the exterior of the spacecraft to generate power. Nine Pegasus launches may be used to deploy fifty such satellites to orbits with inclinations greater than 45 deg. Piggyback deployment from other launch vehicles such as the DELTA 2 is also examined.

  6. Advancing coupled human-earth system models: The integrated Earth System Model Project

    NASA Astrophysics Data System (ADS)

    Thomson, A. M.; Edmonds, J. A.; Collins, W.; Thornton, P. E.; Hurtt, G. C.; Janetos, A. C.; Jones, A.; Mao, J.; Chini, L. P.; Calvin, K. V.; Bond-Lamberty, B. P.; Shi, X.

    2012-12-01

    As human and biogeophysical models develop, opportunities for connections between them evolve and can be used to advance our understanding of human-earth systems interaction in the context of a changing climate. One such integration is taking place with the Community Earth System Model (CESM) and the Global Change Assessment Model (GCAM). A multi-disciplinary, multi-institution team has succeeded in integrating the GCAM integrated assessment model of human activity into CESM to dynamically represent the feedbacks between changing climate and human decision making, in the context of greenhouse gas mitigation policies. The first applications of this capability have focused on the feedbacks between climate change impacts on terrestrial ecosystem productivity and human decisions affecting future land use change, which are in turn connected to human decisions about energy systems and bioenergy production. These experiments have been conducted in the context of the RCP4.5 scenario, one of four pathways of future radiative forcing being used in CMIP5, which constrains future human-induced greenhouse gas emissions from energy and land activities to stabilize radiative forcing at 4.5 W/m2 (~650 ppm CO2 -eq) by 2100. When this pathway is run in GCAM with the climate feedback on terrestrial productivity from CESM, there are implications for both the land use and energy system changes required for stabilization. Early findings indicate that traditional definitions of radiative forcing used in scenario development are missing a critical component of the biogeophysical consequences of land use change and their contribution to effective radiative forcing. Initial full coupling of the two global models has important implications for how climate impacts on terrestrial ecosystems changes the dynamics of future land use change for agriculture and forestry, particularly in the context of a climate mitigation policy designed to reduce emissions from land use as well as energy systems

  7. Final Status Survey for the Largest Decommissioning Project on Earth

    SciT

    Dubiel, R.W.; Miller, J.; Quayle, D.

    2006-07-01

    To assist the United States Department of Energy's (US DOE's) re-industrialization efforts at its gaseous diffusion site in Oak Ridge, Tennessee, known as the East Tennessee Technology Park (ETTP), the US DOE awarded a 6-year Decontamination and Decommissioning (D and D) contract to BNG America (formerly BNFL Inc.) in 1997. The ETTP 3-Building D and D Project included the removal and disposition of the materials and equipment from the K-33, K-31, and K-29 Gaseous Diffusion Plant buildings. The three buildings comprise more than 4.8 million square feet (446,000 square meters) of floor surface area and more than 350 million poundsmore » (148 million kilograms) of hazardous and radioactively contaminated material, making it the largest nuclear D and D project in progress anywhere in the world. The logistical hurdles involved in a project of this scope and magnitude required an extensive amount of Engineering and Health Physics professionals. In order to accomplish the Final Status Survey (FSS) for a project of this scope, the speed and efficiency of automated survey equipment was essential. Surveys of floors, structural steel and ceilings up to 60 feet (18 meters) were required. The FSS had to be expanded to include additional remediation and surveys due to characterization surveys and assumptions regarding the nature and extent of contamination provided by the US DOE. Survey design and technical bases had to consider highly variable constituents; including uranium from depleted to low enrichment, variable levels of Technetium-99 and transuranic nuclides, which were introduced into the cascade during the 1960's when recycled uranium (RU) from Savannah River was re-enriched at the facility. The RU was transported to unexpected locations from leaks in the cascade by complex building ventilation patterns. The primary survey tool used for the post remediation and FSS was the Surface Contamination Monitor (SCM) and the associated Survey Information Management System

  8. Magnetic Earth Ionosphere Resonant Frequencies (NASA-MEIRF Project)

    NASA Technical Reports Server (NTRS)

    1994-01-01

    During this current reporting period, the project has focused on completing Phase 1 of the field monitoring work and documenting research results. Highlights of these efforts include presentations of papers at the annual joint meeting of the American Physical Society/American Association of Physics Teachers, April 18-22, 1994, in Crystal City, Virginia, and at the International Space, Time, and Gravitation Conference and Etoiles de L'Ecole Polytechnique Symposium, May 23-28, 1994, in St. Petersburg, Russia. Field measurements of the background ultra low frequency (ULF) electromagnetic spectrum in the New Mexico and Texas regions show interesting differences. Included are papers entitled 'Triplet Solution of the Twin Paradox' and 'Classical Electron Mass and Fields, Part 3.'

  9. Dagik Earth: A Digital Globe Project for Classrooms, Science Museums, and Research Institutes

    NASA Astrophysics Data System (ADS)

    Saito, A.; Tsugawa, T.

    2017-12-01

    Digital globe system is a powerful tool to make the audiences understand phenomena on the Earth and planets in intuitive way. Geo-cosmos of Miraikan, Japan uses 6-m spherical LED, and is one of the largest systems of digital globe. Science on a Sphere (SOS) by NOAA is a digital globe system that is most widely used in science museums around the world. These systems are so expensive that the usage of the digital globes is mainly limited to large-scale science museums. Dagik Earth is a digital globe project that promotes educational programs using digital globe with low cost. It aims to be used especially in classrooms. The cost for the digital globe of Dagik Earth is from several US dollars if PC and PC projector are available. It uses white spheres, such as balloons and balance balls, as the screen. The software is provided by the project with free of charge for the educational usage. The software runs on devices of Windows, Mac and iOS. There are English and Chinese language versions of the PC software besides Japanese version. The number of the registered users of Dagik Earth is about 1,400 in Japan. About 60% of them belongs to schools, 30% to universities and research institutes, and 8% to science museums. In schools, it is used in classes by teachers, and science activities by students. Several teachers have used the system for five years and more. In a students' activity, Dagik Earth contents on the typhoon, solar eclipse, and satellite launch were created and presented in a school festival. This is a good example of the usage of Dagik Earth for STEM education. In the presentation, the system and activity of Dagik Earth will be presented, and the future expansion of the project will be discussed.

  10. Hot Spots in the Earth's Crust. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

    ERIC Educational Resources Information Center

    Stoever, Edward C., Jr.

    Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

  11. Earth BioGenome Project: Sequencing life for the future of life.

    PubMed

    Lewin, Harris A; Robinson, Gene E; Kress, W John; Baker, William J; Coddington, Jonathan; Crandall, Keith A; Durbin, Richard; Edwards, Scott V; Forest, Félix; Gilbert, M Thomas P; Goldstein, Melissa M; Grigoriev, Igor V; Hackett, Kevin J; Haussler, David; Jarvis, Erich D; Johnson, Warren E; Patrinos, Aristides; Richards, Stephen; Castilla-Rubio, Juan Carlos; van Sluys, Marie-Anne; Soltis, Pamela S; Xu, Xun; Yang, Huanming; Zhang, Guojie

    2018-04-24

    Increasing our understanding of Earth's biodiversity and responsibly stewarding its resources are among the most crucial scientific and social challenges of the new millennium. These challenges require fundamental new knowledge of the organization, evolution, functions, and interactions among millions of the planet's organisms. Herein, we present a perspective on the Earth BioGenome Project (EBP), a moonshot for biology that aims to sequence, catalog, and characterize the genomes of all of Earth's eukaryotic biodiversity over a period of 10 years. The outcomes of the EBP will inform a broad range of major issues facing humanity, such as the impact of climate change on biodiversity, the conservation of endangered species and ecosystems, and the preservation and enhancement of ecosystem services. We describe hurdles that the project faces, including data-sharing policies that ensure a permanent, freely available resource for future scientific discovery while respecting access and benefit sharing guidelines of the Nagoya Protocol. We also describe scientific and organizational challenges in executing such an ambitious project, and the structure proposed to achieve the project's goals. The far-reaching potential benefits of creating an open digital repository of genomic information for life on Earth can be realized only by a coordinated international effort.

  12. The Changing Earth Science Network- Projects and Results from the First Call

    NASA Astrophysics Data System (ADS)

    Dransfeld, Steffen; Fernandez, Diego; Doron, Maeva; Martinez, Elodie; Shutler, Jamie; Papandrea, Enzo; Biggs, Juliet; Dagestad, Knut-Frode; Palazzi, Elisa; Garcia-Comas, Maya; de Graaf, Martin; Schneising, Oliver; Pavon, Patricia Oliva

    2010-12-01

    To better understand the different processes and interactions that govern the earth system and to determine whether recent human-induced changes could ultimately de-stabilise its dynamics, both natural system variability and the consequences of human activities have to be observed and quantified. In this context, the European Space Agency published in 2006 "The Changing Earth: New Scientific Challenges for ESA's living Planet Programme" as the main driver of ESA's new EO science strategy. The document outlines 25 major scientific challenges covering all the different aspects of the Earth system, where EO technology and ESA missions may provide a key contribution. In this context, and responding to a request from ESAC (Earth Science Advisory Committee) to enhance the ESA scientific support towards the achievement of "The Challenges", the Agency has launched the Changing Earth Science Network as an important programmatic component of the new Support To Science Element (STSE) of the Earth Observation Envelope Programme (EOEP). In this paper we summarize the objectives of this initive and provide a review of the first projects that were selected in 2009 and are now generating their first results.

  13. Gut microbiome and bone.

    PubMed

    Ibáñez, Lidia; Rouleau, Matthieu; Wakkach, Abdelilah; Blin-Wakkach, Claudine

    2018-04-11

    The gut microbiome is now viewed as a tissue that interacts bidirectionally with the gastrointestinal, immune, endocrine and nervous systems, affecting the cellular responses in numerous organs. Evidence is accumulating of gut microbiome involvement in a growing number of pathophysiological processes, many of which are linked to inflammatory responses. More specifically, data acquired over the last decade point to effects of the gut microbiome on bone mass regulation and on the development of bone diseases (such as osteoporosis) and of inflammatory joint diseases characterized by bone loss. Mice lacking a gut microbiome have bone mass alteration that can be reversed by gut recolonization. Changes in the gut microbiome composition have been reported in mice with estrogen-deficiency osteoporosis and have also been found in a few studies in humans. Probiotic therapy decreases bone loss in estrogen-deficient animals. The effect of the gut microbiome on bone tissue involves complex mechanisms including modulation of CD4 + T cell activation, control of osteoclastogenic cytokine production and modifications in hormone levels. This complexity may contribute to explain the discrepancies observed betwwen some studies whose results vary depending on the age, gender, genetic background and treatment duration. Further elucidation of the mechanisms involved is needed. However, the available data hold promise that gut microbiome manipulation may prove of interest in the management of bone diseases. Copyright © 2018 Société française de rhumatologie. Published by Elsevier SAS. All rights reserved.

  14. Biodiversity and Functional Genomics in the Human Microbiome

    PubMed Central

    Morgan, Xochitl C.; Segata, Nicola; Huttenhower, Curtis

    2012-01-01

    Over the course of our lives, humans are colonized by a tremendous diversity of commensal microbes, which comprise the human microbiome. The collective genetic potential (metagenome) of the human microbiome is orders of magnitude more than the human genome, and it profoundly affects human health and disease in ways we are only beginning to understand. Advances in computing and high-throughput sequencing have enabled population-level surveys such as MetaHIT and the recently-released Human Microbiome Project, detailed investigations of the microbiome in human disease, and mechanistic studies employing gnotobiotic model organisms. The resulting knowledge of human microbiome composition, function, and range of variation across multiple body sites has begun to assemble a rich picture of commensal host-microbe and microbe- microbe interactions as well as their roles in human health and disease and their potential as diagnostic and therapeutic tools. PMID:23140990

  15. The MY NASA DATA Project: Preparing Future Earth and Environmental Scientists, and Future Citizens

    NASA Astrophysics Data System (ADS)

    Chambers, L. H.; Phelps, C. S.; Phipps, M.; Holzer, M.; Daugherty, P.; Poling, E.; Vanderlaan, S.; Oots, P. C.; Moore, S. W.; Diones, D. D.

    2008-12-01

    For the past 5 years, the MY NASA DATA (MND) project at NASA Langley has developed and adapted tools and materials aimed at enabling student access to real NASA Earth science satellite data. These include web visualization tools including Google Earth capabilities, but also GPS and graphing calculator exercises, Excel spreadsheet analyses, and more. The project team, NASA scientists, and over 80 classroom science teachers from around the country, have created over 85 lesson plans and science fair project ideas that demonstrate NASA satellite data use in the classroom. With over 150 Earth science parameters to choose from, the MND Live Access Server enables scientific inquiry on numerous interconnected Earth and environmental science topics about the Earth system. Teachers involved in the project report a number of benefits, including networking with other teachers nationwide who emphasize data collection and analysis in the classroom, as well as learning about other NASA resources and programs for educators. They also indicate that the MND website enhances the inquiry process and facilitates the formation of testable questions by students (a task that is typically difficult for students to do). MND makes science come alive for students because it allows them to develop their own questions using the same data scientists use. MND also provides educators with a rich venue for science practice skills, which are often overlooked in traditional curricula as teachers concentrate on state and national standards. A teacher in a disadvantaged school reports that her students are not exposed to many educational experiences outside the classroom. MND allows inner city students to be a part of NASA directly. They are able to use the same information that scientists are using and this gives them inspiration. In all classrooms, the MND microsets move students out of their local area to explore global data and then zoom back into their homes realizing that they are a part of the

  16. Methodology and Ontology in Microbiome Research.

    PubMed

    Huss, John

    2014-01-01

    Research on the human microbiome has generated a staggering amount of sequence data, revealing variation in microbial diversity at the community, species (or phylotype), and genomic levels. In order to make this complexity more manageable and easier to interpret, new units-the metagenome, core microbiome, and enterotype-have been introduced in the scientific literature. Here, I argue that analytical tools and exploratory statistical methods, coupled with a translational imperative, are the primary drivers of this new ontology. By reducing the dimensionality of variation in the human microbiome, these new units render it more tractable and easier to interpret, and hence serve an important heuristic role. Nonetheless, there are several reasons to be cautious about these new categories prematurely "hardening" into natural units: a lack of constraints on what can be sequenced metagenomically, freedom of choice in taxonomic level in defining a "core microbiome," typological framing of some of the concepts, and possible reification of statistical constructs. Finally, lessons from the Human Genome Project have led to a translational imperative: a drive to derive results from the exploration of microbiome variation that can help to articulate the emerging paradigm of personalized genomic medicine (PGM). There is a tension between the typologizing inherent in much of this research and the personal in PGM.

  17. Improving Future Ecosystem Benefits through Earth Observations: the H2020 Project ECOPOTENTIAL

    NASA Astrophysics Data System (ADS)

    Provenzale, Antonello; Beierkuhnlein, Carl; Ziv, Guy

    2016-04-01

    Terrestrial and marine ecosystems provide essential goods and services to human societies. In the last decades, however, anthropogenic pressures caused serious threats to ecosystem integrity, functions and processes, potentially leading to the loss of essential ecosystem services. ECOPOTENTIAL is a large European-funded H2020 project which focuses its activities on a targeted set of internationally recognised protected areas in Europe, European Territories and beyond, blending Earth Observations from remote sensing and field measurements, data analysis and modelling of current and future ecosystem conditions and services. The definition of future scenarios is based on climate and land-use change projections, addressing the issue of uncertainties and uncertainty propagation across the modelling chain. The ECOPOTENTIAL project addresses cross-scale geosphere-biosphere interactions and landscape-ecosystem dynamics at regional to continental scales, using geostatistical methods and the emerging approaches in Macrosystem Ecology and Earth Critical Zone studies, addressing long-term and large-scale environmental and ecological challenges. The project started its activities in 2015, by defining a set of storylines which allow to tackle some of the most crucial issues in the assessment of present conditions and the estimate of the future state of selected ecosystem services. In this contribution, we focus on some of the main storylines of the project and discuss the general approach, focusing on the interplay of data and models and on the estimate of projection uncertainties.

  18. Homogenisation in project management for large German research projects in the Earth system sciences: overcoming the institutional coordination bias

    NASA Astrophysics Data System (ADS)

    Rauser, Florian; Vamborg, Freja

    2016-04-01

    The interdisciplinary project on High Definition Clouds and Precipitation for advancing climate prediction HD(CP)2 (hdcp2.eu) is an example for the trend in fundamental research in Europe to increasingly focus on large national and international research programs that require strong scientific coordination. The current system has traditionally been host-based: project coordination activities and funding is placed at the host institute of the central lead PI of the project. This approach is simple and has the advantage of strong collaboration between project coordinator and lead PI, while exhibiting a list of strong, inherent disadvantages that are also mentioned in this session's description: no community best practice development, lack of integration between similar projects, inefficient methodology development and usage, and finally poor career development opportunities for the coordinators. Project coordinators often leave the project before it is finalized, leaving some of the fundamentally important closing processes to the PIs. This systematically prevents the creation of professional science management expertise within academia, which leads to an automatic imbalance that hinders the outcome of large research programs to help future funding decisions. Project coordinators in academia often do not work in a professional project office environment that could distribute activities and use professional tools and methods between different projects. Instead, every new project manager has to focus on methodological work anew (communication infrastructure, meetings, reporting), even though the technological needs of large research projects are similar. This decreases the efficiency of the coordination and leads to funding that is effectively misallocated. We propose to challenge this system by creating a permanent, virtual "Centre for Earth System Science Management CESSMA" (cessma.com), and changing the approach from host- based to centre-based. This should

  19. USGS microbiome research

    Kellogg, Christina A.; Hopkins, M. Camille

    2017-09-26

    Microbiomes are the communities of microorganisms (for example, bacteria, viruses, and fungi) that live on, in, and around people, plants, animals, soil, water, and the atmosphere. Microbiomes are active in the functioning of diverse ecosystems, for instance, by influencing water quality, nutrient acquisition 
and stress tolerance in plants, and stability of soil and aquatic environments. Microbiome research conducted by the U.S. Geological Survey spans many of our mission areas. Key research areas include water quality, understanding climate effects on soil and permafrost, ecosystem and wildlife health, invasive species, contaminated environments to improve bioremediation, and enhancing energy production. Microbiome research will fundamentally strengthen the ability to address the global challenges of maintaining clean water, ensuring adequate food supply, meeting energy needs, and preserving human and ecosystem health.

  20. NextGEOSS project: A user-driven approach to build a Earth Observations Data Hub

    NASA Astrophysics Data System (ADS)

    Percivall, G.; Voidrot, M. F.; Bye, B. L.; De Lathouwer, B.; Catarino, N.; Concalves, P.; Kraft, C.; Grosso, N.; Meyer-Arnek, J.; Mueller, A.; Goor, E.

    2017-12-01

    Several initiatives and projects contribute to support Group on Earth Observation's (GEO) global priorities including support to the UN 2030 Agenda for sustainable development, the Paris Agreement on climate change, and the Sendai Framework for Disaster Risk Reduction . Running until 2020, the NextGEOSS project evolves the European vision of a user driven GEOSS data exploitation for innovation and business, relying on the three main pillars: engaging communities of practice delivering technological advancements advocating the use of GEOSS These 3 pillars support the creation and deployment of Earth observation based innovative research activities and commercial services. In this presentation we will emphasise how the NextGEOSS project uses a pilot-driven approach to ramp up and consolidate the system in a pragmatique way, integrating the complexity of the existing global ecosystem, leveraging previous investments, adding new cloud technologies and resources and engaging the diverse communities to address all types of Sustainable Development Goals (SDGs). A set of 10 initial pilots have been defined by the project partners to address the main challenges and include as soon as possible contributions to SDGs associated with Food Sustainability, Bio Diversity, Space and Security, Cold Regions, Air Pollutions, Disaster Risk Reduction, Territorial Planning, Energy. In 2018 and 2019 the project team will work on two new series of Architecture Implementation Pilots (AIP-10 and AIP-11), opened world-wide, to increase discoverability, accessibility and usability of data with a strong User Centric approach for innovative GEOSS powered applications for multiple societal areas. All initiatives with an interest in and need of Earth observations (data, processes, models, ...) are welcome to participate to these pilots initiatives. NextGEOSS is a H2020 Research and Development Project from the European Community under grant agreement 730329.

  1. A new research project on the interaction of the solid Earth and the Antarctic Ice Sheet

    NASA Astrophysics Data System (ADS)

    Fukuda, Y.; Nishijima, J.; Kazama, T.; Nakamura, K.; Doi, K.; Suganuma, Y.; Okuno, J.; Araya, A.; Kaneda, H.; Aoyama, Y.

    2017-12-01

    A new research project of "Grant-in-Aid for Scientific Research on Innovative Areas" funded by JSPS (Japan Society for the Promotion of Science) has recently been launched. The title of the project is "Giant reservoirs of heat/water/material: Global environmental changes driven by Southern Ocean and Antarctic Ice Sheet", and as a five years project, is aiming to establish a new research area for Antarctic environmental system science. The project consists of 7 research topics, including Antarctic ice sheet and Southern ocean sciences, new observation methodology, modeling and other interdisciplinary topics, and we are involved in the topic A02-2, "Interaction of the solid Earth and the Antarctic Ice Sheet". The Antarctic ice sheet, which relates to the global climate changes through the sea level rise and ocean circulation, is an essential element of the Earth system for predicting the future environment changes. Thus many studies of the ice sheet changes have been conducted by means of geomorphological, geological, geodetic surveys, as well as satellite gravimetry and satellite altimetry. For these studies, one of the largest uncertainties is the effects of GIA. Therefore, GIA as a key to investigate the interaction between the solid Earth and the ice sheet changes, we plan to conduct geomorphological, geological and geodetic surveys in the inland mountain areas and the coastal areas including the surrounding areas of a Japanese station Syowa in East Antarctica, where the in-situ data for constraining GIA models are very few. Combining these new observations with other in-site data, various satellite data and numerical modeling, we aim to estimating a precise GIA model, constructing a reliable ice melting history after the last glacial maximum and obtaining the viscoelastic structure of the Earth's interior. In the presentation, we also show the five years research plans as well. This study was partially supported by JSPS KAKENHI Grant No. 17H06321.

  2. Project of a laser gyroscope to determine continuously the Earth's rotation.

    NASA Astrophysics Data System (ADS)

    Blinov, N. S.; Zharov, V. E.; Sazhin, M. V.; Fedoseev, E. N.; Vlasov, B. I.; Rusakov, V. K.

    The Time Service of the Sternberg State Astronomical Institute together with specialists of VNIIFTRI began to work at the project of the laser gyroscope to determine continuously the Earth's rotation. It is assumed to measure both the high-frequency variations with periods of 100 - 1000 sec and the low-frequency variations with periods of a few days. It gives the opportunity to combine these data with the VLBI data.

  3. "Arising from Sullen Earth": The 52nd Street Project's Transformative Teen Shakespeare Project

    ERIC Educational Resources Information Center

    Sandberg-Zakian, Megan

    2010-01-01

    The author of this document spent time as the Associate Artistic Director of The 52nd Street Project, a not-for-profit theater company dedicated to the creation and production of new plays for, and often by, kids between the ages of nine and eighteen that reside in the Hell's Kitchen neighborhood of New York City. Through a series of unique…

  4. Host genetic variation impacts microbiome composition across human body sites.

    PubMed

    Blekhman, Ran; Goodrich, Julia K; Huang, Katherine; Sun, Qi; Bukowski, Robert; Bell, Jordana T; Spector, Timothy D; Keinan, Alon; Ley, Ruth E; Gevers, Dirk; Clark, Andrew G

    2015-09-15

    The composition of bacteria in and on the human body varies widely across human individuals, and has been associated with multiple health conditions. While microbial communities are influenced by environmental factors, some degree of genetic influence of the host on the microbiome is also expected. This study is part of an expanding effort to comprehensively profile the interactions between human genetic variation and the composition of this microbial ecosystem on a genome- and microbiome-wide scale. Here, we jointly analyze the composition of the human microbiome and host genetic variation. By mining the shotgun metagenomic data from the Human Microbiome Project for host DNA reads, we gathered information on host genetic variation for 93 individuals for whom bacterial abundance data are also available. Using this dataset, we identify significant associations between host genetic variation and microbiome composition in 10 of the 15 body sites tested. These associations are driven by host genetic variation in immunity-related pathways, and are especially enriched in host genes that have been previously associated with microbiome-related complex diseases, such as inflammatory bowel disease and obesity-related disorders. Lastly, we show that host genomic regions associated with the microbiome have high levels of genetic differentiation among human populations, possibly indicating host genomic adaptation to environment-specific microbiomes. Our results highlight the role of host genetic variation in shaping the composition of the human microbiome, and provide a starting point toward understanding the complex interaction between human genetics and the microbiome in the context of human evolution and disease.

  5. Pharmacomicrobiomics: The Impact of Human Microbiome Variations on Systems Pharmacology and Personalized Therapeutics

    PubMed Central

    ElRakaiby, Marwa; Dutilh, Bas E.; Rizkallah, Mariam R.; Boleij, Annemarie; Cole, Jason N.

    2014-01-01

    Abstract The Human Microbiome Project (HMP) is a global initiative undertaken to identify and characterize the collection of human-associated microorganisms at multiple anatomic sites (skin, mouth, nose, colon, vagina), and to determine how intra-individual and inter-individual alterations in the microbiome influence human health, immunity, and different disease states. In this review article, we summarize the key findings and applications of the HMP that may impact pharmacology and personalized therapeutics. We propose a microbiome cloud model, reflecting the temporal and spatial uncertainty of defining an individual's microbiome composition, with examples of how intra-individual variations (such as age and mode of delivery) shape the microbiome structure. Additionally, we discuss how this microbiome cloud concept explains the difficulty to define a core human microbiome and to classify individuals according to their biome types. Detailed examples are presented on microbiome changes related to colorectal cancer, antibiotic administration, and pharmacomicrobiomics, or drug–microbiome interactions, highlighting how an improved understanding of the human microbiome, and alterations thereof, may lead to the development of novel therapeutic agents, the modification of antibiotic policies and implementation, and improved health outcomes. Finally, the prospects of a collaborative computational microbiome research initiative in Africa are discussed. PMID:24785449

  6. Pharmacomicrobiomics: the impact of human microbiome variations on systems pharmacology and personalized therapeutics.

    PubMed

    ElRakaiby, Marwa; Dutilh, Bas E; Rizkallah, Mariam R; Boleij, Annemarie; Cole, Jason N; Aziz, Ramy K

    2014-07-01

    The Human Microbiome Project (HMP) is a global initiative undertaken to identify and characterize the collection of human-associated microorganisms at multiple anatomic sites (skin, mouth, nose, colon, vagina), and to determine how intra-individual and inter-individual alterations in the microbiome influence human health, immunity, and different disease states. In this review article, we summarize the key findings and applications of the HMP that may impact pharmacology and personalized therapeutics. We propose a microbiome cloud model, reflecting the temporal and spatial uncertainty of defining an individual's microbiome composition, with examples of how intra-individual variations (such as age and mode of delivery) shape the microbiome structure. Additionally, we discuss how this microbiome cloud concept explains the difficulty to define a core human microbiome and to classify individuals according to their biome types. Detailed examples are presented on microbiome changes related to colorectal cancer, antibiotic administration, and pharmacomicrobiomics, or drug-microbiome interactions, highlighting how an improved understanding of the human microbiome, and alterations thereof, may lead to the development of novel therapeutic agents, the modification of antibiotic policies and implementation, and improved health outcomes. Finally, the prospects of a collaborative computational microbiome research initiative in Africa are discussed.

  7. Live Storybook Outcomes of Pilot Multidisciplinary Elementary Earth Science Collaborative Project

    NASA Astrophysics Data System (ADS)

    Soeffing, C.; Pierson, R.

    2017-12-01

    Live Storybook Outcomes of pilot multidisciplinary elementary earth science collaborative project Anchoring phenomena leading to student led investigations are key to applying the NGSS standards in the classroom. This project employs the GLOBE elementary storybook, Discoveries at Willow Creek, as an inspiration and operational framework for a collaborative pilot project engaging 4th grade students in asking questions, collecting relevant data, and using analytical tools to document and understand natural phenomena. The Institute of Global Environmental Strategies (IGES), a GLOBE Partner, the Outdoor Campus, an informal educational outdoor learning facility managed by South Dakota Game, Fish and Parks, University of Sioux Falls, and All City Elementary, Sioux Falls are collaborating partners in this project. The Discoveries at Willow Creek storyline introduces young students to the scientific process, and models how they can apply science and engineering practices (SEPs) to discover and understand the Earth system in which they live. One innovation associated with this project is the formal engagement of elementary students in a global citizen science program (for all ages), GLOBE Observer, and engaging them in data collection using GLOBE Observer's Cloud and Mosquito Habitat Mapper apps. As modeled by the fictional students from Willow Creek, the 4th grade students will identify their 3 study sites at the Outdoor Campus, keep a journal, and record observations. The students will repeat their investigations at the Outdoor Campus to document and track change over time. Students will be introduced to "big data" in a manageable way, as they see their observations populate GLOBE's map-based data visualization and . Our research design recognizes the comfort and familiarity factor of literacy activities in the elementary classroom for students and teachers alike, and postulates that connecting a science education project to an engaging storybook text will contribute to a

  8. ForM@Ter: a French Solid Earth Research Infrastructure Project

    NASA Astrophysics Data System (ADS)

    Mandea, M.; Diament, M.; Jamet, O.; Deschamps-Ostanciaux, E.

    2017-12-01

    Recently, some noteworthy initiatives to develop efficient research e-infrastructures for the study of the Earth's system have been set up. However, some gaps between the data availability and their scientific use still exists, either because technical reasons (big data issues) or because of the lack of a dedicated support in terms of expert knowledge of the data, software availability, or data cost. The need for thematic cooperative platforms has been underlined over the last years, as well as the need to create thematic centres designed to federate the scientific community of Earth's observation. Four thematic data centres have been developed in France, covering the domains of ocean, atmosphere, land, and solid Earth sciences. For the Solid Earth science community, a research infrastructure project named ForM@Ter was launched by the French Space Agency (CNES) and the National Centre for Scientific Research (CNRS), with the active participation of the National institute for geographical and forestry information (IGN). Currently, it relies on the contributions of scientists from more than 20 French Earth science laboratories.Preliminary analysis have showed that a focus on the determination of the shape and movements of the Earth surface (ForM@Ter: Formes et Mouvements de la Terre) can federate a wide variety of scientific areas (earthquake cycle, tectonics, morphogenesis, volcanism, erosion dynamics, mantle rheology, geodesy) and offers many interfaces with other geoscience domains, such as glaciology or snow evolution. This choice motivates the design of an ambitious data distribution scheme, including a wide variety of sources - optical imagery, SAR, GNSS, gravity, satellite altimetry data, in situ observations (inclinometers, seismometers, etc.) - as well as a wide variety of processing techniques. In the evolving context of the current and forthcoming national and international e-infrastructures, the challenge of the project is to design a non

  9. EarthCube as an information resource marketplace; the GEAR Project conceptual design

    NASA Astrophysics Data System (ADS)

    Richard, S. M.; Zaslavsky, I.; Gupta, A.; Valentine, D.

    2015-12-01

    Geoscience Architecture for Research (GEAR) is approaching EarthCube design as a complex and evolving socio-technical federation of systems. EarthCube is intended to support the science research enterprise, for which there is no centralized command and control, requirements are a moving target, the function and behavior of the system must evolve and adapt as new scientific paradigms emerge, and system participants are conducting research that inherently implies seeking new ways of doing things. EarthCube must address evolving user requirements and enable domain and project systems developed under different management and for different purposes to work together. The EC architecture must focus on creating a technical environment that enables new capabilities by combining existing and newly developed resources in various ways, and encourages development of new resource designs intended for re-use and interoperability. In a sense, instead of a single architecture design, GEAR provides a way to accommodate multiple designs tuned to different tasks. This agile, adaptive, evolutionary software development style is based on a continuously updated portfolio of compatible components that enable new sub-system architecture. System users make decisions about which components to use in this marketplace based on performance, satisfaction, and impact metrics collected continuously to evaluate components, determine priorities, and guide resource allocation decisions by the system governance agency. EC is designed as a federation of independent systems, and although the coordinator of the EC system may be named an enterprise architect, the focus of the role needs to be organizing resources, assessing their readiness for interoperability with the existing EC component inventory, managing dependencies between transient subsystems, mechanisms of stakeholder engagement and inclusion, and negotiation of standard interfaces, rather than actual specification of components. Composition of

  10. The Airplane Cabin Microbiome.

    PubMed

    Weiss, Howard; Hertzberg, Vicki Stover; Dupont, Chris; Espinoza, Josh L; Levy, Shawn; Nelson, Karen; Norris, Sharon

    2018-06-06

    Serving over three billion passengers annually, air travel serves as a conduit for infectious disease spread, including emerging infections and pandemics. Over two dozen cases of in-flight transmissions have been documented. To understand these risks, a characterization of the airplane cabin microbiome is necessary. Our study team collected 229 environmental samples on ten transcontinental US flights with subsequent 16S rRNA sequencing. We found that bacterial communities were largely derived from human skin and oral commensals, as well as environmental generalist bacteria. We identified clear signatures for air versus touch surface microbiome, but not for individual types of touch surfaces. We also found large flight-to-flight beta diversity variations with no distinguishing signatures of individual flights, rather a high between-flight diversity for all touch surfaces and particularly for air samples. There was no systematic pattern of microbial community change from pre- to post-flight. Our findings are similar to those of other recent studies of the microbiome of built environments. In summary, the airplane cabin microbiome has immense airplane to airplane variability. The vast majority of airplane-associated microbes are human commensals or non-pathogenic, and the results provide a baseline for non-crisis-level airplane microbiome conditions.

  11. The Sky on Earth project: a synergy between formal and informal astronomy education

    NASA Astrophysics Data System (ADS)

    Rossi, Sabrina; Giordano, Enrica; Lanciano, Nicoletta

    2016-09-01

    In this paper we present the Sky on Earth project funded in 2008 by the Italian Ministry of Instruction, Research and University, inside its annual public outreach education program. The project’s goal was to realise a stable and open-access astronomical garden, where children, teachers and citizens could be engaged in investigations about day and night sky phenomena. The project was designed taking into account our prior researches in formal and informal astronomy education. It was realised in the garden of GiocheriaLaboratori, an out-of-school K-6 educational structure of Sesto San Giovanni municipality (near Milan, Italy). Setting and tools were designed with the help of some students of the ‘Altiero Spinelli’ vocational school and their science and technology teachers. Since its installation, the astronomical garden has been used in workshops and open-days, teachers’ preparation courses and research experiences. We might conclude that the Sky on Earth project represents an example of a positive and constructive collaboration between researchers, educators, high school students and teachers. It may also be considered as a potential attempt to face on the well-known gap between research in science education and school practices.

  12. Climate Data Service in the FP7 EarthServer Project

    NASA Astrophysics Data System (ADS)

    Mantovani, Simone; Natali, Stefano; Barboni, Damiano; Grazia Veratelli, Maria

    2013-04-01

    EarthServer is a European Framework Program project that aims at developing and demonstrating the usability of open standards (OGC and W3C) in the management of multi-source, any-size, multi-dimensional spatio-temporal data - in short: "Big Earth Data Analytics". In order to demonstrate the feasibility of the approach, six thematic Lighthouse Applications (Cryospheric Science, Airborne Science, Atmospheric/ Climate Science, Geology, Oceanography, and Planetary Science), each with 100+ TB, are implemented. Scope of the Atmospheric/Climate lighthouse application (Climate Data Service) is to implement the system containing global to regional 2D / 3D / 4D datasets retrieved either from satellite observations, from numerical modelling and in-situ observations. Data contained in the Climate Data Service regard atmospheric profiles of temperature / humidity, aerosol content, AOT, and cloud properties provided by entities such as the European Centre for Mesoscale Weather Forecast (ECMWF), the Austrian Meteorological Service (Zentralanstalt für Meteorologie und Geodynamik - ZAMG), the Italian National Agency for new technologies, energies and sustainable development (ENEA), and the Sweden's Meteorological and Hydrological Institute (Sveriges Meteorologiska och Hydrologiska Institut -- SMHI). The system, through an easy-to-use web application permits to browse the loaded data, visualize their temporal evolution on a specific point with the creation of 2D graphs of a single field, or compare different fields on the same point (e.g. temperatures from different models and satellite observations), and visualize maps of specific fields superimposed with high resolution background maps. All data access operations and display are performed by means of OGC standard operations namely WMS, WCS and WCPS. The EarthServer project has just started its second year over a 3-years development plan: the present status the system contains subsets of the final database, with the scope of

  13. The past, present and future of microbiome analyses

    SciT

    White, Richard Allen; Callister, Stephen J.; Moore, Ronald J.

    Microbes evolved on Earth approximately 3.5 billion years ago and eventually occupied every habitable environment in its biosphere. While microorganisms are responsible for key functions on Earth including carbon and nutrient cycling and determining the health and disease of its inhabitants (i.e. plants and animals), >99% of the estimated trillions of microbes have yet to be discovered.1 In addition, high microbial diversity has made it difficult to study specific functions carried out by complex microbial communities within "microbiomes", such as those inhabiting the soil and human gut.2,3 Fortunately, technological advances over the last few decades have greatly facilitated studies ofmore » complex microbiomes and their functions. Here we will specifically discuss advances related to nucleic acid sequencing and mass spectrometry analyses that have enabled exploration and understanding of complex microbiomes in a range of environments and our own bodies.4,5,6,7« less

  14. Project ALERT: Forging New Partnerships to Improve Earth System Science Education for Pre-Service and In-Service Teachers

    NASA Astrophysics Data System (ADS)

    Metzger, E. P.; Ambos, E. L.; Ng, E. W.; Skiles, J.; Simila, G.; Garfield, N.

    2002-05-01

    Project ALERT (Augmented Learning Environment and Renewable Teaching) was founded in 1998, with funding from NASA and the California State University (CSU), to improve earth system science education for pre-service teachers. Project ALERT has formed linkages between ten campuses of the CSU, which prepares about 60 percent of California's teachers, and two NASA centers, Ames Research Center and the Jet Propulsion Laboratory. ALERT has also fostered alliances between earth science and science education faculty. The combined expertise of Project ALERT's diverse partners has led to a wide array of activities and products, including: 1) incorporation in university classrooms of NASA-developed imagery, data, and educational resources; 2) creation and/or enhancement of several courses that bring earth systems science to pre-service teachers; 3) fellowships for CSU faculty to participate in collaborative research and education projects at the NASA Centers; 4) development of teaching modules on such varied topics as volcanoes, landslides, and paleoclimate; and 5) a central web site that highlights resources for teaching introductory Earth system science. An outgrowth of Project ALERT is the increased interest on the part of CSU earth scientists in education issues. This has catalyzed their participation in other projects, including NASA's Project NOVA, Earth System Science Education Alliance, and Sun-Earth Connection Education Forum, the Digital Library for Earth System Science Education, and the California Science Project. Project ALERT has also expanded to provide professional development opportunities for in-service teachers, as exemplified by its support of the Bay Area Earth Science Institute (BAESI) at San Jose State University. Each year, BAESI offers 10-15 full-day workshops that supply teachers and teachers-to-be with a blend of science concepts and classroom activities, free instructional materials, and the opportunity to earn inexpensive university credit. These

  15. Ancient human microbiomes

    PubMed Central

    Warinner, Christina; Speller, Camilla; Collins, Matthew J.; Lewis, Cecil M.

    2015-01-01

    Very recently, we discovered a vast new microbial self: the human microbiome. Our native microbiota interface with our biology and culture to influence our health, behavior, and quality of life, and yet we know very little about their origin, evolution, or ecology. With the advent of industrialization, globalization, and modern sanitation, it is intuitive that we have changed our relationship with microbes, but we have little information about the ancestral state of our microbiome, and therefore, we lack a foundation for characterizing this change. High-throughput sequencing has opened up new opportunities in the field of paleomicrobiology, allowing us to investigate the evolution of the complex microbial ecologies that inhabit our bodies. By focusing on recent coprolite and dental calculus research, we explore how emerging research on ancient human microbiomes is changing the way we think about ancient disease and how archaeological studies can contribute to a medical understanding of health and nutrition today. PMID:25559298

  16. A Multidisciplinary Approach to Study the Role of the Gut Microbiome in Relapsing and Progressive MS

    DTIC Science & Technology

    2016-10-01

    AWARD NUMBER: W81XWH-15-1-0653 TITLE: A Multidisciplinary Approach to Study the Role of the Gut Microbiome in Relapsing and Progressive MS...Approach to Study the Role of the Gut Microbiome in Relapsing and Progressive MS 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e...compare the gut microbiome of subjects with RMS and PPMS. Major Task 1: To seek and obtain HRPO approval Major Task 2: Identification and

  17. A Multidisciplinary Approach to Study the Role of the Gut Microbiome in Relapsing and Progressive MS

    DTIC Science & Technology

    2016-10-01

    AWARD NUMBER: W81XWH-15-1-0654 TITLE: A Multidisciplinary Approach to Study the Role of the Gut Microbiome in Relapsing and Progressive MS...Multidisciplinary Approach to Study the Role of the Gut Microbiome in Relapsing and Progressive MS 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT...Major Tasks and subtasks: Aim#1: To compare the gut microbiome of subjects with RMS and PPMS. Major Task 1: To seek and obtain HRPO approval Major

  18. Oligotyping analysis of the human oral microbiome

    PubMed Central

    Eren, A. Murat; Borisy, Gary G.; Huse, Susan M.; Mark Welch, Jessica L.

    2014-01-01

    The Human Microbiome Project provided a census of bacterial populations in healthy individuals, but an understanding of the biomedical significance of this census has been hindered by limited taxonomic resolution. A high-resolution method termed oligotyping overcomes this limitation by evaluating individual nucleotide positions using Shannon entropy to identify the most information-rich nucleotide positions, which then define oligotypes. We have applied this method to comprehensively analyze the oral microbiome. Using Human Microbiome Project 16S rRNA gene sequence data for the nine sites in the oral cavity, we identified 493 oligotypes from the V1-V3 data and 360 oligotypes from the V3-V5 data. We associated these oligotypes with species-level taxon names by comparison with the Human Oral Microbiome Database. We discovered closely related oligotypes, differing sometimes by as little as a single nucleotide, that showed dramatically different distributions among oral sites and among individuals. We also detected potentially pathogenic taxa in high abundance in individual samples. Numerous oligotypes were preferentially located in plaque, others in keratinized gingiva or buccal mucosa, and some oligotypes were characteristic of habitat groupings such as throat, tonsils, tongue dorsum, hard palate, and saliva. The differing habitat distributions of closely related oligotypes suggest a level of ecological and functional biodiversity not previously recognized. We conclude that the Shannon entropy approach of oligotyping has the capacity to analyze entire microbiomes, discriminate between closely related but distinct taxa and, in combination with habitat analysis, provide deep insight into the microbial communities in health and disease. PMID:24965363

  19. The Sphagnum microbiome: new insights from an ancient plant lineage.

    PubMed

    Kostka, Joel E; Weston, David J; Glass, Jennifer B; Lilleskov, Erik A; Shaw, A Jonathan; Turetsky, Merritt R

    2016-07-01

    57 I. 57 II. 58 III. 59 IV. 59 V. 61 VI. 62 63 References 63 SUMMARY: Peat mosses of the genus Sphagnum play a major role in global carbon storage and dominate many northern peatland ecosystems, which are currently being subjected to some of the most rapid climate changes on Earth. A rapidly expanding database indicates that a diverse community of microorganisms is intimately associated with Sphagnum, inhabiting the tissues and surface of the plant. Here we summarize the current state of knowledge regarding the Sphagnum microbiome and provide a perspective for future research directions. Although the majority of the microbiome remains uncultivated and its metabolic capabilities uncharacterized, prokaryotes and fungi have the potential to act as mutualists, symbionts, or antagonists of Sphagnum. For example, methanotrophic and nitrogen-fixing bacteria may benefit the plant host by providing up to 20-30% of Sphagnum carbon and nitrogen, respectively. Next-generation sequencing approaches have enabled the detailed characterization of microbiome community composition in peat mosses. However, as with other ecologically or economically important plants, our knowledge of Sphagnum-microbiome associations is in its infancy. In order to attain a predictive understanding of the role of the microbiome in Sphagnum productivity and ecosystem function, the mechanisms of plant-microbiome interactions and the metabolic potential of constituent microbial populations must be revealed. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  20. The Sphagnum microbiome: New insights from an ancient plant lineage

    DOE PAGES

    Kostka, Joel E.; Weston, David J.; Glass, Jennifer B.; ...

    2016-05-13

    Here, peat mosses of the genus Sphagnum play a major role in global carbon storage and dominate many northern peatland ecosystems, which are currently being subjected to some of the most rapid climate changes on Earth. A rapidly expanding database indicates that a diverse community of microorganisms is intimately associated with Sphagnum, inhabiting the tissues and surface of the plant. Here we summarize the current state of knowledge regarding the Sphagnum microbiome and provide a perspective for future research directions. Although the majority of the microbiome remains uncultivated and its metabolic capabilities uncharacterized, prokaryotes and fungi have the potential tomore » act as mutualists, symbionts, or antagonists of Sphagnum. For example, methanotrophic and nitrogen-fixing bacteria may benefit the plant host by providing up to 20–30% of Sphagnum carbon and nitrogen, respectively. Next-generation sequencing approaches have enabled the detailed characterization of microbiome community composition in peat mosses. However, as with other ecologically or economically important plants, our knowledge of Sphagnum–microbiome associations is in its infancy. In order to attain a predictive understanding of the role of the microbiome in Sphagnum productivity and ecosystem function, the mechanisms of plant–microbiome interactions and the metabolic potential of constituent microbial populations must be revealed.« less

  1. The Sphagnum microbiome: New insights from an ancient plant lineage

    SciT

    Kostka, Joel E.; Weston, David J.; Glass, Jennifer B.

    Here, peat mosses of the genus Sphagnum play a major role in global carbon storage and dominate many northern peatland ecosystems, which are currently being subjected to some of the most rapid climate changes on Earth. A rapidly expanding database indicates that a diverse community of microorganisms is intimately associated with Sphagnum, inhabiting the tissues and surface of the plant. Here we summarize the current state of knowledge regarding the Sphagnum microbiome and provide a perspective for future research directions. Although the majority of the microbiome remains uncultivated and its metabolic capabilities uncharacterized, prokaryotes and fungi have the potential tomore » act as mutualists, symbionts, or antagonists of Sphagnum. For example, methanotrophic and nitrogen-fixing bacteria may benefit the plant host by providing up to 20–30% of Sphagnum carbon and nitrogen, respectively. Next-generation sequencing approaches have enabled the detailed characterization of microbiome community composition in peat mosses. However, as with other ecologically or economically important plants, our knowledge of Sphagnum–microbiome associations is in its infancy. In order to attain a predictive understanding of the role of the microbiome in Sphagnum productivity and ecosystem function, the mechanisms of plant–microbiome interactions and the metabolic potential of constituent microbial populations must be revealed.« less

  2. Saving seed microbiomes.

    PubMed

    Berg, Gabriele; Raaijmakers, Jos M

    2018-05-01

    Plant seeds are home to diverse microbial communities whose composition is determined by plant genotype, environment, and management practices. Plant domestication is now recognized as an important driver of plant-associated microbial diversity. To what extent and how domestication affects seed microbiomes is less well studied. Here we propose a 'back-to-the-future' approach to harness seed microbiomes of wild relatives of crop cultivars to save and re-instate missing beneficial seed microbes for improved plant tolerance to biotic and abiotic stress.

  3. ENVRI PLUS project: Developing an ethical framework for Environmental and Earth System Research Infrastructures

    NASA Astrophysics Data System (ADS)

    Peppoloni, Silvia; Di Capua, Giuseppe; Haslinger, Florian

    2016-04-01

    ENVRI PLUS is a Horizon 2020 project bringing together Environmental and Earth System Research Infrastructures (RIs), projects and networks with technical specialist partners to create a more coherent, interdisciplinary and interoperable cluster of Environmental Research Infrastructures across Europe (http://www.envriplus.eu/). One theme of the project deals with the societal relevance and understanding, and within that theme an entire work-package (WP) aims at developing an ethical framework for RIs. Objectives of this WP are: • increase the awareness of both the scientists and the public on the importance of ethical aspects in Earth sciences; • establish a shared ethical framework of reference, to be adopted by RIs governing bodies; • increase the awareness of RIs management and operational levels and of the individual involved scientists on their social role in conducting research activities and research work environment; • assess the ethical and social aspects related to the results achieved and deliverables released within the project. The ongoing activities include: • reviewing the state of art on ethical issues useful for the goals of the project (collection and analysis of materials already existing within scientific organizations, institutions all over the world); • the creation of a questionnaire, through which to investigate how each RI participating in ENVRI PLUS faces ethical issues in relation to its activities, and so to understand the level of perception that researchers and technicians involved in the project have on the ethical implications of their scientific activities; • the definition of ethics guidelines to be used by partners for building their policies and their own codes of conduct; • the elaboration of an ethical label template to characterize each product of the project, that partners will be able to use in order to give essential information about the ethical and social implications of their products; • the

  4. The AmericaView Project - Putting the Earth into Your Hands

    ,

    2005-01-01

    The U.S. Geological Survey (USGS) is a leader in collecting, archiving, and distributing geospatial data and information about the Earth. Providing quick, reliable access to remotely sensed images and geospatial data is the driving principle behind the AmericaView Project. A national not-for-profit organization, AmericaView, Inc. was established and is supported by the USGS to coordinate the activities of a national network of university-led consortia with the primary objective of the advancement of the science of remote sensing. Individual consortia members include academic institutions, as well as state, local, and tribal government agencies. AmericaView's focus is to expand the understanding and use of remote sensing through education and outreach efforts and to provide affordable, integrated remote sensing information access and delivery to the American public. USGS's Landsat and NASA's Earth Observing System (EOS) satellite data are downlinked from satellites or transferred from other facilities to the USGS Center for Earth Resources Observation and Science (EROS) ground receiving station in Sioux Falls, South Dakota. The data can then be transferred over high-speed networks to consortium members, where it is archived and made available for public use.

  5. Final Report Collaborative Project. Improving the Representation of Coastal and Estuarine Processes in Earth System Models

    SciT

    Bryan, Frank; Dennis, John; MacCready, Parker

    This project aimed to improve long term global climate simulations by resolving and enhancing the representation of the processes involved in the cycling of freshwater through estuaries and coastal regions. This was a collaborative multi-institution project consisting of physical oceanographers, climate model developers, and computational scientists. It specifically targeted the DOE objectives of advancing simulation and predictive capability of climate models through improvements in resolution and physical process representation. The main computational objectives were: 1. To develop computationally efficient, but physically based, parameterizations of estuary and continental shelf mixing processes for use in an Earth System Model (CESM). 2. Tomore » develop a two-way nested regional modeling framework in order to dynamically downscale the climate response of particular coastal ocean regions and to upscale the impact of the regional coastal processes to the global climate in an Earth System Model (CESM). 3. To develop computational infrastructure to enhance the efficiency of data transfer between specific sources and destinations, i.e., a point-to-point communication capability, (used in objective 1) within POP, the ocean component of CESM.« less

  6. The GeoBus project: a mobile Earth science outreach project for secondary schools in the UK

    NASA Astrophysics Data System (ADS)

    Robinson, R. A.; Roper, K. A.; Macfarlane, D.; Pike, C.

    2013-12-01

    GeoBus is an educational outreach project that was developed in 2012 by the Department of Earth and Environmental Sciences at the University of St Andrews. It is sponsored jointly by industry and the UK Research Councils (NERC and EPSRC). The aims of GeoBus are to support the teaching of Earth Science in secondary (high) schools by providing teaching resources that are not readily available to educators, to inspire young learners by incorporating new science research outcomes in teaching activities, and to provide a bridge between industry, higher education institutions, research councils and schools. These linkages are important for introducing career opportunities in Earth sciences. Since its launch, GeoBus has visited over 140 different schools across the length and breadth of Scotland. Over 20,000 pupils will have been involved in practical hands-on Earth science learning activities by December 2013, including many in remote and disadvantaged regions. The resources that GeoBus brings to schools include all the materials and equipment needed to run workshops, field excursions and Enterprise Challenges. GeoBus provides 16 workshops which can be adapted for different learning levels. Workshops are 50 to 80 minute sessions for up to 30 pupils and topics include minerals, rocks, fossils, geological time, natural resources, climate change, volcanoes, earthquakes, and geological mapping. As with all GeoBus activities, the inclusion of equipment and technology otherwise unavailable to schools substantially increases the engagement of pupils in workshops. Field excursions are popular, as many teachers have little or no field trainng and feel unable to lead this type of activity. The excursions comprise half or full day sessions for up to 30 pupils and are tailored to cover the local geology or geomorphology. The Enterprise Challenges are half or full day sessions for up to 100 pupils. Current topics are Drilling for Oil, Renewable Energy, a Journey to Mars and Scotland

  7. ENES the European Network for Earth System modelling and its infrastructure projects IS-ENES

    NASA Astrophysics Data System (ADS)

    Guglielmo, Francesca; Joussaume, Sylvie; Parinet, Marie

    2016-04-01

    The scientific community working on climate modelling is organized within the European Network for Earth System modelling (ENES). In the past decade, several European university departments, research centres, meteorological services, computer centres, and industrial partners engaged in the creation of ENES with the purpose of working together and cooperating towards the further development of the network, by signing a Memorandum of Understanding. As of 2015, the consortium counts 47 partners. The climate modelling community, and thus ENES, faces challenges which are both science-driven, i.e. analysing of the full complexity of the Earth System to improve our understanding and prediction of climate changes, and have multi-faceted societal implications, as a better representation of climate change on regional scales leads to improved understanding and prediction of impacts and to the development and provision of climate services. ENES, promoting and endorsing projects and initiatives, helps in developing and evaluating of state-of-the-art climate and Earth system models, facilitates model inter-comparison studies, encourages exchanges of software and model results, and fosters the use of high performance computing facilities dedicated to high-resolution multi-model experiments. ENES brings together public and private partners, integrates countries underrepresented in climate modelling studies, and reaches out to different user communities, thus enhancing European expertise and competitiveness. In this need of sophisticated models, world-class, high-performance computers, and state-of-the-art software solutions to make efficient use of models, data and hardware, a key role is played by the constitution and maintenance of a solid infrastructure, developing and providing services to the different user communities. ENES has investigated the infrastructural needs and has received funding from the EU FP7 program for the IS-ENES (InfraStructure for ENES) phase I and II

  8. The SeaView EarthCube project: Lessons Learned from Integrating Across Repositories

    NASA Astrophysics Data System (ADS)

    Diggs, S. C.; Stocks, K. I.; Arko, R. A.; Kinkade, D.; Shepherd, A.; Olson, C. J.; Pham, A.

    2017-12-01

    SeaView is an NSF-funded EarthCube Integrative Activity Project working with 5 existing data repositories* to provide oceanographers with highly integrated thematic data collections in user-requested formats. The project has three complementary goals: Supporting Scientists: SeaView targets scientists' need for easy access to data of interest that are ready to import into their preferred tool. Strengthening Repositories: By integrating data from multiple repositories for science use, SeaView is helping the ocean data repositories align their data and processes and make ocean data more accessible and easily integrated. Informing EarthCube (earthcube.org): SeaView's experience as an integration demonstration can inform the larger NSF EarthCube architecture and design effort. The challenges faced in this small-scale effort are informative to geosciences cyberinfrastructure more generally. Here we focus on the lessons learned that may inform other data facilities and integrative architecture projects. (The SeaView data collections will be presented at the Ocean Sciences 2018 meeting.) One example is the importance of shared semantics, with persistent identifiers, for key integration elements across the data sets (e.g. cruise, parameter, and project/program.) These must allow for revision through time and should have an agreed authority or process for resolving conflicts: aligning identifiers and correcting errors were time consuming and often required both deep domain knowledge and "back end" knowledge of the data facilities. Another example is the need for robust provenance, and tools that support automated or semi-automated data transform pipelines that capture provenance. Multiple copies and versions of data are now flowing into repositories, and onward to long-term archives such as NOAA NCEI and umbrella portals such as DataONE. Exact copies can be identified with hashes (for those that have the skills), but it can be painfully difficult to understand the processing

  9. The chicken gastrointestinal microbiome

    We are in the midst of what may, in retrospect, come to be referred to as the golden age of microbial ecology. Once considered as only a relatively few pathogens, the microorganisms and their genes (the microbiome) associated with higher organisms are now recognized as complex communities with impo...

  10. The caprine abomasal microbiome

    Parasitism is considered the number one health problem in small ruminants. The barber's pole worm Haemonchus contortus infection in goats elicits a strong host immune response. However, the effect of the parasitic infection on the structure and function of the gut microbiome remains largely unknown....

  11. Toward more realistic projections of soil carbon dynamics by Earth system models

    DOE PAGES

    Luo, Yiqi; Ahlstrom, Anders; Allison, Steven D.; ...

    2016-01-21

    Soil carbon (C) is a critical component of Earth system models (ESMs), and its diverse representations are a major source of the large spread across models in the terrestrial C sink from the third to fifth assessment reports of the Intergovernmental Panel on Climate Change (IPCC). Improving soil C projections is of a high priority for Earth system modeling in the future IPCC and other assessments. To achieve this goal, we suggest that (1) model structures should reflect real-world processes, (2) parameters should be calibrated to match model outputs with observations, and (3) external forcing variables should accurately prescribe themore » environmental conditions that soils experience. First, most soil C cycle models simulate C input from litter production and C release through decomposition. The latter process has traditionally been represented by first-order decay functions, regulated primarily by temperature, moisture, litter quality, and soil texture. While this formulation well captures macroscopic soil organic C (SOC) dynamics, better understanding is needed of their underlying mechanisms as related to microbial processes, depth-dependent environmental controls, and other processes that strongly affect soil C dynamics. Second, incomplete use of observations in model parameterization is a major cause of bias in soil C projections from ESMs. Optimal parameter calibration with both pool-and flux-based data sets through data assimilation is among the highest priorities for near-term research to reduce biases among ESMs. Third, external variables are represented inconsistently among ESMs, leading to differences in modeled soil C dynamics. Furthermore, we recommend the implementation of traceability analyses to identify how external variables and model parameterizations influence SOC dynamics in different ESMs. Overall, projections of the terrestrial C sink can be substantially improved when reliable data sets are available to select the most representative

  12. Toward more realistic projections of soil carbon dynamics by Earth system models

    Luo, Y.; Ahlström, Anders; Allison, Steven D.; Batjes, Niels H.; Brovkin, V.; Carvalhais, Nuno; Chappell, Adrian; Ciais, Philippe; Davidson, Eric A.; Finzi, Adien; Georgiou, Katerina; Guenet, Bertrand; Hararuk, Oleksandra; Harden, Jennifer; He, Yujie; Hopkins, Francesca; Jiang, L.; Koven, Charles; Jackson, Robert B.; Jones, Chris D.; Lara, M.; Liang, J.; McGuire, A. David; Parton, William; Peng, Changhui; Randerson, J.; Salazar, Alejandro; Sierra, Carlos A.; Smith, Matthew J.; Tian, Hanqin; Todd-Brown, Katherine E. O; Torn, Margaret S.; van Groenigen, Kees Jan; Wang, Ying; West, Tristram O.; Wei, Yaxing; Wieder, William R.; Xia, Jianyang; Xu, Xia; Xu, Xiaofeng; Zhou, T.

    2016-01-01

    Soil carbon (C) is a critical component of Earth system models (ESMs), and its diverse representations are a major source of the large spread across models in the terrestrial C sink from the third to fifth assessment reports of the Intergovernmental Panel on Climate Change (IPCC). Improving soil C projections is of a high priority for Earth system modeling in the future IPCC and other assessments. To achieve this goal, we suggest that (1) model structures should reflect real-world processes, (2) parameters should be calibrated to match model outputs with observations, and (3) external forcing variables should accurately prescribe the environmental conditions that soils experience. First, most soil C cycle models simulate C input from litter production and C release through decomposition. The latter process has traditionally been represented by first-order decay functions, regulated primarily by temperature, moisture, litter quality, and soil texture. While this formulation well captures macroscopic soil organic C (SOC) dynamics, better understanding is needed of their underlying mechanisms as related to microbial processes, depth-dependent environmental controls, and other processes that strongly affect soil C dynamics. Second, incomplete use of observations in model parameterization is a major cause of bias in soil C projections from ESMs. Optimal parameter calibration with both pool- and flux-based data sets through data assimilation is among the highest priorities for near-term research to reduce biases among ESMs. Third, external variables are represented inconsistently among ESMs, leading to differences in modeled soil C dynamics. We recommend the implementation of traceability analyses to identify how external variables and model parameterizations influence SOC dynamics in different ESMs. Overall, projections of the terrestrial C sink can be substantially improved when reliable data sets are available to select the most representative model structure

  13. Assessing Student Learning about the Earth through the InTeGrate Project

    NASA Astrophysics Data System (ADS)

    Gilbert, L. A.; Iverson, E. A. R.; Steer, D. N.; Birnbaum, S. J.; Manduca, C. A.

    2016-12-01

    InTeGrate, a five-year community-based project comprised of faculty in the sciences and other disciplines, educational specialists, and evaluation experts at diverse institutions, instills learning about Earth in the context of societal issues through teaching materials developed into 2-3 week modules or courses. Materials were tested by over 135 materials authors and faculty interested in using these materials in undergraduate courses at a range of institution types across the US in geoscience, engineering, humanities, and social science courses. To assess impact on student learning, the InTeGrate project has collected student work from over 4,600 students enrolled in courses using these materials. To evaluate the influence of the materials on learning gains related to geoscience literacy, a set of 8 multiple choice items were developed, tested, and then administered in the first and last week of class in approximately 180 courses. The items were developed by 14 community members with assessment expertise and address content and concepts in the Earth, Climate, Atmosphere, and Ocean Science literacy documents. In a sample of 2,023 paired first and last week responses, students exhibit a 10% normalized gain (equivalent to 1 point of a 12 point total) regardless of their initial score. Students in the lowest quartile at the beginning of the course demonstrate the highest gains (4th quartile gain of 1.8) versus the higher quartile where a ceiling effect is present. In addition, a free-response essay was administered in the last week of the course which tests students' understanding for how Earth system interactions influence people's ability to make decisions about global societal challenges. Analysis of these essays demonstrates a strong relationship between the InTeGrate content and the subject matter of the student essay. These preliminary findings suggest that the use of InTeGrate materials increases students' understanding of geoscience literacies and the

  14. NASA ARIA Project Provides New Look at Earth Surface Deformation from Nepal Quake

    2015-05-04

    NASA and its partners are contributing important observations and expertise to the ongoing response to the April 25, 2015, magnitude 7.8 Gorkha earthquake in Nepal. The quake was the strongest to occur in that area since the 1934 Nepal-Bihar magnitude 8.0 event and caused significant regional damage and a humanitarian crisis. Scientists with the Advanced Rapid Imaging and Analysis project (ARIA), a collaboration between NASA's Jet Propulsion Laboratory, Pasadena, California, and the California Institute of Technology in Pasadena, analyzed interferometric synthetic aperture radar images from the PALSAR-2 instrument on the ALOS-2 satellite operated by the Japan Aerospace Exploration Agency (JAXA) to calculate a map of the deformation of Earth's surface caused by the quake. This false-color map shows the amount of permanent surface movement caused almost entirely by the earthquake, as viewed by the satellite, during a 70-day interval between two ALOS-2 images, acquired February 21 and May 2, 2015. In the map, surface displacements are seen as color contours (or "fringes"), where each color cycle represents 4.7 inches (11.9 centimeters) of surface motion. The contours show the land around Kathmandu has moved toward the satellite by up to 4.6 feet (1.4 meter), or 5.2 feet (1.6 meters) if we assume purely vertical motion. Areas without the color contours have snow or heavy vegetation that affects the radar measurements. Scientists use these maps to build detailed models of the fault and associated land movements to better understand the impact on future earthquake activity. The PALSAR-2 data were provided by JAXA through the Committee on Earth Observation Satellite (CEOS) in support of the response effort. The background image is from Google Earth. http://photojournal.jpl.nasa.gov/catalog/PIA19383

  15. Exploiting Earth observation data pools for urban analysis: the TEP URBAN project

    NASA Astrophysics Data System (ADS)

    Heldens, W.; Esch, T.; Asamer, H.; Boettcher, M.; Brito, F.; Hirner, A.; Marconcini, M.; Mathot, E.; Metz, A.; Permana, H.; Zeidler, J.; Balhar, J.; Soukop, T.; Stankek, F.

    2017-10-01

    Large amounts of Earth observation (EO) data have been collected to date, to increase even more rapidly with the upcoming Sentinel data. All this data contains unprecedented information, yet it is hard to retrieve, especially for nonremote sensing specialists. As we live in an urban era, with more than 50% of the world population living in cities, urban studies can especially benefit from the EO data. Information is needed for sustainable development of cities, for the understanding of urban growth patterns or for studying the threats of natural hazards or climate change. Bridging this gap between the technology-driven EO sector and the information needs of environmental science, planning, and policy is the driver behind the TEP-Urban project. Modern information technology functionalities and services are tested and implemented in the Urban Thematic Exploitation Platform (U-TEP). The platform enables interested users to easily exploit and generate thematic information on the status and development of the environment based on EO data and technologies. The beta version of the web platform contains value added basic earth observation data, global thematic data sets, and tools to derive user specific indicators and metrics. The code is open source and the architecture of the platform allows adding of new data sets and tools. These functionalities and concepts support the four basic use scenarios of the U-TEP platform: explore existing thematic content; task individual on-demand analyses; develop, deploy and offer your own content or application; and, learn more about innovative data sets and methods.

  16. Earth Resources Technology Satellite data collection project, ERTS - Bolivia. [thematic mapping

    NASA Technical Reports Server (NTRS)

    Brockmann, C. E.

    1974-01-01

    The Earth Resources Technology Satellite program of Bolivia has developed a multidisciplinary project to carry out investigations in cartography and to prepare various thematic maps. In cartography, investigations are being carried out with the ERTS-1 images and with existing maps, to determine their application to the preparation of new cartographic products on one hand and on the other to map those regions where the cartography is still deficient. The application of the MSS images to the geological mapping has given more than satisfactory results. Working with conventional photointerpretation, it has been possible to prepare regional geological maps, tectonic maps, studies relative to mining, geomorphological maps, studies relative to petroleum exploration, volcanological maps and maps of hydrologic basins. In agriculture, the ERTS images are used to study land classification and forest and soils mapping.

  17. A photometric survey of Near-Earth Objects in support of the NEOShield-2 project

    NASA Astrophysics Data System (ADS)

    Ieva, S.; Dotto, E.; Mazzotta Epifani, E.; Perna, D.; Barucci, M. A.; Di Paola, A.; Micheli, M.; Perozzi, E.; Speziali, R.; Lazzarin, M.; Bertini, I.; Giunta, A.; Lazzaro, D.; Arcoverde, P.

    2017-09-01

    More than 85% of the 16,000 NEOs discovered up to now lack a physical characterization. The study of their physical properties is essential to define a proper mitigation scenario. One of the main aims of the NEOShield-2 project (2015-2017), financed by the European Community in the framework of the Horizon 2020 program, is therefore to retrieve physical properties of a wide number of NEOs, in order to design impact mitigation missions and assess the consequences of an impact on Earth. We present the results obtained during a 2-year Long-Term Program at the Telescopio Nazionale Galileo (TNG, La Palma, Spain), where we carried out BVRI photometry of about 150 NEOs, and the analysis of the phase curves obtained at the Campo Imperatore telescope (L'Aquila, Italy) and the Observatório Astronômico do Sertão de Itaparica (Nova Itacuruba, Brazil).

  18. MIT Project Apophis: Surface Evaulation & Tomography (SET) Mission Study for the April 2029 Earth Encounter

    NASA Astrophysics Data System (ADS)

    Binzel, R. P.; Earle, A. M.; Vanatta, M.; Miller, D. W.

    2017-12-01

    Nature is providing a once-per-thousand year opportunity to study the geophysical outcome induced on an unprecedentedly large (350 meter) asteroid making an extremely close passage by the Earth (inside the distance of geosynchronous satellites) on Friday April 13, 2029. The aircraft carrier-sized (estimated 20 million metric ton) asteroid is named Apophis. While many previous spacecraft missions have studied asteroids, none has ever had the opportunity to study "live" the outcome of planetary tidal forces on their shapes, spin states, surface geology, and internal structure. Beyond the science interest directly observing this planetary process, the Apophis encounter provides an invaluable opportunity to gain knowledge for any eventuality of a known asteroid found to be on a certain impact trajectory. MIT's Project Apophis [1] is our response to nature's generous opportunity by developing a detailed mission concept for sending a spacecraft to orbit Apophis with the objectives of surveying its surface and interior structure before, during, and after its 2029 near-Earth encounter. The Surface Evaluation & Tomography (SET) mission concept we present is designed toward accomplishing three key science objectives: (1) bulk physical characterization, (2) internal structure, and (3) long-term orbit tracking. For its first mission objective, SET will study Apophis' bulk properties, including: shape, size, mass, volume, bulk density, surface geology, and composition, rotation rate, and spin state. The second mission objective is to characterize Apophis' internal structure before and after the encounter to determine its strength and cohesion - including tidally induced changes. Finally, the third objective studies the process of thermal re-radiation and consequential Yarkovsky drift, whose results will improve orbit predictions for Apophis as well as other potentially hazardous asteroids. [1] https://eapsweb.mit.edu/mit-project-apophis

  19. Uncertainty Assessment of the NASA Earth Exchange Global Daily Downscaled Climate Projections (NEX-GDDP) Dataset

    NASA Technical Reports Server (NTRS)

    Wang, Weile; Nemani, Ramakrishna R.; Michaelis, Andrew; Hashimoto, Hirofumi; Dungan, Jennifer L.; Thrasher, Bridget L.; Dixon, Keith W.

    2016-01-01

    The NASA Earth Exchange Global Daily Downscaled Projections (NEX-GDDP) dataset is comprised of downscaled climate projections that are derived from 21 General Circulation Model (GCM) runs conducted under the Coupled Model Intercomparison Project Phase 5 (CMIP5) and across two of the four greenhouse gas emissions scenarios (RCP4.5 and RCP8.5). Each of the climate projections includes daily maximum temperature, minimum temperature, and precipitation for the periods from 1950 through 2100 and the spatial resolution is 0.25 degrees (approximately 25 km x 25 km). The GDDP dataset has received warm welcome from the science community in conducting studies of climate change impacts at local to regional scales, but a comprehensive evaluation of its uncertainties is still missing. In this study, we apply the Perfect Model Experiment framework (Dixon et al. 2016) to quantify the key sources of uncertainties from the observational baseline dataset, the downscaling algorithm, and some intrinsic assumptions (e.g., the stationary assumption) inherent to the statistical downscaling techniques. We developed a set of metrics to evaluate downscaling errors resulted from bias-correction ("quantile-mapping"), spatial disaggregation, as well as the temporal-spatial non-stationarity of climate variability. Our results highlight the spatial disaggregation (or interpolation) errors, which dominate the overall uncertainties of the GDDP dataset, especially over heterogeneous and complex terrains (e.g., mountains and coastal area). In comparison, the temporal errors in the GDDP dataset tend to be more constrained. Our results also indicate that the downscaled daily precipitation also has relatively larger uncertainties than the temperature fields, reflecting the rather stochastic nature of precipitation in space. Therefore, our results provide insights in improving statistical downscaling algorithms and products in the future.

  20. Microbiome and Malignancy

    PubMed Central

    Plottel, Claudia S.; Blaser, Martin J.

    2011-01-01

    Current knowledge is insufficient to explain why only a proportion of individuals exposed to environmental carcinogens or carrying a genetic predisposition to cancer develop disease. Clearly, other factors must be important and one such element that has recently received attention is the human microbiome, the residential microbes including Bacteria, Archaea, Eukaryotes, and viruses that colonize humans. Here, we review principles and paradigms of microbiome-related malignancy, as illustrated by three specific microbial-host interactions. We review the effects of the microbiota on local and adjacent-neoplasia, present the estrobolome model of distant effects, and discuss the complex interactions with a latent virus leading to malignancy. These are separate facets of a complex biology interfacing all the microbial species we harbor from birth onward toward early reproductive success and eventual senescence. PMID:22018233

  1. NASA's NPOESS Preparatory Project Science Data Segment: A Framework for Measurement-based Earth Science Data Systems

    NASA Technical Reports Server (NTRS)

    Schwaller, Mathew R.; Schweiss, Robert J.

    2007-01-01

    The NPOESS Preparatory Project (NPP) Science Data Segment (SDS) provides a framework for the future of NASA s distributed Earth science data systems. The NPP SDS performs research and data product assessment while using a fully distributed architecture. The components of this architecture are organized around key environmental data disciplines: land, ocean, ozone, atmospheric sounding, and atmospheric composition. The SDS thus establishes a set of concepts and a working prototypes. This paper describes the framework used by the NPP Project as it enabled Measurement-Based Earth Science Data Systems for the assessment of NPP products.

  2. "Urban Fossils": a project enabling reflections concerning human impact on planet Earth.

    NASA Astrophysics Data System (ADS)

    Lozar, Francesca; Delfino, Massimo; Magagna, Alessandra; Ferrero, Elena; Cirilli, Francesca; Bernardi, Massimo; Giardino, Marco

    2016-04-01

    -Piemonte and the Regional Museum of Natural History of Torino; starting from autumn 2015, it is hosted by several Italian museums of Natural History. Since many of the "urban fossils" are ephemeral and doomed to destruction at "catastrophic" events (eg. maintenance of roads and sidewalks), a virtual collection (www.progeopiemonte.it) will preserve in time their photographs, allowing and promoting continue discussion on aspects of paleontology generally neglected outside the academia, such as ichnology and taphonomy, and on the traces that we, humans, will leave on planet Earth and will ultimately be buried in the Anthropocene rocks. "Urban Fossils" is therefore an ongoing project, with a great interdisciplinary value, that represents an opportunity for both geoscientists and society to become more conscious of their role and responsibility in everyday life activities.

  3. The Perinatal Microbiome and Pregnancy: Moving Beyond the Vaginal Microbiome

    PubMed Central

    Prince, Amanda L.; Chu, Derrick M.; Seferovic, Maxim D.; Antony, Kathleen M.; Ma, Jun; Aagaard, Kjersti M.

    2015-01-01

    The human microbiome, the collective genome of the microbial community that is on and within us, has recently been mapped. The initial characterization of healthy subjects has provided investigators with a reference population for interrogating the microbiome in metabolic, intestinal, and reproductive health and disease states. Although it is known that bacteria can colonize the vagina, recent metagenomic studies have shown that the vaginal microbiome varies among reproductive age women. Similarly, the richness and diversity of intestinal microbiota also naturally fluctuate among gravidae in both human and nonhuman primates, as well as mice. Moreover, recent evidence suggests that microbiome niches in pregnancy are not limited to maternal body sites, as the placenta appears to harbor a low biomass microbiome that is presumptively established in early pregnancy and varies in association with a remote history of maternal antenatal infection as well as preterm birth. In this article, we will provide a brief overview on metagenomics science as a means to investigate the microbiome, observations pertaining to both variation and the presumptive potential role of a varied microbiome during pregnancy, and how future studies of the microbiome in pregnancy may lend to a better understanding of human biology, reproductive health, and parturition. PMID:25775922

  4. The ClearEarth Project: Preliminary Findings from Experiments in Applying the CLEARTK NLP Pipeline and Annotation Tools Developed for Biomedicine to the Earth Sciences

    NASA Astrophysics Data System (ADS)

    Duerr, R.; Thessen, A.; Jenkins, C. J.; Palmer, M.; Myers, S.; Ramdeen, S.

    2016-12-01

    The ability to quickly find, easily use and effortlessly integrate data from a variety of sources is a grand challenge in Earth sciences, one around which entire research programs have been built. A myriad of approaches to tackling components of this challenge have been demonstrated, often with some success. Yet finding, assessing, accessing, using and integrating data remains a major challenge for many researchers. A technology that has shown promise in nearly every aspect of the challenge is semantics. Semantics has been shown to improve data discovery, facilitate assessment of a data set, and through adoption of the W3C's Linked Data Platform to have improved data integration and use at least for data amenable to that paradigm. Yet the creation of semantic resources has been slow. Why? Amongst a plethora of other reasons, it is because semantic expertise is rare in the Earth and Space sciences; the creation of semantic resources for even a single discipline is labor intensive and requires agreement within the discipline; best practices, methods and tools for supporting the creation and maintenance of the resources generated are in flux; and the human and financial capital needed are rarely available in the Earth sciences. However, other fields, such as biomedicine, have made considerable progress in these areas. The NSF-funded ClearEarth project is adapting the methods and tools from these communities for the Earth sciences in the expectation that doing so will enhance progress and the rate at which the needed semantic resources are created. We discuss progress and results to date, lessons learned from this adaptation process, and describe our upcoming efforts to extend this knowledge to the next generation of Earth and data scientists.

  5. ESIP's Earth Science Knowledge Graph (ESKG) Testbed Project: An Automatic Approach to Building Interdisciplinary Earth Science Knowledge Graphs to Improve Data Discovery

    NASA Astrophysics Data System (ADS)

    McGibbney, L. J.; Jiang, Y.; Burgess, A. B.

    2017-12-01

    Big Earth observation data have been produced, archived and made available online, but discovering the right data in a manner that precisely and efficiently satisfies user needs presents a significant challenge to the Earth Science (ES) community. An emerging trend in information retrieval community is to utilize knowledge graphs to assist users in quickly finding desired information from across knowledge sources. This is particularly prevalent within the fields of social media and complex multimodal information processing to name but a few, however building a domain-specific knowledge graph is labour-intensive and hard to keep up-to-date. In this work, we update our progress on the Earth Science Knowledge Graph (ESKG) project; an ESIP-funded testbed project which provides an automatic approach to building a dynamic knowledge graph for ES to improve interdisciplinary data discovery by leveraging implicit, latent existing knowledge present within across several U.S Federal Agencies e.g. NASA, NOAA and USGS. ESKG strengthens ties between observations and user communities by: 1) developing a knowledge graph derived from various sources e.g. Web pages, Web Services, etc. via natural language processing and knowledge extraction techniques; 2) allowing users to traverse, explore, query, reason and navigate ES data via knowledge graph interaction. ESKG has the potential to revolutionize the way in which ES communities interact with ES data in the open world through the entity, spatial and temporal linkages and characteristics that make it up. This project enables the advancement of ESIP collaboration areas including both Discovery and Semantic Technologies by putting graph information right at our fingertips in an interactive, modern manner and reducing the efforts to constructing ontology. To demonstrate the ESKG concept, we will demonstrate use of our framework across NASA JPL's PO.DAAC, NOAA's Earth Observation Requirements Evaluation System (EORES) and various USGS

  6. Enhancement of the Earth Science and Remote Sensing Group's Website and Related Projects

    NASA Technical Reports Server (NTRS)

    Coffin, Ashley; Vanderbloemen, Lisa

    2014-01-01

    The major problem addressed throughout the term was the need to update the group's current website, as it was outdated and required streamlining and modernization. The old Gateway to Astronaut Photography of the Earth website had multiple components, many of which involved searches through expansive databases. The amount of work required to update the website was large and due to a desired release date, assistance was needed to help build new pages and to transfer old information. Additionally, one of the tools listed on the website called Image Detective had been underutilized in the past. It was important to address why the public was not using the tool and how it could potentially become more of a resource for the team. In order to help with updating the website, it was necessary to first learn HTML. After assisting with small edits, I began creating new pages. I utilized the "view page source" and "developer" tools in the internet browser to observe how other websites created their features and to test changes without editing the code. I then edited the code to create an interactive feature on the new page. For the Image Detective Page I began an evaluation of the current page. I also asked my fellow interns and friends at my University to offer their input. I took all of the opinions into account and wrote up a document regarding my recommendations. The recommendations will be considered as I help to improve the Image Detective page for the updated website. In addition to the website, other projects included the need for additional, and updated image collections, along with various project requests. The image collections have been used by educators in the classroom and the impact crater collection was highly requested. The glaciers collection focused mostly on South American glaciers and needed to include more of the earth's many glaciers. The collections had not been updated or created due to the fact that related imagery had not been catalogued. The process

  7. The human gut microbiome: current knowledge, challenges, and future directions.

    PubMed

    Dave, Maneesh; Higgins, Peter D; Middha, Sumit; Rioux, Kevin P

    2012-10-01

    The Human Genome Project was completed a decade ago, leaving a legacy of process, tools, and infrastructure now being turned to the study of the microbes that reside in and on the human body as determinants of health and disease, and has been branded "The Human Microbiome Project." Of the various niches under investigation, the human gut houses the most complex and abundant microbial community and is an arena for important host-microbial interactions that have both local and systemic impact. Initial studies of the human microbiome have been largely descriptive, a testing ground for innovative molecular techniques and new hypotheses. Methods for studying the microbiome have quickly evolved from low-resolution surveys of microbial community structure to high-definition description of composition, function, and ecology. Next-generation sequencing technologies combined with advanced bioinformatics place us at the doorstep of revolutionary insight into the composition, capability, and activity of the human intestinal microbiome. Renewed efforts to cultivate previously "uncultivable" microbes will be important to the overall understanding of gut ecology. There remain numerous methodological challenges to the effective study and understanding of the gut microbiome, largely relating to study design, sample collection, and the number of predictor variables. Strategic collaboration of clinicians, microbiologists, molecular biologists, computational scientists, and bioinformaticians is the ideal paradigm for success in this field. Meaningful interpretation of the gut microbiome requires that host genetic and environmental influences be controlled or accounted for. Understanding the gut microbiome in healthy humans is a foundation for discovering its influence in various important gastrointestinal and nutritional diseases (eg, inflammatory bowel disease, diabetes, and obesity), and for rational translation to human health gains. Copyright © 2012 Mosby, Inc. All rights

  8. To Create Space on Earth: The Space Environment Simulation Laboratory and Project Apollo

    NASA Technical Reports Server (NTRS)

    Walters, Lori C.

    2003-01-01

    Few undertakings in the history of humanity can compare to the great technological achievement known as Project Apollo. Among those who witnessed Armstrong#s flickering television image were thousands of people who had directly contributed to this historic moment. Amongst those in this vast anonymous cadre were the personnel of the Space Environment Simulation Laboratory (SESL) at the Manned Spacecraft Center (MSC) in Houston, Texas. SESL houses two large thermal-vacuum chambers with solar simulation capabilities. At a time when NASA engineers had a limited understanding of the effects of extremes of space on hardware and crews, SESL was designed to literally create the conditions of space on Earth. With interior dimensions of 90 feet in height and a 55-foot diameter, Chamber A dwarfed the Apollo command/service module (CSM) it was constructed to test. The chamber#s vacuum pumping capacity of 1 x 10(exp -6) torr can simulate an altitude greater than 130 miles above the Earth. A "lunar plane" capable of rotating a 150,000-pound test vehicle 180 deg replicates the revolution of a craft in space. To reproduce the temperature extremes of space, interior chamber walls cool to -280F as two banks of carbon arc modules simulate the unfiltered solar light/heat of the Sun. With capabilities similar to that of Chamber A, early Chamber B tests included the Gemini modular maneuvering unit, Apollo EVA mobility unit and the lunar module. Since Gemini astronaut Charles Bassett first ventured into the chamber in 1966, Chamber B has assisted astronauts in testing hardware and preparing them for work in the harsh extremes of space.

  9. NASA ARIA Project Maps Deformation of Earth Surface from Nepal Quake

    2015-05-02

    NASA and its partners are contributing important observations and expertise to the ongoing response to the April 25, 2015, magnitude 7.8 Gorkha earthquake in Nepal. The quake was the strongest to occur in that area since the 1934 Nepal-Bihar magnitude 8.0 event and caused significant regional damage and a humanitarian crisis. Scientists with the Advanced Rapid Imaging and Analysis project (ARIA), a collaboration between NASA's Jet Propulsion Laboratory, Pasadena, California, and the California Institute of Technology in Pasadena, analyzed interferometric synthetic aperture radar images from the European Union's Copernicus Sentinel-1A satellite, operated by the European Space Agency and also available from the Alaska Satellite Facility (https://www.asf.alaska.edu), to calculate a map of the deformation of Earth's surface caused by the quake. This false-color map shows the amount of permanent surface movement caused almost entirely by the earthquake, as viewed by the satellite, during a 12-day interval between two Sentinel-1 images acquired on April 17 and April 29, 2015. In the map, surface displacements are seen as color contours (or "fringes"), where each color cycle represents 8 inches (20 centimeters) of surface motion. The contours show the land around Kathmandu has moved upward by more than 40 inches (1 meter). Areas without the color contours have snow or heavy vegetation that affects the radar measurements. Scientists use these maps to build detailed models of the fault and associated land movements to better understand the impact on future earthquake activity. The background image is from Google Earth. The map contains Copernicus data (2015). http://photojournal.jpl.nasa.gov/catalog/PIA19535

  10. A hundred-year-old insight into the gut microbiome!

    PubMed

    Aziz, Ramy Karam

    2009-12-07

    As the National Institutes of Health-funded Human Microbiome Project enters its second phase, and as a major part of this project focuses on the human gut microbiome and its effects on human health, it might help us to travel a century back in time and examine how microbiologists dealt with microbiome-related challenges similar to those of the 21st century using the tools of their time. An article by Arthur I. Kendall, published in The Journal of Biological Chemistry in November 1909 (Some observations on the study of the intestinal bacteria J Biol Chem 1909, 6:499-507), offers a visionary insight into many of today's hot research questions.

  11. Realizing NASA's Goal of Societal Benefits From Earth Observations in Mesoamerica Through the SERVIR Project

    NASA Astrophysics Data System (ADS)

    Hardin, D. M.; Irwin, D.; Sever, T.; Graves, S.

    2006-12-01

    One of the goals of NASA's Applied Sciences Program is to manifest societal benefits from the vast store of Earth Observations through partnerships with public, private and academic organizations. The SERVIR project represents an early success toward this goal. By combining Earth Observations from NASA missions, results from environmental models and decision support tools from its partners the SERVIR project has produced an integrated systems solution that is yielding societal benefits for the region of Mesoamerica. The architecture of the SERVIR system consists of an operational facility in Panama with regional nodes in Costa Rica, Nicaragua, Honduras, Guatemala, El Salvador and Belize plus a Rapid Prototyping Center (RPC), located in Huntsville, Alabama. The RPC, funded by NASA's Applied Sciences Division, and developed by the Information Technology and Systems Center at the University of Alabama in Huntsville, and NASA Marshall Space Flight Center, produces scientifically strong decision support products and applications. When mature, the products and applications migrate to the operational center in Panama. There, they are available to environmental ministers and decision makers in Mesoamerica. In June 2004, the SERVIR project was contacted by the environmental ministry of El Salvador, which urgently requested remote sensing imagery of the location, direction, and extent of a HAB event off the coast of El Salvador and Guatemala. Using MODIS data the SERVIR team developed a value added product that predicts the location, direction, and extent of HABs. The products are produced twice daily and are used by the El Salvadoran and Guatemalan governments to alert their tourism and fishing industries of potential red tide events. This has enabled these countries to save millions of dollars for their industries as well as improve the health of harvested fish. In the area of short term weather forecasting the SERVIR team, in collaboration with the NASA Short

  12. Tick microbiome: the force within

    PubMed Central

    Narasimhan, Sukanya; Fikrig, Erol

    2015-01-01

    Ticks are obligate blood-feeders and serve as vectors of human and livestock pathogens worldwide. Defining the tick microbiome and deciphering the interactions between the tick and its symbiotic bacteria in the context of tick development and pathogen transmission, will likely reveal new insights and spawn new paradigms to control tick-borne diseases. Descriptive observations on the tick microbiome that began almost a century ago serve as forerunners to the gathering momentum to define the tick microbiome in greater detail. This review will focus on the current efforts to address the microbiomes of diverse ticks, and the evolving understanding of tick microbiomes. There is hope that these efforts will bring a holistic understanding of pathogen transmission by ticks. PMID:25936226

  13. Q & A with Kathleen M. Reilly, Author of "Planet Earth: 25 Environmental Projects You Can Build Yourself"

    ERIC Educational Resources Information Center

    Curriculum Review, 2008

    2008-01-01

    This article presents an interview with Kathleen M. Reilly, author of "Planet Earth: 25 Environmental Projects You Can Build Yourself." Environmental awareness needs to begin in childhood, and, through this book, Kathleen M. Reilly encourages children to learn about ecology and ecosystems to begin conservation early in their lives. Children ages 9…

  14. A framework for human microbiome research

    PubMed Central

    Methé, Barbara A.; Nelson, Karen E.; Pop, Mihai; Creasy, Heather H.; Giglio, Michelle G.; Huttenhower, Curtis; Gevers, Dirk; Petrosino, Joseph F.; Abubucker, Sahar; Badger, Jonathan H.; Chinwalla, Asif T.; Earl, Ashlee M.; FitzGerald, Michael G.; Fulton, Robert S.; Hallsworth-Pepin, Kymberlie; Lobos, Elizabeth A.; Madupu, Ramana; Magrini, Vincent; Martin, John C.; Mitreva, Makedonka; Muzny, Donna M.; Sodergren, Erica J.; Versalovic, James; Wollam, Aye M.; Worley, Kim C.; Wortman, Jennifer R.; Young, Sarah K.; Zeng, Qiandong; Aagaard, Kjersti M.; Abolude, Olukemi O.; Allen-Vercoe, Emma; Alm, Eric J.; Alvarado, Lucia; Andersen, Gary L.; Anderson, Scott; Appelbaum, Elizabeth; Arachchi, Harindra M.; Armitage, Gary; Arze, Cesar A.; Ayvaz, Tulin; Baker, Carl C.; Begg, Lisa; Belachew, Tsegahiwot; Bhonagiri, Veena; Bihan, Monika; Blaser, Martin J.; Bloom, Toby; Vivien Bonazzi, J.; Brooks, Paul; Buck, Gregory A.; Buhay, Christian J.; Busam, Dana A.; Campbell, Joseph L.; Canon, Shane R.; Cantarel, Brandi L.; Chain, Patrick S.; Chen, I-Min A.; Chen, Lei; Chhibba, Shaila; Chu, Ken; Ciulla, Dawn M.; Clemente, Jose C.; Clifton, Sandra W.; Conlan, Sean; Crabtree, Jonathan; Cutting, Mary A.; Davidovics, Noam J.; Davis, Catherine C.; DeSantis, Todd Z.; Deal, Carolyn; Delehaunty, Kimberley D.; Dewhirst, Floyd E.; Deych, Elena; Ding, Yan; Dooling, David J.; Dugan, Shannon P.; Dunne, Wm. Michael; Durkin, A. Scott; Edgar, Robert C.; Erlich, Rachel L.; Farmer, Candace N.; Farrell, Ruth M.; Faust, Karoline; Feldgarden, Michael; Felix, Victor M.; Fisher, Sheila; Fodor, Anthony A.; Forney, Larry; Foster, Leslie; Di Francesco, Valentina; Friedman, Jonathan; Friedrich, Dennis C.; Fronick, Catrina C.; Fulton, Lucinda L.; Gao, Hongyu; Garcia, Nathalia; Giannoukos, Georgia; Giblin, Christina; Giovanni, Maria Y.; Goldberg, Jonathan M.; Goll, Johannes; Gonzalez, Antonio; Griggs, Allison; Gujja, Sharvari; Haas, Brian J.; Hamilton, Holli A.; Harris, Emily L.; Hepburn, Theresa A.; Herter, Brandi; Hoffmann, Diane E.; Holder, Michael E.; Howarth, Clinton; Huang, Katherine H.; Huse, Susan M.; Izard, Jacques; Jansson, Janet K.; Jiang, Huaiyang; Jordan, Catherine; Joshi, Vandita; Katancik, James A.; Keitel, Wendy A.; Kelley, Scott T.; Kells, Cristyn; Kinder-Haake, Susan; King, Nicholas B.; Knight, Rob; Knights, Dan; Kong, Heidi H.; Koren, Omry; Koren, Sergey; Kota, Karthik C.; Kovar, Christie L.; Kyrpides, Nikos C.; La Rosa, Patricio S.; Lee, Sandra L.; Lemon, Katherine P.; Lennon, Niall; Lewis, Cecil M.; Lewis, Lora; Ley, Ruth E.; Li, Kelvin; Liolios, Konstantinos; Liu, Bo; Liu, Yue; Lo, Chien-Chi; Lozupone, Catherine A.; Lunsford, R. Dwayne; Madden, Tessa; Mahurkar, Anup A.; Mannon, Peter J.; Mardis, Elaine R.; Markowitz, Victor M.; Mavrommatis, Konstantinos; McCorrison, Jamison M.; McDonald, Daniel; McEwen, Jean; McGuire, Amy L.; McInnes, Pamela; Mehta, Teena; Mihindukulasuriya, Kathie A.; Miller, Jason R.; Minx, Patrick J.; Newsham, Irene; Nusbaum, Chad; O’Laughlin, Michelle; Orvis, Joshua; Pagani, Ioanna; Palaniappan, Krishna; Patel, Shital M.; Pearson, Matthew; Peterson, Jane; Podar, Mircea; Pohl, Craig; Pollard, Katherine S.; Priest, Margaret E.; Proctor, Lita M.; Qin, Xiang; Raes, Jeroen; Ravel, Jacques; Reid, Jeffrey G.; Rho, Mina; Rhodes, Rosamond; Riehle, Kevin P.; Rivera, Maria C.; Rodriguez-Mueller, Beltran; Rogers, Yu-Hui; Ross, Matthew C.; Russ, Carsten; Sanka, Ravi K.; Pamela Sankar, J.; Sathirapongsasuti, Fah; Schloss, Jeffery A.; Schloss, Patrick D.; Schmidt, Thomas M.; Scholz, Matthew; Schriml, Lynn; Schubert, Alyxandria M.; Segata, Nicola; Segre, Julia A.; Shannon, William D.; Sharp, Richard R.; Sharpton, Thomas J.; Shenoy, Narmada; Sheth, Nihar U.; Simone, Gina A.; Singh, Indresh; Smillie, Chris S.; Sobel, Jack D.; Sommer, Daniel D.; Spicer, Paul; Sutton, Granger G.; Sykes, Sean M.; Tabbaa, Diana G.; Thiagarajan, Mathangi; Tomlinson, Chad M.; Torralba, Manolito; Treangen, Todd J.; Truty, Rebecca M.; Vishnivetskaya, Tatiana A.; Walker, Jason; Wang, Lu; Wang, Zhengyuan; Ward, Doyle V.; Warren, Wesley; Watson, Mark A.; Wellington, Christopher; Wetterstrand, Kris A.; White, James R.; Wilczek-Boney, Katarzyna; Wu, Yuan Qing; Wylie, Kristine M.; Wylie, Todd; Yandava, Chandri; Ye, Liang; Ye, Yuzhen; Yooseph, Shibu; Youmans, Bonnie P.; Zhang, Lan; Zhou, Yanjiao; Zhu, Yiming; Zoloth, Laurie; Zucker, Jeremy D.; Birren, Bruce W.; Gibbs, Richard A.; Highlander, Sarah K.; Weinstock, George M.; Wilson, Richard K.; White, Owen

    2012-01-01

    A variety of microbial communities and their genes (microbiome) exist throughout the human body, playing fundamental roles in human health and disease. The NIH funded Human Microbiome Project (HMP) Consortium has established a population-scale framework which catalyzed significant development of metagenomic protocols resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 to 18 body sites up to three times, which to date, have generated 5,177 microbial taxonomic profiles from 16S rRNA genes and over 3.5 Tb of metagenomic sequence. In parallel, approximately 800 human-associated reference genomes have been sequenced. Collectively, these data represent the largest resource to date describing the abundance and variety of the human microbiome, while providing a platform for current and future studies. PMID:22699610

  15. A framework for human microbiome research.

    PubMed

    2012-06-13

    A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies.

  16. Integration of Earth System Models and Workflow Management under iRODS for the Northeast Regional Earth System Modeling Project

    NASA Astrophysics Data System (ADS)

    Lengyel, F.; Yang, P.; Rosenzweig, B.; Vorosmarty, C. J.

    2012-12-01

    The Northeast Regional Earth System Model (NE-RESM, NSF Award #1049181) integrates weather research and forecasting models, terrestrial and aquatic ecosystem models, a water balance/transport model, and mesoscale and energy systems input-out economic models developed by interdisciplinary research team from academia and government with expertise in physics, biogeochemistry, engineering, energy, economics, and policy. NE-RESM is intended to forecast the implications of planning decisions on the region's environment, ecosystem services, energy systems and economy through the 21st century. Integration of model components and the development of cyberinfrastructure for interacting with the system is facilitated with the integrated Rule Oriented Data System (iRODS), a distributed data grid that provides archival storage with metadata facilities and a rule-based workflow engine for automating and auditing scientific workflows.

  17. The Microbiome-Gut-Behavior Axis: Crosstalk Between the Gut Microbiome and Oligodendrocytes Modulates Behavioral Responses.

    PubMed

    Ntranos, Achilles; Casaccia, Patrizia

    2018-01-01

    Environmental and dietary stimuli have always been implicated in brain development and behavioral responses. The gut, being the major portal of communication with the external environment, has recently been brought to the forefront of this interaction with the establishment of a gut-brain axis in health and disease. Moreover, recent breakthroughs in germ-free and antibiotic-treated mice have demonstrated the significant impact of the microbiome in modulating behavioral responses in mice and have established a more specific microbiome-gut-behavior axis. One of the mechanisms by which this axis affects social behavior is by regulating myelination at the prefrontal cortex, an important site for complex cognitive behavior planning and decision-making. The prefrontal cortex exhibits late myelination of its axonal projections that could extend into the third decade of life in humans, which make it susceptible to external influences, such as microbial metabolites. Changes in the gut microbiome were shown to alter the composition of the microbial metabolome affecting highly permeable bioactive compounds, such as p-cresol, which could impair oligodendrocyte differentiation. Dysregulated myelination in the prefrontal cortex is then able to affect behavioral responses in mice, shifting them towards social isolation. The reduced social interactions could then limit microbial exchange, which could otherwise pose a threat to the survival of the existing microbial community in the host and, thus, provide an evolutionary advantage to the specific microbial community. In this review, we will analyze the microbiome-gut-behavior axis, describe the interactions between the gut microbiome and oligodendrocytes and highlight their role in the modulation of social behavior.

  18. Evaluation of the Earth System CoG Infrastructure in Supporting a Model Intercomparison Project

    NASA Astrophysics Data System (ADS)

    Wallis, J. C.; Rood, R. B.; Murphy, S.; Cinquini, L.; DeLuca, C.

    2013-12-01

    Earth System CoG is a web-based collaboration environment that combines data services with metadata and project management services. The environment is particularly suited to support software development and model intercomparison projects. CoG was recently used to support the National Climate Predictions and Projections Platform (NCPP) Quantitative Evaluation of Downscaling (QED-2013) workshop. QED-2013 was a workshop with a community approach for the objective, quantitative evaluation of techniques to downscale climate model predictions and projections. This paper will present a brief introduction to CoG, QED-2013, and findings from an ethnographic evaluation of how CoG supported QED-2013. The QED-2013 workshop focused on real-world application problems drawn from several sectors, and contributed to the informed use of downscaled data. This workshop is a part of a larger effort by NCPP and partner organizations to develop a standardized evaluation framework for local and regional climate information. The main goals of QED-2013 were to a) coordinate efforts for quantitative evaluation, b) develop software infrastructure, c) develop a repository of information, d) develop translational and guidance information, e) identify and engage key user communities, and f) promote collaboration and interoperability. CoG was a key player in QED-2013 support. NCPP was an early adopter of the CoG platform, providing valuable recommendations for overall development plus specific workshop-related requirements. New CoG features developed for QED-2013 included: the ability to publish images and associated metadata contained within XML files to its associated data node combine both artifacts into an integrated display. The ability to modify data search facets into scientifically relevant groups and display dynamic lists of workshop participants and their interests was also added to the interface. During the workshop, the QED-2013 project page on CoG provided meeting logistics, meeting

  19. The ERESE Project: Interfacing with the ERDA Digital Archive and ERR Reference Database in EarthRef.org

    NASA Astrophysics Data System (ADS)

    Koppers, A. A.; Staudigel, H.; Mills, H.; Keller, M.; Wallace, A.; Bachman, N.; Helly, J.; Helly, M.; Miller, S. P.; Massell Symons, C.

    2004-12-01

    To bridge the gap between Earth science teachers, librarians, scientists and data archive managers, we have started the ERESE project that will create, archive and make available "Enduring Resources in Earth Science Education" through information technology (IT) portals. In the first phase of this National Science Digital Library (NSDL) project, we are focusing on the development of these ERESE resources for middle and high school teachers to be used in lesson plans with "plate tectonics" and "magnetics" as their main theme. In this presentation, we will show how these new ERESE resources are being generated, how they can be uploaded via online web wizards, how they are archived, how we make them available via the EarthRef.org Digital Archive (ERDA) and Reference Database (ERR), and how they relate to the SIOExplorer database containing data objects for all seagoing cruises carried out by the Scripps Institution of Oceanography. The EarthRef.org web resource uses the vision of a "general description" of the Earth as a geological system to provide an IT infrastructure for the Earth sciences. This emphasizes the marriage of the "scientific process" (and its results) with an educational cyber-infrastructure for teaching Earth sciences, on any level, from middle school to college and graduate levels. Eight different databases reside under EarthRef.org from which ERDA holds any digital object that has been uploaded by other scientists, teachers and students for free, while the ERR holds more than 80,000 publications. For more than 1,500 of these publications, this latter database makes available for downloading JPG/PDF images of the abstracts, data tables, methods and appendices, together with their digitized contents in Microsoft Word and Excel format. Both holdings are being used to store the ERESE objects that are being generated by a group of undergraduate students majoring in Environmental Systems (ESYS) program at the UCSD with an emphasis on the Earth Sciences

  20. Voxel Advanced Digital-Manufacturing for Earth and Regolith in Space Project

    NASA Technical Reports Server (NTRS)

    Zeitlin, Nancy; Mueller, Robert P.

    2015-01-01

    A voxel is a discrete three-dimensional (3D) element of material that is used to construct a larger 3D object. It is the 3D equivalent of a pixel. This project will conceptualize and study various approaches in order to develop a proof of concept 3D printing device that utilizes regolith as the material of the voxels. The goal is to develop a digital printer head capable of placing discrete self-aligning voxels in additive layers in order to fabricate small parts that can be given structural integrity through a post-printing sintering or other binding process. The quicker speeds possible with the voxel 3D printing approach along with the utilization of regolith material as the substrate will advance the use of this technology to applications for In-Situ Resource Utilization (ISRU), which is key to reducing logistics from Earth to Space, thus making long-duration human exploration missions to other celestial bodies more possible.

  1. Earth Observation in Support of Sustainable Urban Planning: Results of the Dragon-3 Monitor Project

    NASA Astrophysics Data System (ADS)

    Cartalis, C.; Polydoros, A.; Mavrakou, T.; Asimakopoulos, D. N.

    2016-08-01

    Sustainable urban planning increasingly demands innovative concepts and techniques to obtain up-to-date and area-wide information on the characteristics and development of the urban system. In this paper, a thorough and conclusive presentation is made in terms of the results of the DRAGON-3 MONITOR project as based on the use of Earth Observation. Results refer in particular to a set of EO based dynamic urban indicators (i.e. urban form and expansion, land use/land cover changes, land surface temperature distribution, the presence and strength of urban heat island) with the capacity to describe the state, dynamic changes and interaction of the land and thermal environment in urban areas. Furthermore results are assessed in terms of their potential to operationally support sustainable urban planning and bridge the gap between EO scientists and urban planners. Constraints related to the spatial resolution and revisit time of satellite sensors are discussed as they influence the accuracy and applicability of the indicators. Methodologies to improve the applicability of the indicators are also discussed along with the presentation of the respective results.

  2. Holistic Approach to Secondary Earth Science Teacher Professional Development: the Triad of Project-based Instruction, Earth Science Content, and GIS Technology

    NASA Astrophysics Data System (ADS)

    Rubino-Hare, L.; Sample, J. C.; Fredrickson, K.; Claesgens, J.; Bloom, N.; Henderson-Dahms, C.; Manone, M.

    2011-12-01

    We have provided two years of professional development for secondary and middle school teachers with a focus on project-based instruction (PBI) using GIS. The EYE-POD project (funded by NSF-ITEST) involved pairs of teachers from Arizona and the surrounding region in two-week institutes during Summer, 2010, and an advanced institute in Summer, 2011. The NAz-POD project (funded by Arizona Department of Education and administered by Science Foundation Arizona) provided similar PD experiences, but the institutes occurred during weekends in the academic year. The institutes were led by a team with expertise in Earth science content, professional development and pedagogy, and GIS. The teachers developed learning modules using the project based learning instructional model. Pedagogy, content, and GIS skills were combined throughout the professional development activities. Academic year follow up by NAU personnel included classroom observations and technical support. For assessing student work we provided a rubric, but learned that teachers were not prepared to assess GIS products in order to determine the level of student understanding. In year two of the project we incorporated strategies for assessment of student products into the professional development. Teacher-participants and their students completed several pre- and post- assessments. Teacher assessments included a geospatial performance assessment, classroom observations, and content tests. Student data collection included attitude and efficacy questionnaires, content tests, and authentic assessments including products using GIS. Content tests were the same for teachers and students and included spatial reasoning, data analysis, and Earth science content. Data was also collected on teacher perception of professional development delivery and self-reported confidence in teaching with PBI and geospatial technology. Student assessments show that improvement occurred in all areas on the content test. Possible factors

  3. Learning about the Earth through Societally-relevant Interdisciplinary Research Projects: the Honours Integrated Science Program at McMaster

    NASA Astrophysics Data System (ADS)

    Eyles, C.; Symons, S. L.; Harvey, C. T.

    2016-12-01

    Students in the Honours Integrated Science (iSci) program at McMaster University (Hamilton, Ontario, Canada) learn about the Earth through interdisciplinary research projects that focus on important societal issues. The iSci program is a new and innovative undergraduate program that emphasizes the links between scientific disciplines and focuses on learning through research and the development of scientific communication skills. The program accepts up to 60 students each year and is taught by a team of 18 instructors comprising senior and junior faculty, post-doctoral fellows, a lab coordinator, instructional assistant, a librarian and library staff, and an administrator. The program is designed around a pedagogical model that emphasizes hands-on learning through interdisciplinary research (Research-based Integrated Education: RIE) and is mostly project-based and experiential. In their freshman year students learn fundamental Earth science concepts (in conjunction with chemistry, physics, mathematics and biology) through research projects focused on environmental contamination, interplanetary exploration, the effect of drugs on the human body and environment, sustainable energy, and cancer. In subsequent years they conduct research on topics such as the History of the Earth, Thermodynamics, Plant-Animal Interactions, Wine Science, Forensics, and Climate Change. The iSci program attracts students with a broad interest in science and has been particularly effective in directing high quality students into the Earth sciences as they are introduced to the discipline in their first year of study through research projects that are interesting and stimulating. The structure of the iSci program encourages consideration of geoscientific applications in a broad range of societally relevant research projects; these projects are reviewed and modified each year to ensure their currency and ability to meet program learning objectives.

  4. Captivity humanizes the primate microbiome.

    PubMed

    Clayton, Jonathan B; Vangay, Pajau; Huang, Hu; Ward, Tonya; Hillmann, Benjamin M; Al-Ghalith, Gabriel A; Travis, Dominic A; Long, Ha Thang; Tuan, Bui Van; Minh, Vo Van; Cabana, Francis; Nadler, Tilo; Toddes, Barbara; Murphy, Tami; Glander, Kenneth E; Johnson, Timothy J; Knights, Dan

    2016-09-13

    The primate gastrointestinal tract is home to trillions of bacteria, whose composition is associated with numerous metabolic, autoimmune, and infectious human diseases. Although there is increasing evidence that modern and Westernized societies are associated with dramatic loss of natural human gut microbiome diversity, the causes and consequences of such loss are challenging to study. Here we use nonhuman primates (NHPs) as a model system for studying the effects of emigration and lifestyle disruption on the human gut microbiome. Using 16S rRNA gene sequencing in two model NHP species, we show that although different primate species have distinctive signature microbiota in the wild, in captivity they lose their native microbes and become colonized with Prevotella and Bacteroides, the dominant genera in the modern human gut microbiome. We confirm that captive individuals from eight other NHP species in a different zoo show the same pattern of convergence, and that semicaptive primates housed in a sanctuary represent an intermediate microbiome state between wild and captive. Using deep shotgun sequencing, chemical dietary analysis, and chloroplast relative abundance, we show that decreasing dietary fiber and plant content are associated with the captive primate microbiome. Finally, in a meta-analysis including published human data, we show that captivity has a parallel effect on the NHP gut microbiome to that of Westernization in humans. These results demonstrate that captivity and lifestyle disruption cause primates to lose native microbiota and converge along an axis toward the modern human microbiome.

  5. Captivity humanizes the primate microbiome

    PubMed Central

    Vangay, Pajau; Huang, Hu; Ward, Tonya; Hillmann, Benjamin M.; Al-Ghalith, Gabriel A.; Travis, Dominic A.; Long, Ha Thang; Tuan, Bui Van; Minh, Vo Van; Cabana, Francis; Nadler, Tilo; Toddes, Barbara; Murphy, Tami; Glander, Kenneth E.; Johnson, Timothy J.; Knights, Dan

    2016-01-01

    The primate gastrointestinal tract is home to trillions of bacteria, whose composition is associated with numerous metabolic, autoimmune, and infectious human diseases. Although there is increasing evidence that modern and Westernized societies are associated with dramatic loss of natural human gut microbiome diversity, the causes and consequences of such loss are challenging to study. Here we use nonhuman primates (NHPs) as a model system for studying the effects of emigration and lifestyle disruption on the human gut microbiome. Using 16S rRNA gene sequencing in two model NHP species, we show that although different primate species have distinctive signature microbiota in the wild, in captivity they lose their native microbes and become colonized with Prevotella and Bacteroides, the dominant genera in the modern human gut microbiome. We confirm that captive individuals from eight other NHP species in a different zoo show the same pattern of convergence, and that semicaptive primates housed in a sanctuary represent an intermediate microbiome state between wild and captive. Using deep shotgun sequencing, chemical dietary analysis, and chloroplast relative abundance, we show that decreasing dietary fiber and plant content are associated with the captive primate microbiome. Finally, in a meta-analysis including published human data, we show that captivity has a parallel effect on the NHP gut microbiome to that of Westernization in humans. These results demonstrate that captivity and lifestyle disruption cause primates to lose native microbiota and converge along an axis toward the modern human microbiome. PMID:27573830

  6. The Plastisphere "Microbiome"

    NASA Astrophysics Data System (ADS)

    Amaral-Zettler, L. A.; Dupont, C. L.; Zettler, E. R.; Slikas, B.; Kaul, D.; Mincer, T. J.

    2016-02-01

    Alongside other ocean stressors, plastic marine debris (PMD) is now considered a major source of marine pollution and potential source of invasive alien species, two important ocean health index criteria. While macroplastics are recognized as a visible problem in coastal environments, the less conspicuous microplastics (< 5 mm) numerically dominate pristine open ocean gyres where their impact is much less understood. Central to biological interactions with plastic is the almost instant colonization upon entry into the sea by a thin film of microorganisms, the Plastisphere microbiome. While the phylogenetic diversity of the Plastisphere is now recognized to be highly variable and diverse in nature, less is known about its metabolic potential. Using shotgun metagenomics techniques, we characterized the metabolic potential of Plastisphere microbiomes from ocean gyre-collected microplastics and contrasted it with those of known biotic substrates such as macroalgae. Our data reveal that microbial eukaryotic assemblages dominate some Plastisphere communities, and bacteria dominate others, while archaea appear to be consistently rare inhabitants. We have successfully recovered dozens of draft bacterial genomes and several partial eukaryotic genomes from our libraries. Our data allow us to conduct comparative genomics on commonly occurring Plastisphere residents, further gaining insights into their physiology, ecology, pathogenicity, and substrate transformation potential.

  7. The Interactive Virtual Earth Science Teaching (InVEST) project: preliminary results

    NASA Astrophysics Data System (ADS)

    Gallus, W.; Cervato, C.; Parham, T.; Larsen, M.; Cruz-Neira, C.; Boudreaux, H.

    2009-04-01

    The InVEST (Interactive Virtual Earth Science Teaching) project has as its goal the development of state-of-the-art virtual reality geoscience tools that can be used to correct student misunderstandings about some geoscience phenomena. One tool, originally developed several years ago, the virtual tornadic thunderstorm, was recently modified based on feedback from instructors given the opportunity to use the tool. The modified virtual storm will be demonstrated during the presentation. In addition, a virtual volcano application is currently under development. To steer the development of this application, a Volcanic Concept Survey was recently administered to over 600 students at six U.S. institutions with the goal of identifying areas of greatest misconception relating to volcanoes. Both mean and median scores on the instrument were exceptionally low, indicating that students generally possessed minimal understanding of volcanic systems. High scores were restricted to the simplest aspects of volcanism (terminology, basic volcano shape) while questions requiring higher thinking and deeper conceptual connections (analysis of patterns, eruptive controls, and hazards) saw much lower scores. Categorical analysis of response types revealed the extent of specific misconceptions, the most predominant of which demonstrated a failure to link tectonics to a global volcanic pattern. Eruptive catalysts and controls also appear poorly understood, as are volcanic impacts on the environment and human endeavors. The survey also included demographic information which has been analyzed. Analysis of student sources of knowledge found that over 41% of students said that they had acquired most of their understanding about volcanoes from non-traditional sources such as the popular media and Hollywood films. Application of a multiple linear regression model and an expanded model suggests that these students were much less likely to receive high scores on questions relating to understanding

  8. Sewage reflects the microbiomes of human populations.

    PubMed

    Newton, Ryan J; McLellan, Sandra L; Dila, Deborah K; Vineis, Joseph H; Morrison, Hilary G; Eren, A Murat; Sogin, Mitchell L

    2015-02-24

    Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker gene studies that consider microbiome trends among human populations scale with the number of individuals sampled from each population. As an alternative strategy for sampling populations, we examined whether sewage accurately reflects the microbial community of a mixture of stool samples. We used oligotyping of high-throughput 16S rRNA gene sequence data to compare the bacterial distribution in a stool data set to a sewage influent data set from 71 U.S. cities. On average, only 15% of sewage sample sequence reads were attributed to human fecal origin, but sewage recaptured most (97%) human fecal oligotypes. The most common oligotypes in stool matched the most common and abundant in sewage. After informatically separating sequences of human fecal origin, sewage samples exhibited ~3× greater diversity than stool samples. Comparisons among municipal sewage communities revealed the ubiquitous and abundant occurrence of 27 human fecal oligotypes, representing an apparent core set of organisms in U.S. populations. The fecal community variability among U.S. populations was significantly lower than among individuals. It clustered into three primary community structures distinguished by oligotypes from either: Bacteroidaceae, Prevotellaceae, or Lachnospiraceae/Ruminococcaceae. These distribution patterns reflected human population variation and predicted whether samples represented lean or obese populations with 81 to 89% accuracy. Our findings demonstrate that sewage represents the fecal microbial community of human populations and captures population-level traits of the human microbiome. The gut microbiota serves important functions in healthy humans. Numerous projects aim to define a healthy gut microbiome and its association with health states. However

  9. Construction of Hierarchical Models for Fluid Dynamics in Earth and Planetary Sciences : DCMODEL project

    NASA Astrophysics Data System (ADS)

    Takahashi, Y. O.; Takehiro, S.; Sugiyama, K.; Odaka, M.; Ishiwatari, M.; Sasaki, Y.; Nishizawa, S.; Ishioka, K.; Nakajima, K.; Hayashi, Y.

    2012-12-01

    Toward the understanding of fluid motions of planetary atmospheres and planetary interiors by performing multiple numerical experiments with multiple models, we are now proceeding ``dcmodel project'', where a series of hierarchical numerical models with various complexity is developed and maintained. In ``dcmodel project'', a series of the numerical models are developed taking care of the following points: 1) a common ``style'' of program codes assuring readability of the software, 2) open source codes of the models to the public, 3) scalability of the models assuring execution on various scales of computational resources, 4) stressing the importance of documentation and presenting a method for writing reference manuals. The lineup of the models and utility programs of the project is as follows: Gtool5, ISPACK/SPML, SPMODEL, Deepconv, Dcpam, and Rdoc-f95. In the followings, features of each component are briefly described. Gtool5 (Ishiwatari et al., 2012) is a Fortran90 library, which provides data input/output interfaces and various utilities commonly used in the models of dcmodel project. A self-descriptive data format netCDF is adopted as a IO format of Gtool5. The interfaces of gtool5 library can reduce the number of operation steps for the data IO in the program code of the models compared with the interfaces of the raw netCDF library. Further, by use of gtool5 library, procedures for data IO and addition of metadata for post-processing can be easily implemented in the program codes in a consolidated form independent of the size and complexity of the models. ``ISPACK'' is the spectral transformation library and ``SPML (SPMODEL library)'' (Takehiro et al., 2006) is its wrapper library. Most prominent feature of SPML is a series of array-handling functions with systematic function naming rules, and this enables us to write codes with a form which is easily deduced from the mathematical expressions of the governing equations. ``SPMODEL'' (Takehiro et al., 2006

  10. A communal catalogue reveals Earth's multiscale microbial diversity.

    PubMed

    Thompson, Luke R; Sanders, Jon G; McDonald, Daniel; Amir, Amnon; Ladau, Joshua; Locey, Kenneth J; Prill, Robert J; Tripathi, Anupriya; Gibbons, Sean M; Ackermann, Gail; Navas-Molina, Jose A; Janssen, Stefan; Kopylova, Evguenia; Vázquez-Baeza, Yoshiki; González, Antonio; Morton, James T; Mirarab, Siavash; Zech Xu, Zhenjiang; Jiang, Lingjing; Haroon, Mohamed F; Kanbar, Jad; Zhu, Qiyun; Jin Song, Se; Kosciolek, Tomasz; Bokulich, Nicholas A; Lefler, Joshua; Brislawn, Colin J; Humphrey, Gregory; Owens, Sarah M; Hampton-Marcell, Jarrad; Berg-Lyons, Donna; McKenzie, Valerie; Fierer, Noah; Fuhrman, Jed A; Clauset, Aaron; Stevens, Rick L; Shade, Ashley; Pollard, Katherine S; Goodwin, Kelly D; Jansson, Janet K; Gilbert, Jack A; Knight, Rob

    2017-11-23

    Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.

  11. The Intestinal Microbiome and Health

    PubMed Central

    Tuddenham, Susan; Sears, Cynthia L.

    2015-01-01

    Purpose of Review A diverse array of microbes colonizes the human intestine. In this review we seek to outline the current state of knowledge on what characterizes a “healthy” or “normal” intestinal microbiome, what factors modify the intestinal microbiome in the healthy state and how the intestinal microbiome affects normal host physiology Recent Findings What constitutes a “normal” or “healthy” intestinal microbiome is an area of active research, but key characteristics may include diversity, richness and a microbial community’s resilience and ability to resist change. A number of factors, including age, the host immune system, host genetics, diet and antibiotic use appear to modify the intestinal microbiome in the normal state. New research shows that the microbiome likely plays a critical role in the healthy human immune system and metabolism. Summary It is clear that there is a complicated bi-directional relationship between the intestinal microbiota and host which is vital to health. An enhanced understanding of this relationship will be critical not only to maximize and maintain human health but also to shape our understanding of disease and to foster new therapeutic approaches. PMID:26237547

  12. The microbiome of uncontacted Amerindians.

    PubMed

    Clemente, Jose C; Pehrsson, Erica C; Blaser, Martin J; Sandhu, Kuldip; Gao, Zhan; Wang, Bin; Magris, Magda; Hidalgo, Glida; Contreras, Monica; Noya-Alarcón, Óscar; Lander, Orlana; McDonald, Jeremy; Cox, Mike; Walter, Jens; Oh, Phaik Lyn; Ruiz, Jean F; Rodriguez, Selena; Shen, Nan; Song, Se Jin; Metcalf, Jessica; Knight, Rob; Dantas, Gautam; Dominguez-Bello, M Gloria

    2015-04-03

    Most studies of the human microbiome have focused on westernized people with life-style practices that decrease microbial survival and transmission, or on traditional societies that are currently in transition to westernization. We characterize the fecal, oral, and skin bacterial microbiome and resistome of members of an isolated Yanomami Amerindian village with no documented previous contact with Western people. These Yanomami harbor a microbiome with the highest diversity of bacteria and genetic functions ever reported in a human group. Despite their isolation, presumably for >11,000 years since their ancestors arrived in South America, and no known exposure to antibiotics, they harbor bacteria that carry functional antibiotic resistance (AR) genes, including those that confer resistance to synthetic antibiotics and are syntenic with mobilization elements. These results suggest that westernization significantly affects human microbiome diversity and that functional AR genes appear to be a feature of the human microbiome even in the absence of exposure to commercial antibiotics. AR genes are likely poised for mobilization and enrichment upon exposure to pharmacological levels of antibiotics. Our findings emphasize the need for extensive characterization of the function of the microbiome and resistome in remote nonwesternized populations before globalization of modern practices affects potentially beneficial bacteria harbored in the human body.

  13. The microbiome of uncontacted Amerindians

    PubMed Central

    Clemente, Jose C.; Pehrsson, Erica C.; Blaser, Martin J.; Sandhu, Kuldip; Gao, Zhan; Wang, Bin; Magris, Magda; Hidalgo, Glida; Contreras, Monica; Noya-Alarcón, Óscar; Lander, Orlana; McDonald, Jeremy; Cox, Mike; Walter, Jens; Oh, Phaik Lyn; Ruiz, Jean F.; Rodriguez, Selena; Shen, Nan; Song, Se Jin; Metcalf, Jessica; Knight, Rob; Dantas, Gautam; Dominguez-Bello, M. Gloria

    2015-01-01

    Most studies of the human microbiome have focused on westernized people with life-style practices that decrease microbial survival and transmission, or on traditional societies that are currently in transition to westernization. We characterize the fecal, oral, and skin bacterial microbiome and resistome of members of an isolated Yanomami Amerindian village with no documented previous contact with Western people. These Yanomami harbor a microbiome with the highest diversity of bacteria and genetic functions ever reported in a human group. Despite their isolation, presumably for >11,000 years since their ancestors arrived in South America, and no known exposure to antibiotics, they harbor bacteria that carry functional antibiotic resistance (AR) genes, including those that confer resistance to synthetic antibiotics and are syntenic with mobilization elements. These results suggest that westernization significantly affects human microbiome diversity and that functional AR genes appear to be a feature of the human microbiome even in the absence of exposure to commercial antibiotics. AR genes are likely poised for mobilization and enrichment upon exposure to pharmacological levels of antibiotics. Our findings emphasize the need for extensive characterization of the function of the microbiome and resistome in remote nonwesternized populations before globalization of modern practices affects potentially beneficial bacteria harbored in the human body. PMID:26229982

  14. Organic nutrient chemistry and the marine microbiome

    SciT

    Repeta, Daniel J.; Boiteau, Rene M.

    Vast expanses of the ocean are characterized by extraordinarily low concentrations of nutrients but nevertheless support vibrant communities of marine microbes. In aggregate, these communities drive many of the important elemental cycles that sustain life on Earth. Microbial communities are organized to maximize nutrient and energy transfer between cells, and efficiently recycle organic carbon, nitrogen, phosphorus and trace metals. Energy and nutrient transfer occurs across a broad range of spatial scales. Large-sized marine algae and bacteria support epibiont communities that are physically in contact, exchanging nutrients and energy across cell membranes, while other communities that are physically far apart, relymore » on the horizontal mixing of ocean currents or the vertical pull of gravity to transfer nutrient and energy containing organic matter. Marine organic geochemists are making rapid progress in understanding the chemistry of the marine microbiome. These advances have benefited from parallel developments in analytical chemistry, microbial isolation and culture techniques, and advances in microbial genomics, transcriptomics, and proteomics. The combination of all three approaches has proven to be quite powerful. Here we highlight two aspects of the chemistry of organic phosphorus and trace metal cycling and the marine microbiome. In each study, advances in chemical analyses, microbial culture, and microbial genomics played key roles in understanding how microbial communities interact to facilitate nutrient cycling in the open ocean.« less

  15. Global Modeling and Projection of Short-Lived Climate Pollutants in an Earth System Model

    NASA Astrophysics Data System (ADS)

    Sudo, K.; Takemura, T.; Klimont, Z.; Kurokawa, J.; Akimoto, H.

    2013-12-01

    In predicting and mitigating future global warming, short-lived climate pollutants (SLCPs) such as tropospheric ozone (O3), black carbon (BC), and other related components including CH4/VOCs and aerosols play crucial roles as well as long-lived species like CO2 or N2O. Several recent studies suggests that reduction of heating SLCPs (i.e., O3 and black carbon) together with CH4 can decrease and delay the expected future warming, and can be an alternative to CO2 mitigation (Shindell et al., 2012). However it should be noted that there are still large uncertainties in simulating SLCPs and their climate impacts. For instance, present global models generally have a severe tendency to underestimate BC especially in remote areas like the polar regions as shown by the recent model intercomparison project under the IPCC (ACCMIP/AeroCOM). This problem in global BC modeling, basically coming from aging and removal processes of BC, causes still a large uncertainty in the estimate of BC's atmospheric heating and climate impacts (Bond et al., 2013; Kerr et al., 2013). This study attempted to improve global simulation of BC by developing a new scheme for simulating aging process of BC and re-evaluate radiative forcing of BC in the framework of a chemistry-aerosol coupled climate model (Earth system model) MIROC-ESM-CHEM. Our improved model with the new aging scheme appears to relatively well reproduce the observed BC concentrations and seasonality in the Arctic/Antarctic region. The new model estimates radiative forcing of BC to be 0.83 W m-2 which is about two times larger than the estimate by our original model with no aging scheme (0.41 W m-2), or the model ensemble mean in the IPCC report. Using this model, future projection of SLCPs and their climate impacts is conducted following the recent IIASA emission scenarios for the year 2030 (Klimont et al., 2006; Cofala et al., 2007). Our simulation suggests that heating SLCPs components (O3, BC, and CH4) are significantly reduced

  16. The SCIDIP-ES project - towards an international collaboration strategy for long term preservation of earth science data

    NASA Astrophysics Data System (ADS)

    Riddick, Andrew; Glaves, Helen; Marelli, Fulvio; Albani, Mirko; Tona, Calogera; Marketakis, Yannis; Tzitzikas, Yannis; Guarino, Raffaele; Giaretta, David; Di Giammatteo, Ugo

    2013-04-01

    The capability for long term preservation of earth science data is a key requirement to support on-going research and collaboration within and between many earth science disciplines. A number of critically important current research directions (e.g. understanding climate change, and ensuring sustainability of natural resources) rely on the preservation of data often collected over several decades in a form in which it can be accessed and used easily. Another key driver for strategic long term data preservation is that key research challenges (such as those described above) frequently require cross disciplinary research utilising raw and interpreted data from a number of earth science disciplines. Effective data preservation strategies can support this requirement for interoperability and collaboration, and thereby stimulate scientific innovation. The SCIDIP-ES project (EC FP7 grant agreement no. 283401) seeks to address these and other data preservation challenges by developing a Europe wide infrastructure for long term data preservation comprising appropriate software tools and infrastructure services to enable and promote long term preservation of earth science data. Because we define preservation in terms of continued usability of the digitally encoded information, the generic infrastructure services will allow a wide variety of data to be made usable by researchers from many different domains. This approach promotes international collaboration between researchers and will enable the cost for long-term usability across disciplines to be shared supporting the creation of strong business cases for the long term support of that data. This paper will describe our progress to date, including the results of community engagement and user consultation exercises designed to specify and scope the required tools and services. Our user engagement methodology, ensuring that we are capturing the views of a representative sample of institutional users, will be described. Key

  17. Projected Near-Earth Object Discovery Performance of the Large Synoptic Survey Telescope

    NASA Technical Reports Server (NTRS)

    Chesley, Steven R.; Veres, Peter

    2017-01-01

    This report describes the methodology and results of an assessment study of the performance of the Large Synoptic Survey Telescope (LSST) in its planned efforts to detect and catalog near-Earth objects (NEOs).

  18. Super-Earth and Sub-Neptune Exoplanets: a First Look from the MEarth Project

    NASA Astrophysics Data System (ADS)

    Berta, Zachory K.

    Exoplanets that transit nearby M dwarfs allow us to measure the sizes, masses, and atmospheric properties of distant worlds. Between 2008 and 2013, we searched for such planets with the MEarth Project, a photometric survey of the closest and smallest main-sequence stars. This thesis uses the first planet discovered with MEarth, the warm 2.7 Earth radius exoplanet GJ1214b, to explore the possibilities that planets transiting M dwarfs provide. First, we perform a broad reconnaissance of the GJ1214b planetary system to refine the system's physical properties. We fit many transits to improve the planetary parameters, use starspots to measure GJ1214's rotation period (>50 days), and search for additional transiting planets, placing strong limits on habitable-zone Neptune-sized exoplanets in the system. We present Hubble Space Telescope observations of GJ1214b's atmosphere. We find the transmission spectrum to be flat between 1.1 and 1.7 microns, ruling out at 8 sigma the presence of a clear hydrogen-rich envelope that had been proposed to explain GJ1214b's large radius. Additional observations will determine whether the absence of deep absorption features in GJ1214b's transmission spectrum is due to the masking influence of high altitude clouds or to the presence of a compact, hydrogen-poor atmosphere. We describe a new algorithm to find transiting planets in light curves plagued by stellar variability and systematic noise sources. This Method to Include Starspots and Systematics in the Marginalized Probability of a Lone Eclipse (MISS MarPLE) reliably assesses the significance of individual transit events, a necessary requirement for detecting habitable zone planets from the ground with MEarth. We compare MEarth's achieved sensitivity to planet occurrence statistics from the NASA Kepler Mission, and find that MEarth's single discovery of GJ1214b is consistent with expectations. We find that warm Neptunes are rare around mid-to-late M dwarfs (<0.15 planets

  19. Project CUES: A New Middle-School Earth System Science Curriculum Being Developed by the American Geological Institute

    NASA Astrophysics Data System (ADS)

    Smith, M. C.; Smith, M. J.; Lederman, N.; Southard, J. B.; Rogers, E. A.; Callahan, C. N.

    2002-12-01

    Project CUES is a middle-school earth systems science curriculum project under development by the American Geological Institute (AGI) and funded by the National Science Foundation (ESI-0095938). CUES features a student-centered, inquiry pedagogy and approaches earth science from a systems perspective. CUES will use the expanded learning cycle approach of Trowbridge and Bybee (1996), known as the 5E model (engage-explore-explain-elaborate-evaluate). Unlike AGI's Investigating Earth Systems (IES) curriculum modules, CUES will include a single hard-bound textbook, and will take one school-year to complete. The textbook includes a prologue that addresses systems concepts and four main units: Geosphere, Hydrosphere, Atmosphere, and Biosphere. Each eight-week unit takes students through a progression from guided inquiry to open-ended, student-driven inquiry. During first 4 to 5 weeks of each unit, students explore important earth science phenomena and concepts through scripted investigations and narrative reading passages written by scientists as "inquiry narratives". The narratives address the development of scientific ideas and relay the personal experiences of a scientist during their scientific exploration. Aspects of the nature of science will be explicitly addressed in investigations and inquiry narratives. After the guided inquiry, students will develop a research proposal and conduct their own inquiry into local or regional scientific problems. Each unit culminates with a science conference at which students present their research. CUES will be the first NSF-funded, comprehensive earth systems textbook for middle school that is based on national standards. CUES will be pilot tested in 12 classrooms in January 2003, with a national field test of the program in 50 classrooms during the 2003-2004 school year.

  20. Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data.

    PubMed

    Robertson, Charles E; Harris, J Kirk; Wagner, Brandie D; Granger, David; Browne, Kathy; Tatem, Beth; Feazel, Leah M; Park, Kristin; Pace, Norman R; Frank, Daniel N

    2013-12-01

    Studies of the human microbiome, and microbial community ecology in general, have blossomed of late and are now a burgeoning source of exciting research findings. Along with the advent of next-generation sequencing platforms, which have dramatically increased the scope of microbiome-related projects, several high-performance sequence analysis pipelines (e.g. QIIME, MOTHUR, VAMPS) are now available to investigators for microbiome analysis. The subject of our manuscript, the graphical user interface-based Explicet software package, fills a previously unmet need for a robust, yet intuitive means of integrating the outputs of the software pipelines with user-specified metadata and then visualizing the combined data.

  1. The TRUST Project: A Formal-Informal Teacher Education Partnership for the Promotion of Earth Science Teacher Certification

    NASA Astrophysics Data System (ADS)

    Sloan, H.; Miele, E.; Powell, W.; MacDonald, M.

    2004-12-01

    The American Museum of Natural History (AMNH) in partnership with Lehman and Brooklyn Colleges of the City University of New York (CUNY) has initiated The Teacher Renewal for Urban Science Teaching (TRUST) project. TRUST combines informal and formal teacher education in a four-year initiative to enhance professional development and masters of science education programs, grades K-8 at Brooklyn College and 7-12 at Lehman College. This NSF-funded partnership brings together the resources of AMNH, CUNY, New York City school districts, New York City Department of Education-Museum Partnerships, and the expertise of scientists and teachers with research experiences. Following an initial planning year, TRUST will recruit and sustain 90 teachers over a period of 3 years as well as engage 30 school administrators in support of Earth science instruction. Program components include two new formal Earth systems science courses, intensive informal summer institutes, and a lecture and workshop series during which participants gain new Earth science content knowledge, develop action plans, and present their work on the local and national level. In addition, participants have access to ongoing resource and material support to enhance their learning and instruction. Continuous documentation and data collection by project investigators are being used to address questions regarding the impact various aspects of the TRUST participant experience on classroom instruction and learning, the acquisition of scientific knowledge in the new courses and institutes, and to examine the nature of the Museum experience in meeting certification goals. External formative and summative evaluation of the project is addressing issues surrounding the value of the program as a model for formal-informal partnership in urban Earth science teacher education and certification, analysis of policies that facilitate partnership arrangements, and how socialization of novices with experts affects retention and

  2. Geomicrobiology and Metagenomics of Terrestrial Deep Subsurface Microbiomes.

    PubMed

    Itävaara, M; Salavirta, H; Marjamaa, K; Ruskeeniemi, T

    2016-01-01

    Fractures in the deep subsurface of Earth's crust are inhabited by diverse microbial communities that participate in biogeochemical cycles of the Earth. Life on Earth, which arose c. 3.5-4.0 billion years ago, reaches down at least 5 km in the crust. Deep mines, caves, and boreholes have provided scientists with opportunities to sample deep subsurface microbiomes and to obtain information on the species diversity and functions. A wide variety of bacteria, archaea, eukaryotes, and viruses are now known to reside in the crust, but their functions are still largely unknown. The crust at different depths has varying geological composition and hosts endemic microbiomes accordingly. The diversity is driven by geological formations and gases evolving from deeper depths. Cooperation among different species is still mostly unexplored, but viruses are known to restrict density of bacterial and archaeal populations. Due to the complex growth requirements of the deep subsurface microbiomes, the new knowledge about their diversity and functions is mostly obtained by molecular methods, eg, meta'omics'. Geomicrobiology is a multidisciplinary research area combining disciplines from geology, mineralogy, geochemistry, and microbiology. Geomicrobiology is concerned with the interaction of microorganisms and geological processes. At the surface of mineralogical or rock surfaces, geomicrobial processes occur mainly under aerobic conditions. In the deep subsurface, however, the environmental conditions are reducing and anaerobic. The present chapter describes the world of microbiomes in deep terrestrial geological environments as well as metagenomic and metatranscriptomic methods suitable for studies of these enigmatic communities. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. Precovery of near-Earth asteroids by a citizen-science project of the Spanish Virtual Observatory

    NASA Astrophysics Data System (ADS)

    Solano, E.; Rodrigo, C.; Pulido, R.; Carry, B.

    2014-02-01

    This article describes a citizen-science project conducted by the Spanish Virtual Observatory (SVO) to improve the orbits of near-Earth asteroids (NEAs) using data from astronomical archives. The list of NEAs maintained at the Minor Planet Center (MPC) is checked daily to identify new objects or changes in the orbital parameters of already catalogued objects. Using NEODyS we compute the position and magnitude of these objects at the observing epochs of the 938 046 images comprising the Eigth Data Release of the Sloan Digitised Sky Survey (SDSS). If the object lies within the image boundaries and the magnitude is brighter than the limiting magnitude, then the associated image is visually inspected by the project's collaborators ({the citizens}) to confirm or discard the presence of the NEA. If confirmed, accurate coordinates and, sometimes, magnitudes are submitted to the MPC. Using this methodology, 3226 registered users have made during the first fifteen months of the project more than 167 000 measurements which have improved the orbital elements of 551 NEAs (6 % of the total number of this type of asteroids). Even more remarkable is the fact that these results have been obtained at zero cost to telescope time as NEAs were serendipitously observed while the survey was being carried out. This demonstrates the enormous scientific potential hidden in astronomical archives. The great reception of the project as well as the results obtained makes it a valuable and reliable tool for improving the orbital parameters of near-Earth asteroids.

  4. ELF-VLF communications through the Earth Project report for calendar year 1984, revision 1

    NASA Astrophysics Data System (ADS)

    Buettner, H. M.; Burker, G. J.; Didwall, E. M.; Holladay, G.; Lytle, R. J.

    1985-08-01

    We use computer models and experiments to explore the feasibility of communication between points underground and on the Earth's surface. Emphasis is placed on ELF-VLF electromagnetic propagation through the Earth; nominally, we investigated propagation in the 200 Hz-30 kHz frequency range. The computer modeling included calculations of the fields of a point electric or magnetic source in a homogeneous half space or a stratified earth. Initial results for an insulated antenna of finite length are also considered. The experiments involved through-the-Earth transmissions at two locations in Pennsylvania, both of which had large formations of limestone. Initial results indicate that information rates as high as kbits/s may be possible for subsurface depths of 300 m or less. Accuracy of these estimates depends on the electromagnetic propagation constant of the rock, the noise characteristics, and the modulation scheme. Although a nuisance for evaluating through-the-Earth propagation, the existence of subsurface metal conductors can improve the transmission character of the site.

  5. The saliva microbiome of Pan and Homo

    PubMed Central

    2013-01-01

    Background It is increasingly recognized that the bacteria that live in and on the human body (the microbiome) can play an important role in health and disease. The composition of the microbiome is potentially influenced by both internal factors (such as phylogeny and host physiology) and external factors (such as diet and local environment), and interspecific comparisons can aid in understanding the importance of these factors. Results To gain insights into the relative importance of these factors on saliva microbiome diversity, we here analyze the saliva microbiomes of chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) from two sanctuaries in Africa, and from human workers at each sanctuary. The saliva microbiomes of the two Pan species are more similar to one another, and the saliva microbiomes of the two human groups are more similar to one another, than are the saliva microbiomes of human workers and apes from the same sanctuary. We also looked for the existence of a core microbiome and find no evidence for a taxon-based core saliva microbiome for Homo or Pan. In addition, we studied the saliva microbiome from apes from the Leipzig Zoo, and found an extraordinary diversity in the zoo ape saliva microbiomes that is not found in the saliva microbiomes of the sanctuary animals. Conclusions The greater similarity of the saliva microbiomes of the two Pan species to one another, and of the two human groups to one another, are in accordance with both the phylogenetic relationships of the hosts as well as with host physiology. Moreover, the results from the zoo animals suggest that novel environments can have a large impact on the microbiome, and that microbiome analyses based on captive animals should be viewed with caution as they may not reflect the microbiome of animals in the wild. PMID:24025115

  6. EarthServer - an FP7 project to enable the web delivery and analysis of 3D/4D models

    NASA Astrophysics Data System (ADS)

    Laxton, John; Sen, Marcus; Passmore, James

    2013-04-01

    EarthServer aims at open access and ad-hoc analytics on big Earth Science data, based on the OGC geoservice standards Web Coverage Service (WCS) and Web Coverage Processing Service (WCPS). The WCS model defines "coverages" as a unifying paradigm for multi-dimensional raster data, point clouds, meshes, etc., thereby addressing a wide range of Earth Science data including 3D/4D models. WCPS allows declarative SQL-style queries on coverages. The project is developing a pilot implementing these standards, and will also investigate the use of GeoSciML to describe coverages. Integration of WCPS with XQuery will in turn allow coverages to be queried in combination with their metadata and GeoSciML description. The unified service will support navigation, extraction, aggregation, and ad-hoc analysis on coverage data from SQL. Clients will range from mobile devices to high-end immersive virtual reality, and will enable 3D model visualisation using web browser technology coupled with developing web standards. EarthServer is establishing open-source client and server technology intended to be scalable to Petabyte/Exabyte volumes, based on distributed processing, supercomputing, and cloud virtualization. Implementation will be based on the existing rasdaman server technology developed. Services using rasdaman technology are being installed serving the atmospheric, oceanographic, geological, cryospheric, planetary and general earth observation communities. The geology service (http://earthserver.bgs.ac.uk/) is being provided by BGS and at present includes satellite imagery, superficial thickness data, onshore DTMs and 3D models for the Glasgow area. It is intended to extend the data sets available to include 3D voxel models. Use of the WCPS standard allows queries to be constructed against single or multiple coverages. For example on a single coverage data for a particular area can be selected or data with a particular range of pixel values. Queries on multiple surfaces can be

  7. Living the lesson: can the Lifestyle Project be used to achieve deep learning in environmental earth science?

    NASA Astrophysics Data System (ADS)

    Padden, M.; Whalen, K.

    2013-12-01

    Students in a large, second-year environmental earth science class made significant changes to their daily lives over a three-week period to learn how small-scale actions interact with global-scaled issues such as water and energy supplies, waste management and agriculture. The Lifestyle Project (Kirk and Thomas, 2003) was slightly adapted to fit a large-class setting (350 students). Students made changes to their lifestyle in self-selected categories (water, home heating, transportation, waste, food) and created journals over a three-week period as the changes increased in difficulty. The goal of this study is to gain an understanding of which aspects of the project played a pivotal role in impacting long-term learning. Content analysis of the journal entries and follow-up interviews are used to investigate if the Lifestyle Project is having a lasting impact on the students 18 months after the initial assignment.

  8. Herpesviruses and the microbiome.

    PubMed

    Dreyfus, David H

    2013-12-01

    The focus of this article will be to examine the role of common herpesviruses as a component of the microbiome of atopic patients and to review clinical observations suggesting that atopic patients might be predisposed to more severe and atypical herpes-related illness because their immune response is biased toward a TH2 cytokine profile. Human populations are infected with 8 herpesviruses, including herpes simplex virus HSV1 and HSV2 (also termed HHV1 and HHV2), varicella zoster virus (VZV or HHV3), EBV (HHV4), cytomegalovirus (HHV5), HHV6, HHV7, and Kaposi sarcoma-associated herpesvirus (termed KSV or HHV8). Herpesviruses are highly adapted to lifelong infection of their human hosts and thus can be considered a component of the human "microbiome" in addition to their role in illness triggered by primary infection. HSV1 and HSV2 infection and reactivation can present with more severe cutaneous symptoms termed eczema herpeticum in the atopic population, similar to the more severe eczema vaccinatum, and drug reaction with eosinophilia and systemic symptoms syndrome (DRESS) is associated with reactivation of HSV6 and possibly other herpesviruses in both atopic and nonatopic patients. In this review evidence is reviewed that primary infection with herpesviruses may have an atypical presentation in the atopic patient and conversely that childhood infection might alter the atopic phenotype. Reactivation of latent herpesviruses can directly alter host cytokine profiles through viral expression of cytokine-like proteins, such as IL-10 (EBV) or IL-6 (cytomegalovirus and HHV8), viral encoded and secreted siRNA and microRNAs, and modulation of expression of host transcription pathways, such as nuclear factor κB. Physicians caring for allergic and atopic populations should be aware of common and uncommon presentations of herpes-related disease in atopic patients to provide accurate diagnosis and avoid unnecessary laboratory testing or incorrect diagnosis of other conditions

  9. The Microbiome and Sustainable Healthcare

    PubMed Central

    Dietert, Rodney R.; Dietert, Janice M.

    2015-01-01

    Increasing prevalences, morbidity, premature mortality and medical needs associated with non-communicable diseases and conditions (NCDs) have reached epidemic proportions and placed a major drain on healthcare systems and global economies. Added to this are the challenges presented by overuse of antibiotics and increased antibiotic resistance. Solutions are needed that can address the challenges of NCDs and increasing antibiotic resistance, maximize preventative measures, and balance healthcare needs with available services and economic realities. Microbiome management including microbiota seeding, feeding, and rebiosis appears likely to be a core component of a path toward sustainable healthcare. Recent findings indicate that: (1) humans are mostly microbial (in terms of numbers of cells and genes); (2) immune dysfunction and misregulated inflammation are pivotal in the majority of NCDs; (3) microbiome status affects early immune education and risk of NCDs, and (4) microbiome status affects the risk of certain infections. Management of the microbiome to reduce later-life health risk and/or to treat emerging NCDs, to spare antibiotic use and to reduce the risk of recurrent infections may provide a more effective healthcare strategy across the life course particularly when a personalized medicine approach is considered. This review will examine the potential for microbiome management to contribute to sustainable healthcare. PMID:27417751

  10. A Multidisciplinary Approach to Study the Role of the Gut Microbiome in Relapsing and Progressive MS

    DTIC Science & Technology

    2017-10-01

    AWARD NUMBER: W81XWH-15-1-0654 TITLE: A Multidisciplinary Approach to Study the Role of the Gut Microbiome in Relapsing and Progressive MS...valid OMB control number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS. 1. REPORT DATE Oct 2017 2. REPORT TYPE Annual 3. DATES COVERED 30...Multidisciplinary Approach to Study the Role of the Gut Microbiome in Relapsing and Progressive MS 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT

  11. Interaction between drilled shaft and mechanically stabilized earth (MSE) wall : project summary.

    DOT National Transportation Integrated Search

    2015-08-31

    Drilled shafts are being constructed within the reinforced zone of mechanically stabilized earth (MSE) walls (Figure 1). The drilled shafts may be subjected to horizontal loads and push against the front of the wall. Distress of MSE wall panels has b...

  12. Planning for the Future on Spaceship Earth. Environmental Ecological Education Project. Revised.

    ERIC Educational Resources Information Center

    Parkway School District, Chesterfield, MO.

    This unit, designed for upper elementary school students, examines the role of the individual in society in determining the status of the environment. Viewing the earth as an ecosystem, it looks at past and present human events that have influenced the quality of the environment and attempts to provide students with an awareness of the knowledge…

  13. Scope and Sequence. Life Sciences, Physical Sciences, Earth and Space Sciences. A Summer Curriculum Development Project.

    ERIC Educational Resources Information Center

    Cortland-Madison Board of Cooperative Educational Services, Cortland, NY.

    Presented is a booklet containing scope and sequence charts for kindergarten and grades 1 to 6 science units. Overviews and lists of major concepts for units in the life, physical, and earth/space sciences are provided in tables for each grade level. Also presented are seven complete units, one for each grade level. Following a table of contents,…

  14. Microbiome and Food Allergy

    PubMed Central

    Blázquez, Ana B.; Berin, M. Cecilia

    2016-01-01

    Food allergy is a common disease affecting approximately 8% of children and 5% of adults. The prevalence has increased over the last two decades, suggesting an important environmental contribution to susceptibility. Studies have identified mode of birth, pet exposure, and having older siblings as being significant risk modifying factors in the development of food allergy. With the discovery that these factors significantly impact the composition of the intestinal microbiome, which is known to play a critical role in shaping the immune system, recent studies have begun to address the role of the intestinal microbiota in the development of food allergy. Studies in human cohorts support a dysbiosis in food allergy, and limited data suggest that this dysbiosis occurs early in life, preceding the onset of sensitization. Studies from animal models have clearly shown that the composition of the intestinal microbiota confers susceptibility to food allergy, and that there are organisms such as Clostridia species that are protective in the development of food allergy. Our understanding of microbial regulation of food allergy is in its nascency, but the state of the field supports an important contribution of intestinal microbes to susceptibility. Challenges going forward are to identify commensal-derived microorganisms that could be used therapeutically to prevent or perhaps treat food allergy. PMID:27686718

  15. Observationally-based Metrics of Ocean Carbon and Biogeochemical Variables are Essential for Evaluating Earth System Model Projections

    NASA Astrophysics Data System (ADS)

    Russell, J. L.; Sarmiento, J. L.

    2017-12-01

    The Southern Ocean is central to the climate's response to increasing levels of atmospheric greenhouse gases as it ventilates a large fraction of the global ocean volume. Global coupled climate models and earth system models, however, vary widely in their simulations of the Southern Ocean and its role in, and response to, the ongoing anthropogenic forcing. Due to its complex water-mass structure and dynamics, Southern Ocean carbon and heat uptake depend on a combination of winds, eddies, mixing, buoyancy fluxes and topography. Understanding how the ocean carries heat and carbon into its interior and how the observed wind changes are affecting this uptake is essential to accurately projecting transient climate sensitivity. Observationally-based metrics are critical for discerning processes and mechanisms, and for validating and comparing climate models. As the community shifts toward Earth system models with explicit carbon simulations, more direct observations of important biogeochemical parameters, like those obtained from the biogeochemically-sensored floats that are part of the Southern Ocean Carbon and Climate Observations and Modeling project, are essential. One goal of future observing systems should be to create observationally-based benchmarks that will lead to reducing uncertainties in climate projections, and especially uncertainties related to oceanic heat and carbon uptake.

  16. Towards the creation of a European Network of Earth Observation Networks within GEO. The ConnectinGEO project.

    NASA Astrophysics Data System (ADS)

    Masó, Joan; Serral, Ivette; Menard, Lionel; Wald, Lucien; Nativi, Stefano; Plag, Hans-Peter; Jules-Plag, Shelley; Nüst, Daniel; Jirka, Simon; Pearlman, Jay; De Maziere, Martine

    2015-04-01

    ConnectinGEO (Coordinating an Observation Network of Networks EnCompassing saTellite and IN-situ to fill the Gaps in European Observations" is a new H2020 Coordination and Support Action with the primary goal of linking existing Earth Observation networks with science and technology (S&T) communities, the industry sector, the Group on Earth Observations (GEO), and Copernicus. ConnectinGEO aims to facilitate a broader and more accessible knowledge base to support the needs of GEO, its Societal Benefit Areas (SBAs) and the users of the Global Earth Observing System of Systems (GEOSS). A broad range of subjects from climate, natural resources and raw materials, to the emerging UN Sustainable Development Goals (SDGs) will be addressed. The project will generate a prioritized list of critical gaps within available observation data and models to translate observations into practice-relevant knowledge, based on stakeholder consultation and systematic analysis. Ultimately, it will increase coherency of European observation networks, increase the use of Earth observations for assessments and forecasts and inform the planning for future observation systems. ConnectinGEO will initiate a European Network of Earth Observation Networks (ENEON) that will encompass space-based, airborne and in-situ observations networks. ENEON will be composed by project partners representing thematic observation networks along with the GEOSS Science and Technology Stakeholder Network, GEO Communities of Practices, Copernicus services, Sentinel missions and in-situ support data representatives, representatives of the space-based, airborne and in-situ observations European networks (e.g. EPOS, EMSO and GROOM, etc), representatives of the industry sector and European and national funding agencies, in particular those participating in the future ERA-PlaNET. At the beginning, the ENEON will be created and managed by the project. Then the management will be transferred to the network itself to ensure

  17. Discover Earth

    NASA Technical Reports Server (NTRS)

    Steele, Colleen

    1998-01-01

    Discover Earth is a NASA-sponsored project for teachers of grades 5-12, designed to: (1) enhance understanding of the Earth as an integrated system; (2) enhance the interdisciplinary approach to science instruction; and (3) provide classroom materials that focus on those goals. Discover Earth is conducted by the Institute for Global Environmental Strategies in collaboration with Dr. Eric Barron, Director, Earth System Science Center, The Pennsylvania State University; and Dr. Robert Hudson, Chair, the Department of Meteorology, University of Maryland at College Park. The enclosed materials: (1) represent only part of the Discover Earth materials; (2) were developed by classroom teachers who are participating in the Discover Earth project; (3) utilize an investigative approach and on-line data; and (4) can be effectively adjusted to classrooms with greater/without technology access. The Discover Earth classroom materials focus on the Earth system and key issues of global climate change including topics such as the greenhouse effect, clouds and Earth's radiation balance, surface hydrology and land cover, and volcanoes and climate change. All the materials developed to date are available on line at (http://www.strategies.org) You are encouraged to submit comments and recommendations about these materials to the Discover Earth project manager, contact information is listed below. You are welcome to duplicate all these materials.

  18. Constructing a Cross-Domain Resource Inventory: Key Components and Results of the EarthCube CINERGI Project.

    NASA Astrophysics Data System (ADS)

    Zaslavsky, I.; Richard, S. M.; Malik, T.; Hsu, L.; Gupta, A.; Grethe, J. S.; Valentine, D. W., Jr.; Lehnert, K. A.; Bermudez, L. E.; Ozyurt, I. B.; Whitenack, T.; Schachne, A.; Giliarini, A.

    2015-12-01

    While many geoscience-related repositories and data discovery portals exist, finding information about available resources remains a pervasive problem, especially when searching across multiple domains and catalogs. Inconsistent and incomplete metadata descriptions, disparate access protocols and semantic differences across domains, and troves of unstructured or poorly structured information which is hard to discover and use are major hindrances toward discovery, while metadata compilation and curation remain manual and time-consuming. We report on methodology, main results and lessons learned from an ongoing effort to develop a geoscience-wide catalog of information resources, with consistent metadata descriptions, traceable provenance, and automated metadata enhancement. Developing such a catalog is the central goal of CINERGI (Community Inventory of EarthCube Resources for Geoscience Interoperability), an EarthCube building block project (earthcube.org/group/cinergi). The key novel technical contributions of the projects include: a) development of a metadata enhancement pipeline and a set of document enhancers to automatically improve various aspects of metadata descriptions, including keyword assignment and definition of spatial extents; b) Community Resource Viewers: online applications for crowdsourcing community resource registry development, curation and search, and channeling metadata to the unified CINERGI inventory, c) metadata provenance, validation and annotation services, d) user interfaces for advanced resource discovery; and e) geoscience-wide ontology and machine learning to support automated semantic tagging and faceted search across domains. We demonstrate these CINERGI components in three types of user scenarios: (1) improving existing metadata descriptions maintained by government and academic data facilities, (2) supporting work of several EarthCube Research Coordination Network projects in assembling information resources for their domains

  19. Design of Community Resource Inventories as a Component of Scalable Earth Science Infrastructure: Experience of the Earthcube CINERGI Project

    NASA Astrophysics Data System (ADS)

    Zaslavsky, I.; Richard, S. M.; Valentine, D. W., Jr.; Grethe, J. S.; Hsu, L.; Malik, T.; Bermudez, L. E.; Gupta, A.; Lehnert, K. A.; Whitenack, T.; Ozyurt, I. B.; Condit, C.; Calderon, R.; Musil, L.

    2014-12-01

    EarthCube is envisioned as a cyberinfrastructure that fosters new, transformational geoscience by enabling sharing, understanding and scientifically-sound and efficient re-use of formerly unconnected data resources, software, models, repositories, and computational power. Its purpose is to enable science enterprise and workforce development via an extensible and adaptable collaboration and resource integration framework. A key component of this vision is development of comprehensive inventories supporting resource discovery and re-use across geoscience domains. The goal of the EarthCube CINERGI (Community Inventory of EarthCube Resources for Geoscience Interoperability) project is to create a methodology and assemble a large inventory of high-quality information resources with standard metadata descriptions and traceable provenance. The inventory is compiled from metadata catalogs maintained by geoscience data facilities, as well as from user contributions. The latter mechanism relies on community resource viewers: online applications that support update and curation of metadata records. Once harvested into CINERGI, metadata records from domain catalogs and community resource viewers are loaded into a staging database implemented in MongoDB, and validated for compliance with ISO 19139 metadata schema. Several types of metadata defects detected by the validation engine are automatically corrected with help of several information extractors or flagged for manual curation. The metadata harvesting, validation and processing components generate provenance statements using W3C PROV notation, which are stored in a Neo4J database. Thus curated metadata, along with the provenance information, is re-published and accessed programmatically and via a CINERGI online application. This presentation focuses on the role of resource inventories in a scalable and adaptable information infrastructure, and on the CINERGI metadata pipeline and its implementation challenges. Key project

  20. Significant Impacts of Increasing Aridity on the Arid Soil Microbiome.

    PubMed

    Neilson, Julia W; Califf, Katy; Cardona, Cesar; Copeland, Audrey; van Treuren, Will; Josephson, Karen L; Knight, Rob; Gilbert, Jack A; Quade, Jay; Caporaso, J Gregory; Maier, Raina M

    2017-01-01

    Global deserts occupy one-third of the Earth's surface and contribute significantly to organic carbon storage, a process at risk in dryland ecosystems that are highly vulnerable to climate-driven ecosystem degradation. The forces controlling desert ecosystem degradation rates are poorly understood, particularly with respect to the relevance of the arid-soil microbiome. Here we document correlations between increasing aridity and soil bacterial and archaeal microbiome composition along arid to hyperarid transects traversing the Atacama Desert, Chile. A meta-analysis reveals that Atacama soil microbiomes exhibit a gradient in composition, are distinct from a broad cross-section of nondesert soils, and yet are similar to three deserts from different continents. Community richness and diversity were significantly positively correlated with soil relative humidity (SoilRH). Phylogenetic composition was strongly correlated with SoilRH, temperature, and electrical conductivity. The strongest and most significant correlations between SoilRH and phylum relative abundance were observed for Acidobacteria , Proteobacteria , Planctomycetes , Verrucomicrobia , and Euryarchaeota (Spearman's rank correlation [ r s ] = >0.81; false-discovery rate [ q ] = ≤0.005), characterized by 10- to 300-fold decreases in the relative abundance of each taxon. In addition, network analysis revealed a deterioration in the density of significant associations between taxa along the arid to hyperarid gradient, a pattern that may compromise the resilience of hyperarid communities because they lack properties associated with communities that are more integrated. In summary, results suggest that arid-soil microbiome stability is sensitive to aridity as demonstrated by decreased community connectivity associated with the transition from the arid class to the hyperarid class and the significant correlations observed between soilRH and both diversity and the relative abundances of key microbial phyla

  1. Project Planet Earth: A Joint Project Between the NASA/Goddard Space Flight Center and the Girl Scouts of Central Maryland

    NASA Technical Reports Server (NTRS)

    Mattoo, Shana; Remer, Lorraine; Anderson, Terry; Johnson, Courtrina; Lau, William K. M. (Technical Monitor)

    2001-01-01

    Scientists of the NASA/GSFC and the staff of the Girl Scouts of Central Maryland (GSCM) have teamed up to introduce more girls and young women to earth system science. The girls now have the opportunity to earn the specially designed Planet Earth Council Patch. The Patch program includes a set of requirements tailored to the specific age level of the girl and the resource material to help the girl complete the requirements. At completion of the requirements the girl is awarded a patch to sew onto the back of her sash or vest. Girls do hands-on physical experiments, practice taking data, visit science centers and perform skits in order to complete the requirements. In addition to the Patch program, Project Planet Earth continues to encourage strong collaboration between the Girl Scouts of Maryland and NASA/GSFC. Girls volunteer at the GSFC visitor center during community events and in turn scientists are called on as keynote speakers and consultants for the Council. A special science interest group is forming for the teenage Girl Scouts of the Council that will network with scientists and help these young women pursue their interests, find internships and make career decisions.

  2. Microbiome engineering: Current applications and its future.

    PubMed

    Foo, Jee Loon; Ling, Hua; Lee, Yung Seng; Chang, Matthew Wook

    2017-03-01

    Microbiomes exist in all ecosystems and are composed of diverse microbial communities. Perturbation to microbiomes brings about undesirable phenotypes in the hosts, resulting in diseases and disorders, and disturbs the balance of the associated ecosystems. Engineering of microbiomes can be used to modify structures of the microbiota and restore ecological balance. Consequently, microbiome engineering has been employed for improving human health and agricultural productivity. The importance and current applications of microbiome engineering, particularly in humans, animals, plants and soil is reviewed. Furthermore, we explore the challenges in engineering microbiome and the future of this field, thus providing perspectives and outlook of microbiome engineering. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. NASA Global Hawk Project Update and Future Plans: A New Tool for Earth Science Research

    NASA Technical Reports Server (NTRS)

    Naftel, Chris

    2009-01-01

    Science objectives include: First demonstration of the Global Hawk unmanned aircraft system (UAS) for NASA and NOAA Earth science research and applications; Validation of instruments on-board the Aura satellite; Exploration of trace gases, aerosols, and dynamics of remote upper Troposphere/lower Stratosphere regions; Sample polar vortex fragments and atmospheric rivers; Risk reduction for future missions that will study hurricanes and atmospheric rivers.

  4. Testing the Neutral Theory of Biodiversity with Human Microbiome Datasets.

    PubMed

    Li, Lianwei; Ma, Zhanshan Sam

    2016-08-16

    The human microbiome project (HMP) has made it possible to test important ecological theories for arguably the most important ecosystem to human health-the human microbiome. Existing limited number of studies have reported conflicting evidence in the case of the neutral theory; the present study aims to comprehensively test the neutral theory with extensive HMP datasets covering all five major body sites inhabited by the human microbiome. Utilizing 7437 datasets of bacterial community samples, we discovered that only 49 communities (less than 1%) satisfied the neutral theory, and concluded that human microbial communities are not neutral in general. The 49 positive cases, although only a tiny minority, do demonstrate the existence of neutral processes. We realize that the traditional doctrine of microbial biogeography "Everything is everywhere, but the environment selects" first proposed by Baas-Becking resolves the apparent contradiction. The first part of Baas-Becking doctrine states that microbes are not dispersal-limited and therefore are neutral prone, and the second part reiterates that the freely dispersed microbes must endure selection by the environment. Therefore, in most cases, it is the host environment that ultimately shapes the community assembly and tip the human microbiome to niche regime.

  5. Testing the Neutral Theory of Biodiversity with Human Microbiome Datasets

    PubMed Central

    Li, Lianwei; Ma, Zhanshan (Sam)

    2016-01-01

    The human microbiome project (HMP) has made it possible to test important ecological theories for arguably the most important ecosystem to human health—the human microbiome. Existing limited number of studies have reported conflicting evidence in the case of the neutral theory; the present study aims to comprehensively test the neutral theory with extensive HMP datasets covering all five major body sites inhabited by the human microbiome. Utilizing 7437 datasets of bacterial community samples, we discovered that only 49 communities (less than 1%) satisfied the neutral theory, and concluded that human microbial communities are not neutral in general. The 49 positive cases, although only a tiny minority, do demonstrate the existence of neutral processes. We realize that the traditional doctrine of microbial biogeography “Everything is everywhere, but the environment selects” first proposed by Baas-Becking resolves the apparent contradiction. The first part of Baas-Becking doctrine states that microbes are not dispersal-limited and therefore are neutral prone, and the second part reiterates that the freely dispersed microbes must endure selection by the environment. Therefore, in most cases, it is the host environment that ultimately shapes the community assembly and tip the human microbiome to niche regime. PMID:27527985

  6. Monitoring of Space and Earth electromagnetic environment by MAGDAS project: Collaboration with IKIR - Introduction to ICSWSE/MAGDAS project

    NASA Astrophysics Data System (ADS)

    Yoshikawa, Akimasa; Fujimoto, Akiko; Ikeda, Akihiro; Uozumi, Teiji; Abe, Shuji

    2017-10-01

    For study of coupling processes in the Solar-Terrestrial System, International Center for Space Weather Science and Education (ICSWSE), Kyushu University has developed a real time magnetic data acquisition system (the MAGDAS project) around the world. The number of observational sites is increasing every year with the collaboration of host countries. Now at this time, the MAGDAS Project has installed 78 real time magnetometers - so it is the largest magnetometer array in the world. The history of global observation at Kyushu University is over 30 years and number of developed observational sites is over 140. Especially, Collaboration between IKIR is extended back to 1990's. Now a time, we are operating Flux-gate magnetometer and FM-CW Radar. It is one of most important collaboration for space weather monitoring. By using MAGDAS data, ICSWSE produces many types of space weather index, such as EE-index (for monitoring long tern and shot term variation of equatorial electrojet), Pc5 index (for monitoring solar-wind velocity and high energy electron flux), Sq-index (for monitoring global change of ionospheric low and middle latitudinal current system), and Pc3 index (for monitoring of plasma density variation at low latitudes). In this report, we will introduce recent development of MAGDAS/ICSWSE Indexes project and topics for new open policy for MAGDAS data will be also discussed.

  7. Childhood Malnutrition and the Intestinal Microbiome Malnutrition and the microbiome

    PubMed Central

    Kane, Anne V.; Dinh, Duy M.; Ward, Honorine D.

    2015-01-01

    Malnutrition contributes to almost half of all deaths in children under the age of 5 years, particularly those who live in resource-constrained areas. Those who survive frequently suffer from long-term sequelae including growth failure and neurodevelopmental impairment. Malnutrition is part of a vicious cycle of impaired immunity, recurrent infections and worsening malnutrition. Recently, alterations in the gut microbiome have also been strongly implicated in childhood malnutrition. It has been suggested that malnutrition may delay the normal development of the gut microbiota in early childhood or force it towards an altered composition that lacks the required functions for healthy growth and/or increases the risk for intestinal inflammation. This review addresses our current understanding of the beneficial contributions of gut microbiota to human nutrition (and conversely the potential role of changes in that community to malnutrition), the process of acquiring an intestinal microbiome, potential influences of malnutrition on the developing microbiota and the evidence directly linking alterations in the intestinal microbiome to childhood malnutrition. We review recent studies on the association between alterations in the intestinal microbiome and early childhood malnutrition and discuss them in the context of implications for intervention or prevention of the devastation caused by malnutrition. PMID:25356748

  8. The Serpentinite Subsurface Microbiome

    NASA Astrophysics Data System (ADS)

    Schrenk, M. O.; Nelson, B. Y.; Brazelton, W. J.

    2011-12-01

    Microbial habitats hosted in ultramafic rocks constitute substantial, globally-distributed portions of the subsurface biosphere, occurring both on the continents and beneath the seafloor. The aqueous alteration of ultramafics, in a process known as serpentinization, creates energy rich, high pH conditions, with low concentrations of inorganic carbon which place fundamental constraints upon microbial metabolism and physiology. Despite their importance, very few studies have attempted to directly access and quantify microbial activities and distributions in the serpentinite subsurface microbiome. We have initiated microbiological studies of subsurface seeps and rocks at three separate continental sites of serpentinization in Newfoundland, Italy, and California and compared these results to previous analyses of the Lost City field, near the Mid-Atlantic Ridge. In all cases, microbial cell densities in seep fluids are extremely low, ranging from approximately 100,000 to less than 1,000 cells per milliliter. Culture-independent analyses of 16S rRNA genes revealed low-diversity microbial communities related to Gram-positive Firmicutes and hydrogen-oxidizing bacteria. Interestingly, unlike Lost City, there has been little evidence for significant archaeal populations in the continental subsurface to date. Culturing studies at the sites yielded numerous alkaliphilic isolates on nutrient-rich agar and putative iron-reducing bacteria in anaerobic incubations, many of which are related to known alkaliphilic and subsurface isolates. Finally, metagenomic data reinforce the culturing results, indicating the presence of genes associated with organotrophy, hydrogen oxidation, and iron reduction in seep fluid samples. Our data provide insight into the lifestyles of serpentinite subsurface microbial populations and targets for future quantitative exploration using both biochemical and geochemical approaches.

  9. Microbiome and Gluten.

    PubMed

    Sanz, Yolanda

    2015-01-01

    Celiac disease (CD) is a frequent chronic inflammatory enteropathy caused by gluten in genetically predisposed individuals that carry disease susceptibility genes (HLA-DQ2/8). These genes are present in about 30-40% of the general population, but only a small percentage of carriers develops CD. Gluten is the key environmental trigger of CD, but its intake does not fully explain disease onset; indeed, an increased number of cases experience gluten intolerance in late adulthood after many years of gluten exposure. Consequently, additional environmental factors seem to be involved in CD. Epidemiological studies indicate that common perinatal and early postnatal factors influence both CD risk and intestinal microbiota structure. Prospective studies in healthy infants at risk of developing CD also reveal that the HLA-DQ genotype, in conjunction with other environmental factors, influences the microbiota composition. Furthermore, CD patients have imbalances in the intestinal microbiota (dysbiosis), which are not fully normalized despite their adherence to a gluten-free diet. Therefore, it is hypothesized that the disease can promote dysbiosis that aggravates CD pathogenesis, and dysbiosis, in turn, can initiate and sustain inflammation through the expansion of proinflammatory pathobionts and decline of anti-inflammatory mutualistic bacteria. Studies in experimental models are also contributing to understand the role of intestinal bacteria and its interactions with a predisposed genotype in promoting CD. Advances in this area could aid in the development of microbiome-informed intervention strategies that optimize the partnership between the gut microbiota and host immunity for improving CD management. © 2015 S. Karger AG, Basel.

  10. The TOPOMOD-ITN project: unravel the origin of Earth's topography from modelling deep-surface processes

    NASA Astrophysics Data System (ADS)

    Faccenna, C.; Funiciello, F.

    2012-04-01

    EC-Marie Curie Initial Training Networks (ITN) projects aim to improve the career perspectives of young generations of researchers. Institutions from both academic and industry sectors form a collaborative network to recruit research fellows and provide them with opportunities to undertake research in the context of a joint research training program. In this frame, TOPOMOD - one of the training activities of EPOS, the new-born European Research Infrastructure for Geosciences - is a funded ITN project designed to investigate and model how surface processes interact with crustal tectonics and mantle convection to originate and develop topography of the continents over a wide range of spatial and temporal scales. The multi-disciplinary approach combines geophysics, geochemistry, tectonics and structural geology with advanced geodynamic numerical/analog modelling. TOPOMOD involves 8 European research teams internationally recognized for their excellence in complementary fields of Earth Sciences (Roma TRE, Utrecht, GFZ, ETH, Cambridge, Durham, Rennes, Barcelona), to which are associated 5 research institutions (CNR-Italy, Univ. Parma, Univ. Lausanne, Univ. Montpellier, Univ. Mainz) , 3 high-technology enterprises (Malvern Instruments, TNO, G.O. Logical Consulting) and 1 large multinational oil and gas company (ENI). This unique network places emphasis in experience-based training increasing the impact and international visibility of European research in modeling. Long-term collaboration and synergy are established among the overmentioned research teams through 15 cross-disciplinary research projects that combine case studies in well-chosen target areas from the Mediterranean, the Middle and Far East, west Africa, and South America, with new developments in structural geology, geomorphology, seismology, geochemistry, InSAR, laboratory and numerical modelling of geological processes from the deep mantle to the surface. These multidisciplinary projects altogether aim to

  11. Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis.

    PubMed

    Weber, Nick; Liou, David; Dommer, Jennifer; MacMenamin, Philip; Quiñones, Mariam; Misner, Ian; Oler, Andrew J; Wan, Joe; Kim, Lewis; Coakley McCarthy, Meghan; Ezeji, Samuel; Noble, Karlynn; Hurt, Darrell E

    2018-04-15

    Widespread interest in the study of the microbiome has resulted in data proliferation and the development of powerful computational tools. However, many scientific researchers lack the time, training, or infrastructure to work with large datasets or to install and use command line tools. The National Institute of Allergy and Infectious Diseases (NIAID) has created Nephele, a cloud-based microbiome data analysis platform with standardized pipelines and a simple web interface for transforming raw data into biological insights. Nephele integrates common microbiome analysis tools as well as valuable reference datasets like the healthy human subjects cohort of the Human Microbiome Project (HMP). Nephele is built on the Amazon Web Services cloud, which provides centralized and automated storage and compute capacity, thereby reducing the burden on researchers and their institutions. https://nephele.niaid.nih.gov and https://github.com/niaid/Nephele. darrell.hurt@nih.gov.

  12. Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis

    PubMed Central

    Weber, Nick; Liou, David; Dommer, Jennifer; MacMenamin, Philip; Quiñones, Mariam; Misner, Ian; Oler, Andrew J; Wan, Joe; Kim, Lewis; Coakley McCarthy, Meghan; Ezeji, Samuel; Noble, Karlynn; Hurt, Darrell E

    2018-01-01

    Abstract Motivation Widespread interest in the study of the microbiome has resulted in data proliferation and the development of powerful computational tools. However, many scientific researchers lack the time, training, or infrastructure to work with large datasets or to install and use command line tools. Results The National Institute of Allergy and Infectious Diseases (NIAID) has created Nephele, a cloud-based microbiome data analysis platform with standardized pipelines and a simple web interface for transforming raw data into biological insights. Nephele integrates common microbiome analysis tools as well as valuable reference datasets like the healthy human subjects cohort of the Human Microbiome Project (HMP). Nephele is built on the Amazon Web Services cloud, which provides centralized and automated storage and compute capacity, thereby reducing the burden on researchers and their institutions. Availability and implementation https://nephele.niaid.nih.gov and https://github.com/niaid/Nephele Contact darrell.hurt@nih.gov PMID:29028892

  13. The Right Chemistry. Lawn Care Project Brings Science down to Earth.

    ERIC Educational Resources Information Center

    Dollar, David

    1992-01-01

    At Southwest High School in Fort Worth, Texas, an applied learning project enables chemistry students to determine the most effective, economical, and environmentally safe fertilizer for the lawns of schools in the district. (SK)

  14. Collaborative Project: Improving the Representation of Coastal and Estuarine Processes in Earth System Models

    SciT

    Bryan, Frank; Dennis, John; MacCready, Parker

    This project aimed to improve long term global climate simulations by resolving and enhancing the representation of the processes involved in the cycling of freshwater through estuaries and coastal regions. This was a collaborative multi-institution project consisting of physical oceanographers, climate model developers, and computational scientists. It specifically targeted the DOE objectives of advancing simulation and predictive capability of climate models through improvements in resolution and physical process representation.

  15. Final Report Collaborative Project: Improving the Representation of Coastal and Estuarine Processes in Earth System Models

    SciT

    Bryan, Frank; Dennis, John; MacCready, Parker

    This project aimed to improve long term global climate simulations by resolving and enhancing the representation of the processes involved in the cycling of freshwater through estuaries and coastal regions. This was a collaborative multi-institution project consisting of physical oceanographers, climate model developers, and computational scientists. It specifically targeted the DOE objectives of advancing simulation and predictive capability of climate models through improvements in resolution and physical process representation.

  16. Characterization of the human gut microbiome during travelers' diarrhea

    PubMed Central

    Youmans, Bonnie P; Ajami, Nadim J; Jiang, Zhi-Dong; Campbell, Frederick; Wadsworth, W Duncan; Petrosino, Joseph F; DuPont, Herbert L; Highlander, Sarah K

    2015-01-01

    Alterations in the gut microbiota are correlated with ailments such as obesity, inflammatory bowel disease, and diarrhea. Up to 60% of individuals traveling from industrialized to developing countries acquire a form of secretory diarrhea known as travelers' diarrhea (TD), and enterotoxigenic Escherichia coli (ETEC) and norovirus (NoV) are the leading causative pathogens. Presumably, TD alters the gut microbiome, however the effect of TD on gut communities has not been studied. We report the first analysis of bacterial gut populations associated with TD. We examined and compared the gut microbiomes of individuals who developed TD associated with ETEC, NoV, or mixed pathogens, and TD with no pathogen identified, to healthy travelers. We observed a signature dysbiotic gut microbiome profile of high Firmicutes:Bacteroidetes ratios in the travelers who developed diarrhea, regardless of etiologic agent or presence of a pathogen. There was no significant difference in α-diversity among travelers. The bacterial composition of the microbiota of the healthy travelers was similar to the diarrheal groups, however the β-diversity of the healthy travelers was significantly different than any pathogen-associated TD group. Further comparison of the healthy traveler microbiota to those from healthy subjects who were part of the Human Microbiome Project also revealed a significantly higher Firmicutes:Bacteriodetes ratio in the healthy travelers and significantly different β-diversity. Thus, the composition of the gut microbiome in healthy, diarrhea-free travelers has characteristics of a dysbiotic gut, suggesting that these alterations could be associated with factors such as travel. PMID:25695334

  17. Characterization of the human gut microbiome during travelers' diarrhea.

    PubMed

    Youmans, Bonnie P; Ajami, Nadim J; Jiang, Zhi-Dong; Campbell, Frederick; Wadsworth, W Duncan; Petrosino, Joseph F; DuPont, Herbert L; Highlander, Sarah K

    2015-01-01

    Alterations in the gut microbiota are correlated with ailments such as obesity, inflammatory bowel disease, and diarrhea. Up to 60% of individuals traveling from industrialized to developing countries acquire a form of secretory diarrhea known as travelers' diarrhea (TD), and enterotoxigenic Escherichia coli (ETEC) and norovirus (NoV) are the leading causative pathogens. Presumably, TD alters the gut microbiome, however the effect of TD on gut communities has not been studied. We report the first analysis of bacterial gut populations associated with TD. We examined and compared the gut microbiomes of individuals who developed TD associated with ETEC, NoV, or mixed pathogens, and TD with no pathogen identified, to healthy travelers. We observed a signature dysbiotic gut microbiome profile of high Firmicutes:Bacteroidetes ratios in the travelers who developed diarrhea, regardless of etiologic agent or presence of a pathogen. There was no significant difference in α-diversity among travelers. The bacterial composition of the microbiota of the healthy travelers was similar to the diarrheal groups, however the β-diversity of the healthy travelers was significantly different than any pathogen-associated TD group. Further comparison of the healthy traveler microbiota to those from healthy subjects who were part of the Human Microbiome Project also revealed a significantly higher Firmicutes:Bacteriodetes ratio in the healthy travelers and significantly different β-diversity. Thus, the composition of the gut microbiome in healthy, diarrhea-free travelers has characteristics of a dysbiotic gut, suggesting that these alterations could be associated with factors such as travel.

  18. The mobile GeoBus outreach project: hands-on Earth and Mars activities for secondary schools in the UK

    NASA Astrophysics Data System (ADS)

    Robinson, Ruth; Pike, Charlotte; Roper, Kathryn

    2015-04-01

    GeoBus (www.geobus.org.uk) is an educational outreach project that was developed in 2012 by the Department of Earth and Environmental Sciences at the University of St Andrews, and it is sponsored jointly by industry and the UK Research Councils (NERC and EPSRC). The aims of GeoBus are to support the teaching of Earth Science in secondary schools by providing teaching resources that are not readily available to educators, to inspire young learners by incorporating new science research outcomes in teaching activities, and to provide a bridge between industry, higher education institutions, research councils and schools. Since its launch, GeoBus has visited over 160 different schools across the length and breadth of Scotland. Just under 35,000 pupils have been involved in practical hands-on Earth science learning activities since the project began in 2012, including many in remote and disadvantaged regions. The resources that GeoBus brings to schools include all the materials and equipment needed to run 50 - 80 minute workshops, and half- or whole-day Enterprise Challenges and field excursions. Workshops are aimed at a class of up to 30 pupils and topics include minerals, rocks, fossils, geological time, natural resources, climate change, volcanoes, earthquakes, and geological mapping. As with all GeoBus activities, the inclusion of equipment and technology otherwise unavailable to schools substantially increases the engagement of pupils in workshops. Field excursions are increasingly popular, as many teachers have little or no field trainng and feel unable to lead this type of activity. The excursions comprise half or full day sessions for up to 30 pupils and are tailored to cover the local geology or geomorphology. Enterprise Challenge are half or full day sessions for up to 100 pupils. Topics include "Journey to Mars", "Scotland's Rocks", "Drilling for Oil", and "Renewable Energy". Both of the energy Enterprise Challenges were designed to incorporates ideas and

  19. The Mission Accessible Near-Earth Object Survey (MANOS): Project Overview

    NASA Astrophysics Data System (ADS)

    Moskovitz, Nicholas; Polishook, David; Thomas, Cristina; Willman, Mark; DeMeo, Francesca; Mommert, Michael; Endicott, Thomas; Trilling, David; Binzel, Richard; Hinkle, Mary; Siu, Hosea; Neugent, Kathryn; Christensen, Eric; Person, Michael; Burt, Brian; Grundy, Will; Roe, Henry; Abell, Paul; Busch, Michael

    2014-11-01

    The Mission Accessible Near-Earth Object Survey (MANOS) began in August 2013 as a multi-year physical characterization survey that was awarded survey status by NOAO. MANOS will target several hundred mission-accessible NEOs across visible and near-infrared wavelengths, ultimately providing a comprehensive catalog of physical properties (astrometry, light curves, spectra). Particular focus is paid to sub-km NEOs, for which little data currently exists. These small bodies are essential to understanding the link between meteorites and asteroids, pose the most immediate impact hazard to the Earth, and are highly relevant to a variety of planetary mission scenarios. Accessing these targets is enabled through a combination of classical, queue, and target-of-opportunity observations carried out at 1- to 8-meter class facilities in both the northern and southern hemispheres. The MANOS observing strategy is specifically designed to rapidly characterize newly discovered NEOs before they fade beyond observational limits. MANOS will provide major advances in our understanding of the NEO population as a whole and for specific objects of interest. Here we present an overview of the survey, progress to date, and early science highlights including: (1) an estimate of the taxonomic distribution of spectral types for NEOs smaller than ~100 meters, (2) the distribution of rotational properties for approximately 100 previously unstudied objects, (3) models for the dynamical evolution of the overall NEO population over the past 0.5 Myr, and (4) progress in developing a new set of online tools at asteroid.lowell.edu that will enable near realtime public dissemination of our data while providing a portal to facilitate coordination efforts within the small body observer community.MANOS is supported through telescope allocations from NOAO and Lowell Observatory. We acknowledge funding support from an NSF Astronomy and Astrophysics Postdoctoral Fellowship to N. Moskovitz and NASA NEOO grant

  20. Making Earth Science Data Records for Use in Research Environments (MEaSUREs) Projects Data and Services at the GES DISC

    NASA Technical Reports Server (NTRS)

    Vollmer, Bruce E.; Ostrenga, D.; Savtchenko, A.; Johnson, J.; Wei, J.; Teng, W.; Gerasimov, I.

    2011-01-01

    NASA's Earth Science Program is dedicated to advancing Earth remote sensing and pioneering the scientific use of satellite measurements to improve human understanding of our home planet. Through the MEaSUREs Program, NASA is continuing its commitment to expand understanding of the Earth system using consistent data records. Emphasis is on linking together multiple data sources to form coherent time-series, and facilitating the use of extensive data in the development of comprehensive Earth system models. A primary focus of the MEaSUREs Program is the creation of Earth System Data Records (ESDRs). An ESDR is defined as a unified and coherent set of observations of a given parameter of the Earth system, which is optimized to meet specific requirements for addressing science questions. These records are critical for understanding Earth System processes; for the assessment of variability, long-term trends, and change in the Earth System; and for providing input and validation means to modeling efforts. Seven MEaSUREs projects will be archived and distributed through services at the Goddard Earth Sciences Data and Information Services Center (GES DISC).

  1. Review: Maternal health and the placental microbiome.

    PubMed

    Pelzer, Elise; Gomez-Arango, Luisa F; Barrett, Helen L; Nitert, Marloes Dekker

    2017-06-01

    Over the past decade, the role of the microbiome in regulating metabolism, immune function and behavior in humans has become apparent. It has become clear that the placenta is not a sterile organ, but rather has its own endogenous microbiome. The composition of the placental microbiome is distinct from that of the vagina and has been reported to resemble the oral microbiome. Compared to the gut microbiome, the placental microbiome exhibits limited microbial diversity. This review will focus on the current understanding of the placental microbiota in normal healthy pregnancy and also in disease states including preterm birth, chorioamnionitis and maternal conditions such as obesity, gestational diabetes mellitus and preeclampsia. Factors known to alter the composition of the placental microbiota will be discussed in the final part of this review. Copyright © 2016. Published by Elsevier Ltd.

  2. Microbiome in parturition and preterm birth.

    PubMed

    Mysorekar, Indira U; Cao, Bin

    2014-01-01

    Preterm parturition is a one of the most significant global maternal-child health problem. In recent years, there has been an explosion in reports on a role for microbiomes (i.e., a microbial biomass) on a plethora of physiologic and pathologic human conditions. This review aims to describe our current understanding of the microbiome and its impact on parturition, with particular emphasis on preterm birth. We will focus on the roles of vaginal and oral mucosal microbiomes in premature parturition and describe the state-of-the-art methodologies used in microbiome studies. Next, we will present new studies on a potential microbiome in the placenta and how it may affect pregnancy outcomes. Finally, we will propose that host genetic factors can perturb the normal "pregnancy microbiome" and trigger adverse pregnancy outcomes. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

  3. Extending netCDF and CF conventions to support enhanced Earth Observation Ontology services: the Prod-Trees project

    NASA Astrophysics Data System (ADS)

    Mazzetti, Paolo; Valentin, Bernard; Koubarakis, Manolis; Nativi, Stefano

    2013-04-01

    Access to Earth Observation products remains not at all straightforward for end users in most domains. Semantically-enabled search engines, generally accessible through Web portals, have been developed. They allow searching for products by selecting application-specific terms and specifying basic geographical and temporal filtering criteria. Although this mostly suits the needs of the general public, the scientific communities require more advanced and controlled means to find products. Ranges of validity, traceability (e.g. origin, applied algorithms), accuracy, uncertainty, are concepts that are typically taken into account in research activities. The Prod-Trees (Enriching Earth Observation Ontology Services using Product Trees) project will enhance the CF-netCDF product format and vocabulary to allow storing metadata that better describe the products, and in particular EO products. The project will bring a standardized solution that permits annotating EO products in such a manner that official and third-party software libraries and tools will be able to search for products using advanced tags and controlled parameter names. Annotated EO products will be automatically supported by all the compatible software. Because the entire product information will come from the annotations and the standards, there will be no need for integrating extra components and data structures that have not been standardized. In the course of the project, the most important and popular open-source software libraries and tools will be extended to support the proposed extensions of CF-netCDF. The result will be provided back to the respective owners and maintainers for ensuring the best dissemination and adoption of the extended format. The project, funded by ESA, has started in December 2012 and will end in May 2014. It is coordinated by Space Applications Services, and the Consortium includes CNR-IIA and the National and Kapodistrian University of Athens. The first activities included

  4. Applying the design-build-test paradigm in microbiome engineering.

    PubMed

    Pham, Hoang Long; Ho, Chun Loong; Wong, Adison; Lee, Yung Seng; Chang, Matthew Wook

    2017-12-01

    The recently discovered roles of human microbiome in health and diseases have inspired research efforts across many disciplines to engineer microbiome for health benefits. In this review, we highlight recent progress in human microbiome research and how modifications to the microbiome could result in implications to human health. Furthermore, we discuss the application of a 'design-build-test' framework to expedite microbiome engineering efforts by reviewing current literature on three key aspects: design principles to engineer the human microbiome, methods to engineer microbiome with desired functions, and analytical techniques to examine complex microbiome samples. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Development of a High-Resolution Climate Model for Future Climate Change Projection on the Earth Simulator

    NASA Astrophysics Data System (ADS)

    Kanzawa, H.; Emori, S.; Nishimura, T.; Suzuki, T.; Inoue, T.; Hasumi, H.; Saito, F.; Abe-Ouchi, A.; Kimoto, M.; Sumi, A.

    2002-12-01

    The fastest supercomputer of the world, the Earth Simulator (total peak performance 40TFLOPS) has recently been available for climate researches in Yokohama, Japan. We are planning to conduct a series of future climate change projection experiments on the Earth Simulator with a high-resolution coupled ocean-atmosphere climate model. The main scientific aims for the experiments are to investigate 1) the change in global ocean circulation with an eddy-permitting ocean model, 2) the regional details of the climate change including Asian monsoon rainfall pattern, tropical cyclones and so on, and 3) the change in natural climate variability with a high-resolution model of the coupled ocean-atmosphere system. To meet these aims, an atmospheric GCM, CCSR/NIES AGCM, with T106(~1.1o) horizontal resolution and 56 vertical layers is to be coupled with an oceanic GCM, COCO, with ~ 0.28ox 0.19o horizontal resolution and 48 vertical layers. This coupled ocean-atmosphere climate model, named MIROC, also includes a land-surface model, a dynamic-thermodynamic seaice model, and a river routing model. The poles of the oceanic model grid system are rotated from the geographic poles so that they are placed in Greenland and Antarctic land masses to avoild the singularity of the grid system. Each of the atmospheric and the oceanic parts of the model is parallelized with the Message Passing Interface (MPI) technique. The coupling of the two is to be done with a Multi Program Multi Data (MPMD) fashion. A 100-model-year integration will be possible in one actual month with 720 vector processors (which is only 14% of the full resources of the Earth Simulator).

  6. The Mission Accessible Near-Earth Object Survey (MANOS): Project Status

    NASA Astrophysics Data System (ADS)

    Moskovitz, Nicholas; Thirouin, Audrey; Mommert, Michael; Thomas, Cristina A.; Skiff, Brian; Polishook, David; Burt, Brian; Trilling, David E.; DeMeo, Francesca E.; Binzel, Richard P.; Christensen, Eric J.; Willman, Mark; Hinkle, Mary

    2017-10-01

    The Mission Accessible Near-Earth Object Survey (MANOS) is a physical characterization survey of sub-km, low delta-v, newly discovered near-Earth objects (NEOs). MANOS aims to collect astrometry, lightcurve photometry, and reflectance spectra for a representative sample of these important target of opportunity objects in a rarely observed size range. We employ a diverse set of large aperture (2-8 meter) telescopes and observing modes (queue, remote, classical) to overcome the challenge of observing faint NEOs moving at high non-sidereal rates with short observing windows. We target approximately 10% of newly discovered NEOs every month for follow-up characterization.The first generation MANOS ran from late 2013 to early 2017, using telescopes at Lowell Observatory, NOAO, and the University of Hawaii. This resulted in the collection of data for over 500 targets. These data are continuing to provide new insights into the NEO population as a whole as well as for individual objects of interest. Science highlights include identification of the four fastest rotating minor planets found to date with rotation periods under 20 seconds, constraints on the distribution of NEO morphologies as quantified by de-biased estimates for lightcurve-derived axis ratios, and the compositional distribution of NEOs at sizes under 100 meters.The second generation MANOS will begin in late 2017 and will employ much of the same strategies while continuing to build a comprehensive dataset of NEO physical properties. This will grow the MANOS sample to ~1000 objects and provide the means to better address key questions related to understanding the physical properties of NEOs, their viability as exploration mission targets, and their relationship to Main Belt asteroids and meteorites. This continuation of MANOS will include an increased focus on spectroscopic observations at near-IR wavelengths using a new instrument called NIHTS (the Near-Infrared High-Throughput Spectrograph) at Lowell

  7. The Lung Microbiome in Moderate and Severe Chronic Obstructive Pulmonary Disease

    PubMed Central

    Pragman, Alexa A.; Kim, Hyeun Bum; Reilly, Cavan S.; Wendt, Christine; Isaacson, Richard E.

    2012-01-01

    Chronic obstructive pulmonary disease (COPD) is an inflammatory disorder characterized by incompletely reversible airflow obstruction. Bacterial infection of the lower respiratory tract contributes to approximately 50% of COPD exacerbations. Even during periods of stable lung function, the lung harbors a community of bacteria, termed the microbiome. The role of the lung microbiome in the pathogenesis of COPD remains unknown. The COPD lung microbiome, like the healthy lung microbiome, appears to reflect microaspiration of oral microflora. Here we describe the COPD lung microbiome of 22 patients with Moderate or Severe COPD compared to 10 healthy control patients. The composition of the lung microbiomes was determined using 454 pyrosequencing of 16S rDNA found in bronchoalveolar lavage fluid. Sequences were analyzed using mothur, Ribosomal Database Project, Fast UniFrac, and Metastats. Our results showed a significant increase in microbial diversity with the development of COPD. The main phyla in all samples were Actinobacteria, Firmicutes, and Proteobacteria. Principal coordinate analyses demonstrated separation of control and COPD samples, but samples did not cluster based on disease severity. However, samples did cluster based on the use of inhaled corticosteroids and inhaled bronchodilators. Metastats analyses demonstrated an increased abundance of several oral bacteria in COPD samples. PMID:23071781

  8. The Large Synoptic Survey Telescope: Projected Near-Earth Object Discovery Performance

    NASA Technical Reports Server (NTRS)

    Chesley, Steven R.; Veres, Peter

    2016-01-01

    The Large Synoptic Survey Telescope (LSST) is a large-aperture, wide-field survey that has the potential to detect millions of asteroids. LSST is under construction with survey operations slated to begin in 2022. We describe an independent study to assess the performance of LSST for detecting and cataloging near-Earth objects (NEOs). A significant component of the study will be to assess the survey's ability to link observations of a single object from among the large numbers of false detections and detections of other objects. We also will explore the survey's basic performance in terms of fraction of NEOs discovered and cataloged, both for the planned baseline survey, but also for enhanced surveys that are more carefully tuned for NEO search, generally at the expense of other science drivers. Preliminary results indicate that with successful linkage under the current baseline survey LSST would discover approximately 65% of NEOs with absolute magnitude H is less than 22, which corresponds approximately to 140m diameter.

  9. Insights of the dental calculi microbiome of pre-Columbian inhabitants from Puerto Rico

    PubMed Central

    Narganes-Storde, Yvonne; Toranzos, Gary A.; Cano, Raul J.

    2017-01-01

    Background The study of ancient microorganisms in mineralized dental plaque or calculi is providing insights into microbial evolution, as well as lifestyles and disease states of extinct cultures; yet, little is still known about the oral microbial community structure and function of pre-Columbian Caribbean cultures. In the present study, we investigated the dental calculi microbiome and predicted function of one of these cultures, known as the Saladoid. The Saladoids were horticulturalists that emphasized root-crop production. Fruits, as well as small marine and terrestrial animals were also part of the Saladoid diet. Methods Dental calculi samples were recovered from the archaeological site of Sorcé, in the municipal island of Vieques, Puerto Rico, characterized using 16S rRNA gene high-throughput sequencing, and compared to the microbiome of previously characterized coprolites of the same culture, as well modern plaque, saliva and stool microbiomes available from the Human Microbiome Project. Results Actinobacteria, Proteobacteria and Firmicutes comprised the majority of the Saladoid dental calculi microbiome. The Saladoid dental calculi microbiome was distinct when compared to those of modern saliva and dental plaque, but showed the presence of common inhabitants of modern oral cavities including Streptococcus sp., Veillonella dispar and Rothia mucilaginosa. Cell motility, signal transduction and biosynthesis of other secondary metabolites may be unique features of the Saladoid microbiome. Discussion Results suggest that the Saladoid dental calculi microbiome structure and function may possibly reflect a horticulturalist lifestyle and distinct dietary habits. Results also open the opportunity to further elucidate oral disease states in extinct Caribbean cultures and extinct indigenous cultures with similar lifestyles. PMID:28480145

  10. Insights of the dental calculi microbiome of pre-Columbian inhabitants from Puerto Rico.

    PubMed

    Santiago-Rodriguez, Tasha M; Narganes-Storde, Yvonne; Chanlatte-Baik, Luis; Toranzos, Gary A; Cano, Raul J

    2017-01-01

    The study of ancient microorganisms in mineralized dental plaque or calculi is providing insights into microbial evolution, as well as lifestyles and disease states of extinct cultures; yet, little is still known about the oral microbial community structure and function of pre-Columbian Caribbean cultures. In the present study, we investigated the dental calculi microbiome and predicted function of one of these cultures, known as the Saladoid. The Saladoids were horticulturalists that emphasized root-crop production. Fruits, as well as small marine and terrestrial animals were also part of the Saladoid diet. Dental calculi samples were recovered from the archaeological site of Sorcé, in the municipal island of Vieques, Puerto Rico, characterized using 16S rRNA gene high-throughput sequencing, and compared to the microbiome of previously characterized coprolites of the same culture, as well modern plaque, saliva and stool microbiomes available from the Human Microbiome Project. Actinobacteria, Proteobacteria and Firmicutes comprised the majority of the Saladoid dental calculi microbiome. The Saladoid dental calculi microbiome was distinct when compared to those of modern saliva and dental plaque, but showed the presence of common inhabitants of modern oral cavities including Streptococcus sp., Veillonella dispar and Rothia mucilaginosa . Cell motility, signal transduction and biosynthesis of other secondary metabolites may be unique features of the Saladoid microbiome. Results suggest that the Saladoid dental calculi microbiome structure and function may possibly reflect a horticulturalist lifestyle and distinct dietary habits. Results also open the opportunity to further elucidate oral disease states in extinct Caribbean cultures and extinct indigenous cultures with similar lifestyles.

  11. Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality.

    PubMed

    Jiang, Yue; Xiong, Xuejian; Danska, Jayne; Parkinson, John

    2016-01-12

    reference genomes can impact comprehensive annotation of metatranscriptomes. Consequently, beyond the application of standardized pipelines, additional caution must be taken when interpreting their output and performing downstream, microbiome-specific, analyses. The pipeline used in these analyses along with a tutorial has been made freely available for download from our project website: http://www.compsysbio.org/microbiome .

  12. Collaborative Project. A Flexible Atmospheric Modeling Framework for the Community Earth System Model (CESM)

    SciT

    Gettelman, Andrew

    2015-10-01

    In this project we have been upgrading the Multiscale Modeling Framework (MMF) in the Community Atmosphere Model (CAM), also known as Super-Parameterized CAM (SP-CAM). This has included a major effort to update the coding standards and interface with CAM so that it can be placed on the main development trunk. It has also included development of a new software structure for CAM to be able to handle sub-grid column information. These efforts have formed the major thrust of the work.

  13. EC FP6 Enviro-RISKS project outcomes in area of Earth and Space Science Informatics applications

    NASA Astrophysics Data System (ADS)

    Gordov, E. P.; Zakarin, E. A.

    2009-04-01

    exploit completely huge potential of web bases technologies. In particular, development of a region devoted web portal using approached suggested by the Open Geospatial Consortium has been started recently. The state of the art of the information-computational infrastructure in the targeted region is quite a step in the process of development of a distributed collaborative information-computational environment to support multidisciplinary investigations of Earth regional environment, especially those required meteorology, atmospheric pollution transport and climate modeling. Established in process of the Project carrying out cooperative links, new Partners initiatives, and gained expertise allow us to hope that this infrastructure rather soon will make significant input into understanding regional environmental processes in their relationships with Global Change. In particular, this infrastructure will play a role of the 'underlying mechanics' of the research work, leaving the earth scientists to concentrate on their investigations as well as providing the environment to make research results available and understandable to everyone. Additionally to the core FP6 Enviro-RISKS project (INCO-CT-2004-013427) support this activity was partially supported by SB RAS Integration Project 34, SB RAS Basic Program Project 4.5.2.2 and APN Project CBA2007-08NSY. Valuable input into the expert group work and elaborated outcomes of Profs. V. Lykosov and A. Starchenko, Drs. D. Belikov, , M. Korets, S. Kostrykin, B. Mirkarimova, I. Okladnikov, , A. Titov and A. Tridvornov is acknowledged.

  14. Microbiome Tools for Forensic Science.

    PubMed

    Metcalf, Jessica L; Xu, Zhenjiang Z; Bouslimani, Amina; Dorrestein, Pieter; Carter, David O; Knight, Rob

    2017-09-01

    Microbes are present at every crime scene and have been used as physical evidence for over a century. Advances in DNA sequencing and computational approaches have led to recent breakthroughs in the use of microbiome approaches for forensic science, particularly in the areas of estimating postmortem intervals (PMIs), locating clandestine graves, and obtaining soil and skin trace evidence. Low-cost, high-throughput technologies allow us to accumulate molecular data quickly and to apply sophisticated machine-learning algorithms, building generalizable predictive models that will be useful in the criminal justice system. In particular, integrating microbiome and metabolomic data has excellent potential to advance microbial forensics. Copyright © 2017. Published by Elsevier Ltd.

  15. Human Gut Microbiome: Function Matters.

    PubMed

    Heintz-Buschart, Anna; Wilmes, Paul

    2017-11-22

    The human gut microbiome represents a complex ecosystem contributing essential functions to its host. Recent large-scale metagenomic studies have provided insights into its structure and functional potential. However, the functional repertoire which is actually contributed to human physiology remains largely unexplored. Here, by leveraging recent omics datasets, we challenge current assumptions regarding key attributes of the functional gut microbiome, in particular with respect to its variability. We further argue that the closing of existing gaps in functional knowledge should be addressed by a most-wanted gene list, the development and application of molecular and cellular high-throughput measurements, the development and sensible use of experimental models, as well as the direct study of observable molecular effects in the human host. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Helping Italian science teachers to make earth and climate active lessons. Results of 3 years support with the ICLEEN project

    NASA Astrophysics Data System (ADS)

    Cattadori, M.

    2013-12-01

    It has been demonstrated that in Italy Earth and Climate System Sciences Education (ESS) is one of the scientific disciplines where science teachers show a greatest need in terms of professional support. Among the causes that have been reported we should mention: the predominance of science teachers with a degree in biological disciplines rather then geo-logical or physical topics, and the high interdisciplinarity of certain topics, in particular those related to the climate system. Furthermore, it was found that ESS topics are predominant in the science curricula of those grades in which have been reported the major students dropout rates during the whole italian school cycle . In this context, in 2010, the MUSE, the Museum of Science of Trento (Italy), created a web-based service named I-Cleen (Inquring on Climate and Energy www.icleen.muse.it). This is a tool aimed at promoting the collaboration among science teachers in order to share resources and enhance the professional collaboration by means of participatory methods and models belonging to the world of open source and open content. The main instrument of the I-CLEEN project is an online repository (with metadata compliant with the DCMI and LOM international standards) of teaching resources focused on Earth and Climate Sciences all published under the Creative Commons license Attribution 3.0 and therefore, belonging to the model of OER (Open Educational Resources). The service has been designed, developed and managed by a team consisting of very experiencing science teachers and scientists from the Museum and other partners research institutions. The editorial work is carried out online utilizing a specific platform made with LifeRay, a CMS (Content Management System) software that is open source and manageable in a single Java-frameworked environment using the dbase, the website, the editorial process and several web 2.0 services. The project has been subjected to two distinct testing activities in

  17. A Software Engineering Paradigm for Quick-turnaround Earth Science Data Projects

    NASA Astrophysics Data System (ADS)

    Moore, K.

    2016-12-01

    As is generally the case with applied sciences professional and educational programs, the participants of such programs can come from a variety of technical backgrounds. In the NASA DEVELOP National Program, the participants constitute an interdisciplinary set of backgrounds, with varying levels of experience with computer programming. DEVELOP makes use of geographically explicit data sets, and it is necessary to use geographic information systems and geospatial image processing environments. As data sets cover longer time spans and include more complex sets of parameters, automation is becoming an increasingly prevalent feature. Though platforms such as ArcGIS, ERDAS Imagine, and ENVI facilitate the batch-processing of geospatial imagery, these environments are naturally constricting to the user in that they limit him or her to the tools that are available. Users must then turn to "homemade" scripting in more traditional programming languages such as Python, JavaScript, or R, to automate workflows. However, in the context of quick-turnaround projects like those in DEVELOP, the programming learning curve may be prohibitively steep. In this work, we consider how to best design a software development paradigm that addresses two major constants: an arbitrarily experienced programmer and quick-turnaround project timelines.

  18. Menopause and the vaginal microbiome.

    PubMed

    Muhleisen, Alicia L; Herbst-Kralovetz, Melissa M

    2016-09-01

    For over a century it has been well documented that bacteria in the vagina maintain vaginal homeostasis, and that an imbalance or dysbiosis may be associated with poor reproductive and gynecologic health outcomes. Vaginal microbiota are of particular significance to postmenopausal women and may have a profound effect on vulvovaginal atrophy, vaginal dryness, sexual health and overall quality of life. As molecular-based techniques have evolved, our understanding of the diversity and complexity of this bacterial community has expanded. The objective of this review is to compare the changes that have been identified in the vaginal microbiota of menopausal women, outline alterations in the microbiome associated with specific menopausal symptoms, and define how hormone replacement therapy impacts the vaginal microbiome and menopausal symptoms; it concludes by considering the potential of probiotics to reinstate vaginal homeostasis following menopause. This review details the studies that support the role of Lactobacillus species in maintaining vaginal homeostasis and how the vaginal microbiome structure in postmenopausal women changes with decreasing levels of circulating estrogen. In addition, the associated transformations in the microanatomical features of the vaginal epithelium that can lead to vaginal symptoms associated with menopause are described. Furthermore, hormone replacement therapy directly influences the dominance of Lactobacillus in the microbiota and can resolve vaginal symptoms. Oral and vaginal probiotics hold great promise and initial studies complement the findings of previous research efforts concerning menopause and the vaginal microbiome; however, additional trials are required to determine the efficacy of bacterial therapeutics to modulate or restore vaginal homeostasis. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  19. Xenobiotic Metabolism and Gut Microbiomes

    PubMed Central

    Das, Anubhav; Srinivasan, Meenakshi; Ghosh, Tarini Shankar; Mande, Sharmila S.

    2016-01-01

    Humans are exposed to numerous xenobiotics, a majority of which are in the form of pharmaceuticals. Apart from human enzymes, recent studies have indicated the role of the gut bacterial community (microbiome) in metabolizing xenobiotics. However, little is known about the contribution of the plethora of gut microbiome in xenobiotic metabolism. The present study reports the results of analyses on xenobiotic metabolizing enzymes in various human gut microbiomes. A total of 397 available gut metagenomes from individuals of varying age groups from 8 nationalities were analyzed. Based on the diversities and abundances of the xenobiotic metabolizing enzymes, various bacterial taxa were classified into three groups, namely, least versatile, intermediately versatile and highly versatile xenobiotic metabolizers. Most interestingly, specific relationships were observed between the overall drug consumption profile and the abundance and diversity of the xenobiotic metabolizing repertoire in various geographies. The obtained differential abundance patterns of xenobiotic metabolizing enzymes and bacterial genera harboring them, suggest their links to pharmacokinetic variations among individuals. Additional analyses of a few well studied classes of drug modifying enzymes (DMEs) also indicate geographic as well as age specific trends. PMID:27695034

  20. Introduction: Microbiome in human reproduction.

    PubMed

    Franasiak, Jason M; Scott, Richard T

    2015-12-01

    The human microbiome has been termed the "second human genome" and data that has come about of late certainly makes it appear every bit as complex. The human body contains 10-fold more microbial cells than the human cells and accounts for 1%-3% of our total body mass. As we learn more about this symbiotic relationship, it appears this complex interaction occurs in nearly every part of the body, even those areas at one time considered to be sterile. Indeed, the microbiome in human reproduction has been investigated in terms of both the lower and upper reproductive tract and includes interactions even at the point of gametogenesis. What is all the more fascinating is that we have known about the importance of microbes for over 150 years, even before they existed in name. And now, with the assistance of an exciting technologic revolution which has pushed forward our understanding of the microbiome, we appear to stand on the precipice of a higher level of understanding of microbes, the biofilms they create, and their impact of health and disease in human reproduction. Copyright © 2015. Published by Elsevier Inc.

  1. Microbiome/microbiota and allergies.

    PubMed

    Inoue, Yuzaburo; Shimojo, Naoki

    2015-01-01

    Allergies are characterized by a hypersensitive immune reaction to originally harmless antigens. In recent decades, the incidence of allergic diseases has markedly increased, especially in developed countries. The increase in the frequency of allergic diseases is thought to be primarily due to environmental changes related to a westernized lifestyle, which affects the commensal microbes in the human body. The human gut is the largest organ colonized by bacteria and contains more than 1000 bacterial species, called the "gut microbiota." The recent development of sequencing technology has enabled researchers to genetically investigate and clarify the diversity of all species of commensal microbes. The collective genomes of commensal microbes are together called the "microbiome." Although the detailed mechanisms remain unclear, it has been proposed that the microbiota/microbiome, especially that in the gut, impacts the systemic immunity and metabolism, thus affecting the development of various immunological diseases, including allergies. In this review, we summarize the recent findings regarding the importance of the microbiome/microbiota in the development of allergic diseases and also the results of interventional studies using probiotics or prebiotics to prevent allergies.

  2. The Examining Your Environment through the Power of Data Project (EYE-POD) Project at NAU: Professional Development for Secondary Education Teachers Using Earth Sciences and GIS

    NASA Astrophysics Data System (ADS)

    Sample, J. C.; Rubino-Hare, L.; Claesgens, J.; Fredrickson, K.; Manone, M.; White, M.

    2010-12-01

    The EYE-POD project at Northern Arizona University is an NSF-ITEST-funded professional development program for secondary science (SS) and career technical education (CTE) teachers. The program recruited SS-CTE teacher pairs from Arizona and the surrounding region to participate in two-week workshops during Summer, 2010, and an advanced workshop ins Summer, 2011. The workshops are led by a team with distinct expertise in science content, professional development and pedagogy, GIS, and project evaluation. Learning modules and a workshop agenda are developed using the Legacy Cycle of learning. Rather than compartmentalize pedagogical, content, and GIS learning activities, they have been combined throughout the workshop timeline. Early activities focus on learning of climate and weather processes through GIS modules provided by ESRI-“Mapping our World” and “Analyzing our World”. Participants learn the technical aspects of GIS software while investigating real phenomena. The science/GIS learning activities are augmented by laboratory demonstrations and field data collection using Labquest handheld field measurement systems with a variety of probes. At the end of the first week teacher-participants presented the solution to a problem, using GIS-based climate and weather data, involving travel to various locations on Earth. The second week focused on classroom, lab, and field activities devoted to recommendations to the City of Flagstaff for development in the Rio de Flag floodplain. Teacher-participant groups presented solutions making claims and recommendations supported by evidence from georeferenced field data and other GIS data acquired from various sources. At the close of the workshop teachers were provided with GIS software, hardware for field data collection, and several reference materials to aid in curriculum development. They have been tasked with implementing two GIS-based Earth science content modules in their schools, to one science class and one

  3. Geophysics Integrated Studies in the Sun Earth System: A Cooperative Project of Vietnam, Europe, and Africa

    NASA Astrophysics Data System (ADS)

    Amory-Mazaudier, C.; et al.

    2006-11-01

    lhminh@igp.ncst.ac.vn The Hanoi Institute of Geophysics (Vietnam) will participate to international Heliophysical Year. This paper presents Vietnam‘s participation into this International cooperative project : the Vietnamese network of magnetometers, meteorological stations, ionosondes and GPS receivers involved in campaigns of measurements, the research field selected for the training of young Vietnamese scientists, and the Institutes involve in this training. This paper also presents some particularities of geophysical parameters in Vietnam : the strong amplitude of the equatorial electrojet observed by satellite data and confirmed by magnetic observations at the ground level presented for the first time to the international community, the monsoon signature etc. Finally the differences between the Asian sector and the African sector lead to the development of comparative studies between Asia and Africa.

  4. Power law analysis of the human microbiome.

    PubMed

    Ma, Zhanshan Sam

    2015-11-01

    Taylor's (1961, Nature, 189:732) power law, a power function (V = am(b) ) describing the scaling relationship between the mean and variance of population abundances of organisms, has been found to govern the population abundance distributions of single species in both space and time in macroecology. It is regarded as one of few generalities in ecology, and its parameter b has been widely applied to characterize spatial aggregation (i.e. heterogeneity) and temporal stability of single-species populations. Here, we test its applicability to bacterial populations in the human microbiome using extensive data sets generated by the US-NIH Human Microbiome Project (HMP). We further propose extending Taylor's power law from the population to the community level, and accordingly introduce four types of power-law extensions (PLEs): type I PLE for community spatial aggregation (heterogeneity), type II PLE for community temporal aggregation (stability), type III PLE for mixed-species population spatial aggregation (heterogeneity) and type IV PLE for mixed-species population temporal aggregation (stability). Our results show that fittings to the four PLEs with HMP data were statistically extremely significant and their parameters are ecologically sound, hence confirming the validity of the power law at both the population and community levels. These findings not only provide a powerful tool to characterize the aggregations of population and community in both time and space, offering important insights into community heterogeneity in space and/or stability in time, but also underscore the three general properties of power laws (scale invariance, no average and universality) and their specific manifestations in our four PLEs. © 2015 John Wiley & Sons Ltd.

  5. Tuned in to the Earth from the classroom with `O3E' european project

    NASA Astrophysics Data System (ADS)

    Berenguer, J.; Courboulex, F.; Tocheport, A.; Eva, C.; Ferretti, G.; Solarino, S.; Giardini, D.; Sornette, A.; Ponzone, M.; Cremonini, R.; Virieux, J.

    2010-12-01

    In lines with diverse initiatives regarding scientific culture and education, the ‘O3E’ experience (http://O3E.geoazur.eu) has set up a permanent educational network of schools in the Alpine and Mediterranean areas, building an exchange of knowledge on natural risks prevention. The “O3E” innovative project (European Educational Observatory for Environment) is established after 12 years (1996-2008) of regional and national original programs for education (“Seismometers at School” in France and Swiss, “Edurisk” in Italy and “ClimAtscope” in Switzerland). The project is born to promote a responsible behavior of citizens in front of the evolution of a society where scientific information is promptly available. Since 2008, a school network in the Alpine and Mediterranean areas has been equipped with environmental sensors of an educational vocation. The data on the ground motion (seismometers), the temperatures and precipitations (weather stations), the flows of rivers (hydrogeology) recorded in the schools and processed by the students are collected on dedicated servers and then made available through internet to the entire community. This network “O3E”, once installed, is the starting point of activities for students. Indeed, various general objectives are pursued: - To promote the applied sciences and new technologies. - To put in network the actors of Education and formative teaching. - To develop the sense of the autonomy and the responsibility in the young people. - To reinforce and develop relationships with regional partners of the educational and university fields. - To support a rational awakening for the prevention of the natural risks Teachers from this network can share experiences and produce new didactic tools for the classroom. This collaborative work could illustrate the conjugated efforts of researchers and teachers for a better education and awareness of the risk culture especially in young populations. Some student’s and

  6. Bespoke microbiome therapy to manage plant diseases.

    PubMed

    Gopal, Murali; Gupta, Alka; Thomas, George V

    2013-01-01

    Information gathered with advanced nucleotide sequencing technologies, small molecule detection systems and computational biology is revealing that a community of microbes and their genes, now termed "the microbiome," located in gut and rhizosphere, is responsible for maintaining the health of human beings and plants, respectively. Within the complete microbiome a "core-microbiome" exists that plays the pivotal role in well being of humans and plants. Recent studies in medicine have shown that an artificial mixture of bacteria representing the core gut microbiome of healthy person when transferred into gut of diseased person results in re-establishment of normal microflora in the latter leading to alleviation from diseased condition. In agriculture, though not exactly in similar manner as in medicine, success in plant disease management has been achieved through transfer of microbiome by mixing disease suppressive soils with disease conducive soils. A study more similar to artificial gut microbiome transfer in medical field has been recently reported in agriculture, in which transfer of microbiome via soil solutions (filtered and unfiltered) has shown ability to alleviate drought stress in Arabidopsis thaliana. However, the exact practice of transferring artificially cultivated core-microbiome as in medicine has not thus far been attempted in plant disease management. Nonetheless, as the gut and rhizosphere microbiome are known to share many common traits, there exists a good scope for accomplishing similar studies in agriculture. Based upon the information drawn from all recent works in microbiome studies of gut and rhizosphere, we propose that tailor-made core-microbiome transfer therapy can be a success in agriculture too and it could become a viable strategy for management of plant diseases in future.

  7. Undergraduate Earth System Science Education: Project-Based Learning, Land-Atmosphere Interaction, and a Newly Established Student Weather Station

    NASA Astrophysics Data System (ADS)

    Baker, D.

    2004-12-01

    Undergraduate students conducted a semester-long research project as part of a special topics course that launched the Austin College Weather Station in spring 2001. The weather station is located on restored prairie roughly 100 km north of Dallas, Texas. In addition to standard meteorological observations, the Austin College Weather Station measures surface quantities such as soil moisture, soil temperature, solar radiation, infrared radiation, and soil heat flux. These additional quantities are used to calculate the surface energy balance using the Bowen ratio method. Thus, the Austin College Weather Station provides valuable information on land-atmosphere interaction in a prairie environment. This project provided a remarkable learning experience for the students. Each student supervised two instruments on the weather station. Students skillfully learned instrumentation details and the physical phenomena measured by the instruments. Team meetings were held each week to discuss issues such as station location, power requirements, telecommunication options, and data acquisition. Students made important decisions during the meetings. They would then work collaboratively on specific tasks that needed to be accomplished before the next meeting. Students also assessed the validity of their measurements after the weather station came on-line. With this approach, students became the experts. They utilized the scientific method to think critically and to solve problems. For at least a semester, students became Earth system scientists.

  8. New perspectives on interdisciplinary earth science at the Dead Sea: The DESERVE project.

    PubMed

    Kottmeier, Christoph; Agnon, Amotz; Al-Halbouni, Djamil; Alpert, Pinhas; Corsmeier, Ulrich; Dahm, Torsten; Eshel, Adam; Geyer, Stefan; Haas, Michael; Holohan, Eoghan; Kalthoff, Norbert; Kishcha, Pavel; Krawczyk, Charlotte; Lati, Joseph; Laronne, Jonathan B; Lott, Friederike; Mallast, Ulf; Merz, Ralf; Metzger, Jutta; Mohsen, Ayman; Morin, Efrat; Nied, Manuela; Rödiger, Tino; Salameh, Elias; Sawarieh, Ali; Shannak, Benbella; Siebert, Christian; Weber, Michael

    2016-02-15

    The Dead Sea region has faced substantial environmental challenges in recent decades, including water resource scarcity, ~1m annual decreases in the water level, sinkhole development, ascending-brine freshwater pollution, and seismic disturbance risks. Natural processes are significantly affected by human interference as well as by climate change and tectonic developments over the long term. To get a deep understanding of processes and their interactions, innovative scientific approaches that integrate disciplinary research and education are required. The research project DESERVE (Helmholtz Virtual Institute Dead Sea Research Venue) addresses these challenges in an interdisciplinary approach that includes geophysics, hydrology, and meteorology. The project is implemented by a consortium of scientific institutions in neighboring countries of the Dead Sea (Israel, Jordan, Palestine Territories) and participating German Helmholtz Centres (KIT, GFZ, UFZ). A new monitoring network of meteorological, hydrological, and seismic/geodynamic stations has been established, and extensive field research and numerical simulations have been undertaken. For the first time, innovative measurement and modeling techniques have been applied to the extreme conditions of the Dead Sea and its surroundings. The preliminary results show the potential of these methods. First time ever performed eddy covariance measurements give insight into the governing factors of Dead Sea evaporation. High-resolution bathymetric investigations reveal a strong correlation between submarine springs and neo-tectonic patterns. Based on detailed studies of stratigraphy and borehole information, the extension of the subsurface drainage basin of the Dead Sea is now reliably estimated. Originality has been achieved in monitoring flash floods in an arid basin at its outlet and simultaneously in tributaries, supplemented by spatio-temporal rainfall data. Low-altitude, high resolution photogrammetry, allied to

  9. ["Let's play with the Earth": a project of environmental education for primary school children].

    PubMed

    Gallotti, Cristina; Ferloni, Paolo; Roncarolo, Federico; Maccagni, Marinella; Alessi, Luca; Scorletti, Eleonora; Sacco, Sara; Tenconi, Maria Teresa

    2012-01-01

    Raising awareness and knowledge in Pavia Public Primary School students, and indirectly in their parents, about environmental problems like waste recycling and energy saving, developing with games the concept of separate collection of rubbish; creating an environmentally conscious awareness and sense of responsibility towards sustainable behavior. The educational program lasted six months. Data collection was performed using anonymous questionnaires, administered to "treated" students at the beginning and at the end of the program. The "control" population only answered a single questionnaire at the end of the project. It was also carried out an assessment of the fallout of the project on parents, through a questionnaire at the beginning and at the end of the program. At the end of the educational intervention, a satisfaction questionnaire was administered to teachers. The enrolled population was composed of 1,358 students from 3rd, 4th and 5th classes of Public Primary Schools of the four Pavia School Districts: 938 "treated" students followed the program and 420 "controls" only answered the final questionnaire. The data concerning the pupils' knowledge are expressed in terms of frequencies: at first, we evaluated the comparison between "treated" students knowledge at the beginning and at the end of the program in each class, then we made the comparison between "treated" and "control" students at the end of the program. The comparison of the final questionnaires ("treated" students vs "controls") revealed in "treated" students higher knowledge of terms "waste" (94.5% vs 89.0%) and "separate collection" (97.3% vs 90.7%): the differences are statistically significant. Also the practice of separate collection of rubbish is more frequent in "treated" students' families than in "control" ones (83.5% vs 71.4%, p =0.0001).The analysis of teachers' satisfaction questionnaires showed positive ratings with high average scores for each item investigated. The analysis of

  10. Discover Earth

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Discover Earth is a NASA-funded project for teachers of grades 5-12 who want to expand their knowledge of the Earth system, and prepare to become master teachers who promote Earth system science in their own schools, counties, and throughout their state. Participants from the following states are invited to apply: Connecticut, Delaware, Maine, Maryland, Massachusetts, New Hampshire, New Jersey, New York, Pennsylvania, Rhode Island, Vermont, and Washington, DC. Teachers selected for the project participate in a two-week summer workshop conducted at the University of Maryland, College Park; develop classroom-ready materials during the workshop for broad dissemination; conduct a minimum of two peer training activities during the coming school year; and participate in other enrichment/education opportunities as available and desired. Discover Earth is a team effort that utilizes expertise from a range of contributors, and balances science content with hands-on classroom applications.

  11. Microbiome Data Science: Understanding Our Microbial Planet.

    PubMed

    Kyrpides, Nikos C; Eloe-Fadrosh, Emiley A; Ivanova, Natalia N

    2016-06-01

    Microbiology is experiencing a revolution brought on by recent developments in sequencing technology. The unprecedented volume of microbiome data being generated poses significant challenges that are currently hindering progress in the field. Here, we outline the major bottlenecks and propose a vision to advance microbiome research as a data-driven science. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Embracing Community Ecology in Plant Microbiome Research.

    PubMed

    Dini-Andreote, Francisco; Raaijmakers, Jos M

    2018-06-01

    Community assembly is mediated by selection, dispersal, drift, and speciation. Environmental selection is mostly used to date to explain patterns in plant microbiome assembly, whereas the influence of the other processes remains largely elusive. Recent studies highlight that adopting community ecology concepts provides a mechanistic framework for plant microbiome research. Copyright © 2018 Elsevier Ltd. All rights reserved.

  13. Visualizing Earth Science Data for Environmental Monitoring and Decision Support in Mesoamerica: The SERVIR Project

    NASA Astrophysics Data System (ADS)

    Hardin, D.; Graves, S.; Sever, T.; Irwin, D.

    2005-05-01

    different scales. One of these is a 15 meter resolution mosaic of the entire Mesoamerican region. This paper gives an overview of the SERVIR project and its associated visualization methods.

  14. Climate change projections using the IPSL-CM5 Earth System Model: from CMIP3 to CMIP5

    NASA Astrophysics Data System (ADS)

    Dufresne, J.-L.; Foujols, M.-A.; Denvil, S.; Caubel, A.; Marti, O.; Aumont, O.; Balkanski, Y.; Bekki, S.; Bellenger, H.; Benshila, R.; Bony, S.; Bopp, L.; Braconnot, P.; Brockmann, P.; Cadule, P.; Cheruy, F.; Codron, F.; Cozic, A.; Cugnet, D.; de Noblet, N.; Duvel, J.-P.; Ethé, C.; Fairhead, L.; Fichefet, T.; Flavoni, S.; Friedlingstein, P.; Grandpeix, J.-Y.; Guez, L.; Guilyardi, E.; Hauglustaine, D.; Hourdin, F.; Idelkadi, A.; Ghattas, J.; Joussaume, S.; Kageyama, M.; Krinner, G.; Labetoulle, S.; Lahellec, A.; Lefebvre, M.-P.; Lefevre, F.; Levy, C.; Li, Z. X.; Lloyd, J.; Lott, F.; Madec, G.; Mancip, M.; Marchand, M.; Masson, S.; Meurdesoif, Y.; Mignot, J.; Musat, I.; Parouty, S.; Polcher, J.; Rio, C.; Schulz, M.; Swingedouw, D.; Szopa, S.; Talandier, C.; Terray, P.; Viovy, N.; Vuichard, N.

    2013-05-01

    We present the global general circulation model IPSL-CM5 developed to study the long-term response of the climate system to natural and anthropogenic forcings as part of the 5th Phase of the Coupled Model Intercomparison Project (CMIP5). This model includes an interactive carbon cycle, a representation of tropospheric and stratospheric chemistry, and a comprehensive representation of aerosols. As it represents the principal dynamical, physical, and bio-geochemical processes relevant to the climate system, it may be referred to as an Earth System Model. However, the IPSL-CM5 model may be used in a multitude of configurations associated with different boundary conditions and with a range of complexities in terms of processes and interactions. This paper presents an overview of the different model components and explains how they were coupled and used to simulate historical climate changes over the past 150 years and different scenarios of future climate change. A single version of the IPSL-CM5 model (IPSL-CM5A-LR) was used to provide climate projections associated with different socio-economic scenarios, including the different Representative Concentration Pathways considered by CMIP5 and several scenarios from the Special Report on Emission Scenarios considered by CMIP3. Results suggest that the magnitude of global warming projections primarily depends on the socio-economic scenario considered, that there is potential for an aggressive mitigation policy to limit global warming to about two degrees, and that the behavior of some components of the climate system such as the Arctic sea ice and the Atlantic Meridional Overturning Circulation may change drastically by the end of the twenty-first century in the case of a no climate policy scenario. Although the magnitude of regional temperature and precipitation changes depends fairly linearly on the magnitude of the projected global warming (and thus on the scenario considered), the geographical pattern of these changes

  15. Human Microbiome and HIV/AIDS

    PubMed Central

    Li, Yihong; Yang, Liying; Pei, Zhiheng; Poles, Michael; Abrams, William R.; Malamud, Daniel

    2013-01-01

    Understanding of the human microbiome continues to grow rapidly; however, reports on changes in the microbiome after HIV infection are still limited. This review surveys the progress made in methodology associated with microbiome studies and highlights the remaining challenges to this field. Studies have shown that commensal oral, gut, vaginal, and penile bacteria are vital to the health of the human immune system. Our studies on crosstalk among oral and gastrointestinal soluble innate factors, HIV, and microbes indicated that the oral and gut microbiome was altered in the HIV-positive samples compared to the negative controls. The importance of understanding the bacterial component of HIV/AIDS, and likelihood of “crosstalk” between viral and bacterial pathogens, will help in understanding the role of the microbiome in HIV-infected individuals and facilitate identification of novel antiretroviral factors for use as novel diagnostics, microbicides, or therapeutics against HIV infection. PMID:22193889

  16. Emerging Technologies for Gut Microbiome Research

    PubMed Central

    Arnold, Jason W.; Roach, Jeffrey; Azcarate-Peril, M. Andrea

    2016-01-01

    Understanding the importance of the gut microbiome on modulation of host health has become a subject of great interest for researchers across disciplines. As an intrinsically multidisciplinary field, microbiome research has been able to reap the benefits of technological advancements in systems and synthetic biology, biomaterials engineering, and traditional microbiology. Gut microbiome research has been revolutionized by high-throughput sequencing technology, permitting compositional and functional analyses that were previously an unrealistic undertaking. Emerging technologies including engineered organoids derived from human stem cells, high-throughput culturing, and microfluidics assays allowing for the introduction of novel approaches will improve the efficiency and quality of microbiome research. Here, we will discuss emerging technologies and their potential impact on gut microbiome studies. PMID:27426971

  17. The Espere Project - Environmental Science Published For Everybody Round The Earth

    NASA Astrophysics Data System (ADS)

    Uherek, E.; Gauss, M.

    Within the ESPERE project representatives of the scientific community, mediators to the public, educationists, teachers and students are planning to build up a user-friendly informative Network on climate change and related environmental processes. The aim is to make the address www.espere.net become the multilingual gate to the current knowledge of scientists, presented in an easily understandable way for the public with a strong focus on schools. A group of about 100 supporters from numerous countries have already started to create a multilingual web atlas on the climate system, written in an understandable way for the public and based on the results of the recent IPCC-TAR (2001). The structure of this atlas is based on thematic fields such as ENSO/NAO, solar cycle, paleoclimate, etc. The contents will be reviewed as is usual for scientific journals in order to provide a reliable source of information. This effort is assisted by educationists and teachers in order to compile topics from these fields for the use in classes and to complement the online sources with appropriate teaching material. The dualism of the Internet as a medium of information (e.g. scientific journals) and a medium of communication (e.g. chat rooms) enables, unlike any other former tool, the direct interaction of all groups involved in the field of education. ESPERE is going to use the opportunity of direct feedback in order to evaluate and improve scientific publications already under development. In this way an optimisation of the contents with respect to demands of the user and comprehensibility can be achieved. In partic- ular, this will help to bridge the gap between science and the public and to pave the way leading to a knowledge society. In collaboration with partner schools in Germany, ESPERE is already providing teaching materials, which are being translated into other languages. The current experiences show that this effort could work on an international scale and contribute

  18. Privacy-preserving microbiome analysis using secure computation.

    PubMed

    Wagner, Justin; Paulson, Joseph N; Wang, Xiao; Bhattacharjee, Bobby; Corrada Bravo, Héctor

    2016-06-15

    Developing targeted therapeutics and identifying biomarkers relies on large amounts of research participant data. Beyond human DNA, scientists now investigate the DNA of micro-organisms inhabiting the human body. Recent work shows that an individual's collection of microbial DNA consistently identifies that person and could be used to link a real-world identity to a sensitive attribute in a research dataset. Unfortunately, the current suite of DNA-specific privacy-preserving analysis tools does not meet the requirements for microbiome sequencing studies. To address privacy concerns around microbiome sequencing, we implement metagenomic analyses using secure computation. Our implementation allows comparative analysis over combined data without revealing the feature counts for any individual sample. We focus on three analyses and perform an evaluation on datasets currently used by the microbiome research community. We use our implementation to simulate sharing data between four policy-domains. Additionally, we describe an application of our implementation for patients to combine data that allows drug developers to query against and compensate patients for the analysis. The software is freely available for download at: http://cbcb.umd.edu/∼hcorrada/projects/secureseq.html Supplementary data are available at Bioinformatics online. hcorrada@umiacs.umd.edu. © The Author 2016. Published by Oxford University Press.

  19. The representation of non-equilibrium soil types in earth system models and its impact on carbon cycle projections

    NASA Astrophysics Data System (ADS)

    Hugelius, G.; Ahlström, A.; Canadell, J.; Koven, C. D.; Jackson, R. B.; Luo, Y.

    2016-12-01

    Soils hold the largest reactive pool of carbon (C) on earth. Global soil organic C stocks (0-200 cm depth plus full peatland depth) are estimated to 2200 Pg C (adapted from Hugelius et al., 2014, Köchy et al., 2015 and Batjes, 2016). Soil C stocks in Earth system models (ESMs) can be generated by running the model over a longer time period until soil C pools are in or near steady-state. Inherent in this concept is the idea that soil C stocks are in (quasi)equilibrium as determined by the balance of net ecosystem input to soil organic matter and its turnover. The rate of turnover is sometimes subdivided into several pools and the rates are affected by various environmental factors. Here we break down the empirically based estimates of global soil C pools into equilibrium-type soils which current (Coupled Model Intercomparison Project, phase 5; CMIP5) generation ESMs are set-up to represent and non-equilibrium type soils which are generally not represented in current ESMs. We define equilibrium soils as those where pedogenesis (and associated soil C formation) is not significantly limited by the environmental factors perennial soil freezing, waterlogging/anoxia or limited unconsolidated soil substrate. This is essentially all permafrost-free mineral soils that are not in a wetland or alpine setting. On the other hand, non-equlibrium soils are defined as permafrost soils, peatlands and alpine soils with a limited fine-soil matrix. Based on geospatial analyses of state-of-the-art datasets on soil C stocks, we estimate that the global soil C pool is divided roughly equally between equilibrium and non-equlibrium type soils. We discuss the ways in which this result affects C cycling in ESMs and projections of soil C sensitivity under a changing climate. ReferencesBatjes N.H. (2016) Geoderma, 269, 61-68, doi: 10.1016/j.geoderma.2016.01.034 Hugelius G. et al. (2014) Biogeosciences, 11, 6573-6593, doi:10.5194/bg-11-6573-2014 Köchy M. et al. (2015) Soil 1, 351-365. DOI: doi

  20. Exploring the Cultivable Ectocarpus Microbiome

    PubMed Central

    KleinJan, Hetty; Jeanthon, Christian; Boyen, Catherine; Dittami, Simon M.

    2017-01-01

    Coastal areas form the major habitat of brown macroalgae, photosynthetic multicellular eukaryotes that have great ecological value and industrial potential. Macroalgal growth, development, and physiology are influenced by the microbial community they accommodate. Studying the algal microbiome should thus increase our fundamental understanding of algal biology and may help to improve culturing efforts. Currently, a freshwater strain of the brown macroalga Ectocarpus subulatus is being developed as a model organism for brown macroalgal physiology and algal microbiome studies. It can grow in high and low salinities depending on which microbes it hosts. However, the molecular mechanisms involved in this process are still unclear. Cultivation of Ectocarpus-associated bacteria is the first step toward the development of a model system for in vitro functional studies of brown macroalgal–bacterial interactions during abiotic stress. The main aim of the present study is thus to provide an extensive collection of cultivable E. subulatus-associated bacteria. To meet the variety of metabolic demands of Ectocarpus-associated bacteria, several isolation techniques were applied, i.e., direct plating and dilution-to-extinction cultivation techniques, each with chemically defined and undefined bacterial growth media. Algal tissue and algal growth media were directly used as inoculum, or they were pretreated with antibiotics, by filtration, or by digestion of algal cell walls. In total, 388 isolates were identified falling into 33 genera (46 distinct strains), of which Halomonas (Gammaproteobacteria), Bosea (Alphaproteobacteria), and Limnobacter (Betaproteobacteria) were the most abundant. Comparisons with 16S rRNA gene metabarcoding data showed that culturability in this study was remarkably high (∼50%), although several cultivable strains were not detected or only present in extremely low abundance in the libraries. These undetected bacteria could be considered as part of the

  1. Exploring the Cultivable Ectocarpus Microbiome.

    PubMed

    KleinJan, Hetty; Jeanthon, Christian; Boyen, Catherine; Dittami, Simon M

    2017-01-01

    Coastal areas form the major habitat of brown macroalgae, photosynthetic multicellular eukaryotes that have great ecological value and industrial potential. Macroalgal growth, development, and physiology are influenced by the microbial community they accommodate. Studying the algal microbiome should thus increase our fundamental understanding of algal biology and may help to improve culturing efforts. Currently, a freshwater strain of the brown macroalga Ectocarpus subulatus is being developed as a model organism for brown macroalgal physiology and algal microbiome studies. It can grow in high and low salinities depending on which microbes it hosts. However, the molecular mechanisms involved in this process are still unclear. Cultivation of Ectocarpus -associated bacteria is the first step toward the development of a model system for in vitro functional studies of brown macroalgal-bacterial interactions during abiotic stress. The main aim of the present study is thus to provide an extensive collection of cultivable E . subulatus -associated bacteria. To meet the variety of metabolic demands of Ectocarpus -associated bacteria, several isolation techniques were applied, i.e., direct plating and dilution-to-extinction cultivation techniques, each with chemically defined and undefined bacterial growth media. Algal tissue and algal growth media were directly used as inoculum, or they were pretreated with antibiotics, by filtration, or by digestion of algal cell walls. In total, 388 isolates were identified falling into 33 genera (46 distinct strains), of which Halomonas ( Gammaproteobacteria ), Bosea ( Alphaproteobacteria ), and Limnobacter ( Betaproteobacteria ) were the most abundant. Comparisons with 16S rRNA gene metabarcoding data showed that culturability in this study was remarkably high (∼50%), although several cultivable strains were not detected or only present in extremely low abundance in the libraries. These undetected bacteria could be considered as part

  2. The MEarth project: an all-sky survey for transiting Earth-like exoplanets orbiting nearby M-dwarfs

    NASA Astrophysics Data System (ADS)

    Irwin, Jonathan; Berta-Thompson, Zachory K.; Charbonneau, David; Dittmann, Jason; Newton, Elisabeth R.

    2015-01-01

    The MEarth project is an operational all-sky survey searching for transiting Earth-like exoplanets around 3,000 of the closest mid-to-late M-dwarfs. These will be among the best planets in their size class for atmospheric characterization using present day and near-future instruments such as HST, JWST and ground-based Extremely Large Telescopes (ELTs), by virtue of the large observational signal sizes afforded by their small and bright host stars. We present an update on the status and recent scientific results of the survey from our two observing stations: MEarth-North at Fred Lawrence Whipple Observatory, Mount Hopkins, Arizona, and MEarth-South at Cerro Tololo Inter-American Observatory, Chile. MEarth-North discovered the transiting mini-Neptune exoplanet GJ 1214b, which currently has the best-studied atmosphere of any exoplanet in its size class. In addition to searching for planets, we actively pursue stellar astrophysics topics and characterization of the target star sample using MEarth data and supplementary spectroscopic follow-up. This has included measuring astrometric parallaxes for more than 1500 nearby stars, the discovery of 6 new low-mass eclipsing binaries amenable to direct measurement of the masses and radii of their components, and rotation periods, spectral classifications, metallicities and activity indices for hundreds of stars. The MEarth light curves themselves also provide a detailed record of the photometric behavior of the target stars, which include the most favorable and interesting targets to search for small and potentially habitable planets. This will be a valuable resource for all future surveys searching for planets around these stars. All light curves gathered during the survey are made publicly available after one year.The MEarth project gratefully acknowledges funding from the David and Lucile Packard Fellowship for Science and Engineering, the National Science Foundation under grants AST-0807690, AST-1109468, and AST-1004488

  3. Highlights from the Future Earth Water-Energy-Food (W-E-F) Nexus Cluster Project Consultations

    NASA Astrophysics Data System (ADS)

    Lawford, R. G.

    2017-12-01

    Future Earth launched its W-E-F Nexus project in 2015. The focus of the project was to explore how improved governance and integrated information systems could support sustainability in the W-E-F Nexus. Workshops were held in four regions of the world (North America, Europe, Eastern Asia, and Southern Africa) which facilitated a better understanding of the current role of information in decision-making within the W-E-F Nexus. In each of these workshops, needs and options for improving the provision of relevant integrated data and information to support decision-making were discussed. The workshops provided distinct perspectives on W-E-F issues for each region and each sector. Regional differences arise from climate, geomorphology, natural resources and existing infrastructure as well as the economic and social policies within each country. While the needs associated with this diversity are large, it is still possible to identify unifying themes and requirements for data and information which appeared very similar in all the regions. Important themes involve developing a common rigorous definition of the Nexus, ensuring the availability of data of all types are available in the scales, frequencies, and accuracies needed to support better decision making; and promoting the gathering, analysis and use of information to break down the silos associated with the three sectors are made. Information is also needed to monitor the effects of land ownership and land management on W-E-F issues, to maximize the efficiencies that can be realized from joint planning and increased coherence in the sectoral policy approaches to address climate and environmental issues. After commenting on these opportunities the presentation will outline possible elements of a research agenda for moving the W-E-F Nexus approach forward.

  4. The placenta harbors a unique microbiome.

    PubMed

    Aagaard, Kjersti; Ma, Jun; Antony, Kathleen M; Ganu, Radhika; Petrosino, Joseph; Versalovic, James

    2014-05-21

    Humans and their microbiomes have coevolved as a physiologic community composed of distinct body site niches with metabolic and antigenic diversity. The placental microbiome has not been robustly interrogated, despite recent demonstrations of intracellular bacteria with diverse metabolic and immune regulatory functions. A population-based cohort of placental specimens collected under sterile conditions from 320 subjects with extensive clinical data was established for comparative 16S ribosomal DNA-based and whole-genome shotgun (WGS) metagenomic studies. Identified taxa and their gene carriage patterns were compared to other human body site niches, including the oral, skin, airway (nasal), vaginal, and gut microbiomes from nonpregnant controls. We characterized a unique placental microbiome niche, composed of nonpathogenic commensal microbiota from the Firmicutes, Tenericutes, Proteobacteria, Bacteroidetes, and Fusobacteria phyla. In aggregate, the placental microbiome profiles were most akin (Bray-Curtis dissimilarity <0.3) to the human oral microbiome. 16S-based operational taxonomic unit analyses revealed associations of the placental microbiome with a remote history of antenatal infection (permutational multivariate analysis of variance, P = 0.006), such as urinary tract infection in the first trimester, as well as with preterm birth <37 weeks (P = 0.001). Copyright © 2014, American Association for the Advancement of Science.

  5. An assessment of US microbiome research.

    PubMed

    Stulberg, Elizabeth; Fravel, Deborah; Proctor, Lita M; Murray, David M; LoTempio, Jonathan; Chrisey, Linda; Garland, Jay; Goodwin, Kelly; Graber, Joseph; Harris, M Camille; Jackson, Scott; Mishkind, Michael; Porterfield, D Marshall; Records, Angela

    2016-01-11

    Genome-enabled technologies have supported a dramatic increase in our ability to study microbial communities in environments and hosts. Taking stock of previously funded microbiome research can help to identify common themes, under-represented areas and research priorities to consider moving forward. To assess the status of US microbiome research, a team of government scientists conducted an analysis of federally funded microbiome research. Microbiomes were defined as host-, ecosystem- or habitat-associated communities of microorganisms, and microbiome research was defined as those studies that emphasize community-level analyses using 'omics technologies. Single pathogen, single strain and culture-based studies were not included, except symbiosis studies that served as models for more complex communities. Fourteen governmental organizations participated in the data call. The analysis examined three broad research themes, eight environments and eight microbial categories. Human microbiome research was larger than any other environment studied, and the basic biology research theme accounted for half of the total research activities. Computational biology and bioinformatics, reference databases and biorepositories, standardized protocols and high-throughput tools were commonly identified needs. Longitudinal and functional studies and interdisciplinary research were also identified as needs. This study has implications for the funding of future microbiome research, not only in the United States but beyond.

  6. Pancreatic Cancer, Inflammation and Microbiome

    PubMed Central

    Zambirinis, Constantinos P.; Pushalkar, Smruti; Saxena, Deepak; Miller, George

    2014-01-01

    Pancreatic cancer is one of the most lethal cancers worldwide. No effective screening methods exist and available treatment modalities do not effectively treat the disease. Inflammatory conditions such as pancreatitis represent a well-known risk for pancreatic cancer development. Yet only in the past two decades has pancreatic cancer been recognized as an inflammation-driven cancer, and the precise mechanisms underlying the pathogenic role of inflammation are beginning to be explored in detail. A substantial amount of preclinical and clinical evidence suggests that bacteria are likely to influence this process by activating immune receptors and perpetuating cancer-associated inflammation. The recent explosion of investigations into the human microbiome have highlighted how perturbations of commensal bacterial populations can promote inflammation and promote disease processes, including carcinogenesis. The elucidation of the interplay between inflammation and microbiome in the context of pancreatic carcinogenesis will provide novel targets for intervention in order to both prevent and treat pancreatic cancer more efficiently. Further studies towards this direction are urgently needed. PMID:24855007

  7. Gut microbiome and liver diseases.

    PubMed

    Tilg, Herbert; Cani, Patrice D; Mayer, Emeran A

    2016-12-01

    The gut microbiota has recently evolved as a new important player in the pathophysiology of many intestinal and extraintestinal diseases. The liver is the organ which is in closest contact with the intestinal tract, and is exposed to a substantial amount of bacterial components and metabolites. Various liver disorders such as alcoholic liver disease, non-alcoholic liver disease and primary sclerosing cholangitis have been associated with an altered microbiome. This dysbiosis may influence the degree of hepatic steatosis, inflammation and fibrosis through multiple interactions with the host's immune system and other cell types. Whereas few results from clinical metagenomic studies in liver disease are available, evidence is accumulating that in liver cirrhosis an oral microbiome is overrepresented in the lower intestinal tract, potentially contributing to disease process and severity. A major role for the gut microbiota in liver disorders is also supported by the accumulating evidence that several complications of severe liver disease such as hepatic encephalopathy are efficiently treated by various prebiotics, probiotics and antibiotics. A better understanding of the gut microbiota and its components in liver diseases might provide a more complete picture of these complex disorders and also form the basis for novel therapies. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  8. Antibiotic use and microbiome function.

    PubMed

    Ferrer, Manuel; Méndez-García, Celia; Rojo, David; Barbas, Coral; Moya, Andrés

    2017-06-15

    Our microbiome should be understood as one of the most complex components of the human body. The use of β-lactam antibiotics is one of the microbiome covariates that influence its composition. The extent to which our microbiota changes after an antibiotic intervention depends not only on the chemical nature of the antibiotic or cocktail of antibiotics used to treat specific infections, but also on the type of administration, duration and dose, as well as the level of resistance that each microbiota develops. We have begun to appreciate that not all bacteria within our microbiota are vulnerable or reactive to different antibiotic interventions, and that their influence on both microbial composition and metabolism may differ. Antibiotics are being used worldwide on a huge scale and the prescription of antibiotics is continuing to rise; however, their effects on our microbiota have been reported for only a limited number of them. This article presents a critical review of the antibiotics or antibiotic cocktails whose use in humans has been linked to changes in the composition of our microbial communities, with a particular focus on the gut, oral, respiratory, skin and vaginal microbiota, and on their molecular agents (genes, proteins and metabolites). We review the state of the art as of June 2016, and cover a total of circa 68 different antibiotics. The data herein are the first to compile information about the bacteria, fungi, archaea and viruses most influenced by the main antibiotic treatments prescribed nowadays. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. Astronomy: Project Earth Science.

    ERIC Educational Resources Information Center

    Smith, P. Sean

    This book presents classroom activities and reading materials. The activities use a hands-on approach and address the standards. Each features both a student section and a teacher guide. Eleven activities include: (1) "It's Only a Paper Moon"; (2) "Time Traveler"; (3) "Solar System Scale"; (4) "Hello Out…

  10. Rumen Microbiome, Probiotics, and Fermentation Additives.

    PubMed

    McCann, Joshua C; Elolimy, Ahmed A; Loor, Juan J

    2017-11-01

    Fermentation of a variety of feedstuffs by the ruminal microbiome is the distinctive feature of the ruminant digestive tract. The host derives energy and nutrients from microbiome activity; these organisms are essential to survival. Advances in DNA sequencing and bioinformatics have redefined the rumen microbial community. Current research seeks to connect our understanding of the rumen microbiome with nutritional strategies in ruminant livestock systems and their associated digestive disorders. These efforts align with a growing number of products designed to improve ruminal fermentation to benefit the overall efficiency of ruminant livestock production and health. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. 2-Way k-Means as a Model for Microbiome Samples.

    PubMed

    Jackson, Weston J; Agarwal, Ipsita; Pe'er, Itsik

    2017-01-01

    Motivation . Microbiome sequencing allows defining clusters of samples with shared composition. However, this paradigm poorly accounts for samples whose composition is a mixture of cluster-characterizing ones and which therefore lie in between them in the cluster space. This paper addresses unsupervised learning of 2-way clusters. It defines a mixture model that allows 2-way cluster assignment and describes a variant of generalized k -means for learning such a model. We demonstrate applicability to microbial 16S rDNA sequencing data from the Human Vaginal Microbiome Project.

  12. 2-Way k-Means as a Model for Microbiome Samples

    PubMed Central

    2017-01-01

    Motivation. Microbiome sequencing allows defining clusters of samples with shared composition. However, this paradigm poorly accounts for samples whose composition is a mixture of cluster-characterizing ones and which therefore lie in between them in the cluster space. This paper addresses unsupervised learning of 2-way clusters. It defines a mixture model that allows 2-way cluster assignment and describes a variant of generalized k-means for learning such a model. We demonstrate applicability to microbial 16S rDNA sequencing data from the Human Vaginal Microbiome Project. PMID:29177026

  13. Earth Science

    1992-07-18

    Workers at Launch Complex 17 Pad A, Kennedy Space Center (KSC) encapsulate the Geomagnetic Tail (GEOTAIL) spacecraft (upper) and attached payload Assist Module-D upper stage (lower) in the protective payload fairing. GEOTAIL project was designed to study the effects of Earth's magnetic field. The solar wind draws the Earth's magnetic field into a long tail on the night side of the Earth and stores energy in the stretched field lines of the magnetotail. During active periods, the tail couples with the near-Earth magnetosphere, sometimes releasing energy stored in the tail and activating auroras in the polar ionosphere. GEOTAIL measures the flow of energy and its transformation in the magnetotail and will help clarify the mechanisms that control the imput, transport, storage, release, and conversion of mass, momentum, and energy in the magnetotail.

  14. The Norwegian Earth System Model, NorESM1-M - Part 2: Climate response and scenario projections

    NASA Astrophysics Data System (ADS)

    Iversen, T.; Bentsen, M.; Bethke, I.; Debernard, J. B.; Kirkevåg, A.; Seland, Ø.; Drange, H.; Kristjansson, J. E.; Medhaug, I.; Sand, M.; Seierstad, I. A.

    2013-03-01

    NorESM is a generic name of the Norwegian earth system model. The first version is named NorESM1, and has been applied with medium spatial resolution to provide results for CMIP5 (http://cmip-pcmdi.llnl.gov/cmip5/index.html) without (NorESM1-M) and with (NorESM1-ME) interactive carbon-cycling. Together with the accompanying paper by Bentsen et al. (2012), this paper documents that the core version NorESM1-M is a valuable global climate model for research and for providing complementary results to the evaluation of possible anthropogenic climate change. NorESM1-M is based on the model CCSM4 operated at NCAR, but the ocean model is replaced by a modified version of MICOM and the atmospheric model is extended with online calculations of aerosols, their direct effect and their indirect effect on warm clouds. Model validation is presented in the companion paper (Bentsen et al., 2012). NorESM1-M is estimated to have equilibrium climate sensitivity of ca. 2.9 K and a transient climate response of ca. 1.4 K. This sensitivity is in the lower range amongst the models contributing to CMIP5. Cloud feedbacks dampen the response, and a strong AMOC reduces the heat fraction available for increasing near-surface temperatures, for evaporation and for melting ice. The future projections based on RCP scenarios yield a global surface air temperature increase of almost one standard deviation lower than a 15-model average. Summer sea-ice is projected to decrease considerably by 2100 and disappear completely for RCP8.5. The AMOC is projected to decrease by 12%, 15-17%, and 32% for the RCP2.6, 4.5, 6.0, and 8.5, respectively. Precipitation is projected to increase in the tropics, decrease in the subtropics and in southern parts of the northern extra-tropics during summer, and otherwise increase in most of the extra-tropics. Changes in the atmospheric water cycle indicate that precipitation events over continents will become more intense and dry spells more frequent. Extra

  15. Software tools and e-infrastructure services to support the long term preservation of earth science data - new functionality from the SCIDIP-ES project

    NASA Astrophysics Data System (ADS)

    Riddick, Andrew; Glaves, Helen; Crompton, Shirley; Giaretta, David; Ritchie, Brian; Pepler, Sam; De Smet, Wim; Marelli, Fulvio; Mantovani, Pier-Luca

    2014-05-01

    The ability to preserve earth science data for the long-term is a key requirement to support on-going research and collaboration within and between earth science disciplines. A number of critically important current research initiatives (e.g. understanding climate change or ensuring sustainability of natural resources) typically rely on the continuous availability of data collected over several decades in a form which can be easily accessed and used by scientists. In many earth science disciplines the capture of key observational data may be difficult or even impossible to repeat. For example, a specific geological exposure or subsurface borehole may be only temporarily available, and earth observation data derived from a particular satellite mission is often unique. Another key driver for long-term data preservation is that the grand challenges of the kind described above frequently involve cross-disciplinary research utilising raw and interpreted data from a number of related earth science disciplines. Adopting effective data preservation strategies supports this requirement for interoperability as well as ensuring long term usability of earth science data, and has the added potential for stimulating innovative earth science research. The EU-funded SCIDIP-ES project seeks to address these challenges by developing a Europe-wide e-infrastructure for long-term data preservation by providing appropriate software tools and infrastructure services to enable and promote long-term preservation of earth science data. This poster will describe the current status of this e-infrastructure and outline the integration of the prototype SCIDIP-ES software components into the existing systems used by earth science archives and data providers. These prototypes utilise a system architecture which stores preservation information in a standardised OAIS-compliant way, and connects and adds value to existing earth science archives. A SCIDIP-ES test-bed has been implemented by the

  16. Data Publication Process for CMIP5 Data and the Role of PIDs within Federated Earth System Science Projects

    NASA Astrophysics Data System (ADS)

    Stockhause, M.; Höck, H.; Toussaint, F.; Weigel, T.; Lautenschlager, M.

    2012-12-01

    We present the publication process for the CMIP5 (Coupled Model Intercomparison Project Phase 5) data with special emphasis on the current role of identifiers and the potential future role of PIDs in such distributed technical infrastructures. The DataCite data publication with DOI assignment finalizes the 3 levels quality control procedure for CMIP5 data (Stockhause et al., 2012). WDCC utilizes the Assistant System Atarrabi to support the publication process. Atarrabi is a web-based workflow system for metadata reviews of data creators and Publication Agents (PAs). Within the quality checks for level 3 all available information in the different infrastructure components is cross-checked for consistency by the DataCite PA. This information includes: metadata on data, metadata in the long-term archive of the Publication Agency, quality information, and external metadata on model and simulation (CIM). For these consistency checks metadata related to the data publication has to be identified. The Data Reference Syntax (DRS) convention functions as global identifier for data. Since the DRS structures the data, hierarchically, it can be used to identify data collections like DataCite publication units, i.e. all data belonging to a CMIP5 simulation. Every technical component of the infrastructure uses DRS or maps to it, but there is no central repository storing DRS_ids. Thus they have to be mapped, occasionally. Additional local identifiers are used within the different technical infrastructure components. Identification of related pieces of information in their repositories is cumbersome and tricky for the PA. How could PIDs improve the situation? To establish a reliable distributed data and metadata infrastructure, PIDs for all objects are needed as well as relations between them. An ideal data publication scenario for federated community projects within Earth System Sciences, e.g. CMIP, would be: 1. Data creators at the modeling centers define their simulation

  17. The Human Microbiome: Our Second Genome*

    PubMed Central

    Grice, Elizabeth A.; Segre, Julia A.

    2012-01-01

    The human genome has been referred to as the blueprint of human biology. In this review we consider an essential but largely ignored overlay to that blueprint, the human microbiome, which is composed of those microbes that live in and on our bodies. The human microbiome is a source of genetic diversity, a modifier of disease, an essential component of immunity, and a functional entity that influences metabolism and modulates drug interactions. Characterization and analysis of the human microbiome have been greatly catalyzed by advances in genomic technologies. We discuss how these technologies have shaped this emerging field of study and advanced our understanding of the human microbiome. We also identify future challenges, many of which are common to human genetic studies, and predict that in the future, analyzing genetic variation and risk of human disease will sometimes necessitate the integration of human and microbial genomic data sets. PMID:22703178

  18. Tools for the Microbiome: Nano and Beyond.

    PubMed

    Biteen, Julie S; Blainey, Paul C; Cardon, Zoe G; Chun, Miyoung; Church, George M; Dorrestein, Pieter C; Fraser, Scott E; Gilbert, Jack A; Jansson, Janet K; Knight, Rob; Miller, Jeff F; Ozcan, Aydogan; Prather, Kimberly A; Quake, Stephen R; Ruby, Edward G; Silver, Pamela A; Taha, Sharif; van den Engh, Ger; Weiss, Paul S; Wong, Gerard C L; Wright, Aaron T; Young, Thomas D

    2016-01-26

    The microbiome presents great opportunities for understanding and improving the world around us and elucidating the interactions that compose it. The microbiome also poses tremendous challenges for mapping and manipulating the entangled networks of interactions among myriad diverse organisms. Here, we describe the opportunities, technical needs, and potential approaches to address these challenges, based on recent and upcoming advances in measurement and control at the nanoscale and beyond. These technical needs will provide the basis for advancing the largely descriptive studies of the microbiome to the theoretical and mechanistic understandings that will underpin the discipline of microbiome engineering. We anticipate that the new tools and methods developed will also be more broadly useful in environmental monitoring, medicine, forensics, and other areas.

  19. Tools for the microbiome. Nano and beyond

    SciT

    Biteen, Julie S.; Blainey, Paul C.; Cardon, Zoe G.

    Here, the microbiome presents great opportunities for understanding and improving the world around us and elucidating the interactions that compose it. The microbiome also poses tremendous challenges for mapping and manipulating the entangled networks of interactions among myriad diverse organisms. Here, we describe the opportunities, technical needs, and potential approaches to address these challenges, based on recent and upcoming advances in measurement and control at the nanoscale and beyond. Moreover, these technical needs will provide the basis for advancing the largely descriptive studies of the microbiome to the theoretical and mechanistic understandings that will underpin the discipline of microbiome engineering.more » We anticipate that the new tools and methods developed will also be more broadly useful in environmental monitoring, medicine, forensics, and other areas.« less

  20. Understanding microbiomes for plant disease control

    A rigorous understanding of the microbiomes associated with plants holds tremendous potential for suggesting new management targets that will more effectively manage pathogens and improve plant performance. Characterizing ecological interactions among microbial species within the phytobiome is essen...

  1. Tools for the microbiome. Nano and beyond

    DOE PAGES

    Biteen, Julie S.; Blainey, Paul C.; Cardon, Zoe G.; ...

    2015-12-22

    Here, the microbiome presents great opportunities for understanding and improving the world around us and elucidating the interactions that compose it. The microbiome also poses tremendous challenges for mapping and manipulating the entangled networks of interactions among myriad diverse organisms. Here, we describe the opportunities, technical needs, and potential approaches to address these challenges, based on recent and upcoming advances in measurement and control at the nanoscale and beyond. Moreover, these technical needs will provide the basis for advancing the largely descriptive studies of the microbiome to the theoretical and mechanistic understandings that will underpin the discipline of microbiome engineering.more » We anticipate that the new tools and methods developed will also be more broadly useful in environmental monitoring, medicine, forensics, and other areas.« less

  2. The Lung Microbiome After Lung Transplantation

    PubMed Central

    Becker, Julia B.; Poroyko, Valeriy

    2014-01-01

    Summary Lung transplantation survival remains significantly impacted by infections and the development of chronic rejection manifesting as bronchiolitis obliterans syndrome (BOS). Traditional microbiologic data has provided insight into the role of infections in BOS. Now, new non-culture-based techniques have been developed to characterize the entire population of microbes resident on the surfaces of the body, also known as the human microbiome. Early studies have identified that lung transplant patients have a different lung microbiome and have demonstrated the important finding that the transplant lung microbiome changes over time. Furthermore, both unique bacterial populations and longitudinal changes in the lung microbiome have now been suggested to play a role in the development of BOS. In the future, this technology will need to be combined with functional assays and assessment of the immune responses in the lung to help further explain the microbiome’s role in the failing lung allograft. PMID:24601662

  3. Understanding Caries From the Oral Microbiome Perspective.

    PubMed

    Tanner, Anne C R; Kressirer, Christine A; Faller, Lina L

    2016-07-01

    Dental caries is a major disease of the oral cavity with profound clinical significance. Caries results from a transition of a healthy oral microbiome into an acidogenic community of decreased microbial diversity in response to excessive dietary sugar intake. Microbiological cultivation, molecular identification, gene expression and metabolomic analyses show the importance of the entire microbial community in understanding the role of the microbiome in the pathology of caries.

  4. Metabolome of human gut microbiome is predictive of host dysbiosis.

    PubMed

    Larsen, Peter E; Dai, Yang

    2015-01-01

    Humans live in constant and vital symbiosis with a closely linked bacterial ecosystem called the microbiome, which influences many aspects of human health. When this microbial ecosystem becomes disrupted, the health of the human host can suffer; a condition called dysbiosis. However, the community compositions of human microbiomes also vary dramatically from individual to individual, and over time, making it difficult to uncover the underlying mechanisms linking the microbiome to human health. We propose that a microbiome's interaction with its human host is not necessarily dependent upon the presence or absence of particular bacterial species, but instead is dependent on its community metabolome; an emergent property of the microbiome. Using data from a previously published, longitudinal study of microbiome populations of the human gut, we extrapolated information about microbiome community enzyme profiles and metabolome models. Using machine learning techniques, we demonstrated that the aggregate predicted community enzyme function profiles and modeled metabolomes of a microbiome are more predictive of dysbiosis than either observed microbiome community composition or predicted enzyme function profiles. Specific enzyme functions and metabolites predictive of dysbiosis provide insights into the molecular mechanisms of microbiome-host interactions. The ability to use machine learning to predict dysbiosis from microbiome community interaction data provides a potentially powerful tool for understanding the links between the human microbiome and human health, pointing to potential microbiome-based diagnostics and therapeutic interventions.

  5. Elevated temperature drives kelp microbiome dysbiosis, while elevated carbon dioxide induces water microbiome disruption

    PubMed Central

    Morris, Megan M.; Brown, Matt; Doane, Michael; Edwards, Matthew S.; Michael, Todd P.; Dinsdale, Elizabeth A.

    2018-01-01

    Global climate change includes rising temperatures and increased pCO2 concentrations in the ocean, with potential deleterious impacts on marine organisms. In this case study we conducted a four-week climate change incubation experiment, and tested the independent and combined effects of increased temperature and partial pressure of carbon dioxide (pCO2), on the microbiomes of a foundation species, the giant kelp Macrocystis pyrifera, and the surrounding water column. The water and kelp microbiome responded differently to each of the climate stressors. In the water microbiome, each condition caused an increase in a distinct microbial order, whereas the kelp microbiome exhibited a reduction in the dominant kelp-associated order, Alteromondales. The water column microbiomes were most disrupted by elevated pCO2, with a 7.3 fold increase in Rhizobiales. The kelp microbiome was most influenced by elevated temperature and elevated temperature in combination with elevated pCO2. Kelp growth was negatively associated with elevated temperature, and the kelp microbiome showed a 5.3 fold increase Flavobacteriales and a 2.2 fold increase alginate degrading enzymes and sulfated polysaccharides. In contrast, kelp growth was positively associated with the combination of high temperature and high pCO2 ‘future conditions’, with a 12.5 fold increase in Planctomycetales and 4.8 fold increase in Rhodobacteriales. Therefore, the water and kelp microbiomes acted as distinct communities, where the kelp was stabilizing the microbiome under changing pCO2 conditions, but lost control at high temperature. Under future conditions, a new equilibrium between the kelp and the microbiome was potentially reached, where the kelp grew rapidly and the commensal microbes responded to an increase in mucus production. PMID:29474389

  6. Projections of oceanic N2O emissions in the 21st century using the IPSL Earth system model

    NASA Astrophysics Data System (ADS)

    Martinez-Rey, J.; Bopp, L.; Gehlen, M.; Tagliabue, A.; Gruber, N.

    2015-07-01

    The ocean is a substantial source of nitrous oxide (N2O) to the atmosphere, but little is known about how this flux might change in the future. Here, we investigate the potential evolution of marine N2O emissions in the 21st century in response to anthropogenic climate change using the global ocean biogeochemical model NEMO-PISCES. Assuming nitrification as the dominant N2O formation pathway, we implemented two different parameterizations of N2O production which differ primarily under low-oxygen (O2) conditions. When forced with output from a climate model simulation run under the business-as-usual high-CO2 concentration scenario (RCP8.5), our simulations suggest a decrease of 4 to 12 % in N2O emissions from 2005 to 2100, i.e., a reduction from 4.03/3.71 to 3.54/3.56 TgN yr-1 depending on the parameterization. The emissions decrease strongly in the western basins of the Pacific and Atlantic oceans, while they tend to increase above the oxygen minimum zones (OMZs), i.e., in the eastern tropical Pacific and in the northern Indian Ocean. The reduction in N2O emissions is caused on the one hand by weakened nitrification as a consequence of reduced primary and export production, and on the other hand by stronger vertical stratification, which reduces the transport of N2O from the ocean interior to the ocean surface. The higher emissions over the OMZ are linked to an expansion of these zones under global warming, which leads to increased N2O production, associated primarily with denitrification. While there are many uncertainties in the relative contribution and changes in the N2O production pathways, the increasing storage seems unequivocal and determines largely the decrease in N2O emissions in the future. From the perspective of a global climate system, the averaged feedback strength associated with the projected decrease in oceanic N2O emissions amounts to around -0.009 W m-2 K-1, which is comparable to the potential increase from terrestrial N2O sources. However

  7. The alligator gut microbiome and implications for archosaur symbioses

    PubMed Central

    Keenan, Sarah W.; Engel, Annette Summers; Elsey, Ruth M.

    2013-01-01

    Among vertebrate gastrointestinal microbiome studies, complete representation of taxa is limited, particularly among reptiles. Here, we provide evidence for previously unrecognized host-microbiome associations along the gastrointestinal tract from the American alligator, a crown archosaur with shared ancestry to extinct taxa, including dinosaurs. Microbiome compositional variations reveal that the digestive system consists of multiple, longitudinally heterogeneous microbiomes that strongly correlate to specific gastrointestinal tract organs, regardless of rearing histories or feeding status. A core alligator gut microbiome comprised of Fusobacteria, but depleted in Bacteroidetes and Proteobacteria common to mammalians, is compositionally unique from other vertebrate gut microbiomes, including other reptiles, fish, and herbivorous and carnivorous mammals. As such, modern alligator gut microbiomes advance our understanding of archosaur gut microbiome evolution, particularly if conserved host ecology has retained archosaur-specific symbioses over geologic time. PMID:24096888

  8. Final Report: The Human Microbiome as a Multipurpose Biomarker

    DTIC Science & Technology

    2015-11-23

    Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 microbiome, biomarker, microbial forensics, microbial ecology , identifiability REPORT...temporal variation in the ecology of the human microbiome, this work demonstrated the feasibility of microbiome-based identifiability for the first time...a result with important ethical implications for microbiome study design. In order to construct metagenomic codes that are stable over time, we

  9. Comparisons of microbiomes in conventional and alternative poultry production systems

    With the advent of new sequencing technologies and platforms, entire microbiomes are more easily characterized than ever before, while initially used more as a surveying tool to determine what microbial taxa (and their relative abundance) comprise various microbiomes, using microbiome data in a more...

  10. Analyses of the Microbial Diversity across the Human Microbiome

    PubMed Central

    Li, Kelvin; Bihan, Monika; Yooseph, Shibu; Methé, Barbara A.

    2012-01-01

    Analysis of human body microbial diversity is fundamental to understanding community structure, biology and ecology. The National Institutes of Health Human Microbiome Project (HMP) has provided an unprecedented opportunity to examine microbial diversity within and across body habitats and individuals through pyrosequencing-based profiling of 16 S rRNA gene sequences (16 S) from habits of the oral, skin, distal gut, and vaginal body regions from over 200 healthy individuals enabling the application of statistical techniques. In this study, two approaches were applied to elucidate the nature and extent of human microbiome diversity. First, bootstrap and parametric curve fitting techniques were evaluated to estimate the maximum number of unique taxa, Smax, and taxa discovery rate for habitats across individuals. Next, our results demonstrated that the variation of diversity within low abundant taxa across habitats and individuals was not sufficiently quantified with standard ecological diversity indices. This impact from low abundant taxa motivated us to introduce a novel rank-based diversity measure, the Tail statistic, (“τ”), based on the standard deviation of the rank abundance curve if made symmetric by reflection around the most abundant taxon. Due to τ’s greater sensitivity to low abundant taxa, its application to diversity estimation of taxonomic units using taxonomic dependent and independent methods revealed a greater range of values recovered between individuals versus body habitats, and different patterns of diversity within habitats. The greatest range of τ values within and across individuals was found in stool, which also exhibited the most undiscovered taxa. Oral and skin habitats revealed variable diversity patterns, while vaginal habitats were consistently the least diverse. Collectively, these results demonstrate the importance, and motivate the introduction, of several visualization and analysis methods tuned specifically for next

  11. The microbiome in urogenital schistosomiasis and induced bladder pathologies

    PubMed Central

    Adebayo, Adewale S.; Survayanshi, Mangesh; Bhute, Shrikanth; Agunloye, Atinuke M.; Isokpehi, Raphael D.; Shouche, Yogesh S.

    2017-01-01

    Background Human schistosomiasis is a highly prevalent neglected tropical disease (NTD) caused by Schistosoma species. Research on the molecular mechanisms influencing the outcomes of bladder infection by Schistosoma haematobium is urgently needed to develop new diagnostics, therapeutics and infection prevention strategies. The objective of the research study was to determine the microbiome features and changes in urine during urogenital schistosomiasis and induced bladder pathologies. Methodology Seventy participants from Eggua, southwestern Nigeria provided morning urine samples and were screened for urogenital schistosomiasis infection and bladder pathologies in a cross-sectional study. Highthroughput NGS sequencing was carried out, targeting the 16S V3 region. Filtered reads were processed and analyzed in a bioinformatics pipeline. Principal findings The study participants (36 males and 34 females, between ages 15 and 65) were categorized into four groups according to status of schistosomiasis infection and bladder pathology. Data analytics of the next-generation sequencing reads revealed that Proteobacteria and Firmicutes dominated and had influence on microbiome structure of both non-infected persons and persons with urogenital schistosomiasis. Furthermore, gender and age influenced taxa abundance independent of infection or bladder pathology. Several taxa distinguished urogenital schistosomiasis induced bladder pathologies from urogenital schistosomiasis infection alone and from healthy persons, including known immune-stimulatory taxa such as Fusobacterium, Sphingobacterium and Enterococcus. Some of these significant taxa, especially Sphingobacterium were projected as markers of infection, while several genera including potentially beneficial taxa such as Trabulsiella and Weissella, were markers of the non-infected. Finally, expected changes in protein functional categories were observed to relate to cellular maintenance and lipid metabolism. Conclusion The

  12. Microbial Co-occurrence Relationships in the Human Microbiome

    PubMed Central

    Izard, Jacques; Segata, Nicola; Gevers, Dirk

    2012-01-01

    The healthy microbiota show remarkable variability within and among individuals. In addition to external exposures, ecological relationships (both oppositional and symbiotic) between microbial inhabitants are important contributors to this variation. It is thus of interest to assess what relationships might exist among microbes and determine their underlying reasons. The initial Human Microbiome Project (HMP) cohort, comprising 239 individuals and 18 different microbial habitats, provides an unprecedented resource to detect, catalog, and analyze such relationships. Here, we applied an ensemble method based on multiple similarity measures in combination with generalized boosted linear models (GBLMs) to taxonomic marker (16S rRNA gene) profiles of this cohort, resulting in a global network of 3,005 significant co-occurrence and co-exclusion relationships between 197 clades occurring throughout the human microbiome. This network revealed strong niche specialization, with most microbial associations occurring within body sites and a number of accompanying inter-body site relationships. Microbial communities within the oropharynx grouped into three distinct habitats, which themselves showed no direct influence on the composition of the gut microbiota. Conversely, niches such as the vagina demonstrated little to no decomposition into region-specific interactions. Diverse mechanisms underlay individual interactions, with some such as the co-exclusion of Porphyromonaceae family members and Streptococcus in the subgingival plaque supported by known biochemical dependencies. These differences varied among broad phylogenetic groups as well, with the Bacilli and Fusobacteria, for example, both enriched for exclusion of taxa from other clades. Comparing phylogenetic versus functional similarities among bacteria, we show that dominant commensal taxa (such as Prevotellaceae and Bacteroides in the gut) often compete, while potential pathogens (e.g. Treponema and Prevotella in the

  13. Gut Microbiome of the Canadian Arctic Inuit

    PubMed Central

    Tromas, Nicolas; Amyot, Marc

    2017-01-01

    ABSTRACT Diet is a major determinant of community composition in the human gut microbiome, and “traditional” diets have been associated with distinct and highly diverse communities, compared to Western diets. However, most traditional diets studied have been those of agrarians and hunter-gatherers consuming fiber-rich diets. In contrast, the Inuit of the Canadian Arctic have been consuming a traditional diet low in carbohydrates and rich in animal fats and protein for thousands of years. We hypothesized that the Inuit diet and lifestyle would be associated with a distinct microbiome. We used deep sequencing of the 16S rRNA gene to compare the gut microbiomes of Montrealers with a Western diet to those of the Inuit consuming a range of traditional and Western diets. At the overall microbial community level, the gut microbiomes of Montrealers and Inuit were indistinguishable and contained similar levels of microbial diversity. However, we observed significant differences in the relative abundances of certain microbial taxa down to the subgenus level using oligotyping. For example, Prevotella spp., which have been previously associated with high-fiber diets, were enriched in Montrealers and among the Inuit consuming a Western diet. The gut microbiomes of Inuit consuming a traditional diet also had significantly less genetic diversity within the Prevotella genus, suggesting that a low-fiber diet might not only select against Prevotella but also reduce its diversity. Other microbes, such as Akkermansia, were associated with geography as well as diet, suggesting limited dispersal to the Arctic. Our report provides a snapshot of the Inuit microbiome as Western-like in overall community structure but distinct in the relative abundances and diversity of certain genera and strains. IMPORTANCE Non-Western populations have been shown to have distinct gut microbial communities shaped by traditional diets. The hitherto-uncharacterized microbiome of the Inuit may help us to

  14. Evaluation of the microbiome in children's appendicitis.

    PubMed

    Salö, Martin; Marungruang, Nittaya; Roth, Bodil; Sundberg, Tiia; Stenström, Pernilla; Arnbjörnsson, Einar; Fåk, Frida; Ohlsson, Bodil

    2017-01-01

    The role of the microbiome has been widely discussed in the etiology of appendicitis. The primary aim was to evaluate the microbiome in the normal appendix and in appendicitis specifically divided into the three clinically and histopathologically defined grades of inflammation. Secondary aims were to examine whether there were any microbiome differences between proximal and distal appendices, and relate the microbiome with histopathological findings. A prospective pilot study was conducted of children undergoing appendectomy for appendicitis. The diagnosis was based on histopathological analysis. Children with incidental appendectomy were used as controls. The proximal and distal mucosa from the appendices were analyzed with 16S rRNA gene sequencing. A total of 22 children, 3 controls and 19 appendicitis patients; 11 phlegmonous, 4 gangrenous, and 4 perforated appendices, were prospectively included. The amount of Fusobacterium increased and Bacteroides decreased in phlegmonous and perforated appendicitis compared to controls, but statistical significance was not reached, and this pattern was not seen in gangrenous appendicitis. No relation could be seen between different bacteria and the grade of inflammation, and there was a wide variation of abundances at phylum, genus, and species level within every specific group of patients. Further, no significant differences could be detected when comparing the microbiome in proximal and distal mucosa, which may be because the study was underpowered. A trend with more abundance of Fusobacteria in the distal mucosa was seen in appendicitis patients with obstruction (25 and 13 %, respectively, p = 0.06). The pattern of microbiome differed not only between groups, but also within groups. However, no statistically significant differences could be found in the microbiome between groups or clinical conditions. No correlation between a specific bacteria and grade of inflammation was found. In the vast majority of cases of

  15. Metagenomic investigation of gastrointestinal microbiome in cattle

    PubMed Central

    Kim, Minseok; Park, Tansol; Yu, Zhongtang

    2017-01-01

    The gastrointestinal (GI) tract, including the rumen and the other intestinal segments of cattle, harbors a diverse, complex, and dynamic microbiome that drives feed digestion and fermentation in cattle, determining feed efficiency and output of pollutants. This microbiome also plays an important role in affecting host health. Research has been conducted for more than a century to understand the microbiome and its relationship to feed efficiency and host health. The traditional cultivation-based research elucidated some of the major metabolism, but studies using molecular biology techniques conducted from late 1980’s to the late early 2000’s greatly expanded our view of the diversity of the rumen and intestinal microbiome of cattle. Recently, metagenomics has been the primary technology to characterize the GI microbiome and its relationship with host nutrition and health. This review addresses the main methods/techniques in current use, the knowledge gained, and some of the challenges that remain. Most of the primers used in quantitative real-time polymerase chain reaction quantification and diversity analysis using metagenomics of ruminal bacteria, archaea, fungi, and protozoa were also compiled. PMID:28830126

  16. From microbiome to infectome in autoimmunity.

    PubMed

    Bogdanos, Dimitrios P; Sakkas, Lazaros I

    2017-07-01

    The current review discusses the pros and cons of the microbiome studies conducted in search of the association between microbiota and autoimmunity. We focus on the role of infectome and autoinfectome as a bridge to link the findings of microbiome studies with those emerging from investigations of the role of specific viruses and antiviral responses as triggers of autoimmunity (through various mechanisms such as molecular mimicry). The 'usual suspects', such as herpetoviruses and Escherichia coli, are thoroughly discussed in light of the data emerged by the microbiome studies, using as examples specific autoimmune rheumatic diseases and inflammatory bowel diseases. We conclude that the studies of the oral cavity, gastrointestinal, and urinary tract microbiome are informative but can only be useful if further explored from the infectome perspective. This means that the plethora of bacteria associated with autoimmune diseases from microbiome studies can be and must be tested experimentally. If certain bacteria are associated directly or indirectly with autoimmune diseases, specific immunological mechanisms must be identified.

  17. Global diversity in the human salivary microbiome.

    PubMed

    Nasidze, Ivan; Li, Jing; Quinque, Dominique; Tang, Kun; Stoneking, Mark

    2009-04-01

    The human salivary microbiome may play a role in diseases of the oral cavity and interact with microbiomes from other parts of the human body (in particular, the intestinal tract), but little is known about normal variation in the salivary microbiome. We analyzed 14,115 partial ( approximately 500 bp) 16S ribosomal RNA (rRNA) sequences from saliva samples from 120 healthy individuals (10 individuals from each of 12 worldwide locations). These sequences could be assigned to 101 known bacterial genera, of which 39 were not previously reported from the human oral cavity; phylogenetic analysis suggests that an additional 64 unknown genera are present. There is high diversity in the salivary microbiome within and between individuals, but little geographic structure. Overall, approximately 13.5% of the total variance in the composition of genera is due to differences among individuals, which is remarkably similar to the fraction of the total variance in neutral genetic markers that can be attributed to differences among human populations. Investigation of some environmental variables revealed a significant association between the genetic distances among locations and the distance of each location from the equator. Further characterization of the enormous diversity revealed here in the human salivary microbiome will aid in elucidating the role it plays in human health and disease, and in the identification of potentially informative species for studies of human population history.

  18. The core microbiome bonds the Alpine bog vegetation to a transkingdom metacommunity.

    PubMed

    Bragina, Anastasia; Berg, Christian; Berg, Gabriele

    2015-09-01

    Bog ecosystems fulfil important functions in Earth's carbon and water turnover. While plant communities and their keystone species Sphagnum have been well studied, less is known about the microbial communities associated with them. To study our hypothesis that bog plants share an essential core of their microbiome despite their different phylogenetic origins, we analysed four plant community plots with 24 bryophytes, vascular plants and lichen species in two Alpine bogs in Austria by 16S rDNA amplicon sequencing followed by bioinformatic analyses. The overall bog microbiome was classified into 32 microbial phyla, while Proteobacteria (30.8%), Verrucomicrobia (20.3%) and Planctomycetes (15.1%) belonged to the most abundant groups. Interestingly, the archaeal phylum Euryarcheota represented 7.2% of total microbial abundance. However, a high portion of micro-organisms remained unassigned at phylum and class level, respectively. The core microbiome of the bog vegetation contained 177 operational taxonomic units (OTUs) (150 526 seq.) and contributed to 49.5% of the total microbial abundance. Only a minor portion of associated core micro-organisms was host specific for examined plant groups (5.9-11.6%). Using our new approach to analyse plant-microbial communities in an integral framework of ecosystem, vegetation and microbiome, we demonstrated that bog vegetation harboured a core microbiome that is shared between plants and lichens over the whole ecosystem and formed a transkingdom metacommunity. All micro- and macro-organisms are connected to keystone Sphagnum mosses via set of microbial species, for example Burkholderia bryophila which was found associated with a wide spectrum of host plants and is known for a beneficial plant-microbe interaction. © 2015 John Wiley & Sons Ltd.

  19. Earth Science

    1991-01-01

    In July 1990, the Marshall Space Flight Center, in a joint project with the Department of Defense/Air Force Space Test Program, launched the Combined Release and Radiation Effects Satellite (CRRES) using an Atlas I launch vehicle. The mission was designed to study the effects of artificial ion clouds produced by chemical releases on the Earth's ionosphere and magnetosphere, and to monitor the effects of space radiation environment on sophisticated electronics.

  20. Microbiome therapeutics - Advances and challenges.

    PubMed

    Mimee, Mark; Citorik, Robert J; Lu, Timothy K

    2016-10-01

    The microbial community that lives on and in the human body exerts a major impact on human health, from metabolism to immunity. In order to leverage the close associations between microbes and their host, development of therapeutics targeting the microbiota has surged in recent years. Here, we discuss current additive and subtractive strategies to manipulate the microbiota, focusing on bacteria engineered to produce therapeutic payloads, consortia of natural organisms and selective antimicrobials. Further, we present challenges faced by the community in the development of microbiome therapeutics, including designing microbial therapies that are adapted for specific geographies in the body, stable colonization with microbial therapies, discovery of clinically relevant biosensors, robustness of engineered synthetic gene circuits and addressing safety and biocontainment concerns. Moving forward, collaboration between basic and applied researchers and clinicians to address these challenges will poise the field to herald an age of next-generation, cellular therapies that draw on novel findings in basic research to inform directed augmentation of the human microbiota. Copyright © 2016. Published by Elsevier B.V.

  1. Alaska's Secondary Science Teachers and Students Receive Earth Systems Science Knowledge, GIS Know How and University Technical Support for Pre- College Research Experiences: The EDGE Project

    NASA Astrophysics Data System (ADS)

    Connor, C. L.; Prakash, A.

    2007-12-01

    Alaska's secondary school teachers are increasingly required to provide Earth systems science (ESS) education that integrates student observations of local natural processes related to rapid climate change with geospatial datasets and satellite imagery using Geographic Information Systems (GIS) technology. Such skills are also valued in various employment sectors of the state where job opportunities requiring Earth science and GIS training are increasing. University of Alaska's EDGE (Experiential Discoveries in Geoscience Education) program has provided training and classroom resources for 3 cohorts of inservice Alaska science and math teachers in GIS and Earth Systems Science (2005-2007). Summer workshops include geologic field experiences, GIS instruction, computer equipment and technical support for groups of Alaska high school (HS) and middle school (MS) science teachers each June and their students in August. Since 2005, EDGE has increased Alaska science and math teachers' Earth science content knowledge and developed their GIS and computer skills. In addition, EDGE has guided teachers using a follow-up, fall online course that provided more extensive ESS knowledge linked with classroom standards and provided course content that was directly transferable into their MS and HS science classrooms. EDGE teachers were mentored by University faculty and technical staff as they guided their own students through semester-scale, science fair style projects using geospatial data that was student- collected. EDGE program assessment indicates that all teachers have improved their ESS knowledge, GIS knowledge, and the use of technology in their classrooms. More than 230 middle school students have learned GIS, from EDGE teachers and 50 EDGE secondary students have conducted original research related to landscape change and its impacts on their own communities. Longer-term EDGE goals include improving student performance on the newly implemented (spring 2008) 10th grade

  2. Microbiome influences on insect host vector competence

    PubMed Central

    Weiss, Brian

    2011-01-01

    Insect symbioses lack the complexity and diversity of those associated with higher eukaryotic hosts. Symbiotic microbiomes are beneficial to their insect hosts in many ways, including dietary supplementation, tolerance to environmental perturbations and maintenance and/or enhancement of host immune system homeostasis. Recent studies have also highlighted the importance of the microbiome in the context of host pathogen transmission processes. Here we provide an overview of the relationship between insect disease vectors, such as tsetse flies and mosquitoes, and their associated microbiome. Several mechanisms are discussed through which symbiotic microbes may influence their host’s ability to transmit pathogens, as well as potential disease control strategies that harness symbiotic microbes to reduce pathogen transmission through an insect vector. PMID:21697014

  3. Human microbiome visualization using 3D technology.

    PubMed

    Moore, Jason H; Lari, Richard Cowper Sal; Hill, Douglas; Hibberd, Patricia L; Madan, Juliette C

    2011-01-01

    High-throughput sequencing technology has opened the door to the study of the human microbiome and its relationship with health and disease. This is both an opportunity and a significant biocomputing challenge. We present here a 3D visualization methodology and freely-available software package for facilitating the exploration and analysis of high-dimensional human microbiome data. Our visualization approach harnesses the power of commercial video game development engines to provide an interactive medium in the form of a 3D heat map for exploration of microbial species and their relative abundance in different patients. The advantage of this approach is that the third dimension provides additional layers of information that cannot be visualized using a traditional 2D heat map. We demonstrate the usefulness of this visualization approach using microbiome data collected from a sample of premature babies with and without sepsis.

  4. The Maternal Gut Microbiome During Pregnancy.

    PubMed

    Edwards, Sara M; Cunningham, Solveig A; Dunlop, Anne L; Corwin, Elizabeth J

    The gut microbiome is a critical component of an individual's metabolism and overall health. The prenatal period is marked by unique inflammatory and immune changes that alter maternal gut function and bacterial composition as the pregnancy advances. The composition of the maternal gut microbiome contributes to obstetric outcomes with long-term health sequelae for mother and child. Estrogen and progesterone also have an impact on gut function, especially during the prenatal period. These physiologic changes in pregnancy allow for adjustments in maternal metabolism and weight necessary to support the pregnancy. Normal hormonal, metabolic, and immunologic changes to the maternal gut microbiome throughout the prenatal period are reviewed, including relevant implications for nurses providing care for pregnant women.

  5. Human genetic variation and the gut microbiome in disease.

    PubMed

    Hall, Andrew Brantley; Tolonen, Andrew C; Xavier, Ramnik J

    2017-11-01

    Taxonomic and functional changes to the composition of the gut microbiome have been implicated in multiple human diseases. Recent microbiome genome-wide association studies reveal that variants in many human genes involved in immunity and gut architecture are associated with an altered composition of the gut microbiome. Although many factors can affect the microbial organisms residing in the gut, a number of recent findings support the hypothesis that certain host genetic variants predispose an individual towards microbiome dysbiosis. This condition, in which the normal microbiome population structure is disturbed, is a key feature in disorders of metabolism and immunity.

  6. Earth Observation-Supported Service Platform for the Development and Provision of Thematic Information on the Built Environment - the Tep-Urban Project

    NASA Astrophysics Data System (ADS)

    Esch, T.; Asamer, H.; Boettcher, M.; Brito, F.; Hirner, A.; Marconcini, M.; Mathot, E.; Metz, A.; Permana, H.; Soukop, T.; Stanek, F.; Kuchar, S.; Zeidler, J.; Balhar, J.

    2016-06-01

    The Sentinel fleet will provide a so-far unique coverage with Earth observation data and therewith new opportunities for the implementation of methodologies to generate innovative geo-information products and services. It is here where the TEP Urban project is supposed to initiate a step change by providing an open and participatory platform based on modern ICT technologies and services that enables any interested user to easily exploit Earth observation data pools, in particular those of the Sentinel missions, and derive thematic information on the status and development of the built environment from these data. Key component of TEP Urban project is the implementation of a web-based platform employing distributed high-level computing infrastructures and providing key functionalities for i) high-performance access to satellite imagery and derived thematic data, ii) modular and generic state-of-the art pre-processing, analysis, and visualization techniques, iii) customized development and dissemination of algorithms, products and services, and iv) networking and communication. This contribution introduces the main facts about the TEP Urban project, including a description of the general objectives, the platform systems design and functionalities, and the preliminary portfolio products and services available at the TEP Urban platform.

  7. Determining the culturability of the rumen bacterial microbiome

    PubMed Central

    Creevey, Christopher J; Kelly, William J; Henderson, Gemma; Leahy, Sinead C

    2014-01-01

    The goal of the Hungate1000 project is to generate a reference set of rumen microbial genome sequences. Toward this goal we have carried out a meta-analysis using information from culture collections, scientific literature, and the NCBI and RDP databases and linked this with a comparative study of several rumen 16S rRNA gene-based surveys. In this way we have attempted to capture a snapshot of rumen bacterial diversity to examine the culturable fraction of the rumen bacterial microbiome. Our analyses have revealed that for cultured rumen bacteria, there are many genera without a reference genome sequence. Our examination of culture-independent studies highlights that there are few novel but many uncultured taxa within the rumen bacterial microbiome. Taken together these results have allowed us to compile a list of cultured rumen isolates that are representative of abundant, novel and core bacterial species in the rumen. In addition, we have identified taxa, particularly within the phylum Bacteroidetes, where further cultivation efforts are clearly required. This information is being used to guide the isolation efforts and selection of bacteria from the rumen microbiota for sequencing through the Hungate1000. PMID:24986151

  8. Metabolome of human gut microbiome is predictive of host dysbiosis

    DOE PAGES

    Larsen, Peter E.; Dai, Yang

    2015-09-14

    Background: Humans live in constant and vital symbiosis with a closely linked bacterial ecosystem called the microbiome, which influences many aspects of human health. When this microbial ecosystem becomes disrupted, the health of the human host can suffer; a condition called dysbiosis. The community compositions of human microbiomes also vary dramatically from individual to individual, and over time, making it difficult to uncover the underlying mechanisms linking the microbiome to human health. We propose that a microbiome’s interaction with its human host is not necessarily dependent upon the presence or absence of particular bacterial species, but instead is dependent onmore » its community metabolome; an emergent property of the microbiome. Results: Using data from a previously published, longitudinal study of microbiome populations of the human gut, we extrapolated information about microbiome community enzyme profiles and metabolome models. Using machine learning techniques, we demonstrated that the aggregate predicted community enzyme function profiles and modeled metabolomes of a microbiome are more predictive of dysbiosis than either observed microbiome community composition or predicted enzyme function profiles. Conclusions: Specific enzyme functions and metabolites predictive of dysbiosis provide insights into the molecular mechanisms of microbiome–host interactions. The ability to use machine learning to predict dysbiosis from microbiome community interaction data provides a potentially powerful tool for understanding the links between the human microbiome and human health, pointing to potential microbiome-based diagnostics and therapeutic interventions.« less

  9. Metabolome of human gut microbiome is predictive of host dysbiosis

    SciT

    Larsen, Peter E.; Dai, Yang

    Background: Humans live in constant and vital symbiosis with a closely linked bacterial ecosystem called the microbiome, which influences many aspects of human health. When this microbial ecosystem becomes disrupted, the health of the human host can suffer; a condition called dysbiosis. The community compositions of human microbiomes also vary dramatically from individual to individual, and over time, making it difficult to uncover the underlying mechanisms linking the microbiome to human health. We propose that a microbiome’s interaction with its human host is not necessarily dependent upon the presence or absence of particular bacterial species, but instead is dependent onmore » its community metabolome; an emergent property of the microbiome. Results: Using data from a previously published, longitudinal study of microbiome populations of the human gut, we extrapolated information about microbiome community enzyme profiles and metabolome models. Using machine learning techniques, we demonstrated that the aggregate predicted community enzyme function profiles and modeled metabolomes of a microbiome are more predictive of dysbiosis than either observed microbiome community composition or predicted enzyme function profiles. Conclusions: Specific enzyme functions and metabolites predictive of dysbiosis provide insights into the molecular mechanisms of microbiome–host interactions. The ability to use machine learning to predict dysbiosis from microbiome community interaction data provides a potentially powerful tool for understanding the links between the human microbiome and human health, pointing to potential microbiome-based diagnostics and therapeutic interventions.« less

  10. Metabolome of human gut microbiome is predictive of host dysbiosis

    SciT

    Larsen, Peter E.; Dai, Yang

    Background: Humans live in constant and vital symbiosis with a closely linked bacterial ecosystem called the microbiome, which influences many aspects of human health. When this microbial ecosystem becomes disrupted, the health of the human host can suffer; a condition called dysbiosis. However, the community compositions of human microbiomes also vary dramatically from individual to individual, and over time, making it difficult to uncover the underlying mechanisms linking the microbiome to human health. We propose that a microbiome’s interaction with its human host is not necessarily dependent upon the presence or absence of particular bacterial species, but instead is dependentmore » on its community metabolome; an emergent property of the microbiome. Results: Using data from a previously published, longitudinal study of microbiome populations of the human gut, we extrapolated information about microbiome community enzyme profiles and metabolome models. Using machine learning techniques, we demonstrated that the aggregate predicted community enzyme function profiles and modeled metabolomes of a microbiome are more predictive of dysbiosis than either observed microbiome community composition or predicted enzyme function profiles. Conclusions: Specific enzyme functions and metabolites predictive of dysbiosis provide insights into the molecular mechanisms of microbiome–host interactions. The ability to use machine learning to predict dysbiosis from microbiome community interaction data provides a potentially powerful tool for understanding the links between the human microbiome and human health, pointing to potential microbiome-based diagnostics and therapeutic interventions.« less

  11. The noncolonic microbiome: does it really matter?

    PubMed

    Lawson, R Daniel; Coyle, Walter J

    2010-08-01

    About 100 trillion microorganisms compose the microbiome of the gastrointestinal tract and are predominantly found within the colon. Until recently, few bacteria were thought to inhabit the normal healthy esophagus and stomach. However, contemporary studies using molecular techniques have contradicted these assumptions. In this review, we summarize the pertinent findings of these studies that demonstrate established, complex mixed-microbial communities within the foregut in both health and disease. These studies contribute to improved understanding of interactions between the host immunity and the microbiome that may ultimately allow for novel therapeutic targets.

  12. The infant microbiome development: mom matters

    PubMed Central

    Mueller, Noel T.; Bakacs, Elizabeth; Combellick, Joan; Grigoryan, Zoya; Dominguez-Bello, Maria G.

    2015-01-01

    The infant microbiome plays an essential role in human health and its assembly is determined by maternal– offspring exchanges of microbiota. This process is affected by several practices, including Cesarean section (C-section), perinatal antibiotics, and formula feeding, that have been linked to increased risks of metabolic and immune diseases. Here we review recent knowledge about the impacts on infant microbiome assembly, discuss preventive and restorative strategies to ameliorate the effects of these impacts, and highlight where research is needed to advance this field and improve the health of future generations. PMID:25578246

  13. Rapid changes in the gut microbiome during human evolution

    PubMed Central

    Moeller, Andrew H.; Li, Yingying; Mpoudi Ngole, Eitel; Ahuka-Mundeke, Steve; Lonsdorf, Elizabeth V.; Pusey, Anne E.; Peeters, Martine; Hahn, Beatrice H.; Ochman, Howard

    2014-01-01

    Humans are ecosystems containing trillions of microorganisms, but the evolutionary history of this microbiome is obscured by a lack of knowledge about microbiomes of African apes. We sequenced the gut communities of hundreds of chimpanzees, bonobos, and gorillas and developed a phylogenetic approach to reconstruct how present-day human microbiomes have diverged from those of ancestral populations. Compositional change in the microbiome was slow and clock-like during African ape diversification, but human microbiomes have deviated from the ancestral state at an accelerated rate. Relative to the microbiomes of wild apes, human microbiomes have lost ancestral microbial diversity while becoming specialized for animal-based diets. Individual wild apes cultivate more phyla, classes, orders, families, genera, and species of bacteria than do individual humans across a range of societies. These results indicate that humanity has experienced a depletion of the gut flora since diverging from Pan. PMID:25368157

  14. Rapid changes in the gut microbiome during human evolution.

    PubMed

    Moeller, Andrew H; Li, Yingying; Mpoudi Ngole, Eitel; Ahuka-Mundeke, Steve; Lonsdorf, Elizabeth V; Pusey, Anne E; Peeters, Martine; Hahn, Beatrice H; Ochman, Howard

    2014-11-18

    Humans are ecosystems containing trillions of microorganisms, but the evolutionary history of this microbiome is obscured by a lack of knowledge about microbiomes of African apes. We sequenced the gut communities of hundreds of chimpanzees, bonobos, and gorillas and developed a phylogenetic approach to reconstruct how present-day human microbiomes have diverged from those of ancestral populations. Compositional change in the microbiome was slow and clock-like during African ape diversification, but human microbiomes have deviated from the ancestral state at an accelerated rate. Relative to the microbiomes of wild apes, human microbiomes have lost ancestral microbial diversity while becoming specialized for animal-based diets. Individual wild apes cultivate more phyla, classes, orders, families, genera, and species of bacteria than do individual humans across a range of societies. These results indicate that humanity has experienced a depletion of the gut flora since diverging from Pan.

  15. Catalog of earth photographs from the Apollo-Soyuz test project. [listing cloud photographs and data acquired at time photograph was taken

    NASA Technical Reports Server (NTRS)

    El-Baz, F. (Editor)

    1979-01-01

    Information is given on earth photographs obtained by the Apollo astronauts during the Apollo Soyuz Test Project. The data are arranged in three sections. A map index shows the boundaries of each photograph and is used for a quick survey of the coverage for a given geographical area. A tabular index provides the following data: list of photographs by serial number, description of geographic location, latitude and longitude of the center point of the photograph, date when photograph was taken, ground elapsed time, revolution number of Apollo spacecraft, approximate spacecraft altitude, tilt, sun angle, camera, and lens. The photographic index provides same size black and white prints made from the original color negatives.

  16. Insights into the human oral microbiome.

    PubMed

    Verma, Digvijay; Garg, Pankaj Kumar; Dubey, Ashok Kumar

    2018-05-01

    Human oral cavity harbors the second most abundant microbiota after the gastrointestinal tract. The expanded Human Oral Microbiome Database (eHOMD) that was last updated on November 22, 2017, contains the information of approximately 772 prokaryotic species, where 70% is cultivable, and 30% belong to the uncultivable class of microorganisms along with whole genome sequences of 482 taxa. Out of 70% culturable species, 57% have already been assigned to their names. The 16S rDNA profiling of the healthy oral cavity categorized the inhabitant bacteria into six broad phyla, viz. Firmicutes, Actinobacteria, Proteobacteria, Fusobacteria, Bacteroidetes and Spirochaetes constituting 96% of total oral bacteria. These hidden oral micro-inhabitants exhibit a direct influence on human health, from host's metabolism to immune responses. Altered oral microflora has been observed in several diseases such as diabetes, bacteremia, endocarditis, cancer, autoimmune disease and preterm births. Therefore, it becomes crucial to understand the oral microbial diversity and how it fluctuates under diseased/perturbed conditions. Advances in metagenomics and next-generation sequencing techniques generate rapid sequences and provide extensive information of inhabitant microorganisms of a niche. Thus, the retrieved information can be utilized for developing microbiome-based biomarkers for their use in early diagnosis of oral and associated diseases. Besides, several apex companies have shown keen interest in oral microbiome for its diagnostic and therapeutic potential indicating a vast market opportunity. This review gives an insight of various associated aspects of the human oral microbiome.

  17. Childhood malnutrition and the intestinal microbiome.

    PubMed

    Kane, Anne V; Dinh, Duy M; Ward, Honorine D

    2015-01-01

    Malnutrition contributes to almost half of all deaths in children under the age of 5 y, particularly those who live in resource-constrained areas. Those who survive frequently suffer from long-term sequelae including growth failure and neurodevelopmental impairment. Malnutrition is part of a vicious cycle of impaired immunity, recurrent infections, and worsening malnutrition. Recently, alterations in the gut microbiome have also been strongly implicated in childhood malnutrition. It has been suggested that malnutrition may delay the normal development of the gut microbiota in early childhood or force it toward an altered composition that lacks the required functions for healthy growth and/or increases the risk for intestinal inflammation. This review addresses our current understanding of the beneficial contributions of gut microbiota to human nutrition (and conversely the potential role of changes in that community to malnutrition), the process of acquiring an intestinal microbiome, potential influences of malnutrition on the developing microbiota, and the evidence directly linking alterations in the intestinal microbiome to childhood malnutrition. We review recent studies on the association between alterations in the intestinal microbiome and early childhood malnutrition and discuss them in the context of implications for intervention or prevention of the devastation caused by malnutrition.

  18. Sinonasal microbiome sampling: a comparison of techniques.

    PubMed

    Bassiouni, Ahmed; Cleland, Edward John; Psaltis, Alkis James; Vreugde, Sarah; Wormald, Peter-John

    2015-01-01

    The role of the sino-nasal microbiome in CRS remains unclear. We hypothesized that the bacteria within mucosal-associated biofilms may be different from the more superficial-lying, free-floating bacteria in the sinuses and that this may impact on the microbiome results obtained. This study investigates whether there is a significant difference in the microbiota of a sinonasal mucosal tissue sample versus a swab sample. Cross-sectional study with paired design. Mucosal biopsy and swab samples were obtained intra-operatively from the ethmoid sinuses of 6 patients with CRS. Extracted DNA was sequenced on a Roche-454 sequencer using 16S-rRNA gene targeted primers. Data were analyzed using QIIME 1.8 software package. At a maximum subsampling depth of 1,100 reads, the mean observed species richness was 33.3 species (30.6 for swab, versus 36 for mucosa; p > 0.05). There was no significant difference in phylogenetic and non-phylogenetic alpha diversity metrics (Faith's PD_Whole_Tree and Shannon's index) between the two sampling methods (p > 0.05). The type of sample also had no significant effect on phylogenetic and non-phylogenetic beta diversity metrics (Unifrac and Bray-Curtis; p > 0.05). We observed no significant difference between the microbiota of mucosal tissue and swab samples. This suggests that less invasive swab samples are representative of the sinonasal mucosa microbiome and can be used for future sinonasal microbiome studies.

  19. Social attraction mediated by fruit flies' microbiome.

    PubMed

    Venu, Isvarya; Durisko, Zachary; Xu, Jianping; Dukas, Reuven

    2014-04-15

    Larval and adult fruit flies are attracted to volatiles emanating from food substrates that have been occupied by larvae. We tested whether such volatiles are emitted by the larval gut bacteria by conducting tests under bacteria-free (axenic) conditions. We also tested attraction to two bacteria species, Lactobacillus brevis, which we cultured from larvae in our lab, and L. plantarum, a common constituent of fruit flies' microbiome in other laboratory populations and in wild fruit flies. Neither larvae nor adults showed attraction to axenic food that had been occupied by axenic larvae, but both showed the previously reported attraction to standard food that had been occupied by larvae with an intact microbiome. Larvae also showed significant attraction to volatiles from axenic food and larvae to which we added only either L. brevis or L. plantarum, and volatiles from L. brevis reared on its optimal growth medium. Controlled learning experiments indicated that larvae experienced with both standard and axenic used food do not perceive either as superior, while focal larvae experienced with simulated used food, which contains burrows, perceive it as superior to unused food. Our results suggest that flies rely on microbiome-derived volatiles for long-distance attraction to suitable food patches. Under natural settings, fruits often contain harmful fungi and bacteria, and both L. brevis and L. plantarum produce compounds that suppress the growth of some antagonistic fungi and bacteria. The larval microbiome volatiles may therefore lead prospective fruit flies towards substrates with a hospitable microbial environment.

  20. Apollo-Soyuz test project. Volume 1: Astronomy, earth atmosphere and gravity field, life sciences, and materials processing

    NASA Technical Reports Server (NTRS)

    1977-01-01

    The joint U.S.-USSR experiments and the U.S. conducted unilateral experiments performed during the Apollo Soyuz Test Project are described. Scientific concepts and experiment design and operation are discussed along with scientific results of postflight analysis.

  1. "Snake-oil," "quack medicine," and "industrially cultured organisms:" biovalue and the commercialization of human microbiome research.

    PubMed

    Slashinski, Melody J; McCurdy, Sheryl A; Achenbaum, Laura S; Whitney, Simon N; McGuire, Amy L

    2012-10-30

    Continued advances in human microbiome research and technologies raise a number of ethical, legal, and social challenges. These challenges are associated not only with the conduct of the research, but also with broader implications, such as the production and distribution of commercial products promising maintenance or restoration of good physical health and disease prevention. In this article, we document several ethical, legal, and social challenges associated with the commercialization of human microbiome research, focusing particularly on how this research is mobilized within economic markets for new public health uses. We conducted in-depth, semi-structured interviews (2009-2010) with 63 scientists, researchers, and National Institutes of Health project leaders ("investigators") involved with human microbiome research. Interviews explored a range of ethical, legal, and social dimensions of human microbiome research, including investigators' perspectives on commercialization. Using thematic content analysis, we identified and analyzed emergent themes and patterns. Investigators discussed the commercialization of human microbiome research in terms of (1) commercialization, probiotics, and issues of safety, (2) public awareness of the benefits and risks of dietary supplements, and (3) regulation. The prevailing theme of ethical, legal, social concern focused on the need to find a balance between the marketplace, scientific research, and the public's health. The themes we identified are intended to serve as points for discussions about the relationship between scientific research and the manufacture and distribution of over-the-counter dietary supplements in the United States.

  2. The role of microbiome in central nervous system disorders

    PubMed Central

    Wang, Yan; Kasper, Lloyd H.

    2014-01-01

    Mammals live in a co-evolutionary association with the plethora of microorganisms that reside at a variety of tissue microenvironments. The microbiome represents the collective genomes of these co-existing microorganisms, which is shaped by host factors such as genetics and nutrients but in turn is able to influence host biology in health and disease. Niche-specific microbiome, prominently the gut microbiome, has the capacity to effect both local and distal sites within the host. The gut microbiome has played a crucial role in the bidirectional gut-brain axis that integrates the gut and central nervous system (CNS) activities, and thus the concept of microbiome-gut-brain axis is emerging. Studies are revealing how diverse forms of neuro-immune and neuro-psychiatric disorders are correlated with or modulated by variations of microbiome, microbiota-derived products and exogenous antibiotics and probiotics. The microbiome poises the peripheral immune homeostasis and predisposes host susceptibility to CNS autoimmune diseases such as multiple sclerosis. Neural, endocrine and metabolic mechanisms are also critical mediators of the microbiome-CNS signaling, which are more involved in neuro-psychiatric disorders such as autism, depression, anxiety, stress. Research on the role of microbiome in CNS disorders deepens our academic knowledge about host-microbiome commensalism in central regulation and in practicality, holds conceivable promise for developing novel prognostic and therapeutic avenues for CNS disorders. PMID:24370461

  3. Differences in vaginal microbiome in African American women versus women of European ancestry

    PubMed Central

    Fettweis, Jennifer M.; Brooks, J. Paul; Serrano, Myrna G.; Sheth, Nihar U.; Girerd, Philippe H.; Edwards, David J.; Strauss, Jerome F.; Jefferson, Kimberly K.

    2014-01-01

    Women of European ancestry are more likely to harbour a Lactobacillus-dominated microbiome, whereas African American women are more likely to exhibit a diverse microbial profile. African American women are also twice as likely to be diagnosed with bacterial vaginosis and are twice as likely to experience preterm birth. The objective of this study was to further characterize and contrast the vaginal microbial profiles in African American versus European ancestry women. Through the Vaginal Human Microbiome Project at Virginia Commonwealth University, 16S rRNA gene sequence analysis was used to compare the microbiomes of vaginal samples from 1268 African American women and 416 women of European ancestry. The results confirmed significant differences in the vaginal microbiomes of the two groups and identified several taxa relevant to these differences. Major community types were dominated by Gardnerella vaginalis and the uncultivated bacterial vaginosis-associated bacterium-1 (BVAB1) that were common among African Americans. Moreover, the prevalence of multiple bacterial taxa that are associated with microbial invasion of the amniotic cavity and preterm birth, including Mycoplasma, Gardnerella, Prevotella and Sneathia, differed between the two ethnic groups. We investigated the contributions of intrinsic and extrinsic factors, including pregnancy, body mass index, diet, smoking and alcohol use, number of sexual partners, and household income, to vaginal community composition. Ethnicity, pregnancy and alcohol use correlated significantly with the relative abundance of bacterial vaginosis-associated species. Trends between microbial profiles and smoking and number of sexual partners were observed; however, these associations were not statistically significant. These results support and extend previous findings that there are significant differences in the vaginal microbiome related to ethnicity and demonstrate that these differences are pronounced even in healthy women

  4. Cultivated Vaginal Microbiomes Alter HIV-1 Infection and Antiretroviral Efficacy in Colonized Epithelial Multilayer Cultures

    PubMed Central

    Pyles, Richard B.; Vincent, Kathleen L.; Baum, Marc M.; Elsom, Barry; Miller, Aaron L.; Maxwell, Carrie; Eaves-Pyles, Tonyia D.; Li, Guangyu; Popov, Vsevolod L.; Nusbaum, Rebecca J.; Ferguson, Monique R.

    2014-01-01

    There is a pressing need for modeling of the symbiotic and at times dysbiotic relationship established between bacterial microbiomes and human mucosal surfaces. In particular clinical studies have indicated that the complex vaginal microbiome (VMB) contributes to the protection against sexually-transmitted pathogens including the life-threatening human immunodeficiency virus (HIV-1). The human microbiome project has substantially increased our understanding of the complex bacterial communities in the vagina however, as is the case for most microbiomes, very few of the community member species have been successfully cultivated in the laboratory limiting the types of studies that can be completed. A genetically controlled ex vivo model system is critically needed to study the complex interactions and associated molecular dialog. We present the first vaginal mucosal culture model that supports colonization by both healthy and dysbiotic VMB from vaginal swabs collected from routine gynecological patients. The immortalized vaginal epithelial cells used in the model and VMB cryopreservation methods provide the opportunity to reproducibly create replicates for lab-based evaluations of this important mucosal/bacterial community interface. The culture system also contains HIV-1 susceptible cells allowing us to study the impact of representative microbiomes on replication. Our results show that our culture system supports stable and reproducible colonization by VMB representing distinct community state types and that the selected representatives have significantly different effects on the replication of HIV-1. Further, we show the utility of the system to predict unwanted alterations in efficacy or bacterial community profiles following topical application of a front line antiretroviral. PMID:24676219

  5. Association between statin use, the vaginal microbiome, and Gardnerella vaginalis vaginolysin-mediated cytotoxicity.

    PubMed

    Abdelmaksoud, Abdallah A; Girerd, Philippe H; Garcia, Erin M; Brooks, J Paul; Leftwich, Lauren M; Sheth, Nihar U; Bradley, Steven P; Serrano, Myrna G; Fettweis, Jennifer M; Huang, Bernice; Strauss, Jerome F; Buck, Gregory A; Jefferson, Kimberly K

    2017-01-01

    Bacterial vaginosis (BV) is the leading dysbiosis of the vaginal microbiome. The pathways leading towards the development of BV are not well understood. Gardnerella vaginalis is frequently associated with BV. G. vaginalis produces the cholesterol-dependent cytolysin (CDC), vaginolysin, which can lyse a variety of human cells and is thought to play a role in pathogenesis. Because membrane cholesterol is required for vaginolysin to function, and because HMG-CoA reductase inhibitors (statins) affect not only serum levels of cholesterol but membrane levels as well, we hypothesized that statins might affect the vaginal microbiome. To investigate the relationship between use of the statins and the vaginal microbiome, we analyzed 16S rRNA gene taxonomic surveys performed on vaginal samples from 133 women who participated in the Vaginal Human Microbiome Project and who were taking statins at the time of sampling, 152 women who reported high cholesterol levels but were not taking statins, and 316 women who did not report high cholesterol. To examine the effect of statins on the cytolytic effect of vaginolysin, the cholesterol-dependent cytolysin (CDC) produced by Gardnerella vaginalis, we assessed the effect of simvastatin pretreatment of VK2E6/E7 vaginal epithelial cells on vaginolysin-mediated cytotoxicity. The mean proportion of G. vaginalis among women taking statins was significantly lower relative to women not using statins. Women using statins had higher mean proportions of Lactobacillus crispatus relative to women with normal cholesterol levels, and higher levels of Lactobacillus jensenii relative to women with high cholesterol but not taking statins. In vitro, vaginal epithelial cells pretreated with simvastatin were relatively resistant to vaginolysin and this effect was inhibited by cholesterol. In this cross-sectional study, statin use was associated with reduced proportions of G. vaginalis and greater proportions of beneficial lactobacilli within the vaginal

  6. Cultivated vaginal microbiomes alter HIV-1 infection and antiretroviral efficacy in colonized epithelial multilayer cultures.

    PubMed

    Pyles, Richard B; Vincent, Kathleen L; Baum, Marc M; Elsom, Barry; Miller, Aaron L; Maxwell, Carrie; Eaves-Pyles, Tonyia D; Li, Guangyu; Popov, Vsevolod L; Nusbaum, Rebecca J; Ferguson, Monique R

    2014-01-01

    There is a pressing need for modeling of the symbiotic and at times dysbiotic relationship established between bacterial microbiomes and human mucosal surfaces. In particular clinical studies have indicated that the complex vaginal microbiome (VMB) contributes to the protection against sexually-transmitted pathogens including the life-threatening human immunodeficiency virus (HIV-1). The human microbiome project has substantially increased our understanding of the complex bacterial communities in the vagina however, as is the case for most microbiomes, very few of the community member species have been successfully cultivated in the laboratory limiting the types of studies that can be completed. A genetically controlled ex vivo model system is critically needed to study the complex interactions and associated molecular dialog. We present the first vaginal mucosal culture model that supports colonization by both healthy and dysbiotic VMB from vaginal swabs collected from routine gynecological patients. The immortalized vaginal epithelial cells used in the model and VMB cryopreservation methods provide the opportunity to reproducibly create replicates for lab-based evaluations of this important mucosal/bacterial community interface. The culture system also contains HIV-1 susceptible cells allowing us to study the impact of representative microbiomes on replication. Our results show that our culture system supports stable and reproducible colonization by VMB representing distinct community state types and that the selected representatives have significantly different effects on the replication of HIV-1. Further, we show the utility of the system to predict unwanted alterations in efficacy or bacterial community profiles following topical application of a front line antiretroviral.

  7. The effects of family, dentition, and dental caries on the salivary microbiome.

    PubMed

    Foxman, Betsy; Luo, Ting; Srinivasan, Usha; Ramadugu, Kirtana; Wen, Ai; Goldberg, Deborah; Shedden, Kerby; Crout, Richard; McNeil, Daniel W; Weyant, Robert; Marazita, Mary L

    2016-05-01

    Family members share genes, environment, and microbial communities. If there is a strong effect of family on the salivary microbiota, controlling for family will enhance identification of microbial communities associated with cariogenesis. The present study was designed to assess the similarity of the salivary microbiome among families and the association between the salivary microbiome and dental decay taking age into account. We selected families (n = 49) participating in the cohort study of oral health conducted by the Center for Oral Health Research in Appalachia. All families where at least two children and at least one parent gave a saliva sample (n = 173) were included. Saliva samples were collected at least 1 hour after eating or drinking. After DNA extraction, the V6 region of the 16s rRNA gene was sequenced. Paired ends were joined using fast length adjustment of short reads, sequences were demultiplexed and filtered using Quantitative Insights Into Microbial Ecology 1.9.0, and taxonomy was assigned using the Ribosomal Database Project (RDP; http://rdp.cme.msu.edu/) classifier and sequences aligned with the CORE database using PyNAST. The salivary microbiome changed with age and was more similar within families than between families. There was no difference in the diversity of the salivary microbiome by dental decay. After taking into account age and family, signals of dental decay were weak in the saliva, whether examined at the phyla, genus, or operational taxonomic level. The salivary microbiome does not appear to be a good indicator of dental caries. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Proton pump inhibitors affect the gut microbiome

    PubMed Central

    Imhann, Floris; Bonder, Marc Jan; Vich Vila, Arnau; Fu, Jingyuan; Mujagic, Zlatan; Vork, Lisa; Tigchelaar, Ettje F; Jankipersadsing, Soesma A; Cenit, Maria Carmen; Harmsen, Hermie J M; Dijkstra, Gerard; Franke, Lude; Xavier, Ramnik J; Jonkers, Daisy; Wijmenga, Cisca; Weersma, Rinse K; Zhernakova, Alexandra

    2016-01-01

    Background and aims Proton pump inhibitors (PPIs) are among the top 10 most widely used drugs in the world. PPI use has been associated with an increased risk of enteric infections, most notably Clostridium difficile. The gut microbiome plays an important role in enteric infections, by resisting or promoting colonisation by pathogens. In this study, we investigated the influence of PPI use on the gut microbiome. Methods The gut microbiome composition of 1815 individuals, spanning three cohorts, was assessed by tag sequencing of the 16S rRNA gene. The difference in microbiota composition in PPI users versus non-users was analysed separately in each cohort, followed by a meta-analysis. Results 211 of the participants were using PPIs at the moment of stool sampling. PPI use is associated with a significant decrease in Shannon's diversity and with changes in 20% of the bacterial taxa (false discovery rate <0.05). Multiple oral bacteria were over-represented in the faecal microbiome of PPI-users, including the genus Rothia (p=9.8×10−38). In PPI users we observed a significant increase in bacteria: genera Enterococcus, Streptococcus, Staphylococcus and the potentially pathogenic species Escherichia coli. Conclusions The differences between PPI users and non-users observed in this study are consistently associated with changes towards a less healthy gut microbiome. These differences are in line with known changes that predispose to C. difficile infections and can potentially explain the increased risk of enteric infections in PPI users. On a population level, the effects of PPI are more prominent than the effects of antibiotics or other commonly used drugs. PMID:26657899

  9. Proton pump inhibitors affect the gut microbiome.

    PubMed

    Imhann, Floris; Bonder, Marc Jan; Vich Vila, Arnau; Fu, Jingyuan; Mujagic, Zlatan; Vork, Lisa; Tigchelaar, Ettje F; Jankipersadsing, Soesma A; Cenit, Maria Carmen; Harmsen, Hermie J M; Dijkstra, Gerard; Franke, Lude; Xavier, Ramnik J; Jonkers, Daisy; Wijmenga, Cisca; Weersma, Rinse K; Zhernakova, Alexandra

    2016-05-01

    Proton pump inhibitors (PPIs) are among the top 10 most widely used drugs in the world. PPI use has been associated with an increased risk of enteric infections, most notably Clostridium difficile. The gut microbiome plays an important role in enteric infections, by resisting or promoting colonisation by pathogens. In this study, we investigated the influence of PPI use on the gut microbiome. The gut microbiome composition of 1815 individuals, spanning three cohorts, was assessed by tag sequencing of the 16S rRNA gene. The difference in microbiota composition in PPI users versus non-users was analysed separately in each cohort, followed by a meta-analysis. 211 of the participants were using PPIs at the moment of stool sampling. PPI use is associated with a significant decrease in Shannon's diversity and with changes in 20% of the bacterial taxa (false discovery rate <0.05). Multiple oral bacteria were over-represented in the faecal microbiome of PPI-users, including the genus Rothia (p=9.8×10(-38)). In PPI users we observed a significant increase in bacteria: genera Enterococcus, Streptococcus, Staphylococcus and the potentially pathogenic species Escherichia coli. The differences between PPI users and non-users observed in this study are consistently associated with changes towards a less healthy gut microbiome. These differences are in line with known changes that predispose to C. difficile infections and can potentially explain the increased risk of enteric infections in PPI users. On a population level, the effects of PPI are more prominent than the effects of antibiotics or other commonly used drugs. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  10. Oral microbiome in HIV-associated periodontitis.

    PubMed

    Noguera-Julian, Marc; Guillén, Yolanda; Peterson, Jessica; Reznik, David; Harris, Erica V; Joseph, Sandeep J; Rivera, Javier; Kannanganat, Sunil; Amara, Rama; Nguyen, Minh Ly; Mutembo, Simon; Paredes, Roger; Read, Timothy D; Marconi, Vincent C

    2017-03-01

    HIV-associated periodontal diseases (PD) could serve as a source of chronic inflammation. Here, we sought to characterize the oral microbial signatures of HIV+ and HIV- individuals at different levels of PD severity.This cross-sectional study included both HIV+ and HIV- patients with varying degrees of PD. Two tooth, 2 cheek, and 1 saliva samples were obtained for microbiome analysis. Mothur/SILVADB were used to classify sequences. R/Bioconductor (Vegan, PhyloSeq, and DESeq2) was employed to assess overall microbiome structure differences and differential abundance of bacterial genera between groups. Polychromatic flow cytometry was used to assess immune activation in CD4 and CD8 cell populations.Around 250 cheek, tooth, and saliva samples from 50 participants (40 HIV+ and 10 HIV-) were included. Severity of PD was classified clinically as None/Mild (N), Moderate (M), and Severe (S) with 18 (36%), 16 (32%), and 16 (32%) participants in each category, respectively. Globally, ordination analysis demonstrated clustering by anatomic site (R2 = 0.25, P < 0.001). HIV status and PD severity showed a statistically significant impact on microbiome composition but only accounted for a combined 2% of variation. HIV+ samples were enriched in genera Abiotrophia, Neisseria, Kingella, and unclassified Neisseriaceae and depleted in Leptotrichia and Selenomonas. The Neisseria genus was consistently enriched in HIV+ participants regardless of sampling site and PD level. Immune markers were altered in HIV+ participants but did not show association with the oral microbiome.HIV-associated changes in oral microbiome result in subtle microbial signatures along different stages of PD that are common in independent oral anatomic sites.

  11. Oral microbiome in HIV-associated periodontitis

    PubMed Central

    Noguera-Julian, Marc; Guillén, Yolanda; Peterson, Jessica; Reznik, David; Harris, Erica V.; Joseph, Sandeep J.; Rivera, Javier; Kannanganat, Sunil; Amara, Rama; Nguyen, Minh Ly; Mutembo, Simon; Paredes, Roger; Read, Timothy D.; Marconi, Vincent C.

    2017-01-01

    Abstract HIV-associated periodontal diseases (PD) could serve as a source of chronic inflammation. Here, we sought to characterize the oral microbial signatures of HIV+ and HIV– individuals at different levels of PD severity. This cross-sectional study included both HIV+ and HIV– patients with varying degrees of PD. Two tooth, 2 cheek, and 1 saliva samples were obtained for microbiome analysis. Mothur/SILVADB were used to classify sequences. R/Bioconductor (Vegan, PhyloSeq, and DESeq2) was employed to assess overall microbiome structure differences and differential abundance of bacterial genera between groups. Polychromatic flow cytometry was used to assess immune activation in CD4 and CD8 cell populations. Around 250 cheek, tooth, and saliva samples from 50 participants (40 HIV+ and 10 HIV–) were included. Severity of PD was classified clinically as None/Mild (N), Moderate (M), and Severe (S) with 18 (36%), 16 (32%), and 16 (32%) participants in each category, respectively. Globally, ordination analysis demonstrated clustering by anatomic site (R2 = 0.25, P < 0.001). HIV status and PD severity showed a statistically significant impact on microbiome composition but only accounted for a combined 2% of variation. HIV+ samples were enriched in genera Abiotrophia, Neisseria, Kingella, and unclassified Neisseriaceae and depleted in Leptotrichia and Selenomonas. The Neisseria genus was consistently enriched in HIV+ participants regardless of sampling site and PD level. Immune markers were altered in HIV+ participants but did not show association with the oral microbiome. HIV-associated changes in oral microbiome result in subtle microbial signatures along different stages of PD that are common in independent oral anatomic sites. PMID:28328799

  12. CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software.

    PubMed

    Wilkinson, Toby J; Huws, Sharon A; Edwards, Joan E; Kingston-Smith, Alison H; Siu-Ting, Karen; Hughes, Martin; Rubino, Francesco; Friedersdorff, Maximillian; Creevey, Christopher J

    2018-01-01

    Metataxonomic 16S rDNA based studies are a commonplace and useful tool in the research of the microbiome, but they do not provide the full investigative power of metagenomics and metatranscriptomics for revealing the functional potential of microbial communities. However, the use of metagenomic and metatranscriptomic technologies is hindered by high costs and skills barrier necessary to generate and interpret the data. To address this, a tool for Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was developed for inferring the functional potential of an observed microbiome profile, based on 16S data. This allows functional inferences to be made from metataxonomic 16S rDNA studies with little extra work or cost, but its accuracy relies on the availability of completely sequenced genomes of representative organisms from the community being investigated. The rumen microbiome is an example of a community traditionally underrepresented in genome and sequence databases, but recent efforts by projects such as the Global Rumen Census and Hungate 1000 have resulted in a wide sampling of 16S rDNA profiles and almost 500 fully sequenced microbial genomes from this environment. Using this information, we have developed "CowPI," a focused version of the PICRUSt tool provided for use by the wider scientific community in the study of the rumen microbiome. We evaluated the accuracy of CowPI and PICRUSt using two 16S datasets from the rumen microbiome: one generated from rDNA and the other from rRNA where corresponding metagenomic and metatranscriptomic data was also available. We show that the functional profiles predicted by CowPI better match estimates for both the meta-genomic and transcriptomic datasets than PICRUSt, and capture the higher degree of genetic variation and larger pangenomes of rumen organisms. Nonetheless, whilst being closer in terms of predictive power for the rumen microbiome, there were differences when compared to

  13. Total Lipopolysaccharide from the Human Gut Microbiome Silences Toll-Like Receptor Signaling.

    PubMed

    d'Hennezel, Eva; Abubucker, Sahar; Murphy, Leon O; Cullen, Thomas W

    2017-01-01

    Cohabitation of microbial communities with the host enables the formation of a symbiotic relationship that maintains homeostasis in the gut and beyond. One prevailing model suggests that this relationship relies on the capacity of host cells and tissues to remain tolerant to the strong immune stimulation generated by the microbiota such as the activation of Toll-like receptor 4 (TLR4) pathways by lipopolysaccharide (LPS). Indeed, gut microbial LPS is thought to be one of the most potent activators of innate immune signaling and an important mediator of the microbiome's influence on host physiology. In this study, we performed computational and experimental analyses of healthy human fecal samples to examine the TLR4 signaling capacity of the gut microbiota. These analyses revealed that an immunoinhibitory activity of LPS, conserved across the members of the order Bacteroidales and derived from an underacylated structural feature, silences TLR4 signaling for the entire consortium of organisms inhabiting the human gut. Comparative analysis of metagenomic data from the Human Microbiome Project and healthy-donor samples indicates that immune silencing via LPS is a microbe-intrinsic feature in all healthy adults. These findings challenge the current belief that robust TLR4 signaling is a feature of the microbiome and demonstrate that microbiome-derived LPS has the ability to facilitate host tolerance of gut microbes. These findings have broad implications for how we model host-microbe interactions and for our understanding of microbiome-linked disease. IMPORTANCE While the ability for humans to host a complex microbial ecosystem is an essential property of life, the mechanisms allowing for immune tolerance of such a large microbial load are not completely understood and are currently the focus of intense research. This study shows that an important proinflammatory pathway that is commonly triggered by pathogenic bacteria upon interaction with the host is, in fact

  14. Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes: Deterministic assembly of hyporheic microbiomes

    SciT

    Graham, Emily B.; Crump, Alex R.; Resch, Charles T.

    2017-03-28

    Subsurface zones of groundwater and surface water mixing (hyporheic zones) are regions of enhanced rates of biogeochemical cycling, yet ecological processes governing hyporheic microbiome composition and function through space and time remain unknown. We sampled attached and planktonic microbiomes in the Columbia River hyporheic zone across seasonal hydrologic change, and employed statistical null models to infer mechanisms generating temporal changes in microbiomes within three hydrologically-connected, physicochemically-distinct geographic zones (inland, nearshore, river). We reveal that microbiomes remain dissimilar through time across all zones and habitat types (attached vs. planktonic) and that deterministic assembly processes regulate microbiome composition in all data subsets.more » The consistent presence of heterotrophic taxa and members of the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum nonetheless suggests common selective pressures for physiologies represented in these groups. Further, co-occurrence networks were used to provide insight into taxa most affected by deterministic assembly processes. We identified network clusters to represent groups of organisms that correlated with seasonal and physicochemical change. Extended network analyses identified keystone taxa within each cluster that we propose are central in microbiome composition and function. Finally, the abundance of one network cluster of nearshore organisms exhibited a seasonal shift from heterotrophic to autotrophic metabolisms and correlated with microbial metabolism, possibly indicating an ecological role for these organisms as foundational species in driving biogeochemical reactions within the hyporheic zone. Taken together, our research demonstrates a predominant role for deterministic assembly across highly-connected environments and provides insight into niche dynamics associated with seasonal changes in hyporheic microbiome composition and metabolism.« less

  15. Graduate student involvement with designing inquiry-based Earth science field projects for the secondary-level classroom

    NASA Astrophysics Data System (ADS)

    McDermott, J. M.; Scherf, L.; Ward, S.; Cady, P.; Bromley, J.; Varner, R. K.; Froburg, E.

    2008-12-01

    In a secondary-level Earth System Science (ESS) curriculum, the most authentic learning is achieved through the inquiry-based application of real-world research methods in the context of modern understanding of the interconnected components of the Earth System (e.g. lithosphere, hydrosphere, atmosphere, and biosphere). Following the intensive ESST-1 summer institute at UNH, during which teachers enhance their ESS content knowledge via interactions with UNH faculty, staff, and graduate students, each participating teacher is paired with one graduate student fellow for the duration of the school year. This graduate fellow provides a continuing link between the secondary-level school teaching environment and university resources, facilitating the implementation of new content knowledge and current scientific research methodology into the classroom setting. According to the National Science Education Standards (1), scientific inquiry is the central strategy for teaching science. "In successful science classrooms, teachers and students collaborate in the pursuit of ideas... Students formulate questions and devise ways to answer them, they collect data and decide how to represent it, they organize data to generate knowledge, and they test the reliability of the knowledge they have generated. As they proceed, students explain and justify their work to themselves and to one another, learn to cope with problems such as the limitations of equipment, and react to challenges posed by the teacher and by classmates." To speak to these goals, an ongoing local wetland field study has been conceptualized and implemented in three example classrooms (seventh grade general science, ninth grade physical science and tenth grade biology) in two school systems (Oyster River Middle School in Durham, NH and Berlin High School in Berlin, NH). These field studies were conducted using authentic scientific equipment to collect data, including a Li-Cor 840 infrared CO2 analyzer and handmade

  16. Earth Science

    1992-07-24

    A Delta II rocket carrying the Geomagnetic Tail Lab (GEOTAIL) spacecraft lifts off at Launch Complex 17, Kennedy Space Center (KSC) into a cloud-dappled sky. This liftoff marks the first Delta launch under the medium expendable launch vehicle services contract between NASA and McDonnell Douglas Space Systems Co. The GEOTAIL mission, a joint US/Japanese project, is the first in a series of five satellites to study the interactions between the Sun, the Earth's magnetic field, and the Van Allen radiation belts.

  17. Dysbiotic drift and biopsychosocial medicine: how the microbiome links personal, public and planetary health.

    PubMed

    Prescott, Susan L; Wegienka, Ganesa; Logan, Alan C; Katz, David L

    2018-01-01

    The emerging concept of planetary health emphasizes that the health of human civilization is intricately connected to the health of natural systems within the Earth's biosphere; here, we focus on the rapidly progressing microbiome science - the microbiota-mental health research in particular - as a way to illustrate the pathways by which exposure to biodiversity supports health. Microbiome science is illuminating the ways in which stress, socioeconomic disadvantage and social polices interact with lifestyle and behaviour to influence the micro and macro-level biodiversity that otherwise mediates health. Although the unfolding microbiome and mental health research is dominated by optimism in biomedical solutions (e.g. probiotics, prebiotics), we focus on the upstream psychosocial and ecological factors implicated in dysbiosis; we connect grand scale biodiversity in the external environment with differences in human-associated microbiota, and, by extension, differences in immune function and mental outlook. We argue that the success of planetary health as a new concept will be strengthened by a more sophisticated understanding of the ways in which individuals develop emotional connections to nature (nature relatedness) and the social policies and practices which facilitate or inhibit the pro-environmental values that otherwise support personal, public and planetary health.

  18. Joint inversion estimate of regional glacial isostatic adjustment in Antarctica considering a lateral varying Earth structure (ESA STSE Project REGINA)

    NASA Astrophysics Data System (ADS)

    Sasgen, Ingo; Martín-Español, Alba; Horvath, Alexander; Klemann, Volker; Petrie, Elizabeth J.; Wouters, Bert; Horwath, Martin; Pail, Roland; Bamber, Jonathan L.; Clarke, Peter J.; Konrad, Hannes; Drinkwater, Mark R.

    2017-12-01

    A major uncertainty in determining the mass balance of the Antarctic ice sheet from measurements of satellite gravimetry, and to a lesser extent satellite altimetry, is the poorly known correction for the ongoing deformation of the solid Earth caused by glacial isostatic adjustment (GIA). Although much progress has been made in consistently modeling the ice-sheet evolution throughout the last glacial cycle, as well as the induced bedrock deformation caused by these load changes, forward models of GIA remain ambiguous due to the lack of observational constraints on the ice sheet's past extent and thickness and mantle rheology beneath the continent. As an alternative to forward-modeling GIA, we estimate GIA from multiple space-geodetic observations: Gravity Recovery and Climate Experiment (GRACE), Envisat/ICESat and Global Positioning System (GPS). Making use of the different sensitivities of the respective satellite observations to current and past surface-mass (ice mass) change and solid Earth processes, we estimate GIA based on viscoelastic response functions to disc load forcing. We calculate and distribute the viscoelastic response functions according to estimates of the variability of lithosphere thickness and mantle viscosity in Antarctica. We compare our GIA estimate with published GIA corrections and evaluate its impact in determining the ice-mass balance in Antarctica from GRACE and satellite altimetry. Particular focus is applied to the Amundsen Sea Sector in West Antarctica, where uplift rates of several centimetres per year have been measured by GPS. We show that most of this uplift is caused by the rapid viscoelastic response to recent ice-load changes, enabled by the presence of a low-viscosity upper mantle in West Antarctica. This paper presents the second and final contributions summarizing the work carried out within a European Space Agency funded study, REGINA (www.regina-science.eu).

  19. Our Planet Earth. Study Guide. Unit F1. ZIM-SCI, Zimbabwe Secondary School Science Project. Year 2.

    ERIC Educational Resources Information Center

    Stocklmayer, Sue

    The Zimbabwe Secondary School Science Project (ZIM-SCI) developed student study guides, corresponding teaching guides, and science kits for a low-cost science course which could be taught during the first 2 years of secondary school without the aid of qualified teachers and conventional laboratories. This teaching guide, designed to be read in…

  20. Our Planet Earth. Teacher's Guide. Unit F1. ZIM-SCI, Zimbabwe Secondary School Science Project. Year 2.

    ERIC Educational Resources Information Center

    Stocklmayer, Sue

    The Zimbabwe Secondary School Science Project (ZIM-SCI) developed student study guides, corresponding teaching guides, and science kits for a low-cost science course which could be taught during the first 2 years of secondary school without the aid of qualified teachers and conventional laboratories. This ZIM-SCI study guide presents activities,…

  1. The Chemicals of the Earth. Teacher's Guide. Unit F2. ZIM-SCI, Zimbabwe Secondary School Science Project. Year 2.

    ERIC Educational Resources Information Center

    Stocklmayer, Sue

    The Zimbabwe Secondary School Science Project (ZIM-SCI) developed student study guides, corresponding teaching guides, and science kits for a low-cost science course which could be taught during the first 2 years of secondary school without the aid of qualified teachers and conventional laboratories. This teaching guide, designed to be read in…

  2. The Chemicals of the Earth. Study Guide. Unit F2. ZIM-SCI, Zimbabwe Secondary School Science Project. Year 2.

    ERIC Educational Resources Information Center

    Stocklmayer, Sue

    The Zimbabwe Secondary School Science Project (ZIM-SCI) developed student study guides, corresponding teaching guides, and science kits for a low-cost science course which could be taught during the first 2 years of secondary school without the aid of qualified teachers and conventional laboratories. This ZIM-SCI study guide presents activities…

  3. The evidence for microbiome manipulation in inflammatory arthritis.

    PubMed

    Jethwa, Hannah; Abraham, Sonya

    2017-09-01

    The human body consists of millions of commensal bacteria (the microbiome), with the intestinal tract being the most prevalent site of colonization. This colonization process begins at birth, and despite numerous factors such as ageing, diet and drug use affecting the microbiome make-up, by adulthood the composition of the gut bacteria is relatively consistent across local populations. The recent advent of new scientific techniques has enabled us to explore how the microbiome affects health and, in particular, has shed light on the involvement of the microbiome in the pathogenesis of inflammatory disease. In this review we highlight the current evidence for microbiome manipulation in inflammatory arthritis in animal and human models and discuss potential therapeutics targeting the microbiome as treatment for these diseases. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  4. The Gut Microbiome: A New Frontier in Autism Research

    PubMed Central

    Mulle, Jennifer G.; Sharp, William G.; Cubells, Joseph F.

    2013-01-01

    The human gut harbors a complex community of microbes that profoundly influence many aspects of growth and development, including development of the nervous system. Advances in high-throughput DNA sequencing methods have led to rapidly expanding knowledge about this gut microbiome. Here, we review fundamental emerging data on the human gut microbiome, with a focus on potential interactions between the microbiome and autism spectrum disorders (ASD) and consider research on atypical patterns of feeding and nutrition in ASD and how they might interact with the microbiome. Finally we selectively survey results from studies in rodents on the impact of the microbiome on neurobehavioral development. The evidence reviewed here suggests that a deeper understanding of the gut microbiome could open up new avenues of research on ASD, including potential novel treatment strategies. PMID:23307560

  5. Breaking down the gut microbiome composition in multiple sclerosis.

    PubMed

    Budhram, Adrian; Parvathy, Seema; Kremenchutzky, Marcelo; Silverman, Michael

    2017-04-01

    The gut microbiome, which consists of a highly diverse ecologic community of micro-organisms, has increasingly been studied regarding its role in multiple sclerosis (MS) immunopathogenesis. This review critically examines the literature investigating the gut microbiome in MS. A comprehensive search was performed of PubMed databases and ECTRIMS meeting abstracts for literature relating to the gut microbiome in MS. Controlled studies examining the gut microbiome in patients with MS were included for review. Identified studies were predominantly case-control in their design and consistently found differences in the gut microbiome of MS patients compared to controls. We examine plausible mechanistic links between these differences and MS immunopathogenesis, and discuss the therapeutic implications of these findings. Review of the available literature reveals potential immunopathogenic links between the gut microbiome and MS, identifies avenues for therapeutic advancement, and emphasizes the need for further systematic study in this emerging field.

  6. Disseminated Museum Displays and Participation of Students from Underrepresented Populations in Polar Research: Education and Outreach for Joint Projects in GPS and Seismology Solid Earth Science Community

    NASA Astrophysics Data System (ADS)

    Eriksson, S. C.; Wilson, T. J.; Anandakrishnan, S.; Aster, R. C.; Johns, B.; Anderson, K.; Taber, J.

    2006-12-01

    Two Antarctic projects developed by solid earth scientists in the GPS and seismology communities have rich education and outreach activities focused on disseminating information gleaned from this research and on including students from underrepresented groups. Members of the UNAVCO and IRIS research consortia along with international partners from Australia, Canada, Chile, Germany, Italy, New Zealand and the U.K. aim to deploy an ambitious GPS/seismic network to observe the Antarctic glaciological and geologic system using a multidisciplinary and internationally coordinated approach. The second project supports this network. UNAVCO and IRIS are designing and building a reliable power and communication system for autonomous polar station operation which use the latest power and communication technologies for ease of deployment and reliable multi-year operation in severe polar environments. This project will disseminate research results through an IPY/POLENET web-based museum style display based on the next-generation "Museum Lite" capability primarily supported by IRIS. "Museum Lite" uses a standard PC, touch-screen monitor, and standard Internet browsers to exploit the scalability and access of the Internet and to provide customizable content in an interactive setting. The unit is suitable for research departments, public schools, and an assortment of public venues, and can provide wide access to real-time geophysical data, ongoing research, and general information. The POLENET group will work with members of the two consortia to provide content about the project and polar science in general. One unit is to be installed at Barrow's Ilisagvit College through the Barrow Arctic Science Consortium, one at McMurdo Station in Antarctica, and two at other sites to be determined (likely in New Zealand/Australia and in the U.S.). In January, 2006, Museum Lite exhibit was installed at the Amundsen-Scott South Pole Station. Evaluation of this prototype is underway. These

  7. Dental Calculus and the Evolution of the Human Oral Microbiome.

    PubMed

    Warinner, Christina

    2016-07-01

    Characterizing the evolution of the oral microbiome is a challenging, but increasingly feasible, task. Recently, dental calculus has been shown to preserve ancient biomolecules from the oral microbiota, host tissues and diet for tens of thousands of years. As such, it provides a unique window into the ancestral oral microbiome. This article reviews recent advancements in ancient dental calculus research and emerging insights into the evolution and ecology of the human oral microbiome.

  8. Analysis of the Small Intestinal Microbiome of Children With Autism

    DTIC Science & Technology

    2013-05-01

    appears to be some indication of the gut microflora differing between the autistic and control groups. On Figure 6, the whole microbiome of...Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE. (2006). Metagenomic analysis of the human distal gut microbiome ...TITLE AND SUBTITLE 5a. CONTRACT NUMBER W81XWH-10-1-0477 Analysis of the Small Intestinal Microbiome in Children with Autism 5b. GRANT NUMBER

  9. Effects of Host Phylogeny and Habitats on Gut Microbiomes of Oriental River Prawn (Macrobrachium nipponense)

    PubMed Central

    Chen, Po-Cheng; Weng, Francis Cheng-Hsuan; Jean, Wen Dar; Wang, Daryi

    2015-01-01

    The gut microbial community is one of the richest and most complex ecosystems on earth, and the intestinal microbes play an important role in host development and health. Next generation sequencing approaches, which rapidly produce millions of short reads that enable the investigation on a culture independent basis, are now popular for exploring microbial community. Currently, the gut microbiome in fresh water shrimp is unexplored. To explore gut microbiomes of the oriental river prawn (Macrobrachium nipponense) and investigate the effects of host genetics and habitats on the microbial composition, 454 pyrosequencing based on the 16S rRNA gene were performed. We collected six groups of samples, including M. nipponense shrimp from two populations, rivers and lakes, and one sister species (M. asperulum) as an out group. We found that Proteobacteria is the major phylum in oriental river prawn, followed by Firmicutes and Actinobacteria. Compositional analysis showed microbial divergence between the two shrimp species is higher than that between the two populations of one shrimp species collected from river and lake. Hierarchical clustering also showed that host genetics had a greater impact on the divergence of gut microbiome than host habitats. This finding was also congruent with the functional prediction from the metagenomic data implying that the two shrimp species still shared the same type of biological functions, reflecting a similar metabolic profile in their gut environments. In conclusion, this study provides the first investigation of the gut microbiome of fresh water shrimp, and supports the hypothesis of host species-specific signatures of bacterial community composition. PMID:26168244

  10. Effects of Host Phylogeny and Habitats on Gut Microbiomes of Oriental River Prawn (Macrobrachium nipponense).

    PubMed

    Tzeng, Tzong-Der; Pao, Yueh-Yang; Chen, Po-Cheng; Weng, Francis Cheng-Hsuan; Jean, Wen Dar; Wang, Daryi

    2015-01-01

    The gut microbial community is one of the richest and most complex ecosystems on earth, and the intestinal microbes play an important role in host development and health. Next generation sequencing approaches, which rapidly produce millions of short reads that enable the investigation on a culture independent basis, are now popular for exploring microbial community. Currently, the gut microbiome in fresh water shrimp is unexplored. To explore gut microbiomes of the oriental river prawn (Macrobrachium nipponense) and investigate the effects of host genetics and habitats on the microbial composition, 454 pyrosequencing based on the 16S rRNA gene were performed. We collected six groups of samples, including M. nipponense shrimp from two populations, rivers and lakes, and one sister species (M. asperulum) as an out group. We found that Proteobacteria is the major phylum in oriental river prawn, followed by Firmicutes and Actinobacteria. Compositional analysis showed microbial divergence between the two shrimp species is higher than that between the two populations of one shrimp species collected from river and lake. Hierarchical clustering also showed that host genetics had a greater impact on the divergence of gut microbiome than host habitats. This finding was also congruent with the functional prediction from the metagenomic data implying that the two shrimp species still shared the same type of biological functions, reflecting a similar metabolic profile in their gut environments. In conclusion, this study provides the first investigation of the gut microbiome of fresh water shrimp, and supports the hypothesis of host species-specific signatures of bacterial community composition.

  11. Visibiome: an efficient microbiome search engine based on a scalable, distributed architecture.

    PubMed

    Azman, Syafiq Kamarul; Anwar, Muhammad Zohaib; Henschel, Andreas

    2017-07-24

    Given the current influx of 16S rRNA profiles of microbiota samples, it is conceivable that large amounts of them eventually are available for search, comparison and contextualization with respect to novel samples. This process facilitates the identification of similar compositional features in microbiota elsewhere and therefore can help to understand driving factors for microbial community assembly. We present Visibiome, a microbiome search engine that can perform exhaustive, phylogeny based similarity search and contextualization of user-provided samples against a comprehensive dataset of 16S rRNA profiles environments, while tackling several computational challenges. In order to scale to high demands, we developed a distributed system that combines web framework technology, task queueing and scheduling, cloud computing and a dedicated database server. To further ensure speed and efficiency, we have deployed Nearest Neighbor search algorithms, capable of sublinear searches in high-dimensional metric spaces in combination with an optimized Earth Mover Distance based implementation of weighted UniFrac. The search also incorporates pairwise (adaptive) rarefaction and optionally, 16S rRNA copy number correction. The result of a query microbiome sample is the contextualization against a comprehensive database of microbiome samples from a diverse range of environments, visualized through a rich set of interactive figures and diagrams, including barchart-based compositional comparisons and ranking of the closest matches in the database. Visibiome is a convenient, scalable and efficient framework to search microbiomes against a comprehensive database of environmental samples. The search engine leverages a popular but computationally expensive, phylogeny based distance metric, while providing numerous advantages over the current state of the art tool.

  12. The adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition.

    PubMed

    Cremers, Amelieke Jh; Zomer, Aldert L; Gritzfeld, Jenna F; Ferwerda, Gerben; van Hijum, Sacha Aft; Ferreira, Daniela M; Shak, Joshua R; Klugman, Keith P; Boekhorst, Jos; Timmerman, Harro M; de Jonge, Marien I; Gordon, Stephen B; Hermans, Peter Wm

    2014-01-01

    Several cohort studies have indicated associations between S. pneumoniae and other microbes in the nasopharynx. To study causal relationships between the nasopharyngeal microbiome and pneumococcal carriage, we employed an experimental human pneumococcal carriage model. Healthy adult volunteers were assessed for pneumococcal carriage by culture of nasal wash samples (NWS). Those without natural pneumococcal carriage received an intranasal pneumococcal inoculation with serotype 6B or 23F. The composition of the nasopharyngeal microbiome was longitudinally studied by 16S rDNA pyrosequencing on NWS collected before and after challenge. Among 40 selected volunteers, 10 were natural carriers and 30 were experimentally challenged. At baseline, five distinct nasopharyngeal microbiome profiles were identified. The phylogenetic distance between microbiomes of natural pneumococcal carriers was particularly large compared to non-carriers. A more diverse microbiome prior to inoculation was associated with the establishment of pneumococcal carriage. Perturbation of microbiome diversity upon pneumococcal challenge was strain specific. Shifts in microbiome profile occurred after pneumococcal exposure, and those volunteers who acquired carriage more often diverted from their original profile. S. pneumoniae was little prominent in the microbiome of pneumococcal carriers. Pneumococcal acquisition in healthy adults is more likely to occur in a diverse microbiome and appears to promote microbial heterogeneity.

  13. Community assembly of a euryhaline fish microbiome during salinity acclimation.

    PubMed

    Schmidt, Victor T; Smith, Katherine F; Melvin, Donald W; Amaral-Zettler, Linda A

    2015-05-01

    Microbiomes play a critical role in promoting a range of host functions. Microbiome function, in turn, is dependent on its community composition. Yet, how microbiome taxa are assembled from their regional species pool remains unclear. Many possible drivers have been hypothesized, including deterministic processes of competition, stochastic processes of colonization and migration, and physiological 'host-effect' habitat filters. The contribution of each to assembly in nascent or perturbed microbiomes is important for understanding host-microbe interactions and host health. In this study, we characterized the bacterial communities in a euryhaline fish and the surrounding tank water during salinity acclimation. To assess the relative influence of stochastic versus deterministic processes in fish microbiome assembly, we manipulated the bacterial species pool around each fish by changing the salinity of aquarium water. Our results show a complete and repeatable turnover of dominant bacterial taxa in the microbiomes from individuals of the same species after acclimation to the same salinity. We show that changes in fish microbiomes are not correlated with corresponding changes to abundant taxa in tank water communities and that the dominant taxa in fish microbiomes are rare in the aquatic surroundings, and vice versa. Our results suggest that bacterial taxa best able to compete within the unique host environment at a given salinity appropriate the most niche space, independent of their relative abundance in tank water communities. In this experiment, deterministic processes appear to drive fish microbiome assembly, with little evidence for stochastic colonization. © 2015 John Wiley & Sons Ltd.

  14. The microbiome in prostate inflammation and prostate cancer.

    PubMed

    Porter, Corey M; Shrestha, Eva; Peiffer, Lauren B; Sfanos, Karen S

    2018-05-23

    The human microbiome may influence prostate cancer initiation and/or progression through both direct and indirect interactions. To date, the majority of studies have focused on direct interactions including the influence of prostate infections on prostate cancer risk and, more recently, on the composition of the urinary microbiome in relation to prostate cancer. Less well understood are indirect interactions of the microbiome with prostate cancer, such as the influence of the gastrointestinal or oral microbiota on pro- or anti-carcinogenic xenobiotic metabolism, and treatment response. We review the literature to date on direct and indirect interactions of the microbiome with prostate inflammation and prostate cancer. Emerging studies indicate that the microbiome can influence prostate inflammation in relation to benign prostate conditions such as prostatitis/chronic pelvic pain syndrome and benign prostatic hyperplasia, as well as in prostate cancer. We provide evidence that the human microbiome present at multiple anatomic sites (urinary tract, gastrointestinal tract, oral cavity, etc.) may play an important role in prostate health and disease. In health, the microbiome encourages homeostasis and helps educate the immune system. In dysbiosis, a systemic inflammatory state may be induced, predisposing remote anatomical sites to disease, including cancer. The microbiome's ability to affect systemic hormone levels may also be important, particularly in a disease such as prostate cancer that is dually affected by estrogen and androgen levels. Due to the complexity of the potential interconnectedness between prostate cancer and the microbiome, it is vital to further explore and understand the relationships that are involved.

  15. Skylab Explores the Earth.

    ERIC Educational Resources Information Center

    National Aeronautics and Space Administration, Washington, DC.

    This book describes the Skylab 4 Earth Explorations Project. Photographs of the earth taken by the Skylab astronauts are reproduced here and accompanied by an analytical and explanatory text. Some of the geological and geographical topics covered are: (1) global tectonics - some geological analyses of observations and photographs from Skylab; (2)…

  16. The I-Cleen Project (Inquiring on CLimate & ENergy). Research Meets Education in AN Inquiry-Based Approach to Earth System Science in Italian Classrooms

    NASA Astrophysics Data System (ADS)

    Cattadori, M.; Editorial Staff of the I-CLEN Project

    2011-12-01

    Italian citizens' perception of the seriousness of the issue of climate change is one of the lowest in Europe (Eurobarometer survey, 2008), running next to last among the 28 EU Nations. This has recently driven many national science institutions to take action in order to connect society with the complexities and consequences of climate change. These connection initiatives have encountered a certain deal of opposition in Italian schools. A fact most likely due both to a further weakening of the use of inquiry-based educational practices adopted by teachers and to their reluctance to cooperate on a professional level, which hinders the diffusion of educational practices. I-CLEEN (Inquiring on CLimate and Energy, www.icleen.museum) is a service that offers a new type of link between schools and the complexity of climate change. The project took off in 2008 thanks to the Trento Science Museum (former Tridentine Museum of Natural Science), one of the major Italian science museums that includes both research and science education and dissemination departments. The main aim is to create, using the tools of professional cooperation, a free repository of educational resources that can support teachers in preparing inquiry-based lessons on climate change and earth system science topics, making the task less of a burden. I-CLEEN is inspired by many models, which include: the ARISE (Andrill Research Immersion for Science Educators), the OER (Open Educational Resources) models and those of other projects that have developed similar information gateways such as LRE (Learning Resource Exchange) and DLESE (Digital Library on Earth Science Education). One of the strategies devised by I-CLEEN is to rely upon an editorial team made up of a highly selected group of teachers that interacts with the researchers of the museum and of other Earth system science research centres like the National Institute of Geophysics and Volcanology (INGV). Resource selection, production, revision and

  17. Inclusion of ecologically based trait variation in plant functional types reduces the projected land carbon sink in an earth system model.

    PubMed

    Verheijen, Lieneke M; Aerts, Rien; Brovkin, Victor; Cavender-Bares, Jeannine; Cornelissen, Johannes H C; Kattge, Jens; van Bodegom, Peter M

    2015-08-01

    Earth system models demonstrate large uncertainty in projected changes in terrestrial carbon budgets. The lack of inclusion of adaptive responses of vegetation communities to the environment has been suggested to hamper the ability of modeled vegetation to adequately respond to environmental change. In this study, variation in functional responses of vegetation has been added to an earth system model (ESM) based on ecological principles. The restriction of viable mean trait values of vegetation communities by the environment, called 'habitat filtering', is an important ecological assembly rule and allows for determination of global scale trait-environment relationships. These relationships were applied to model trait variation for different plant functional types (PFTs). For three leaf traits (specific leaf area, maximum carboxylation rate at 25 °C, and maximum electron transport rate at 25 °C), relationships with multiple environmental drivers, such as precipitation, temperature, radiation, and CO2 , were determined for the PFTs within the Max Planck Institute ESM. With these relationships, spatiotemporal variation in these formerly fixed traits in PFTs was modeled in global change projections (IPCC RCP8.5 scenario). Inclusion of this environment-driven trait variation resulted in a strong reduction of the global carbon sink by at least 33% (2.1 Pg C yr(-1) ) from the 2nd quarter of the 21st century onward compared to the default model with fixed traits. In addition, the mid- and high latitudes became a stronger carbon sink and the tropics a stronger carbon source, caused by trait-induced differences in productivity and relative respirational costs. These results point toward a reduction of the global carbon sink when including a more realistic representation of functional vegetation responses, implying more carbon will stay airborne, which could fuel further climate change. © 2015 John Wiley & Sons Ltd.

  18. Current understanding of the human microbiome.

    PubMed

    Gilbert, Jack A; Blaser, Martin J; Caporaso, J Gregory; Jansson, Janet K; Lynch, Susan V; Knight, Rob

    2018-04-10

    Our understanding of the link between the human microbiome and disease, including obesity, inflammatory bowel disease, arthritis and autism, is rapidly expanding. Improvements in the throughput and accuracy of DNA sequencing of the genomes of microbial communities that are associated with human samples, complemented by analysis of transcriptomes, proteomes, metabolomes and immunomes and by mechanistic experiments in model systems, have vastly improved our ability to understand the structure and function of the microbiome in both diseased and healthy states. However, many challenges remain. In this review, we focus on studies in humans to describe these challenges and propose strategies that leverage existing knowledge to move rapidly from correlation to causation and ultimately to translation into therapies.

  19. Current understanding of the human microbiome

    SciT

    Gilbert, Jack A.; Blaser, Martin J.; Caporaso, J. Gregory

    Our understanding of the link between the human microbiome and disease, including obesity, inflammatory bowel disease, arthritis and autism, is rapidly expanding. Improvements in the throughput and accuracy of DNA sequencing of the genomes of microbial communities associated with human samples, complemented by analysis of transcriptomes, proteomes, metabolomes and immunomes, and mechanistic experiments in model systems, have vastly improved our ability to understand the structure and function of the microbiome in both diseased and healthy states. However, many challenges remain. In this Review we focus on studies in humans to describe these challenges, and propose strategies that leverage existing knowledgemore » to move rapidly from correlation to causation, and ultimately to translation.« less

  20. An Introductory "How-to" Guide for Incorporating Microbiome Research into Integrative and Comparative Biology.

    PubMed

    Kohl, Kevin D

    2017-10-01

    Research on host-associated microbial communities has grown rapidly. Despite the great body of work, inclusion of microbiota-related questions into integrative and comparative biology is still lagging behind other disciplines. The purpose of this paper is to offer an introduction into the basic tools and techniques of host-microbe research. Specifically, what considerations should be made before embarking on such projects (types of samples, types of controls)? How is microbiome data analyzed and integrated with data measured from the hosts? How can researchers experimentally manipulate the microbiome? With this information, integrative and comparative biologists should be able to include host-microbe studies into their research and push the boundaries of both fields. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

  1. Characterization of the SOS meta-regulon in the human gut microbiome.

    PubMed

    Cornish, Joseph P; Sanchez-Alberola, Neus; O'Neill, Patrick K; O'Keefe, Ronald; Gheba, Jameel; Erill, Ivan

    2014-05-01

    Data from metagenomics projects remain largely untapped for the analysis of transcriptional regulatory networks. Here, we provide proof-of-concept that metagenomic data can be effectively leveraged to analyze regulatory networks by characterizing the SOS meta-regulon in the human gut microbiome. We combine well-established in silico and in vitro techniques to mine the human gut microbiome data and determine the relative composition of the SOS network in a natural setting. Our analysis highlights the importance of translesion synthesis as a primary function of the SOS response. We predict the association of this network with three novel protein clusters involved in cell wall biogenesis, chromosome partitioning and restriction modification, and we confirm binding of the SOS response transcriptional repressor to sites in the promoter of a cell wall biogenesis enzyme, a phage integrase and a death-on-curing protein. We discuss the implications of these findings and the potential for this approach for metagenome analysis.

  2. Combining Project-based Instruction, Earth Science Content, and GIS Technology in Teacher Professional Development: Is this Holistic Approach Sustainable?

    NASA Astrophysics Data System (ADS)

    Rubino-Hare, L.; Bloom, N.; Claesgens, J.; Fredrickson, K.; Henderson-Dahms, C.; Sample, J. C.

    2012-12-01

    From 2009-2011, with support from the National Science Foundation (ITEST, DRL-0929846) and Science Foundation Arizona (MSAG-0412-09), educators, geologists and geographers at Northern Arizona University (NAU) partnered to offer professional development for interdisciplinary teams of secondary and middle school teachers with a focus on project-based instruction (PBI) using geospatial technologies (GST). While participating in professional development teachers received support and were held accountable to NAU staff. They implemented activities and pedagogical strategies presented, increased knowledge, skills, and confidence teaching with project-based instruction integrating GST, and their students demonstrated learning gains. Changes in student understanding are only observed when teachers continue to implement change, so the question remained: did these changes in practice sustain after official project support ended? In order to determine what, if anything, teachers sustained from the professional development and the factors that promoted or hindered sustained use of teaching with GST and PBI, data were collected one to two years following the professional development. Research questions included a) what pedagogical practices did teachers sustain following the professional learning experiences? and b) what contexts were present in schools that supported or limited the use of geospatial technologies as a teaching and learning tool? Findings from this study indicate that teachers fall into three categories of sustaining implementation - reformed implementers, mechanical implementers and non-implementers. School context was less of a factor in level of implementation than teachers' beliefs and philosophy of teaching and teachers' understanding of technology integration (teaching with technology vs. teaching technology). Case studies of teacher experiences will be presented along with implications for future professional development.

  3. The Microbiome in Infectious Disease and Inflammation

    PubMed Central

    Honda, Kenya; Littman, Dan R.

    2015-01-01

    The mammalian alimentary tract harbors hundreds of species of commensal microorganisms (microbiota) that intimately interact with the host and provide it with genetic, metabolic, and immunological attributes. Recent reports have indicated that the microbiota composition and its collective genomes (microbiome) are major factors in predetermining the type and robustness of mucosal immune responses. In this review, we discuss the recent advances in our understanding of host-microbiota interactions and their effect on the health and disease susceptibility of the host. PMID:22224764

  4. Enabling the Direct Detection of Earth-Sized Exoplanets with the LBTI HOSTS Project: A Progress Report

    NASA Technical Reports Server (NTRS)

    Danchi, W.; Bailey, V.; Bryden, G.; Defrere, D.; Ertel, S.; Haniff, C.; Hinz, P.; Kennedy, G.; Mennesson, B.; Millan-Gabet, R.; hide

    2016-01-01

    NASA has funded a project called the Hunt for Observable Signatures of Terrestrial Systems (HOSTS) to survey nearby solar type stars to determine the amount of warm zodiacal dust in their habitable zones. The goal is not only to determine the luminosity distribution function but also to know which individual stars have the least amount of zodiacal dust. It is important to have this information for future missions that directly image exoplanets as this dust is the main source of astrophysical noise for them. The HOSTS project utilizes the Large Binocular Telescope Interferometer (LBTI), which consists of two 8.4-m apertures separated by a 14.4-m baseline on Mt. Graham, Arizona. The LBTI operates in a nulling mode in the mid-infrared spectral window (8-13 micrometers), in which light from the two telescopes is coherently combined with a 180 degree phase shift between them, producing a dark fringe at the location of the target star. In doing so the starlight is greatly reduced, increasing the contrast, analogous to a coronagraph operating at shorter wavelengths. The LBTI is a unique instrument, having only three warm reflections before the starlight reaches cold mirrors, giving it the best photometric sensitivity of any interferometer operating in the mid-infrared. It also has a superb Adaptive Optics (AO) system giving it Strehl ratios greater than 98% at 10 micrometers. In 2014 into early 2015 LBTI was undergoing commissioning. The HOSTS. project team passed its Operational Readiness Review (ORR) in April 2015. The team recently published papers on the target sample, modeling of the nulled disk images, and initial results such as the detection of warm dust around eta Corvi. Recently a paper was published on the data pipeline and on-sky performance. An additional paper is in preparation on Beta Leo. We will discuss the scientific and programmatic context for the LBTI project, and we will report recent progress, new results, and plans for the science verification

  5. The native microbiome of the nematode Caenorhabditis elegans: gateway to a new host-microbiome model.

    PubMed

    Dirksen, Philipp; Marsh, Sarah Arnaud; Braker, Ines; Heitland, Nele; Wagner, Sophia; Nakad, Rania; Mader, Sebastian; Petersen, Carola; Kowallik, Vienna; Rosenstiel, Philip; Félix, Marie-Anne; Schulenburg, Hinrich

    2016-05-09

    Host-microbe associations underlie many key processes of host development, immunity, and life history. Yet, none of the current research on the central model species Caenorhabditis elegans considers the worm's natural microbiome. Instead, almost all laboratories exclusively use the canonical strain N2 and derived mutants, maintained through routine bleach sterilization in monoxenic cultures with an E. coli strain as food. Here, we characterize for the first time the native microbiome of C. elegans and assess its influence on nematode life history characteristics. Nematodes sampled directly from their native habitats carry a species-rich bacterial community, dominated by Proteobacteria such as Enterobacteriaceae and members of the genera Pseudomonas, Stenotrophomonas, Ochrobactrum, and Sphingomonas. The C. elegans microbiome is distinct from that of the worm's natural environment and the congeneric species C. remanei. Exposure to a derived experimental microbiome revealed that bacterial composition is influenced by host developmental stage and genotype. These experiments also showed that the microbes enhance host fitness under standard and also stressful conditions (e.g., high temperature and either low or high osmolarity). Taking advantage of the nematode's transparency, we further demonstrate that several Proteobacteria are able to enter the C. elegans gut and that an Ochrobactrum isolate even seems to be able to persist in the intestines under stressful conditions. Moreover, three Pseudomonas isolates produce an anti-fungal effect in vitro which we show can contribute to the worm's defense against fungal pathogens in vivo. This first systematic analysis of the nematode's native microbiome reveals a species-rich bacterial community to be associated with C. elegans, which is likely of central importance for our understanding of the worm's biology. The information acquired and the microbial isolates now available for experimental work establishes C. elegans as a

  6. The Sea Monitoring Virtual Research Community (VRC) in the EVER-EST Project (a virtual research environment for the Earth Sciences).

    NASA Astrophysics Data System (ADS)

    Foglini, Federica; Boero, Ferdinando; Guarino, Raffaele

    2016-04-01

    The EU's H2020 EVER-EST Project is dedicated to the realization of a Virtual Research Environment (VRE) for Earth Science researchers during 2015-2018. In this framework the Sea monitoring represents one of the four use case VRCs chosen to validate the EVER-EST e-infrastructure, which is aimed at representing a wide and multidisciplinary Earth Science domain. The objective of the Sea Monitoring Virtual Research Community (VRC) is to provide useful and applicable contributions to the identification and definition of variables indicated by the European Commission in the Marine Directive under the framework for Good Environment Status (GES). The European Marine Strategy Framework Directive (MSFD, http://ec.europa.eu/environment/marine/index_en.htm) has defined the descriptors for Good Environmental Status in marine waters. The first descriptor is biodiversity; the second one is the presence of non-indigenous species while the remaining nine (even when they consider physical, chemical or geological variables) require proper functioning of the ecosystem, linked to a good state of biodiversity. The Sea Monitoring VRC is direct to provide practical methods, procedures and protocols to support coherent and widely accepted interpretation of the Descriptors 1(Biodiversity), 2 (non- indigenous species), 4 (food webs) and 6 (seafloor integrity) identified in GES. In that context, the criteria and methodological standards already identified by the European Commission, and at same time considering the activities and projects in progress in the marine framework, will be taken into account. This research of practical methods to estimate and measure GES parameters requires a close cooperation among different disciplines including: biologists, geologists, geophysics, oceanographers, Earth observation experts and others. It will also require a number of different types of scientific data and observations (e.g. biology related, chemico-physical, etc.) from different inputs and sensors

  7. Smoking, pregnancy and the subgingival microbiome

    PubMed Central

    Paropkari, Akshay D.; Leblebicioglu, Binnaz; Christian, Lisa M.; Kumar, Purnima S.

    2016-01-01

    The periodontal microbiome is known to be altered during pregnancy as well as by smoking. However, despite the fact that 2.1 million women in the United States smoke during their pregnancy, the potentially synergistic effects of smoking and pregnancy on the subgingival microbiome have never been studied. Subgingival plaque was collected from 44 systemically and periodontally healthy non-pregnant nonsmokers (control), non-pregnant smokers, pregnant nonsmokers and pregnant smokers and sequenced using 16S-pyrotag sequencing. 331601 classifiable sequences were compared against HOMD. Community ordination methods and co-occurrence networks were used along with non-parametric tests to identify differences between groups. Linear Discriminant Analysis revealed significant clustering based on pregnancy and smoking status. Alpha diversity was similar between groups, however, pregnant women (smokers and nonsmokers) demonstrated higher levels of gram-positive and gram-negative facultatives, and lower levels of gram-negative anaerobes when compared to smokers. Each environmental perturbation induced distinctive co-occurrence patterns between species, with unique network anchors in each group. Our study thus suggests that the impact of each environmental perturbation on the periodontal microbiome is unique, and that when they are superimposed, the sum is greater than its parts. The persistence of these effects following cessation of the environmental disruption warrants further investigation. PMID:27461975

  8. Perna canaliculus and the Intestinal Microbiome.

    PubMed

    Saltzman, Emma Tali; Thomsen, Michael; Hall, Sean; Vitetta, Luis

    2017-06-30

    Natural medicines are often an attractive option for patients diagnosed with chronic conditions. Three main classes of bioactives that have been reported from marine mussel extracts include proteins, lipids and carbohydrates. Commercially, the most relevant species of marine mollusks belong to two genera, Perna and Mytilus. Specifically, the Perna canaliculus species has been repeatedly demonstrated to harbor anti-inflammatory compounds such as omega-3 polyunsaturated fatty acids ( ω -3 PUFAs) that can ameliorate pro-inflammatory conditions, or proteins that can promote thrombin inhibitory activity. Recent clinical studies have posited that extracts from green-lipped mussels may lead to prebiotic activity in the intestinal microbiome that in turn has been reported to improve symptoms of osteoarthritis of the knee. Prebiotics have been reported to favorably interact with the intestinal microbiome through the proliferation of beneficial bacteria in the gut, suppressing exogenous and endogenous intestinal infections and promoting homeostasis by balancing local pro- and anti-inflammatory actions. Bioactive compounds from Perna canaliculus are functional foods and, in this regard, may positively interact with the intestinal microbiome and provide novel therapeutic solutions for intra-intestinal and extra-intestinal inflammatory conditions.

  9. The Norwegian Earth System Model, NorESM1-M - Part 2: Climate response and scenario projections

    NASA Astrophysics Data System (ADS)

    Iversen, T.; Bentsen, M.; Bethke, I.; Debernard, J. B.; Kirkevåg, A.; Seland, Ø.; Drange, H.; Kristjánsson, J. E.; Medhaug, I.; Sand, M.; Seierstad, I. A.

    2012-09-01

    The NorESM1-M simulation results for CMIP5 (http://cmip-pcmdi.llnl.gov/cmip5/index.html) are described and discussed. Together with the accompanying paper by Bentsen et al. (2012), this paper documents that NorESM1-M is a valuable global climate model for research and for providing complementary results to the evaluation of possible man made climate change. NorESM is based on the model CCSM4 operated at NCAR on behalf of many contributors in USA. The ocean model is replaced by a developed version of MICOM and the atmospheric model is extended with on-line calculations of aerosols, their direct effect, and their indirect effect on warm clouds. Model validation is presented in a companion paper (Bentsen et al., 2012). NorESM1-M is estimated to have equilibrium climate sensitivity slightly smaller than 2.9 K, a transient climate response just below 1.4 K, and is less sensitive than most other models. Cloud feedbacks damp the response, and a strong AMOC reduces the heat fraction available for increasing near surface temperatures, for evaporation, and for melting ice. The future projections based on RCP scenarios yield global surface air temperature increase almost one standard deviation lower than a 15-model average. Summer sea-ice is projected to decrease considerably by 2100, and completely for RCP8.5. The AMOC is projected to reduce by 12%, 15-17%, and 32% for the RCP2.6, 4.5, 6.0 and 8.5 respectively. Precipitation is projected to increase in the tropics, decrease in the subtropics and in southern parts of the northern extra-tropics during summer, and otherwise increase in most of the extra-tropics. Changes in the atmospheric water cycle indicate that precipitation events over continents will become more intense and dry spells more frequent. Extra-tropical storminess in the Northern Hemisphere is projected to shift northwards. There are indications of more frequent spring and summer blocking in

  10. Microbiome manipulation with faecal microbiome transplantation as a therapeutic strategy in Clostridium difficile infection

    PubMed Central

    Marchesi, J.R.; Thursz, M.R.; Williams, H.R.T.

    2015-01-01

    Faecal microbiome transplantation (FMT) has generated huge recent interest as it presents a potential solution to a significant clinical problem—the increasing incidence of Clostridium difficile infection (CDI). In the short term, however, there remain many practical questions regarding its use, including the optimal selection of donors, material preparation and the mechanics of delivery. In the longer term, enhanced understanding of the mechanisms of action of FMT may potentiate novel therapies, such as targeted manipulation of the microbiome in CDI and beyond. PMID:25193538

  11. The GLOBE Carbon Cycle Project: Using a systems approach to understand carbon and the Earth's climate system

    NASA Astrophysics Data System (ADS)

    Silverberg, S. K.; Ollinger, S. V.; Martin, M. E.; Gengarelly, L. M.; Schloss, A. L.; Bourgeault, J. L.; Randolph, G.; Albrechtova, J.

    2009-12-01

    National Science Content Standards identify systems as an important unifying concept across the K-12 curriculum. While this standard exists, there is a recognized gap in the ability of students to use a systems thinking approach in their learning. In a similar vein, both popular media as well as some educational curricula move quickly through climate topics to carbon footprint analyses without ever addressing the nature of carbon or the carbon cycle. If students do not gain a concrete understanding of carbon’s role in climate and energy they will not be able to successfully tackle global problems and develop innovative solutions. By participating in the GLOBE Carbon Cycle project, students learn to use a systems thinking approach, while at the same time, gaining a foundation in the carbon cycle and it's relation to climate and energy. Here we present the GLOBE Carbon Cycle project and materials, which incorporate a diverse set of activities geared toward upper middle and high school students with a variety of learning styles. A global carbon cycle adventure story and game let students see the carbon cycle as a complete system, while introducing them to systems thinking concepts including reservoirs, fluxes and equilibrium. Classroom photosynthesis experiments and field measurements of schoolyard vegetation brings the global view to the local level. And the use of computer models at varying levels of complexity (effects on photosynthesis, biomass and carbon storage in global biomes, global carbon cycle) not only reinforces systems concepts and carbon content, but also introduces students to an important scientific tool necessary for understanding climate change.

  12. Impacts of cloud superparameterization on projected daily rainfall intensity climate changes in multiple versions of the Community Earth System Model

    DOE PAGES

    Kooperman, Gabriel J.; Pritchard, Michael S.; Burt, Melissa A.; ...

    2016-09-26

    Changes in the character of rainfall are assessed using a holistic set of statistics based on rainfall frequency and amount distributions in climate change experiments with three conventional and superparameterized versions of the Community Atmosphere Model (CAM and SPCAM). Previous work has shown that high-order statistics of present-day rainfall intensity are significantly improved with superparameterization, especially in regions of tropical convection. Globally, the two modeling approaches project a similar future increase in mean rainfall, especially across the Inter-Tropical Convergence Zone (ITCZ) and at high latitudes, but over land, SPCAM predicts a smaller mean change than CAM. Changes in high-order statisticsmore » are similar at high latitudes in the two models but diverge at lower latitudes. In the tropics, SPCAM projects a large intensification of moderate and extreme rain rates in regions of organized convection associated with the Madden Julian Oscillation, ITCZ, monsoons, and tropical waves. In contrast, this signal is missing in all versions of CAM, which are found to be prone to predicting increases in the amount but not intensity of moderate rates. Predictions from SPCAM exhibit a scale-insensitive behavior with little dependence on horizontal resolution for extreme rates, while lower resolution (~2°) versions of CAM are not able to capture the response simulated with higher resolution (~1°). Furthermore, moderate rain rates analyzed by the “amount mode” and “amount median” are found to be especially telling as a diagnostic for evaluating climate model performance and tracing future changes in rainfall statistics to tropical wave modes in SPCAM.« less

  13. Tailoring Earth Observation To Ranchers For Improved Land Management And Profitability: The VegMachine Online Project

    NASA Astrophysics Data System (ADS)

    Scarth, P.; Trevithick, B.; Beutel, T.

    2016-12-01

    VegMachine Online is a freely available browser application that allows ranchers across Australia to view and interact with satellite derived ground cover state and change maps on their property and extract this information in a graphical format using interactive tools. It supports the delivery and communication of a massive earth observation data set in an accessible, producer friendly way . Around 250,000 Landsat TM, ETM and OLI images were acquired across Australia, converted to terrain corrected surface reflectance and masked for cloud, cloud shadow, terrain shadow and water. More than 2500 field sites across the Australian rangelands were used to derive endmembers used in a constrained unmixing approach to estimate the per-pixel proportion of bare, green and non-green vegetation for all images. A seasonal metoid compositing method was used to produce national fractional cover virtual mosaics for each three month period since 1988. The time series of green fraction is used to estimate the persistent green due to tree and shrub canopies, and this estimate is used to correct the fractional cover to ground cover for our mixed tree-grass rangeland systems. Finally, deciles are produced for key metrics every season to track a pixels relativity to the entire time series. These data are delivered through time series enabled web mapping services and customised web processing services that enable the full time series over any spatial extent to be interrogated in seconds via a RESTful interface. These services interface with a front end browser application that provides product visualization for any date in the time series, tools to draw or import polygon boundaries, plot time series ground cover comparisons, look at the effect of historical rainfall and tools to run the revised universal soil loss equation in web time to assess the effect of proposed changes in cover retention. VegMachine Online is already being used by ranchers monitoring paddock condition

  14. MoMa: From Molecules to Man: Space Research Applied to the improvement of the Quality of Life of the Ageing Population on Earth. Evolution of a project

    NASA Astrophysics Data System (ADS)

    Zambito, Anna Maria; Curcio, Francesco; Meli, Antonella; Saverio Ambesi-Impiombato, Francesco

    The "MoMa" project: "From Molecules to Man: Space Research Applied to the improvement of the Quality of Life of the Ageing Population on Earth started June 16 2006 and finished right on schedule June 25 2009, has been the biggest of the three projects funded by ASI in the sector "Medicine and Biotechnology. In the last years the scientific community had formed a national chain of biomedical spatial research with different research areas. MoMa responds to the necessity of unification in ASI of the two areas "Radiobiology and Protection" and "Cellular and Molecular Biotechnology" in a line of joint research: "Biotechnological Applications" were the interests of all groups would be combined and unified in a goal of social relevance. MoMa is the largest project ever developed in the biomedical area in Italy, the idea was born thinking about the phenomenon of acceleration of the aging process observed in space, and already described in literature, and the aim of studying the effects of the space environment at cellular, molecular and human organism level. "MoMa" was divided into three primary areas of study: Molecules, Cells and Man with an industrial area alongside. This allowed to optimize the work and information flows within the scientific research more similar and more culturally homogeneous and allowed a perfect industrial integration in a project of great scientific importance. Within three scientific areas 10 scientific lines in total are identified, each of them coordinated by a subcontractor. The rapid and efficient exchange of information between different areas of science and the development of industrial applications in various areas of interest have been assured by a strong work of Scientific Coordination of System Engineering and Quality Control. After three years of intense and coordinated activities within the MoMa project, the objectives achieved are very significant not only as regards the scientific results and the important hardware produced but

  15. New Directions in Seismic Hazard Assessment Through Focused Earth Observation in the MARmara SuperSITE - Project Achievements

    NASA Astrophysics Data System (ADS)

    Meral OZel, Nurcan; Necmioǧlu, Öcal; Ergintav, Semih; Ozel, Oǧuz; Favali, Paolo; Bigarre, Pascal; Çakır, Ziyadin; Ozeren, Sinan; Geli, Louis; Douglas, John; Aochi, Hideo; Bossu, Remy; Zülfikar, Can; Şeşetyan, Karin; Erdik, Mustafa

    2016-04-01

    The MARsite Project, which started in November 2012,funded by the EC/ FP7-ENV.2012 6.4-2 (Grant 308417) identifies the Marmara region as a 'Supersite' within European initiatives to aggregate on-shore, off-shore and space-based observations, comprehensive geophysical monitoring, improved hazard and risk assessments encompassed in an integrated set of activities. MARsite aimed to harmonize geological, geophysical, geodetic and geochemical observations to provide a better view of the post-seismic deformation of the 1999 Izmit earthquake (in addition to the post-seismic signature of previous earthquakes), loading of submarine and inland active fault segments and transient pre-earthquake signals, related to stress loading with different tectonic properties in and around Marmara Sea. This presentation provides an overview of the achievements of MARSite which aimed to coordinate research groups ranging from seismology to gas geochemistry in a comprehensive monitoring activity developed in the Marmara Region based on collection of multidisciplinary data to be shared, interpreted and merged in consistent theoretical and practical models suitable for the implementation of good practices to move the necessary information to the end users in charge of seismic risk management of the region. In addition, processes involved in earthquake generation and the physics of short-term seismic transients, 4D deformations to understand earthquake cycle processes, fluid activity monitoring and seismicity under the sea floor using existing autonomous instrumentation, early warning and development of real-time shake and loss information, real- and quasi-real-time earthquake and tsunami hazard monitoring and earthquake-induced landslide hazard topics are also covered within MARSite. In particular, achievements and progress in the design and building of a multi-parameter borehole system consisting of very wide dynamic range and stable borehole (VBB) broad band seismic sensor, with

  16. Functional variation in the gut microbiome of wild Drosophila populations.

    PubMed

    Bost, Alyssa; Martinson, Vincent G; Franzenburg, Soeren; Adair, Karen L; Albasi, Alice; Wells, Martin T; Douglas, Angela E

    2018-05-26

    Most of the evidence that the gut microbiome of animals is functionally variable, with consequences for the health and fitness of the animal host, is based on laboratory studies, often using inbred animals under tightly controlled conditions. It is largely unknown whether these microbiome effects would be evident in outbred animal populations under natural conditions. In this study, we quantified the functional traits of the gut microbiota (metagenome) and host (gut transcriptome) and the taxonomic composition of the gut microorganisms (16S rRNA gene sequence) in natural populations of three mycophagous Drosophila species. Variation in microbiome function and composition was driven principally by the period of sample collection, while host function varied mostly with Drosophila species, indicating that variation in microbiome traits is determined largely by environmental factors, and not host taxonomy. Despite this, significant correlations between microbiome and host functional traits were obtained. In particular, microbiome functions dominated by metabolism were positively associated with host functions relating to gut epithelial turnover. Much of the functional variation in the microbiome could be attributed to variation in abundance of Bacteroidetes, rather than the two other abundant groups, the γ-Proteobacteria or Lactobacillales. We conclude that functional variation in the interactions between animals and their gut microbiome can be detectable in natural populations and, in mycophagous Drosophila, this variation relates primarily to metabolism and homeostasis of the gut epithelium. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  17. Metagenomic and metatranscriptomic analysis of the microbiome of watermelon fruits

    The plant microbiome is a key determinant of plant health and productivity, and alteration of the plant microbiome can increase the quality of agricultural products. Little is known about the microbial population in fruit development of plants. In this study, we aimed to understand the function of m...

  18. Experimental metagenomics and ribosomal profiling of the human skin microbiome.

    PubMed

    Ferretti, Pamela; Farina, Stefania; Cristofolini, Mario; Girolomoni, Giampiero; Tett, Adrian; Segata, Nicola

    2017-03-01

    The skin is the largest organ in the human body, and it is populated by a large diversity of microbes, most of which are co-evolved with the host and live in symbiotic harmony. There is increasing evidence that the skin microbiome plays a crucial role in the defense against pathogens, immune system training and homoeostasis, and microbiome perturbations have been associated with pathological skin conditions. Studying the skin resident microbial community is thus essential to better understand the microbiome-host crosstalk and to associate its specific configurations with cutaneous diseases. Several community profiling approaches have proved successful in unravelling the composition of the skin microbiome and overcome the limitations of cultivation-based assays, but these tools remain largely inaccessible to the clinical and medical dermatology communities. The study of the skin microbiome is also characterized by specific technical challenges, such as the low amount of microbial biomass and the extensive human DNA contamination. Here, we review the available community profiling approaches to study the skin microbiome, specifically focusing on the practical experimental and analytical tools necessary to generate and analyse skin microbiome data. We describe all the steps from the initial samples collection to the final data interpretation, with the goal of enabling clinicians and researchers who are not familiar with the microbiome field to perform skin profiling experiments. © 2016 The Authors. Experimental Dermatology Published by John Wiley & Sons Ltd.

  19. The intestinal microbiome and skeletal fitness: connecting bugs and bones

    PubMed Central

    Charles, Julia F.; Ermann, Joerg; Aliprantis, Antonios O.

    2015-01-01

    Recent advances have dramatically increased our understanding of how organ systems interact. This has been especially true for immunology and bone biology, where the term “osteoimmunology” was coined to capture this relationship. The importance of the microbiome to the immune system has also emerged as a driver of health and disease. It makes sense therefore to ask the question: how does the intestinal microbiome influence bone biology and does dysbiosis promote bone disease? Surprisingly, few studies have analyzed this connection. A broader interpretation of this question reveals many mechanisms whereby the microbiome may affect bone cells. These include effects of the microbiome on immune cells, including myeloid progenitors and Th17 cells, as well as steroid hormones, fatty acids, serotonin and vitamin D. As mechanistic interactions of the microbiome and skeletal system are revealed within and without the immune system, novel strategies to optimize skeletal fitness may emerge. PMID:25840106

  20. The gut microbiome: a clinically significant player in transplantation?

    PubMed

    Vindigni, Stephen M; Surawicz, Christina M

    2015-01-01

    The intestinal microbiome is critical to digestion, metabolism and protection from pathogenic organisms. Dysbiosis, or alteration of this microbiome, can result in Clostridium difficile infection and may play a role in other conditions. Patients undergoing solid organ transplantation (e.g., kidney, lung, liver, small bowel) and hematopoietic stem cell transplantation have a shift in the gut microbiome with a decrease in predominant organisms, a loss of bacterial diversity and emergence of a new dominant population. This translates into increased morbidity and mortality with risk of infection and rejection. We discuss the changes seen in the microbiome and its possible consequences. It may be important to develop strategies to restore the normal microbiome in such patients.

  1. The microbiome in early life: implications for health outcomes.

    PubMed

    Tamburini, Sabrina; Shen, Nan; Wu, Han Chih; Clemente, Jose C

    2016-07-07

    Recent studies have characterized how host genetics, prenatal environment and delivery mode can shape the newborn microbiome at birth. Following this, postnatal factors, such as antibiotic treatment, diet or environmental exposure, further modulate the development of the infant's microbiome and immune system, and exposure to a variety of microbial organisms during early life has long been hypothesized to exert a protective effect in the newborn. Furthermore, epidemiological studies have shown that factors that alter bacterial communities in infants during childhood increase the risk for several diseases, highlighting the importance of understanding early-life microbiome composition. In this review, we describe how prenatal and postnatal factors shape the development of both the microbiome and the immune system. We also discuss the prospects of microbiome-mediated therapeutics and the need for more effective approaches that can reconfigure bacterial communities from pathogenic to homeostatic configurations.

  2. Development of an earth pressure model for design of earth retaining structures in piedmont soil.

    DOT National Transportation Integrated Search

    2008-10-01

    Anecdotal evidence suggests that earth pressure in Piedmont residual soils is typically over estimated. Such estimates of earth pressure impact the design of earth retaining structures used on highway projects. Thus, the development of an appropriate...

  3. The I-Cleen Project (inquiring on Climate & Energy). Enhancing AN Enquiry-Based Approach to Earth System Sciences in Italian Classrooms

    NASA Astrophysics Data System (ADS)

    Cattadori, M.

    2010-12-01

    In the last years, the world of Italian school underwent some slow but deep transformation processes. One of the negative consequences - documented by specific studies - was the further weakening of the use of inquiring educational practices (or kinds of lessons) by science teachers. This occurred in a scholastic framework already traditionally little inclined to those. The I-CLEEN project (Inquiring on CLimate & Energy, www.icleen.museum ) was born in 2008 with the intent to react to (and contrast) this process (trend) by initiative of a staff of science teachers from different regions, all with many years’ experience, coordinated and supported by the local museum, the Natural Science Museum of Trento - Trento, Italy. I-CLEEN is a free instrument of cooperation for Italian teachers, aimed to support and enhance the practice of the inquiring education in explaining themes in range of Climate and Energy and generally about Earth System Sciences. This project is a consequence of what has been experienced and done in Italy by its creators within the Educational and Outreach program of ANDRILL (ANtarctic geological DRILLing). The core of the project is a database of resources potentially useful to a teacher preparing an inquiring lesson. These are selected by a staff following a specific selection policy. There are also lessons ready to be used in the classrooms, prepared according to a specific editorial standard. These are composed by a paper for the teacher and a paper for the student. The database is technically an information gateway and it is constantly enriched thanks to a job of critical research in the teachers’ practices or the worthiest international educational web projects. These are published in Italian or in bilingual format (Italian-English), always through explicit authorization by the authors and under a Creative Commons license when possible. This contribution illustrates details about this service which is on-line since December 2009 and is

  4. Acquisition of Uropygial Gland Microbiome by Hoopoe Nestlings.

    PubMed

    Martín-Vivaldi, Manuel; Soler, Juan José; Martínez-García, Ángela; Arco, Laura; Juárez-García-Pelayo, Natalia; Ruiz-Rodríguez, Magdalena; Martínez-Bueno, Manuel

    2017-12-18

    Mutualistic symbioses between animals and bacteria depend on acquisition of appropriate symbionts while avoiding exploitation by non-beneficial microbes. The mode of acquisition of symbionts would determine, not only the probability of encountering but also evolutionary outcomes of mutualistic counterparts. The microbiome inhabiting the uropygial gland of the European hoopoe (Upupa epops) includes a variety of bacterial strains, some of them providing antimicrobial benefits. Here, the mode of acquisition and stability of this microbiome is analyzed by means of Automated rRNA Intergenic Spacer Analysis and two different experiments. The first experiment impeded mothers' access to their glands, thus avoiding direct transmission of microorganisms from female to offspring secretions. The second experiment explored the stability of the microbiomes by inoculating glands with secretions from alien nests. The first experiment provoked a reduction in similarity of microbiomes of mother and nestlings. Interestingly, some bacterial strains were more often detected when females had not access to their glands, suggesting antagonistic effects among bacteria from different sources. The second experiment caused an increase in richness of the microbiome of receivers in terms of prevalence of Operational Taxonomic Units (OTUs) that reduced differences in microbiomes of donors and receivers. That occurred because OTUs that were present in donors but not in receivers incorporated to the microbiome of the latter, which provoked that cross-inoculated nestlings got similar final microbiomes that included the most prevalent OTUs. The results are therefore consistent with a central role of vertical transmission in bacterial acquisition by nestling hoopoes and support the idea that the typical composition of the hoopoe gland microbiome is reached by the incorporation of some bacteria during the nestling period. This scenario suggests the existence of a coevolved core microbiome composed by

  5. A Machine Learning Approach for Using the Postmortem Skin Microbiome to Estimate the Postmortem Interval

    PubMed Central

    Johnson, Hunter R.; Trinidad, Donovan D.; Guzman, Stephania; Khan, Zenab; Parziale, James V.; DeBruyn, Jennifer M.

    2016-01-01

    Research on the human microbiome, the microbiota that live in, on, and around the human person, has revolutionized our understanding of the complex interactions between microbial life and human health and disease. The microbiome may also provide a valuable tool in forensic death investigations by helping to reveal the postmortem interval (PMI) of a decedent that is discovered after an unknown amount of time since death. Current methods of estimating PMI for cadavers discovered in uncontrolled, unstudied environments have substantial limitations, some of which may be overcome through the use of microbial indicators. In this project, we sampled the microbiomes of decomposing human cadavers, focusing on the skin microbiota found in the nasal and ear canals. We then developed several models of statistical regression to establish an algorithm for predicting the PMI of microbial samples. We found that the complete data set, rather than a curated list of indicator species, was preferred for training the regressor. We further found that genus and family, rather than species, are the most informative taxonomic levels. Finally, we developed a k-nearest- neighbor regressor, tuned with the entire data set from all nasal and ear samples, that predicts the PMI of unknown samples with an average error of ±55 accumulated degree days (ADD). This study outlines a machine learning approach for the use of necrobiome data in the prediction of the PMI and thereby provides a successful proof-of- concept that skin microbiota is a promising tool in forensic death investigations. PMID:28005908

  6. Human microbiomes and their roles in dysbiosis, common diseases, and novel therapeutic approaches.

    PubMed

    Belizário, José E; Napolitano, Mauro

    2015-01-01

    The human body is the residence of a large number of commensal (non-pathogenic) and pathogenic microbial species that have co-evolved with the human genome, adaptive immune system, and diet. With recent advances in DNA-based technologies, we initiated the exploration of bacterial gene functions and their role in human health. The main goal of the human microbiome project is to characterize the abundance, diversity and functionality of the genes present in all microorganisms that permanently live in different sites of the human body. The gut microbiota expresses over 3.3 million bacterial genes, while the human genome expresses only 20 thousand genes. Microbe gene-products exert pivotal functions via the regulation of food digestion and immune system development. Studies are confirming that manipulation of non-pathogenic bacterial strains in the host can stimulate the recovery of the immune response to pathogenic bacteria causing diseases. Different approaches, including the use of nutraceutics (prebiotics and probiotics) as well as phages engineered with CRISPR/Cas systems and quorum sensing systems have been developed as new therapies for controlling dysbiosis (alterations in microbial community) and common diseases (e.g., diabetes and obesity). The designing and production of pharmaceuticals based on our own body's microbiome is an emerging field and is rapidly growing to be fully explored in the near future. This review provides an outlook on recent findings on the human microbiomes, their impact on health and diseases, and on the development of targeted therapies.

  7. Human microbiomes and their roles in dysbiosis, common diseases, and novel therapeutic approaches

    PubMed Central

    Belizário, José E.; Napolitano, Mauro

    2015-01-01

    The human body is the residence of a large number of commensal (non-pathogenic) and pathogenic microbial species that have co-evolved with the human genome, adaptive immune system, and diet. With recent advances in DNA-based technologies, we initiated the exploration of bacterial gene functions and their role in human health. The main goal of the human microbiome project is to characterize the abundance, diversity and functionality of the genes present in all microorganisms that permanently live in different sites of the human body. The gut microbiota expresses over 3.3 million bacterial genes, while the human genome expresses only 20 thousand genes. Microbe gene-products exert pivotal functions via the regulation of food digestion and immune system development. Studies are confirming that manipulation of non-pathogenic bacterial strains in the host can stimulate the recovery of the immune response to pathogenic bacteria causing diseases. Different approaches, including the use of nutraceutics (prebiotics and probiotics) as well as phages engineered with CRISPR/Cas systems and quorum sensing systems have been developed as new therapies for controlling dysbiosis (alterations in microbial community) and common diseases (e.g., diabetes and obesity). The designing and production of pharmaceuticals based on our own body’s microbiome is an emerging field and is rapidly growing to be fully explored in the near future. This review provides an outlook on recent findings on the human microbiomes, their impact on health and diseases, and on the development of targeted therapies. PMID:26500616

  8. The role of the cutaneous microbiome in skin cancer: lessons learned from the gut.

    PubMed

    Yu, Yang; Champer, Jackson; Beynet, David; Kim, Jenny; Friedman, Adam J

    2015-05-01

    The human microbiome has recently gained prominence as a major factor in health and disease. Here we review the literature regarding the microbiome and cancer and suggest how the microbiome may be manipulated for improved health outcomes. The gut microbiome has been relatively well studied, and the mechanisms of how it may increase or decrease the risk of certain cancers may apply to the skin microbiome. Additionally, the gut microbiome may directly impact the risk of cancer in the skin and other organs by promoting systemic inflammation. The skin microbiome itself is as diverse as the gut microbiome, but research has just begun to unravel its influence on the host. Like the gut microbiome, it affects the risk for several diseases, including cancer. By using healthpromoting strains from the microbiome in oral or topical probiotics, it may be possible to reduce the risk of skin cancer and perhaps even increase the likelihood of successful treatment.

  9. Field Studies in Science Teacher Preparation Programs: Examples of Research-Oriented Earth and Environmental Science Field Projects for Pre-service and In-service Teachers

    NASA Astrophysics Data System (ADS)

    O'Neal, M. L.

    2005-12-01

    Science teaching reforms of the past 10 to 20 years have focused on a pedagogical shift from verification-style laboratory exercises, toward hands-on and inquiry-based constructivist teaching methods. Such methods, however, require teachers to be proficient in more than just basic content and teaching strategies. To be effective teachers, these professionals must also be skilled in the design and implementation of research-style investigations. At Loyola College in Maryland, topics in the earth and environmental sciences are used as the basis for field research projects that teach our students science content, along with how to design age-appropriate investigative activities and how to implement them in a stimulating, inquiry-based learning environment. Presented here are examples of three projects, demonstrating how these themes are woven throughout our pre- and in-service teacher preparation programs, at both undergraduate and graduate levels. 1. Watershed Studies - In our undergraduate, pre-service, elementary education teacher preparation program, students design and implement a water quality study in a local watershed. In the classroom, students use topographic maps and aerial photographs to delineate the watersheds' boundaries, to identify current land use patterns, and to select appropriate locations on the trunk stream for testing. Water testing at these sites is conducted during field trips, with data analysis and interpretation performed on-site. On-site work allows students to make connections between stream water quality and adjacent land use practices. Students then relate the content and research results to science teaching standards, in order to develop a unit-plan for use in their future classrooms. 2. Land Use Assessment - In our graduate, in-service, elementary and middle school science program, a local stream valley is used as the basis for an analysis of potential land use changes. Students first construct a topographic base map of the area, and

  10. Microbiome of Yermic Regosol in southern Kazakhstan

    NASA Astrophysics Data System (ADS)

    Kutovaya, Olga; Lebedeva, Marina; Tkhakakhova, Azida

    2014-05-01

    Biological activity is of utmost importance for the genesis of extremely arid desert soils. The soil surface in arid regions is often covered by biofilms representing a complex biocenosis of algae, bacteria, micromycetes, and, sometimes, mosses or lichens. Biofilms of extremely arid soils form a significant part of the living matter in the desert ecosystems and play the central role in their dynamics. Study of the genetic material recovered directly from the soil samples is the main approach in soil metagenomics. Modern sequencing methods were used to describe the diversity of the microorganisms in soil samples. For the first time, such data were obtained for the extremely arid desert soil (Yermic Regosol) in southern Kazakhstan (flat alluvial plain; 43° 42'53.2" N; 79°25'29.1" E; 615 m asl). Taxonomic identification of nucleotide sequences and comparative analysis of microbial communities were performed using VAMPS. The classification of the sequences was performed using RDP. As the primers used were based on the sequences of 16S-rRNA gene of bacteria and archaea, we could analyze the prokaryotic community. Along with bacteria and archaea with established systematic position, all soil samples contained unidentified sequences (5.2-5.3%). Bacteria predominated at the domain level (65.9-74.9%), although their portion was much lower in comparison with that in less arid soils, where it reached 94-100%. Archaea were present as minor components (0.3-0.5%). Dominant groups of bacteria were represented by Proteobacteria (43.9-50.8%), Actinobacteria (9.5-10%), Firmicutes (0.8-2.4%), Verrucomicrobia (1.1-3%), Acidobacteria (1.1-2%), Bacteroidetes (1.2-1.4%). The portion of other phyla was less than 1%. Thus, bacterial phyla Proteobacteria, Actinobacteria and Acidobacteria constitute the core component of the microbiome. Archaea are represented by phylum Crenarchaeota. A key feature of the extremely arid soils is the presence of large numbers (24.7-33.6%) of cyanobacteria

  11. Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

    PubMed Central

    Abubucker, Sahar; Segata, Nicola; Goll, Johannes; Schubert, Alyxandria M.; Izard, Jacques; Cantarel, Brandi L.; Rodriguez-Mueller, Beltran; Zucker, Jeremy; Thiagarajan, Mathangi; Henrissat, Bernard; White, Owen; Kelley, Scott T.; Methé, Barbara; Schloss, Patrick D.; Gevers, Dirk; Mitreva, Makedonka; Huttenhower, Curtis

    2012-01-01

    Microbial communities carry out the majority of the biochemical activity on the planet, and they play integral roles in processes including metabolism and immune homeostasis in the human microbiome. Shotgun sequencing of such communities' metagenomes provides information complementary to organismal abundances from taxonomic markers, but the resulting data typically comprise short reads from hundreds of different organisms and are at best challenging to assemble comparably to single-organism genomes. Here, we describe an alternative approach to infer the functional and metabolic potential of a microbial community metagenome. We determined the gene families and pathways present or absent within a community, as well as their relative abundances, directly from short sequence reads. We validated this methodology using a collection of synthetic metagenomes, recovering the presence and abundance both of large pathways and of small functional modules with high accuracy. We subsequently applied this method, HUMAnN, to the microbial communities of 649 metagenomes drawn from seven primary body sites on 102 individuals as part of the Human Microbiome Project (HMP). This provided a means to compare functional diversity and organismal ecology in the human microbiome, and we determined a core of 24 ubiquitously present modules. Core pathways were often implemented by different enzyme families within different body sites, and 168 functional modules and 196 metabolic pathways varied in metagenomic abundance specifically to one or more niches within the microbiome. These included glycosaminoglycan degradation in the gut, as well as phosphate and amino acid transport linked to host phenotype (vaginal pH) in the posterior fornix. An implementation of our methodology is available at http://huttenhower.sph.harvard.edu/humann. This provides a means to accurately and efficiently characterize microbial metabolic pathways and functional modules directly from high-throughput sequencing reads

  12. Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis.

    PubMed

    Song, Han; Yoo, Young; Hwang, Junghyun; Na, Yun-Cheol; Kim, Heenam Stanley

    2016-03-01

    Atopic dermatitis (AD) is a serious global epidemic associated with a modern lifestyle. Although aberrant interactions between gut microbes and the intestinal immune system have been implicated in this skin disease, the nature of the microbiome dysfunction underlying the disease remains unclear. The gut microbiome from 132 subjects, including 90 patients with AD, was analyzed by using 16S rRNA gene and metagenome sequence analyses. Reference genomes from the Human Microbiome Project and the KEGG Orthology database were used for metagenome analyses. Short-chain fatty acids in fecal samples were compared by using gas chromatographic-mass spectrometric analyses. We show that enrichment of a subspecies of the major gut species Faecalibacterium prausnitzii is strongly associated with AD. In addition, the AD microbiome was enriched in genes encoding the use of various nutrients that could be released from damaged gut epithelium, reflecting a bloom of auxotrophic bacteria. Fecal samples from patients with AD showed decreased levels of butyrate and propionate, which have anti-inflammatory effects. This is likely a consequence of an intraspecies compositional change in F prausnitzii that reduces the number of high butyrate and propionate producers, including those related to the strain A2-165, a lack of which has been implicated in patients with Crohn disease. The data suggest that feedback interactions between dysbiosis in F prausnitzii and dysregulation of gut epithelial inflammation might underlie the chronic progression of AD by resulting in impairment of the gut epithelial barrier, which ultimately leads to aberrant TH2-type immune responses to allergens in the skin. Copyright © 2015 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  13. Effects of moderate, voluntary ethanol consumption on the rat and human gut microbiome.

    PubMed

    Kosnicki, Kassi L; Penprase, Jerrold C; Cintora, Patricia; Torres, Pedro J; Harris, Greg L; Brasser, Susan M; Kelley, Scott T

    2018-05-11

    Many alcohol-induced health complications are directly attributable to the toxicity of alcohol or its metabolites, but another potential health impact of alcohol may be on the microbial communities of the human gut. Clear distinctions between healthy and diseased-state gut microbiota have been observed in subjects with metabolic diseases, and recent studies suggest that chronic alcoholism is linked to gut microbiome dysbiosis. Here, we investigated the effects of moderate levels of alcohol consumption on the gut microbiome in both rats and humans. The gut microbiota of rats voluntarily consuming a 20 percent ethanol solution, on alternate days, were compared with a non-exposed control group to identify differential taxonomic and functional profiles. Gut microbial diversity profiles were determined using culture-independent amplification, next-generation sequencing and bioinformatic analysis of bacterial 16S ribosomal RNA gene sequence libraries. Our results showed that, compared with controls, ethanol-consuming rats experienced a significant decline in the biodiversity of their gut microbiomes, a state generally associated with dysbiosis. We also observed significant shifts in the overall diversity of the gut microbial communities and a dramatic change in the relative abundance of particular microbes, such as the Lactobacilli. We also compared our results to human fecal microbiome data collected as part of the citizen science American Gut Project. In contrast to the rat data, human drinkers had significantly higher gut microbial biodiversity than non-drinkers. However, we also observed that microbes that differed among the human subjects displayed similar trends in the rat model, including bacteria implicated in metabolic disease. © 2018 Society for the Study of Addiction.

  14. ERATOSTHENES: excellence research Centre for Earth surveillance and space-based monitoring of the environment, the EXCELSIOR Horizon 2020 teaming project

    NASA Astrophysics Data System (ADS)

    Hadjimitsis, Diofantos G.; Kontoes, Haris; Schreier, Gunter; Ansmann, Albert; Komodromos, George; Themistocleous, Kyriacos; Mamouri, Rodanthi; Michaelides, Silas; Nisantzi, Argyro; Papoutsa, Christiana; Neocleous, Kyriacos; Mettas, Christodoulos; Tzouvaras, Marios; Evagorou, Evagoras; Christofe, Andreas; Melillos, George; Papoutsis, Ioannis

    2017-10-01

    The aim of this paper is to present the strategy and vision to upgrade the existing ERATOSTHENES Research Centre (ERC) established within the Cyprus University of Technology (CUT) into a sustainable, viable and autonomous Centre of Excellence (CoE) for Earth Surveillance and Space-Based Monitoring of the Environment, which will provide the highest quality of related services on the National, European and International levels. EXCELSIOR is a Horizon 2020 Teaming project which addresses a specific challenge defined by the work program, namely, the reduction of substantial disparities in the European Union by supporting research and innovation activities and systems in low performing countries. It also aims at establishing long-term and strategic partnerships between the Teaming partners, thus reducing internal research and innovation disparities within European Research and Innovation landscape. The proposed CoE envisions the upgrading of the existing ERC into an inspiring environment for conducting basic and applied research and innovation in the areas of the integrated use of remote sensing and space-based techniques for monitoring the environment. Environment has been recognized by the Smart Specialization Strategy of Cyprus as the first horizontal priority for future growth of the island. The foreseen upgrade will regard the expansion of this vision to systematic monitoring of the environment using Earth Observation, space and ground based integrated technologies. Such an approach will lead to the systematic monitoring of all three domains of the Environment (Air, Land, Water). Five partners have united to upgrade the existing ERC into a CoE, with the common vision to become a world-class innovation, research and education centre, actively contributing to the European Research Area (ERA). More specifically, the Teaming project is a team effort between the Cyprus University of Technology (CUT, acting as the coordinator), the German Aerospace Centre (DLR), the

  15. Earth Observation

    NASA Technical Reports Server (NTRS)

    1994-01-01

    For pipeline companies, mapping, facilities inventory, pipe inspections, environmental reporting, etc. is a monumental task. An Automated Mapping/Facilities Management/Geographic Information Systems (AM/FM/GIS) is the solution. However, this is costly and time consuming. James W. Sewall Company, an AM/FM/GIS consulting firm proposed an EOCAP project to Stennis Space Center (SSC) to develop a computerized system for storage and retrieval of digital aerial photography. This would provide its customer, Algonquin Gas Transmission Company, with an accurate inventory of rights-of-way locations and pipeline surroundings. The project took four years to complete and an important byproduct was SSC's Digital Aerial Rights-of-Way Monitoring System (DARMS). DARMS saves substantial time and money. EOCAP enabled Sewall to develop new products and expand its customer base. Algonquin now manages regulatory requirements more efficiently and accurately. EOCAP provides government co-funding to encourage private investment in and broader use of NASA remote sensing technology. Because changes on Earth's surface are accelerating, planners and resource managers must assess the consequences of change as quickly and accurately as possible. Pacific Meridian Resources and NASA's Stennis Space Center (SSC) developed a system for monitoring changes in land cover and use, which incorporated the latest change detection technologies. The goal of this EOCAP project was to tailor existing technologies to a system that could be commercialized. Landsat imagery enabled Pacific Meridian to identify areas that had sustained substantial vegetation loss. The project was successful and Pacific Meridian's annual revenues have substantially increased. EOCAP provides government co-funding to encourage private investment in and broader use of NASA remote sensing technology.

  16. Sewage Reflects the Microbiomes of Human Populations

    PubMed Central

    Newton, Ryan J.; McLellan, Sandra L.; Dila, Deborah K.; Vineis, Joseph H.; Morrison, Hilary G.; Eren, A. Murat

    2015-01-01

    ABSTRACT Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker gene studies that consider microbiome trends among human populations scale with the number of individuals sampled from each population. As an alternative strategy for sampling populations, we examined whether sewage accurately reflects the microbial community of a mixture of stool samples. We used oligotyping of high-throughput 16S rRNA gene sequence data to compare the bacterial distribution in a stool data set to a sewage influent data set from 71 U.S. cities. On average, only 15% of sewage sample sequence reads were attributed to human fecal origin, but sewage recaptured most (97%) human fecal oligotypes. The most common oligotypes in stool matched the most common and abundant in sewage. After informatically separating sequences of human fecal origin, sewage samples exhibited ~3× greater diversity than stool samples. Comparisons among municipal sewage communities revealed the ubiquitous and abundant occurrence of 27 human fecal oligotypes, representing an apparent core set of organisms in U.S. populations. The fecal community variability among U.S. populations was significantly lower than among individuals. It clustered into three primary community structures distinguished by oligotypes from either: Bacteroidaceae, Prevotellaceae, or Lachnospiraceae/Ruminococcaceae. These distribution patterns reflected human population variation and predicted whether samples represented lean or obese populations with 81 to 89% accuracy. Our findings demonstrate that sewage represents the fecal microbial community of human populations and captures population-level traits of the human microbiome. PMID:25714718

  17. Municipal solid waste landfills harbor distinct microbiomes

    Stamps, Blake W.; Lyles, Christopher N.; Suflita, Joseph M.; Masoner, Jason R.; Cozzarelli, Isabelle M.; Kolpin, Dana W.; Stevenson, Bradley S.

    2016-01-01

    Landfills are the final repository for most of the discarded material from human society and its “built environments.” Microorganisms subsequently degrade this discarded material in the landfill, releasing gases (largely CH4 and CO2) and a complex mixture of soluble chemical compounds in leachate. Characterization of “landfill microbiomes” and their comparison across several landfills should allow the identification of environmental or operational properties that influence the composition of these microbiomes and potentially their biodegradation capabilities. To this end, the composition of landfill microbiomes was characterized as part of an ongoing USGS national survey studying the chemical composition of leachates from 19 non-hazardous landfills across 16 states in the continental U.S. The landfills varied in parameters such as size, waste composition, management strategy, geography, and climate zone. The diversity and composition of bacterial and archaeal populations in leachate samples were characterized by 16S rRNA gene sequence analysis, and compared against a variety of physical and chemical parameters in an attempt to identify their impact on selection. Members of the Epsilonproteobacteria, Gammaproteobacteria, Clostridia, and candidate division OP3 were the most abundant. The distribution of the observed phylogenetic diversity could best be explained by a combination of variables and was correlated most strongly with the concentrations of chloride and barium, rate of evapotranspiration, age of waste, and the number of detected household chemicals. This study illustrates how leachate microbiomes are distinct from those of other natural or built environments, and sheds light on the major selective forces responsible for this microbial diversity.

  18. Microbiome Disturbances and Autism Spectrum Disorders.

    PubMed

    Rosenfeld, Cheryl S

    2015-10-01

    Autism spectrum disorders (ASDs) are considered a heterogenous set of neurobehavioral diseases, with the rates of diagnosis dramatically increasing in the past few decades. As genetics alone does not explain the underlying cause in many cases, attention has turned to environmental factors as potential etiological agents. Gastrointestinal disorders are a common comorbidity in ASD patients. It was thus hypothesized that a gut-brain link may account for some autistic cases. With the characterization of the human microbiome, this concept has been expanded to include the microbiota-gut-brain axis. There are mounting reports in animal models and human epidemiologic studies linking disruptive alterations in the gut microbiota or dysbiosis and ASD symptomology. In this review, we will explore the current evidence that gut dysbiosis in animal models and ASD patients correlates with disease risk and severity. The studies to date have surveyed how gut microbiome changes may affect these neurobehavioral disorders. However, we harbor other microbiomes in the body that might impact brain function. We will consider microbial colonies residing in the oral cavity, vagina, and the most recently discovered one in the placenta. Based on the premise that gut microbiota alterations may be causative agents in ASD, several therapeutic options have been tested, such as diet modulations, prebiotics, probiotics, synbiotics, postbiotics, antibiotics, fecal transplantation, and activated charcoal. The potential benefits of these therapies will be considered. Finally, the possible mechanisms by which changes in the gut bacterial communities may result in ASD and related neurobehavioral disorders will be examined. Copyright © 2015 by The American Society for Pharmacology and Experimental Therapeutics.

  19. Municipal Solid Waste Landfills Harbor Distinct Microbiomes

    PubMed Central

    Stamps, Blake W.; Lyles, Christopher N.; Suflita, Joseph M.; Masoner, Jason R.; Cozzarelli, Isabelle M.; Kolpin, Dana W.; Stevenson, Bradley S.

    2016-01-01

    Landfills are the final repository for most of the discarded material from human society and its “built environments.” Microorganisms subsequently degrade this discarded material in the landfill, releasing gases (largely CH4 and CO2) and a complex mixture of soluble chemical compounds in leachate. Characterization of “landfill microbiomes” and their comparison across several landfills should allow the identification of environmental or operational properties that influence the composition of these microbiomes and potentially their biodegradation capabilities. To this end, the composition of landfill microbiomes was characterized as part of an ongoing USGS national survey studying the chemical composition of leachates from 19 non-hazardous landfills across 16 states in the continental U.S. The landfills varied in parameters such as size, waste composition, management strategy, geography, and climate zone. The diversity and composition of bacterial and archaeal populations in leachate samples were characterized by 16S rRNA gene sequence analysis, and compared against a variety of physical and chemical parameters in an attempt to identify their impact on selection. Members of the Epsilonproteobacteria, Gammaproteobacteria, Clostridia, and candidate division OP3 were the most abundant. The distribution of the observed phylogenetic diversity could best be explained by a combination of variables and was correlated most strongly with the concentrations of chloride and barium, rate of evapotranspiration, age of waste, and the number of detected household chemicals. This study illustrates how leachate microbiomes are distinct from those of other natural or built environments, and sheds light on the major selective forces responsible for this microbial diversity. PMID:27148222

  20. DLESE Teaching Box Pilot Project: Developing a Replicable Model for Collaboratively Creating Innovative Instructional Sequences Using Exemplary Resources in the Digital Library for Earth System Education (DLESE)

    NASA Astrophysics Data System (ADS)

    Weingroff, M.

    2004-12-01

    Before the advent of digital libraries, it was difficult for teachers to find suitable high-quality resources to use in their teaching. Digital libraries such as DLESE have eased the task by making high quality resources more easily accessible and providing search mechanisms that allow teachers to 'fine tune' the criteria over which they search. Searches tend to return lists of resources with some contextualizing information. However, teachers who are teaching 'out of discipline' or who have minimal training in science often need additional support to know how to use and sequence them. The Teaching Box Pilot Project was developed to address these concerns, bringing together educators, scientists, and instructional designers in a partnership to build an online framework to fully support innovative units of instruction about the Earth system. Each box integrates DLESE resources and activities, teaching tips, standards, concepts, teaching outcomes, reviews, and assessment information. Online templates and best practice guidelines are being developed that will enable teachers to create their own boxes or customize existing ones. Two boxes have been developed so far, one on weather for high school students, and one on the evidence for plate tectonics for middle schoolers. The project has met with significant enthusiasm and interest, and we hope to expand it by involving individual teachers, school systems, pre-service programs, and universities in the development and use of teaching boxes. A key ingredient in the project's success has been the close collaboration between the partners, each of whom has brought unique experiences, perspectives, knowledge, and skills to the project. This first effort involved teachers in the San Francisco Bay area, the University of California Museum of Paleontology, San Francisco State University, U.S. Geological Survey, and DLESE. This poster will allow participants to explore one of the teaching boxes. We will discuss how the boxes were

  1. Assessment of malaria transmission changes in Africa, due to the climate impact of land use change using Coupled Model Intercomparison Project Phase 5 earth system models.

    PubMed

    Tompkins, Adrian M; Caporaso, Luca

    2016-03-31

    Using mathematical modelling tools, we assessed the potential for land use change (LUC) associated with the Intergovernmental Panel on Climate Change low- and high-end emission scenarios (RCP2.6 and RCP8.5) to impact malaria transmission in Africa. To drive a spatially explicit, dynamical malaria model, data from the four available earth system models (ESMs) that contributed to the LUC experiment of the Fifth Climate Model Intercomparison Project are used. Despite the limited size of the ESM ensemble, stark differences in the assessment of how LUC can impact climate are revealed. In three out of four ESMs, the impact of LUC on precipitation and temperature over the next century is limited, resulting in no significant change in malaria transmission. However, in one ESM, LUC leads to increases in precipitation under scenario RCP2.6, and increases in temperature in areas of land use conversion to farmland under both scenarios. The result is a more intense transmission and longer transmission seasons in the southeast of the continent, most notably in Mozambique and southern Tanzania. In contrast, warming associated with LUC in the Sahel region reduces risk in this model, as temperatures are already above the 25-30°C threshold at which transmission peaks. The differences between the ESMs emphasise the uncertainty in such assessments. It is also recalled that the modelling framework is unable to adequately represent local-scale changes in climate due to LUC, which some field studies indicate could be significant.

  2. The Urinary Tract Microbiome in Health and Disease.

    PubMed

    Aragón, Isabel M; Herrera-Imbroda, Bernardo; Queipo-Ortuño, María I; Castillo, Elisabeth; Del Moral, Julia Sequeira-García; Gómez-Millán, Jaime; Yucel, Gozde; Lara, María F

    2016-11-14

    The urinary tract, previously considered a sterile body niche, has emerged as the host of an array of bacteria in healthy individuals, revolutionizing the urology research field. To review the literature on microbiome implications in the urinary tract and the usefulness of probiotics/prebiotics and diet as treatment for urologic disorders. A systematic review was conducted using PubMed and Medline from inception until July 2016. The initial search identified 1419 studies and 89 were included in this systematic review. Specific bacterial communities have been found in the healthy urinary tract. Changes in this microbiome have been observed in certain urologic disorders such as urinary incontinence, urologic cancers, interstitial cystitis, neurogenic bladder dysfunction, sexually transmitted infections, and chronic prostatitis/chronic pelvic pain syndrome. The role of probiotics, prebiotics, and diet as treatment or preventive agents for urologic disorders requires further investigation. There is a microbiome associated with the healthy urinary tract that can change in urologic disorders. This represents a propitious context to identify new diagnostic, prognostic, and predictive microbiome-based biomarkers that could be used in clinical urology practice. In addition, probiotics, prebiotics, and diet modifications appear to represent an opportunity to regulate the urinary microbiome. We review the urinary microbiome of healthy individuals and its changes in relation to urinary disorders. The question to resolve is how we can modulate the microbiome to improve urinary tract health. Copyright © 2016 European Association of Urology. Published by Elsevier B.V. All rights reserved.

  3. Exploring coral microbiome assemblages in the South China Sea.

    PubMed

    Cai, Lin; Tian, Ren-Mao; Zhou, Guowei; Tong, Haoya; Wong, Yue Him; Zhang, Weipeng; Chui, Apple Pui Yi; Xie, James Y; Qiu, Jian-Wen; Ang, Put O; Liu, Sheng; Huang, Hui; Qian, Pei-Yuan

    2018-02-05

    Coral reefs are significant ecosystems. The ecological success of coral reefs relies on not only coral-algal symbiosis but also coral-microbial partnership. However, microbiome assemblages in the South China Sea corals remain largely unexplored. Here, we compared the microbiome assemblages of reef-building corals Galaxea (G. fascicularis) and Montipora (M. venosa, M. peltiformis, M. monasteriata) collected from five different locations in the South China Sea using massively-parallel sequencing of 16S rRNA gene and multivariate analysis. The results indicated that microbiome assemblages for each coral species were unique regardless of location and were different from the corresponding seawater. Host type appeared to drive the coral microbiome assemblages rather than location and seawater. Network analysis was employed to explore coral microbiome co-occurrence patterns, which revealed 61 and 80 co-occurring microbial species assembling the Galaxea and Montipora microbiomes, respectively. Most of these co-occurring microbial species were commonly found in corals and were inferred to play potential roles in host nutrient metabolism; carbon, nitrogen, sulfur cycles; host detoxification; and climate change. These findings suggest that the co-occurring microbial species explored might be essential to maintain the critical coral-microbial partnership. The present study provides new insights into coral microbiome assemblages in the South China Sea.

  4. Immunomodulatory interplay of the microbiome and therapy of rheumatic diseases.

    PubMed

    Ostrov, Barbara E; Amsterdam, Daniel

    2017-11-01

    Modulation of the immune system by microbes, especially from the gastrointestinal tract, is increasingly considered a key factor in the onset, course and outcome of rheumatic diseases. The interplay of the microbiome, along with genetic predisposition and environmental exposure, is thought to be an important trigger for rheumatic diseases. Improved identification of the relationship of disease-specific genetic alterations and rheumatic diseases has potential diagnostic and therapeutic applications. Treatment of rheumatic disorders is influenced by microbial actions but this interplay can be challenging due to variable and unpredictable responses to therapies. Expanded knowledge of the microbiome now allows clinicians to more precisely select ideal medication regimens and to predict response to and toxicity from drugs. Rheumatic diseases and associated therapies were among the earliest microbiome interactions investigated, yet it is notable that current research is focused on clinical and immunological associations but, in comparison, a limited number of studies regarding the microbiome's impact on treatment for rheumatic diseases have been published. In the coming years, further knowledge of immunomodulating interactions between the microbiome and the immune system will aid our understanding of autoimmunity and will be increasingly important in selection of therapeutic agents for patients with autoimmune and rheumatic diseases. In this review, recent literature regarding the bidirectional immunomodulatory effects of the microbiome with rheumatic diseases and current understanding and gaps regarding the drug-microbiome interface in the management of these disorders is presented.

  5. Interplay between the lung microbiome and lung cancer.

    PubMed

    Mao, Qixing; Jiang, Feng; Yin, Rong; Wang, Jie; Xia, Wenjie; Dong, Gaochao; Ma, Weidong; Yang, Yao; Xu, Lin; Hu, Jianzhong

    2018-02-28

    The human microbiome confers benefits or disease susceptibility to the human body through multiple pathways. Disruption of the symbiotic balance of the human microbiome is commonly found in systematic diseases such as diabetes, obesity, and chronic gastric diseases. Emerging evidence has suggested that dysbiosis of the microbiota may also play vital roles in carcinogenesis at multiple levels, e.g., by affecting metabolic, inflammatory, or immune pathways. Although the impact of the gut microbiome on the digestive cancer has been widely explored, few studies have investigated the interplay between the microbiome and lung cancer. Some recent studies have shown that certain microbes and microbiota dysbiosis are correlated with development of lung cancer. In this mini-review, we briefly summarize current research findings describing the relationship between the lung microbiome and lung cancer. We further discuss the potential mechanisms through which the lung microbiome may play a role in lung carcinogenesis and impact lung cancer treatment. A better knowledge of the interplay between the lung microbiome and lung cancer may promote the development of innovative strategies for early prevention and personalized treatment in lung cancer. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Dynamics of the human gut microbiome in inflammatory bowel disease

    SciT

    Halfvarson, Jonas; Brislawn, Colin J.; Lamendella, Regina

    Inflammatory bowel disease (IBD) is characterized by flares of inflammation with periodic need for increased medication and sometimes even surgery. IBD etiology is partly attributed to a deregulated immune response to gut microbiome dysbiosis. Cross-sectional studies have revealed microbial signatures for different IBD diseases, including ulcerative colitis (UC), colonic Crohn’s Disease (CCD), and ileal CD (ICD). Although IBD is dynamic, microbiome studies have primarily focused on single timepoints or few individuals. Here we dissect the long-term dynamic behavior of the gut microbiome in IBD and differentiate this from normal variation. Microbiomes of IBD subjects fluctuate more than healthy individuals, basedmore » on deviation from a newly-defined healthy plane (HP). ICD subjects deviated most from the HP, especially subjects with surgical resection. Intriguingly, the microbiomes of some IBD subjects periodically visited the HP then deviated away from it. Inflammation was not directly correlated with distance to the healthy plane, but there was some correlation between observed dramatic fluctuations in the gut microbiome and intensified medication due to a flare of the disease. These results help guide therapies that will re-direct the gut microbiome towards a healthy state and maintain remission in IBD.« less

  7. The Microbiome: a Revolution in Treatment for Rheumatic Diseases?

    PubMed

    Rosenbaum, James T; Asquith, Mark J

    2016-10-01

    The microbiome is the term that describes the microbial ecosystem that cohabits an organism such as humans. The microbiome has been implicated in a long list of immune-mediated diseases which include rheumatoid arthritis, ankylosing spondylitis, and even gout. The mechanisms to account for this effect are multiple. The clinical implications from observations on the microbiome and disease are broad. A growing number of microbiota constituents such as Prevotella copri, Porphyromonas gingivalis, and Collinsella have been correlated or causally related to rheumatic disease. The microbiome has a marked effect on the immune system. Our understanding of immune pathways modulated by the microbiota such as the induction of T helper 17 (Th17) cells and secretory immunoglobulin A (IgA) responses to segmented filamentous bacteria continues to expand. In addition to the gut microbiome, bacterial communities of other sites such as the mouth, lung, and skin have also been associated with the pathogenesis of rheumatic diseases. Strategies to alter the microbiome or to alter the immune activation from the microbiome might play a role in the future therapy for rheumatic diseases.

  8. The microbiome of the oral mucosa in irritable bowel syndrome

    PubMed Central

    Fourie, Nicolaas H.; Wang, Dan; Abey, Sarah K.; Sherwin, LeeAnne B.; Joseph, Paule V.; Rahim-Williams, Bridgett; Ferguson, Eric G.; Henderson, Wendy A.

    2016-01-01

    abstract Irritable bowel syndrome (IBS) is a poorly understood disorder characterized by persistent symptoms, including visceral pain. Studies have demonstrated oral microbiome differences in inflammatory bowel diseases suggesting the potential of the oral microbiome in the study of non-oral conditions. In this exploratory study we examine whether differences exist in the oral microbiome of IBS participants and healthy controls, and whether the oral microbiome relates to symptom severity. The oral buccal mucosal microbiome of 38 participants was characterized using PhyloChip microarrays. The severity of visceral pain was assessed by orally administering a gastrointestinal test solution. Participants self-reported their induced visceral pain. Pain severity was highest in IBS participants (P = 0.0002), particularly IBS-overweight participants (P = 0.02), and was robustly correlated to the abundance of 60 OTUs, 4 genera, 5 families and 4 orders of bacteria (r2 > 0.4, P < 0.001). IBS-overweight participants showed decreased richness in the phylum Bacteroidetes (P = 0.007) and the genus Bacillus (P = 0.008). Analysis of β-diversity found significant separation of the IBS-overweight group (P < 0.05). Our oral microbial results are concordant with described fecal and colonic microbiome-IBS and -weight associations. Having IBS and being overweight, rather than IBS-subtypes, was the most important factor in describing the severity of visceral pain and variation in the microbiome. Pain severity was strongly correlated to the abundance of many taxa, suggesting the potential of the oral microbiome in diagnosis and patient phenotyping. The oral microbiome has potential as a source of microbial information in IBS. PMID:26963804

  9. Dysbiosis of the microbiome in gastric carcinogenesis.

    PubMed

    Castaño-Rodríguez, Natalia; Goh, Khean-Lee; Fock, Kwong Ming; Mitchell, Hazel M; Kaakoush, Nadeem O

    2017-11-21

    The gastric microbiome has been proposed as an etiological factor in gastric carcinogenesis. We compared the gastric microbiota in subjects presenting with gastric cancer (GC, n = 12) and controls (functional dyspepsia (FD), n = 20) from a high GC risk population in Singapore and Malaysia. cDNA from 16S rRNA transcripts were amplified (515F-806R) and sequenced using Illumina MiSeq 2 × 250 bp chemistry. Increased richness and phylogenetic diversity but not Shannon's diversity was found in GC as compared to controls. nMDS clustered GC and FD subjects separately, with PERMANOVA confirming a significant difference between the groups. H. pylori serological status had a significant impact on gastric microbiome α-diversity and composition. Several bacterial taxa were enriched in GC, including Lactococcus, Veilonella, and Fusobacteriaceae (Fusobacterium and Leptotrichia). Prediction of bacterial metabolic contribution indicated that serological status had a significant impact on metabolic function, while carbohydrate digestion and pathways were enriched in GC. Our findings highlight three mechanisms of interest in GC, including enrichment of pro-inflammatory oral bacterial species, increased abundance of lactic acid producing bacteria, and enrichment of short chain fatty acid production pathways.

  10. The microbiome: stress, health and disease.

    PubMed

    Moloney, Rachel D; Desbonnet, Lieve; Clarke, Gerard; Dinan, Timothy G; Cryan, John F

    2014-02-01

    Bacterial colonisation of the gut plays a major role in postnatal development and maturation of key systems that have the capacity to influence central nervous system (CNS) programming and signaling, including the immune and endocrine systems. Individually, these systems have been implicated in the neuropathology of many CNS disorders and collectively they form an important bidirectional pathway of communication between the microbiota and the brain in health and disease. Regulation of the microbiome-brain-gut axis is essential for maintaining homeostasis, including that of the CNS. Moreover, there is now expanding evidence for the view that commensal organisms within the gut play a role in early programming and later responsivity of the stress system. Research has focused on how the microbiota communicates with the CNS and thereby influences brain function. The routes of this communication are not fully elucidated but include neural, humoral, immune and metabolic pathways. This view is underpinned by studies in germ-free animals and in animals exposed to pathogenic bacterial infections, probiotic agents or antibiotics which indicate a role for the gut microbiota in the regulation of mood, cognition, pain and obesity. Thus, the concept of a microbiome-brain-gut axis is emerging which suggests that modulation of the gut microflora may be a tractable strategy for developing novel therapeutics for complex stress-related CNS disorders where there is a huge unmet medical need.

  11. A gut (microbiome) feeling about the brain.

    PubMed

    Sherwin, Eoin; Rea, Kieran; Dinan, Timothy G; Cryan, John F

    2016-03-01

    There is an increasing realization that the microorganisms which reside within our gut form part of a complex multidirectional communication network with the brain known as the microbiome-gut-brain axis. In this review, we focus on recent findings which support a role for this axis in modulating neurodevelopment and behavior. A growing body of research is uncovering that under homeostatic conditions and in response to internal and external stressors, the bacterial commensals of our gut can signal to the brain through a variety of mechanisms to influence processes such neurotransmission, neurogenesis, microglia activation, and modulate behavior. Moreover, the mechanisms underlying the ability of stress to modulate the microbiota and also for microbiota to change the set point for stress sensitivity are being unraveled. Dysregulation of the gut microbiota composition has been identified in a number of psychiatric disorders, including depression. This has led to the concept of bacteria that have a beneficial effect upon behavior and mood (psychobiotics) being proposed for potential therapeutic interventions. Understanding the mechanisms by which the bacterial commensals of our gut are involved in brain function may lead to the development of novel microbiome-based therapies for these mood and behavioral disorders.

  12. The Gut Microbiome and the Brain

    PubMed Central

    Galland, Leo

    2014-01-01

    Abstract The human gut microbiome impacts human brain health in numerous ways: (1) Structural bacterial components such as lipopolysaccharides provide low-grade tonic stimulation of the innate immune system. Excessive stimulation due to bacterial dysbiosis, small intestinal bacterial overgrowth, or increased intestinal permeability may produce systemic and/or central nervous system inflammation. (2) Bacterial proteins may cross-react with human antigens to stimulate dysfunctional responses of the adaptive immune system. (3) Bacterial enzymes may produce neurotoxic metabolites such as D-lactic acid and ammonia. Even beneficial metabolites such as short-chain fatty acids may exert neurotoxicity. (4) Gut microbes can produce hormones and neurotransmitters that are identical to those produced by humans. Bacterial receptors for these hormones influence microbial growth and virulence. (5) Gut bacteria directly stimulate afferent neurons of the enteric nervous system to send signals to the brain via the vagus nerve. Through these varied mechanisms, gut microbes shape the architecture of sleep and stress reactivity of the hypothalamic-pituitary-adrenal axis. They influence memory, mood, and cognition and are clinically and therapeutically relevant to a range of disorders, including alcoholism, chronic fatigue syndrome, fibromyalgia, and restless legs syndrome. Their role in multiple sclerosis and the neurologic manifestations of celiac disease is being studied. Nutritional tools for altering the gut microbiome therapeutically include changes in diet, probiotics, and prebiotics. PMID:25402818

  13. Community assembly of the worm gut microbiome

    NASA Astrophysics Data System (ADS)

    Gore, Jeff

    It has become increasingly clear that human health is strongly influenced by the bacteria that live within the gut, known collectively as the gut microbiome. This complex community varies tremendously between individuals, but understanding the sources that lead to this heterogeneity is challenging. To address this challenge, we are using a bottom-up approach to develop a predictive understanding of how the microbiome assembles and functions within a simple and experimentally tractable gut, the gut of the worm C. elegans. We have found that stochastic community assembly in the C. elegansintestine is sufficient to produce strong inter-worm heterogeneity in community composition. When worms are fed with two neutrally-competing fluorescently labeled bacterial strains, we observe stochastically-driven bimodality in community composition, where approximately half of the worms are dominated by each bacterial strain. A simple model incorporating stochastic colonization suggests that heterogeneity between worms is driven by the low rate at which bacteria successfully establish new intestinal colonies. We can increase this rate experimentally by feeding worms at high bacterial density; in these conditions the bimodality disappears. We have also characterized all pairwise interspecies competitions among a set of eleven bacterial species, illuminating the rules governing interspecies community assembly. These results demonstrate the potential importance of stochastic processes in bacterial community formation and suggest a role for C. elegans as a model system for ecology of host-associated communities.

  14. The fecal microbiome of ALS patients.

    PubMed

    Brenner, David; Hiergeist, Andreas; Adis, Carolin; Mayer, Benjamin; Gessner, André; Ludolph, Albert C; Weishaupt, Jochen H

    2018-01-01

    Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative motor neuron disease accompanied by both systemic and central nervous system-specific inflammation as well as deregulated energy metabolism. These potential pathogenetic factors have recently been found to mutually interact with the gut microbiota, raising the hypothesis of a link between microbiome alterations and ALS pathogenesis. The aim of our study was to assess whether ALS is associated with an altered composition of the fecal microbiota. We compared the fecal microbiota of 25 ALS patients with 32 age- and gender-matched healthy persons using 16S rRNA gene sequencing analysis. Confounding factors and secondary disease effects on the microbiome were minimized by selection of patients without dysphagia, gastrostomy, noninvasive ventilation, or reduced body mass index. Comparing the 2 carefully matched groups, the diversity and the abundance of the bacterial taxa on the different taxonomic levels as well as PICRUSt-predicted metagenomes were almost indistinguishable. Significant differences between ALS patients and healthy controls were only observed with regard to the overall number of microbial species (operational taxonomic units) and in the abundance of uncultured Ruminococcaceae. Conclusively, ALS patients do not exhibit a substantial alteration of the gut microbiota composition. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. Performing skin microbiome research: A method to the madness

    PubMed Central

    Kong, Heidi H.; Andersson, Björn; Clavel, Thomas; Common, John E.; Jackson, Scott A.; Olson, Nathan D.; Segre, Julia A.; Traidl-Hoffmann, Claudia

    2017-01-01

    Growing interest in microbial contributions to human health and disease has increasingly led investigators to examine the microbiome in both healthy skin and cutaneous disorders, including acne, psoriasis and atopic dermatitis. The need for common language, effective study design, and validated methods are critical for high-quality, standardized research. Features, unique to skin, pose particular challenges when conducting microbiome research. This review discusses microbiome research standards and highlights important factors to consider, including clinical study design, skin sampling, sample processing, DNA sequencing, control inclusion, and data analysis. PMID:28063650

  16. Which experimental systems should we use for human microbiome science?

    PubMed

    Douglas, Angela E

    2018-03-01

    Microbiome science is revealing that the phenotype and health of animals, including humans, depend on the sustained function of their resident microorganisms. In this essay, I argue for thoughtful choice of model systems for human microbiome science. A greater variety of experimental systems, including wider use of invertebrate models, would benefit biomedical research, while systems ill-suited to experimental and genetic manipulation can be used to address very limited sets of scientific questions. Microbiome science benefits from the coordinated use of multiple systems, which is facilitated by networks of researchers with expertise in different experimental systems.

  17. The development of lower respiratory tract microbiome in mice.

    PubMed

    Singh, Nisha; Vats, Asheema; Sharma, Aditi; Arora, Amit; Kumar, Ashwani

    2017-06-21

    Although culture-independent methods have paved the way for characterization of the lung microbiome, the dynamic changes in the lung microbiome from neonatal stage to adult age have not been investigated. In this study, we tracked changes in composition and diversity of the lung microbiome in C57BL/6N mice, starting from 1-week-old neonates to 8-week-old mice. Towards this, the lungs were sterilely excised from mice of different ages from 1 to 8 weeks. High-throughput DNA sequencing of the 16S rRNA gene followed by composition and diversity analysis was utilized to decipher the microbiome in these samples. Microbiome analysis suggests that the changes in the lung microbiome correlated with age. The lung microbiome was primarily dominated by phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria in all the stages from week 1 to week 8 after birth. Although Defluvibacter was the predominant genus in 1-week-old neonatal mice, Streptococcus became the dominant genus at the age of 2 weeks. Lactobacillus, Defluvibacter, Streptococcus, and Achromobacter were the dominant genera in 3-week-old mice, while Lactobacillus and Achromobacter were the most abundant genera in 4-week-old mice. Interestingly, relatively greater diversity (at the genus level) during the age of 5 to 6 weeks was observed as compared to the earlier weeks. The diversity of the lung microbiome remained stable between 6 and 8 weeks of age. In summary, we have tracked the development of the lung microbiome in mice from an early age of 1 week to adulthood. The lung microbiome is dominated by the phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. However, dynamic changes were observed at the genus level. Relatively higher richness in the microbial diversity was achieved by age of 6 weeks and then maintained at later ages. We believe that this study improves our understanding of the development of the mice lung microbiome and will facilitate further analyses of the role of

  18. Gut microbiomes and their metabolites shape human and animal health.

    PubMed

    Park, Woojun

    2018-03-01

    The host genetic background, complex surrounding environments, and gut microbiome are very closely linked to human and animal health and disease. Although significant correlations between gut microbiota and human and animal health have been revealed, the specific roles of each gut bacterium in shaping human and animal health and disease remain unclear. However, recent omics-based studies using experimental animals and surveys of gut microbiota from unhealthy humans have provided insights into the relationships among microbial community, their metabolites, and human and animal health. This editorial introduces six review papers that provide new discoveries of disease-associated microbiomes and suggest possible microbiome-based therapeutic approaches to human disease.

  19. Earth-Observation based mapping and monitoring of exposure change in the megacity of Istanbul: open-source tools from the MARSITE project

    NASA Astrophysics Data System (ADS)

    De Vecchi, Daniele; Dell'Acqua, Fabio

    2016-04-01

    The EU FP7 MARSITE project aims at assessing the "state of the art" of seismic risk evaluation and management at European level, as a starting point to move a "step forward" towards new concepts of risk mitigation and management by long-term monitoring activities carried out both on land and at sea. Spaceborne Earth Observation (EO) is one of the means through which MARSITE is accomplishing this commitment, whose importance is growing as a consequence of the operational unfolding of the Copernicus initiative. Sentinel-2 data, with its open-data policy, represents an unprecedented opportunity to access global spaceborne multispectral data for various purposes including risk monitoring. In the framework of EU FP7 projects MARSITE, RASOR and SENSUM, our group has developed a suite of geospatial software tools to automatically extract risk-related features from EO data, especially on the exposure and vulnerability side of the "risk equation" [1]. These are for example the extension of a built-up area or the distribution of building density. These tools are available open-source as QGIS plug-ins [2] and their source code can be freely downloaded from GitHub [3]. A test case on the risk-prone mega city of Istanbul has been set up, and preliminary results will be presented in this paper. The output of the algorithms can be incorporated into a risk modeling process, whose output is very useful to stakeholders and decision makers who intend to assess and mitigate the risk level across the giant urban agglomerate. Keywords - Remote Sensing, Copernicus, Istanbul megacity, seismic risk, multi-risk, exposure, open-source References [1] Harb, M.M.; De Vecchi, D.; Dell'Acqua, F., "Physical Vulnerability Proxies from Remotes Sensing: Reviewing, Implementing and Disseminating Selected Techniques," Geoscience and Remote Sensing Magazine, IEEE , vol.3, no.1, pp.20,33, March 2015. doi: 10.1109/MGRS.2015.2398672 [2] SENSUM QGIS plugin, 2016, available online at: https

  20. Proceedings of the 2013 A.S.P.E.N. Research workshop: the interface between nutrition and the gut microbiome: implications and applications for human health [corrected].

    PubMed

    Alverdy, John; Gilbert, Jack; DeFazio, Jennifer R; Sadowsky, Michael J; Chang, Eugene B; Morowitz, Michael J; Teitelbaum, Daniel H

    2014-02-01

    The human and earth microbiomes are among the most important biological agents in understanding and preventing disease. Technology is advancing at a fast pace and allowing for high-resolution analysis of the composition and function of our microbial partners across regions, space, and time. Bioinformaticists and biostatisticians are developing ever more elegant displays to understand the generated megadatasets. A virtual cyberinfrastructure of search engines to cross-reference the rapidly developing data is emerging in line with technologic advances. Nutrition science will reap the benefits of this new field, and its role in preserving the earth and the humans who inhabit it will become evidently clear. In this report we highlight some of the topics of an A.S.P.E.N.-sponsored symposium held during Clinical Nutrition Week in 2013 that address the importance of the human microbiome to human health and disease.

  1. Proceedings of the ASPEN- sponsored workshop: “The Interface Between Nutrition and the Gut Microbiome: Implications and Applications for Human Health”

    PubMed Central

    Alverdy, John; Gilbert, Jack; DeFazio, Jennifer R.; Sadowsky, Michael; Chang, Eugene; Morowitz, Michael; Teitelbaum, Daniel

    2014-01-01

    The human and earth microbiome are emerging as among the most important biological agents in understanding and preventing disease. Technology is advancing at a fast pace and allowing for high resolution analysis of the composition and function of our microbial partners across regions, space, and time. Bioinformaticists and biostatisticians are developing ever more elegant displays to understand the generated mega-datasets. A virtual cyberinfrastruture of search engines to cross reference the rapidly developing data is emerging in line with technologic advances. Nutritional science will reap the benefits of this new field and its role in preserving the earth and the humans that inhabit it will become evidently clear. In this report we highlight some of the topics of an ASPEN sponsored symposium that took place at the Clinical Nutrition Week in 2013 that address the importance of the human microbiome to human health and disease. PMID:24379111

  2. Minorities Striving and Pursuing Higher Degrees of Success in Earth System Science (MS PHD'S) Beyond the PhD Professional Development Program: A Pilot Project

    NASA Astrophysics Data System (ADS)

    Johnson, A.; Jearld, A.; Williamson Whitney, V.; Huggans, M.; Ricciardi, L.; Thomas, S. H.; Jansma, P. E.

    2012-12-01

    In 2011 the Minorities Striving and Pursuing Higher Degrees of Success in Earth System Science (MS PHD'S)® initiative launched its newest activity entitled the MS PHD'S "Beyond the PhD (B-PhD) Professional Development Program." This exciting new program was designed to facilitate the development of a new community of underrepresented minority (URM) doctoral candidates and recent doctorate degree recipients in Earth system science (ESS)-related fields. The MS PHD'S B-PhD provides customized support and advocacy for MS PHD'S B-PhD participants in order to facilitate smoother and informed transitions from graduate school, to postdoctoral and tenure-track positions, as well as other "first" jobs in government, industry, and non-profit organizations. In November 2011 the first cohort of MS PHD'S B-PhD participants engaged in intensive sessions on the following topics: "Toolkits for Success for Academia, Business/Industry, Federal Government and Non-Profits", "Defining Short, Mid and Long Term Career Goals", "Accessing and Refining Skill Sets and Other Door Openers", "International Preparation and Opportunities", "Paying it Forward/Lifting as You Climb", and "Customized Strategies for Next Steps". This pilot event, which was hosted by the University of Texas at Arlington's (UTA) College of Science, also provided opportunities for participants to serve as guest lecturers in the UTA's Colleges of Science and Engineering and included one-on-one discussions with MS PHD'S B-PhD mentors and guest speakers who are well established within their individual ESS fields. Insights regarding opportunities, challenges and obstacles commonly faced by URMs within the ESS fields, as well as strategies for success were shared by MS PHD'S B-PhD mentors and guest speakers. Survey results indicate that MS PHD'S B-PhD participants appreciated not only the material covered during this pilot activity, but also appreciated the opportunity to become part of a community of young URM ESS

  3. “Snake-oil,” “quack medicine,” and “industrially cultured organisms:” biovalue and the commercialization of human microbiome research

    PubMed Central

    2012-01-01

    Background Continued advances in human microbiome research and technologies raise a number of ethical, legal, and social challenges. These challenges are associated not only with the conduct of the research, but also with broader implications, such as the production and distribution of commercial products promising maintenance or restoration of good physical health and disease prevention. In this article, we document several ethical, legal, and social challenges associated with the commercialization of human microbiome research, focusing particularly on how this research is mobilized within economic markets for new public health uses. Methods We conducted in-depth, semi-structured interviews (2009–2010) with 63 scientists, researchers, and National Institutes of Health project leaders (“investigators”) involved with human microbiome research. Interviews explored a range of ethical, legal, and social dimensions of human microbiome research, including investigators’ perspectives on commercialization. Using thematic content analysis, we identified and analyzed emergent themes and patterns. Results Investigators discussed the commercialization of human microbiome research in terms of (1) commercialization, probiotics, and issues of safety, (2) public awareness of the benefits and risks of dietary supplements, and (3) regulation. Conclusion The prevailing theme of ethical, legal, social concern focused on the need to find a balance between the marketplace, scientific research, and the public’s health. The themes we identified are intended to serve as points for discussions about the relationship between scientific research and the manufacture and distribution of over-the-counter dietary supplements in the United States. PMID:23110633

  4. Earth Observation

    2014-06-01

    ISS040-E-006327 (1 June 2014) --- A portion of International Space Station solar array panels and Earth?s horizon are featured in this image photographed by an Expedition 40 crew member on the space station.

  5. Earth Science Applications Showcase

    2014-08-05

    NASA Administrator Charles Bolden speaks with young professionals about their project during the annual DEVELOP Earth Science Application Showcase at NASA headquarters Tuesday, August 5, 2014. The Earth Science Applications Showcase highlights the work of over 150 participants in the 10-week DEVELOP program that started in June. The DEVELOP Program bridges the gap between NASA Earth science and society, building capacity in both its participants and partner organizations, to better prepare them to handle the challenges that face our society and future generations. Photo Credit: (NASA/Aubrey Gemignani)

  6. Earth Science Applications Showcase

    2014-08-05

    NASA Administrator Charles Bolden speaks with young professionals about their project on New England water resources during the annual DEVELOP Earth Science Application Showcase at NASA headquarters Tuesday, August 5, 2014. The Earth Science Applications Showcase highlights the work of over 150 participants in the 10-week DEVELOP program that started in June. The DEVELOP Program bridges the gap between NASA Earth science and society, building capacity in both its participants and partner organizations, to better prepare them to handle the challenges that face our society and future generations. Photo Credit: (NASA/Aubrey Gemignani)

  7. Earth Science Applications Showcase

    2014-08-05

    Lisa Waldron and Justin Roberts-Pierel present their project on Texas health and air quality during the annual DEVELOP Earth Science Application Showcase at NASA headquarters Tuesday, August 5, 2014. The Earth Science Applications Showcase highlights the work of over 150 participants in the 10-week DEVELOP program that started in June. The DEVELOP Program bridges the gap between NASA Earth science and society, building capacity in both its participants and partner organizations, to better prepare them to handle the challenges that face our society and future generations. Photo Credit: (NASA/Aubrey Gemignani)

  8. Earth Science Applications Showcase

    2014-08-05

    Michael Gao presents his project on Southeast Asian disasters during the annual DEVELOP Earth Science Application Showcase at NASA headquarters Tuesday, August 5, 2014. The Earth Science Applications Showcase highlights the work of over 150 participants in the 10-week DEVELOP program that started in June. The DEVELOP Program bridges the gap between NASA Earth science and society, building capacity in both its participants and partner organizations, to better prepare them to handle the challenges that face our society and future generations. Photo Credit: (NASA/Aubrey Gemignani)

  9. Earth Science Applications Showcase

    2014-08-05

    NASA Administrator Charles Bolden asks young professionals about their projects after posing for a group photo during the annual DEVELOP Earth Science Application Showcase at NASA headquarters Tuesday, August 5, 2014. The Earth Science Applications Showcase highlights the work of over 150 participants in the 10-week DEVELOP program that started in June. The DEVELOP Program bridges the gap between NASA Earth science and society, building capacity in both its participants and partner organizations, to better prepare them to handle the challenges that face our society and future generations. Photo Credit: (NASA/Aubrey Gemignani)

  10. The Intestinal Microbiome in Infectious Diseases: The Clinical Relevance of a Rapidly Emerging Field.

    PubMed

    Harris, Vanessa C; Haak, Bastiaan W; Boele van Hensbroek, Michaël; Wiersinga, Willem J

    2017-01-01

    The field of infectious disease is undergoing a paradigm shift as the intestinal microbiome is becoming understood. The aim of this review is to inform infectious disease physicians of the potential relevance of the intestinal microbiome to their practice. We searched Medline using both index and text words relating to infectious diseases, microbiome, and probiotics. Relevant articles published up through 2017 were reviewed within Rayyan. The review illustrates pathophysiologic concepts linking the microbiome and infectious diseases; specifically, the intestinal microbiome's relevance to early immune development, the microbiome and enteric infections, the microbiome's relevance in compromised hosts, and antimicrobial resistance. Within each subject, there are specific examples of diseases and at-risk patient populations where a role for the microbiome has been strongly established. This provides an overview of the significance of the intestinal microbiome to microbiology, pediatric and adult infectious diseases with an underpinning of concepts useful for the practicing clinician.

  11. The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information

    PubMed Central

    Chen, Tsute; Yu, Wen-Han; Izard, Jacques; Baranova, Oxana V.; Lakshmanan, Abirami; Dewhirst, Floyd E.

    2010-01-01

    The human oral microbiome is the most studied human microflora, but 53% of the species have not yet been validly named and 35% remain uncultivated. The uncultivated taxa are known primarily from 16S rRNA sequence information. Sequence information tied solely to obscure isolate or clone numbers, and usually lacking accurate phylogenetic placement, is a major impediment to working with human oral microbiome data. The goal of creating the Human Oral Microbiome Database (HOMD) is to provide the scientific community with a body site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity based on a curated 16S rRNA gene-based provisional naming scheme. Currently, two primary types of information are provided in HOMD—taxonomic and genomic. Named oral species and taxa identified from 16S rRNA gene sequence analysis of oral isolates and cloning studies were placed into defined 16S rRNA phylotypes and each given unique Human Oral Taxon (HOT) number. The HOT interlinks phenotypic, phylogenetic, genomic, clinical and bibliographic information for each taxon. A BLAST search tool is provided to match user 16S rRNA gene sequences to a curated, full length, 16S rRNA gene reference data set. For genomic analysis, HOMD provides comprehensive set of analysis tools and maintains frequently updated annotations for all the human oral microbial genomes that have been sequenced and publicly released. Oral bacterial genome sequences, determined as part of the Human Microbiome Project, are being added to the HOMD as they become available. We provide HOMD as a conceptual model for the presentation of microbiome data for other human body sites. Database URL: http://www.homd.org PMID:20624719

  12. Aquarium Microbiome Response to Ninety-Percent System Water Change: Clues to Microbiome Management

    PubMed Central

    Van Bonn, William; LaPointe, Allen; Gibbons, Sean M.; Frazier, Angel; Hampton-Marcell, Jarrad; Gilbert, Jack

    2016-01-01

    The bacterial community composition and structure of water from an established teleost fish system was examined before, during and after a major water change to explore the impact of such a water-change disturbance on the stability of the aquarium water microbiome. The diversity and evenness of the bacterial community significantly increased following the 90% water replacement. While the change in bacterial community structure was significant, it was slight, and was also weakly correlated with changes in physicochemical parameters. Interestingly there was a significant shift in the correlative network relationships between operational taxonomic units from before to after the water replacement. We suggest this shift in network structure is due to the turnover of many taxa during the course of water replacement. These observations will inform future studies into manipulation of the microbiome by changing system environmental parameter values to optimize resident animal health. PMID:26031788

  13. Aquarium microbiome response to ninety-percent system water change: Clues to microbiome management.

    PubMed

    Van Bonn, William; LaPointe, Allen; Gibbons, Sean M; Frazier, Angel; Hampton-Marcell, Jarrad; Gilbert, Jack

    2015-01-01

    The bacterial community composition and structure of water from an established teleost fish system was examined before, during and after a major water change to explore the impact of such a water-change disturbance on the stability of the aquarium water microbiome. The diversity and evenness of the bacterial community significantly increased following the 90% water replacement. While the change in bacterial community structure was significant, it was slight, and was also weakly correlated with changes in physicochemical parameters. Interestingly there was a significant shift in the correlative network relationships between operational taxonomic units from before to after the water replacement. We suggest this shift in network structure is due to the turnover of many taxa during the course of water replacement. These observations will inform future studies into manipulation of the microbiome by changing system environmental parameter values to optimize resident animal health. © 2015 Wiley Periodicals, Inc.

  14. COREMIC: a web-tool to search for a niche associated CORE MICrobiome.

    PubMed

    Rodrigues, Richard R; Rodgers, Nyle C; Wu, Xiaowei; Williams, Mark A

    2018-01-01

    Microbial diversity on earth is extraordinary, and soils alone harbor thousands of species per gram of soil. Understanding how this diversity is sorted and selected into habitat niches is a major focus of ecology and biotechnology, but remains only vaguely understood. A systems-biology approach was used to mine information from databases to show how it can be used to answer questions related to the core microbiome of habitat-microbe relationships. By making use of the burgeoning growth of information from databases, our tool "COREMIC" meets a great need in the search for understanding niche partitioning and habitat-function relationships. The work is unique, furthermore, because it provides a user-friendly statistically robust web-tool (http://coremic2.appspot.com or http://core-mic.com), developed using Google App Engine, to help in the process of database mining to identify the "core microbiome" associated with a given habitat. A case study is presented using data from 31 switchgrass rhizosphere community habitats across a diverse set of soil and sampling environments. The methodology utilizes an outgroup of 28 non-switchgrass (other grasses and forbs) to identify a core switchgrass microbiome. Even across a diverse set of soils (five environments), and conservative statistical criteria (presence in more than 90% samples and FDR q -val <0.05% for Fisher's exact test) a core set of bacteria associated with switchgrass was observed. These included, among others, closely related taxa from Lysobacter spp., Mesorhizobium spp , and Chitinophagaceae . These bacteria have been shown to have functions related to the production of bacterial and fungal antibiotics and plant growth promotion. COREMIC can be used as a hypothesis generating or confirmatory tool that shows great potential for identifying taxa that may be important to the functioning of a habitat (e.g. host plant). The case study, in conclusion, shows that COREMIC can identify key habitat-specific microbes

  15. A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome.

    PubMed

    Allali, Imane; Arnold, Jason W; Roach, Jeffrey; Cadenas, Maria Belen; Butz, Natasha; Hassan, Hosni M; Koci, Matthew; Ballou, Anne; Mendoza, Mary; Ali, Rizwana; Azcarate-Peril, M Andrea

    2017-09-13

    Advancements in Next Generation Sequencing (NGS) technologies regarding throughput, read length and accuracy had a major impact on microbiome research by significantly improving 16S rRNA amplicon sequencing. As rapid improvements in sequencing platforms and new data analysis pipelines are introduced, it is essential to evaluate their capabilities in specific applications. The aim of this study was to assess whether the same project-specific biological conclusions regarding microbiome composition could be reached using different sequencing platforms and bioinformatics pipelines. Chicken cecum microbiome was analyzed by 16S rRNA amplicon sequencing using Illumina MiSeq, Ion Torrent PGM, and Roche 454 GS FLX Titanium platforms, with standard and modified protocols for library preparation. We labeled the bioinformatics pipelines included in our analysis QIIME1 and QIIME2 (de novo OTU picking [not to be confused with QIIME version 2 commonly referred to as QIIME2]), QIIME3 and QIIME4 (open reference OTU picking), UPARSE1 and UPARSE2 (each pair differs only in the use of chimera depletion methods), and DADA2 (for Illumina data only). GS FLX+ yielded the longest reads and highest quality scores, while MiSeq generated the largest number of reads after quality filtering. Declines in quality scores were observed starting at bases 150-199 for GS FLX+ and bases 90-99 for MiSeq. Scores were stable for PGM-generated data. Overall microbiome compositional profiles were comparable between platforms; however, average relative abundance of specific taxa varied depending on sequencing platform, library preparation method, and bioinformatics analysis. Specifically, QIIME with de novo OTU picking yielded the highest number of unique species and alpha diversity was reduced with UPARSE and DADA2 compared to QIIME. The three platforms compared in this study were capable of discriminating samples by treatment, despite differences in diversity and abundance, leading to similar biological

  16. Epidemiologic studies of the human microbiome and cancer.

    PubMed

    Vogtmann, Emily; Goedert, James J

    2016-02-02

    The human microbiome, which includes the collective genome of all bacteria, archaea, fungi, protists, and viruses found in and on the human body, is altered in many diseases and may substantially affect cancer risk. Previously detected associations of individual bacteria (e.g., Helicobacter pylori), periodontal disease, and inflammation with specific cancers have motivated studies considering the association between the human microbiome and cancer risk. This short review summarises microbiome research, focusing on published epidemiological associations with gastric, oesophageal, hepatobiliary, pancreatic, lung, colorectal, and other cancers. Large, prospective studies of the microbiome that employ multidisciplinary laboratory and analysis methods, as well as rigorous validation of case status, are likely to yield translational opportunities to reduce cancer morbidity and mortality by improving prevention, screening, and treatment.

  17. Epidemiologic studies of the human microbiome and cancer

    PubMed Central

    Vogtmann, Emily; Goedert, James J

    2016-01-01

    The human microbiome, which includes the collective genome of all bacteria, archaea, fungi, protists, and viruses found in and on the human body, is altered in many diseases and may substantially affect cancer risk. Previously detected associations of individual bacteria (e.g., Helicobacter pylori), periodontal disease, and inflammation with specific cancers have motivated studies considering the association between the human microbiome and cancer risk. This short review summarises microbiome research, focusing on published epidemiological associations with gastric, oesophageal, hepatobiliary, pancreatic, lung, colorectal, and other cancers. Large, prospective studies of the microbiome that employ multidisciplinary laboratory and analysis methods, as well as rigorous validation of case status, are likely to yield translational opportunities to reduce cancer morbidity and mortality by improving prevention, screening, and treatment. PMID:26730578

  18. Frequent Replenishment Sustains the Beneficial Microbiome of Drosophila melanogaster

    PubMed Central

    Blum, Jessamina E.; Fischer, Caleb N.; Miles, Jessica; Handelsman, Jo

    2013-01-01

    ABSTRACT We report that establishment and maintenance of the Drosophila melanogaster microbiome depend on ingestion of bacteria. Frequent transfer of flies to sterile food prevented establishment of the microbiome in newly emerged flies and reduced the predominant members, Acetobacter and Lactobacillus spp., by 10- to 1,000-fold in older flies. Flies with a normal microbiome were less susceptible than germfree flies to infection by Serratia marcescens and Pseudomonas aeruginosa. Augmentation of the normal microbiome with higher populations of Lactobacillus plantarum, a Drosophila commensal and probiotic used in humans, further protected the fly from infection. Replenishment represents an unexplored strategy by which animals can sustain a gut microbial community. Moreover, the population behavior and health benefits of L. plantarum resemble features of certain probiotic bacteria administered to humans. As such, L. plantarum in the fly gut may serve as a simple model for dissecting the population dynamics and mode of action of probiotics in animal hosts. PMID:24194543

  19. Unraveling the processes shaping mammalian gut microbiomes over evolutionary time

    PubMed Central

    Groussin, Mathieu; Mazel, Florent; Sanders, Jon G.; Smillie, Chris S.; Lavergne, Sébastien; Thuiller, Wilfried; Alm, Eric J.

    2017-01-01

    Whether mammal–microbiome interactions are persistent and specific over evolutionary time is controversial. Here we show that host phylogeny and major dietary shifts have affected the distribution of different gut bacterial lineages and did so on vastly different bacterial phylogenetic resolutions. Diet mostly influences the acquisition of ancient and large microbial lineages. Conversely, correlation with host phylogeny is mostly seen among more recently diverged bacterial lineages, consistent with processes operating at similar timescales to host evolution. Considering microbiomes at appropriate phylogenetic scales allows us to model their evolution along the mammalian tree and to infer ancient diets from the predicted microbiomes of mammalian ancestors. Phylogenetic analyses support co-speciation as having a significant role in the evolution of mammalian gut microbiome compositions. Highly co-speciating bacterial genera are also associated with immune diseases in humans, laying a path for future studies that probe these co-speciating bacteria for signs of co-evolution. PMID:28230052

  20. Human Microbiome Acquisition and Bioinformatic Challenges in Metagenomic Studies

    PubMed Central

    2018-01-01

    The study of the human microbiome has become a very popular topic. Our microbial counterpart, in fact, appears to play an important role in human physiology and health maintenance. Accordingly, microbiome alterations have been reported in an increasing number of human diseases. Despite the huge amount of data produced to date, less is known on how a microbial dysbiosis effectively contributes to a specific pathology. To fill in this gap, other approaches for microbiome study, more comprehensive than 16S rRNA gene sequencing, i.e., shotgun metagenomics and metatranscriptomics, are becoming more widely used. Methods standardization and the development of specific pipelines for data analysis are required to contribute to and increase our understanding of the human microbiome relationship with health and disease status. PMID:29382070

  1. Changes of Cattle Fecal Microbiome Under Field Conditions.

    EPA Science Inventory

    Next generation sequencing (NGS) has been applied to study the microbiome in wastewater, sewage sludge, and feces. Previous microbial survival studies have shown different fecal-associated microbes have different decay rates and regrowth behaviors.

  2. Changes of Cattle Fecal Microbiome Under Field Conditions

    EPA Science Inventory

    Next generation sequencing (NGS) has been applied to study the microbiome in wastewater, sewage sludge, and feces. Previous microbial survival studies have shown different fecal-associated microbes have different decay rates and regrowth behaviors.

  3. Metagenomics of prebiotic and probiotic supplemented broilers gastrointestinal tract microbiome

    Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) is a recently developed computational approach for prediction of functional composition of a microbiome comparing marker gene data with a reference genome database. The procedure established significant link ...

  4. Microbiomes Have the Power to Help or Hinder Your Health

    SciT

    Jansson, Janet

    They are everywhere: countless microorganisms that inhabit our world—even in your skin, mouth, gut and other parts of your body. Called microbiomes, these communities play a fundamental role in our ecosystem and our bodies, influencing everything from climate to human health. And scientists at PNNL are studying microbiomes to better understand how they influence our daily lives. Scientist Janet Jansson studies complex microbiomes in soil and the human intestine to understand changes in the composition or function of microbes. In the soil, these microbes are associated with carbon cycling and degrading pollutants, as well as plant health. In the intestine,more » they are responsible for digestion of our food and protection from pathogens. When they go awry, they can be associated with numerous inflammatory bowel diseases, such as Crohn’s. Understanding the factors underlying these microbiome changes will ultimately help researchers develop solutions to problems encountered within our world and our bodies.« less

  5. Mining the human gut microbiome for novel stress resistance genes

    PubMed Central

    Culligan, Eamonn P.; Marchesi, Julian R.; Hill, Colin; Sleator, Roy D.

    2012-01-01

    With the rapid advances in sequencing technologies in recent years, the human genome is now considered incomplete without the complementing microbiome, which outnumbers human genes by a factor of one hundred. The human microbiome, and more specifically the gut microbiome, has received considerable attention and research efforts over the past decade. Many studies have identified and quantified “who is there?,” while others have determined some of their functional capacity, or “what are they doing?” In a recent study, we identified novel salt-tolerance loci from the human gut microbiome using combined functional metagenomic and bioinformatics based approaches. Herein, we discuss the identified loci, their role in salt-tolerance and their importance in the context of the gut environment. We also consider the utility and power of functional metagenomics for mining such environments for novel genes and proteins, as well as the implications and possible applications for future research. PMID:22688726

  6. Maternal HIV Infection Influences the Microbiome of HIV Uninfected Infants

    PubMed Central

    Bender, Jeffrey M.; Li, Fan; Martelly, Shoria; Byrt, Erin; Rouzier, Vanessa; Leo, Marguerithe; Tobin, Nicole; Pannaraj, Pia S.; Adisetiyo, Helty; Rollie, Adrienne; Santiskulvong, Chintda; Wang, Shuang; Autran, Chloe; Bode, Lars; Fitzgerald, Daniel; Kuhn, Louise; Aldrovandi, Grace M.

    2017-01-01

    More than one million HIV-exposed, uninfected infants are born annually to HIV-positive mothers worldwide. This growing population of infants experiences twice the mortality of HIV-unexposed infants. We found that although there were very few differences seen in the microbiomes of mothers with and without HIV infection, maternal HIV infection was associated with changes in the microbiome of HIV-exposed, uninfected infants. Furthermore, we observed that human breast milk oligosaccharides were associated with the bacterial species in the infant microbiome. The disruption of the infant’s microbiome associated with maternal HIV infection may contribute to the increased morbidity and mortality of HIV-exposed, uninfected infants. PMID:27464748

  7. Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.

    PubMed

    Schirmer, Melanie; Smeekens, Sanne P; Vlamakis, Hera; Jaeger, Martin; Oosting, Marije; Franzosa, Eric A; Ter Horst, Rob; Jansen, Trees; Jacobs, Liesbeth; Bonder, Marc Jan; Kurilshikov, Alexander; Fu, Jingyuan; Joosten, Leo A B; Zhernakova, Alexandra; Huttenhower, Curtis; Wijmenga, Cisca; Netea, Mihai G; Xavier, Ramnik J

    2016-11-03

    Gut microbial dysbioses are linked to aberrant immune responses, which are often accompanied by abnormal production of inflammatory cytokines. As part of the Human Functional Genomics Project (HFGP), we investigate how differences in composition and function of gut microbial communities may contribute to inter-individual variation in cytokine responses to microbial stimulations in healthy humans. We observe microbiome-cytokine interaction patterns that are stimulus specific, cytokine specific, and cytokine and stimulus specific. Validation of two predicted host-microbial interactions reveal that TNFα and IFNγ production are associated with specific microbial metabolic pathways: palmitoleic acid metabolism and tryptophan degradation to tryptophol. Besides providing a resource of predicted microbially derived mediators that influence immune phenotypes in response to common microorganisms, these data can help to define principles for understanding disease susceptibility. The three HFGP studies presented in this issue lay the groundwork for further studies aimed at understanding the interplay between microbial, genetic, and environmental factors in the regulation of the immune response in humans. PAPERCLIP. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. The Influence of the Gut Microbiome on Cancer, Immunity, and Cancer Immunotherapy.

    PubMed

    Gopalakrishnan, Vancheswaran; Helmink, Beth A; Spencer, Christine N; Reuben, Alexandre; Wargo, Jennifer A

    2018-04-09

    The microbiome is receiving significant attention given its influence on a host of human diseases including cancer. Its role in response to cancer treatment is becoming increasingly apparent, with evidence suggesting that modulating the gut microbiome may affect responses to numerous forms of cancer therapy. A working knowledge of the microbiome is vital as we move forward in this age of precision medicine, and an understanding of the microbiome's influence on immune responses and cancer is key. It is also important to understand factors influencing the gut microbiome and strategies to manipulate the microbiome to augment therapeutic responses. Copyright © 2018 Elsevier Inc. All rights reserved.

  9. Diet may influence the oral microbiome composition in cats.

    PubMed

    Adler, Christina J; Malik, Richard; Browne, Gina V; Norris, Jacqueline M

    2016-06-09

    Periodontal disease is highly prevalent amongst domestic cats, causing pain, gingival bleeding, reduced food intake, loss of teeth and possibly impacts on overall systemic health. Diet has been suggested to play a role in the development of periodontal disease in cats. There is a complete lack of information about how diet (composition and texture) affects the feline oral microbiome, the composition of which may influence oral health and the development of periodontal disease. We undertook a pilot study to assess if lifelong feeding of dry extruded kibble or wet (canned and/or fresh meat combinations) diets to cats (n = 10) with variable oral health affected the microbiome. Oral microbiome composition was assessed by amplifying the V1-V3 region of the 16S gene from supragingival dental plaque DNA extracts. These amplicons were sequenced using Illumina technology. This deep sequencing revealed the feline oral microbiome to be diverse, containing 411 bacterial species from 14 phyla. We found that diet had a significant influence on the overall diversity and abundance of specific bacteria in the oral environment. Cats fed a dry diet exclusively had higher bacterial diversity in their oral microbiome than wet-food diet cats (p < 0.001). Amongst this higher diversity, cats on dry-food diets had a higher abundance of Porphyromonas spp. (p < 0.01) and Treponema spp. (p < 0.01). While we observed differences in the oral microbiome between cats on the two diets assessed, the relationship between these differences and gingival health was unclear. Our preliminary results indicate that further analysis of the influence of dietary constituents and texture on the feline oral microbiome is required to reveal the relationship between diet, the oral microbiome and gingival health in cats.

  10. Characterization of the salivary microbiome in people with obesity

    PubMed Central

    Zhang, Qian

    2018-01-01

    Background The interactions between the gut microbiome and obesity have been extensively studied. Although the oral cavity is the gateway to the gut, and is extensively colonized with microbes, little is known about the oral microbiome in people with obesity. In the present study, we investigated the salivary microbiome in obese and normal weight healthy participants using metagenomic analysis. The subjects were categorized into two groups, obesity and normal weight, based on their BMIs. Methods We characterized the salivary microbiome of 33 adults with obesity and 29 normal weight controls using high-throughput sequencing of the V3–V4 region of the 16S rRNA gene (Illumina MiSeq). None of the selected participants had systemic, oral mucosal, or periodontal diseases. Results The salivary microbiome of the obesity group was distinct from that of the normal weight group. The salivary microbiome of periodontally healthy people with obesity had both significantly lower bacterial diversity and richness compared with the controls. The genus Prevotella, Granulicatella, Peptostreptococcus, Solobacterium, Catonella, and Mogibacterium were significantly more abundant in the obesity group; meanwhile the genus Haemophilus, Corynebacterium, Capnocytophaga, and Staphylococcus were less abundant in the obesity group. We also performed a functional analysis of the inferred metagenomes, and showed that the salivary community associated with obesity had a stronger signature of immune disease and a decreased functional signature related to environmental adaptation and Xenobiotics biodegradation compared with the normal weight controls. Discussion Our study demonstrates that the microbial diversity and structure of the salivary microbiome in people with obesity are significantly different from those of normal weight controls. These results suggested that changes in the structure and function of salivary microbiome in people with obesity might reflect their susceptibility to oral

  11. The oral microbiome - an update for oral healthcare professionals.

    PubMed

    Kilian, M; Chapple, I L C; Hannig, M; Marsh, P D; Meuric, V; Pedersen, A M L; Tonetti, M S; Wade, W G; Zaura, E

    2016-11-18

    For millions of years, our resident microbes have coevolved and coexisted with us in a mostly harmonious symbiotic relationship. We are not distinct entities from our microbiome, but together we form a 'superorganism' or holobiont, with the microbiome playing a significant role in our physiology and health. The mouth houses the second most diverse microbial community in the body, harbouring over 700 species of bacteria that colonise the hard surfaces of teeth and the soft tissues of the oral mucosa. Through recent advances in technology, we have started to unravel the complexities of the oral microbiome and gained new insights into its role during both health and disease. Perturbations of the oral microbiome through modern-day lifestyles can have detrimental consequences for our general and oral health. In dysbiosis, the finely-tuned equilibrium of the oral ecosystem is disrupted, allowing disease-promoting bacteria to manifest and cause conditions such as caries, gingivitis and periodontitis. For practitioners and patients alike, promoting a balanced microbiome is therefore important to effectively maintain or restore oral health. This article aims to give an update on our current knowledge of the oral microbiome in health and disease and to discuss implications for modern-day oral healthcare.

  12. Development of the preterm infant gut microbiome: A research priority

    SciT

    Groer, Maureen W.; Luciano, Angel A.; Dishaw, Larry J.

    The very low birth weight (VLBW) infant is at great risk for marked dysbiosis of the gut microbiome due to multiple factors, including physiological immaturity and prenatal/postnatal influences that disrupt the development of a normal gut flora. However, little is known about the developmental succession of the microbiota in preterm infants as they grow and mature. This review provides a synthesis of our understanding of the normal development of the infant gut microbiome and contrasts this with dysbiotic development in the VLBW infant. The role of human milk in normal gut microbial development is emphasized, along with the role ofmore » the gut microbiome in immune development and gastroenteric health. Current research provides evidence that the gut microbiome interacts extensively with many physiological systems and metabolic processes in the developing infant. However, to the best of our knowledge, there are currently no studies prospectively mapping the gut microbiome of VLBW infants through early childhood. This knowledge gap must be filled to inform a healthcare system that can provide for the growth, health, and development of VLBW infants. In conclusion, the study speculates about how the VLBW infants’ gut microbiome might function through host-microbe interactions to contribute to the sequelae of preterm birth, including its influence on growth, development, and general health of the infant host.« less

  13. The Human Microbiome in the Fight Against Tuberculosis

    PubMed Central

    Wood, Madeleine R.; Yu, Elaine A.; Mehta, Saurabh

    2017-01-01

    The human microbiome is an intriguing potentially modifiable risk factor in our arsenal against Mycobacterium tuberculosis, the leading infectious disease killer globally. Previous studies have shown associations between the human microbiome and pulmonary disease states; however, etiological links between the microbiome and tuberculosis (TB) infection or disease remain unclear. Immunomodulatory roles of the microbiome may prove to be a critical asset in the host response against TB, including in preventing TB infection, reducing progression from latency, mitigating disease severity, and lowering the incidence of drug resistance and coinfections. This review examined the associations between TB and the gut and lung microbiome. Eight studies were identified through a PubMed database search, including one animal study (N = 1), case report (N = 1), and case–control studies (N = 6). TB infection and disease were associated with reduced gastrointestinal microbial diversity in a murine model and human case report. Sputum microbial diversity differed by TB status in case–control studies, although some reported heterogeneous findings. Current evidence suggests that the gut and lung microbiome are associated with TB infection and disease. However, as studies are limited, etiological and longitudinal research is needed to determine clinical relevance. PMID:28719264

  14. Development of the preterm infant gut microbiome: A research priority

    DOE PAGES

    Groer, Maureen W.; Luciano, Angel A.; Dishaw, Larry J.; ...

    2014-10-13

    The very low birth weight (VLBW) infant is at great risk for marked dysbiosis of the gut microbiome due to multiple factors, including physiological immaturity and prenatal/postnatal influences that disrupt the development of a normal gut flora. However, little is known about the developmental succession of the microbiota in preterm infants as they grow and mature. This review provides a synthesis of our understanding of the normal development of the infant gut microbiome and contrasts this with dysbiotic development in the VLBW infant. The role of human milk in normal gut microbial development is emphasized, along with the role ofmore » the gut microbiome in immune development and gastroenteric health. Current research provides evidence that the gut microbiome interacts extensively with many physiological systems and metabolic processes in the developing infant. However, to the best of our knowledge, there are currently no studies prospectively mapping the gut microbiome of VLBW infants through early childhood. This knowledge gap must be filled to inform a healthcare system that can provide for the growth, health, and development of VLBW infants. In conclusion, the study speculates about how the VLBW infants’ gut microbiome might function through host-microbe interactions to contribute to the sequelae of preterm birth, including its influence on growth, development, and general health of the infant host.« less

  15. A psychology of the human brain–gut–microbiome axis

    PubMed Central

    Allen, Andrew P.; Dinan, Timothy G.; Clarke, Gerard

    2017-01-01

    Abstract In recent years, we have seen increasing research within neuroscience and biopsychology on the interactions between the brain, the gastrointestinal tract, the bacteria within the gastrointestinal tract, and the bidirectional relationship between these systems: the brain–gut–microbiome axis. Although research has demonstrated that the gut microbiota can impact upon cognition and a variety of stress‐related behaviours, including those relevant to anxiety and depression, we still do not know how this occurs. A deeper understanding of how psychological development as well as social and cultural factors impact upon the brain–gut–microbiome axis will contextualise the role of the axis in humans and inform psychological interventions that improve health within the brain–gut–microbiome axis. Interventions ostensibly aimed at ameliorating disorders in one part of the brain–gut–microbiome axis (e.g., psychotherapy for depression) may nonetheless impact upon other parts of the axis (e.g., microbiome composition and function), and functional gastrointestinal disorders such as irritable bowel syndrome represent a disorder of the axis, rather than an isolated problem either of psychology or of gastrointestinal function. The discipline of psychology needs to be cognisant of these interactions and can help to inform the future research agenda in this emerging field of research. In this review, we outline the role psychology has to play in understanding the brain–gut–microbiome axis, with a focus on human psychology and the use of research in laboratory animals to model human psychology. PMID:28804508

  16. Targeting gut microbiome: A novel and potential therapy for autism.

    PubMed

    Yang, Yongshou; Tian, Jinhu; Yang, Bo

    2018-02-01

    Autism spectrum disorder (ASD) is a severely neurodevelopmental disorder that impairs a child's ability to communicate and interact with others. Children with neurodevelopmental disorder, including ASD, are regularly affected by gastrointestinal problems and dysbiosis of gut microbiota. On the other hand, humans live in a co-evolutionary association with plenty of microorganisms that resident on the exposed and internal surfaces of our bodies. The microbiome, refers to the collection of microbes and their genetic material, confers a variety of physiologic benefits to the host in many key aspects of life as well as being responsible for some diseases. A large body of preclinical literature indicates that gut microbiome plays an important role in the bidirectional gut-brain axis that communicates between the gut and central nervous system. Moreover, accumulating evidences suggest that the gut microbiome is involved in the pathogenesis of ASD. The present review introduces the increasing evidence suggesting the reciprocal interaction network among microbiome, gut and brain. It also discusses the possible mechanisms by which gut microbiome influences the etiology of ASD via altering gut-brain axis. Most importantly, it highlights the new findings of targeting gut microbiome, including probiotic treatment and fecal microbiota transplant, as novel and potential therapeutics for ASD diseases. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. A psychology of the human brain-gut-microbiome axis.

    PubMed

    Allen, Andrew P; Dinan, Timothy G; Clarke, Gerard; Cryan, John F

    2017-04-01

    In recent years, we have seen increasing research within neuroscience and biopsychology on the interactions between the brain, the gastrointestinal tract, the bacteria within the gastrointestinal tract, and the bidirectional relationship between these systems: the brain-gut-microbiome axis. Although research has demonstrated that the gut microbiota can impact upon cognition and a variety of stress-related behaviours, including those relevant to anxiety and depression, we still do not know how this occurs. A deeper understanding of how psychological development as well as social and cultural factors impact upon the brain-gut-microbiome axis will contextualise the role of the axis in humans and inform psychological interventions that improve health within the brain-gut-microbiome axis. Interventions ostensibly aimed at ameliorating disorders in one part of the brain-gut-microbiome axis (e.g., psychotherapy for depression) may nonetheless impact upon other parts of the axis (e.g., microbiome composition and function), and functional gastrointestinal disorders such as irritable bowel syndrome represent a disorder of the axis, rather than an isolated problem either of psychology or of gastrointestinal function. The discipline of psychology needs to be cognisant of these interactions and can help to inform the future research agenda in this emerging field of research. In this review, we outline the role psychology has to play in understanding the brain-gut-microbiome axis, with a focus on human psychology and the use of research in laboratory animals to model human psychology.

  18. BMPOS: a Flexible and User-Friendly Tool Sets for Microbiome Studies.

    PubMed

    Pylro, Victor S; Morais, Daniel K; de Oliveira, Francislon S; Dos Santos, Fausto G; Lemos, Leandro N; Oliveira, Guilherme; Roesch, Luiz F W

    2016-08-01

    Recent advances in science and technology are leading to a revision and re-orientation of methodologies, addressing old and current issues under a new perspective. Advances in next generation sequencing (NGS) are allowing comparative analysis of the abundance and diversity of whole microbial communities, generating a large amount of data and findings at a systems level. The current limitation for biologists has been the increasing demand for computational power and training required for processing of NGS data. Here, we describe the deployment of the Brazilian Microbiome Project Operating System (BMPOS), a flexible and user-friendly Linux distribution dedicated to microbiome studies. The Brazilian Microbiome Project (BMP) has developed data analyses pipelines for metagenomic studies (phylogenetic marker genes), conducted using the two main high-throughput sequencing platforms (Ion Torrent and Illumina MiSeq). The BMPOS is freely available and possesses the entire requirement of bioinformatics packages and databases to perform all the pipelines suggested by the BMP team. The BMPOS may be used as a bootable live USB stick or installed in any computer with at least 1 GHz CPU and 512 MB RAM, independent of the operating system previously installed. The BMPOS has proved to be effective for sequences processing, sequences clustering, alignment, taxonomic annotation, statistical analysis, and plotting of metagenomic data. The BMPOS has been used during several metagenomic analyses courses, being valuable as a tool for training, and an excellent starting point to anyone interested in performing metagenomic studies. The BMPOS and its documentation are available at http://www.brmicrobiome.org .

  19. Earth Observation

    2013-10-14

    ISS037-E-011470 (14 Oct. 2013) --- Man-made archipelagos near Dubai, United Arab Emirates, are featured in this image photographed by an Expedition 37 crew member on the International Space Station, flying at approximately 220 miles above Earth. The municipality of Dubai is the largest city of the Persian Gulf emirate of the same name, and has built a global reputation for large-scale developments and architectural works. Among the most visible of these developments -- particularly from the perspective of astronauts onboard the space station -- are three man-made archipelagos. The two Palm Islands -- Palm Jumeirah (right) and Palm Jebel Ali (out of frame further to the right) -- appear as stylized palm trees when viewed from above. The World Islands (center frame) evoke a rough map of the world from an air- or space-borne perspective. The Palm Jumeirah project began in 2001 and required more than 50 million cubic meters of dredged sand to raise the islands above the Persian Gulf sea level. Construction of the Palm Jumeirah islands was completed in 2006; for several years now they have been developed for residential and commercial housing and infrastructure. Creation of the World Islands was begun in 2003 and completed in 2008, using 320 million cubic meters of sand and 37 million tons of rock for the surrounding 27 kilometer-long protective breakwater.

  20. [The importance of maternal microbiome in pregnancy].

    PubMed

    Záhumenský, J; Hederlingová, J; Pšenková, P

    2017-01-01

    To bring the most actual published findings of the influence of maternal microbiome on the development of pregnancy and possibilities of its adjusting. Review. 2nd Department of Gyneacology and Obstetrics of the Faculty of Medicine and the University Hospital, Bratislava. Review of the literature. The appearance of microbes on various body surface areas determines the overall health status of the individual in significant manner. The change in composition of microbioma in pregnant woman is well known. It was believed that the placenta and the body of the newborn is sterile environment. Modern diagnostic methods proved the presence of microorganisms inside the fetoplacentar unit without the signs of inflammation. Mutual interaction between the immune system of the mother, microbioma and immune system of the newborn can decrease the risk of serious obstetrical syndromes as well as define the lifelong health status of the newborn. The risk can be decreased by the administration of probiotics during the pregnancy.

  1. The Microbiome in Psychology and Cognitive Neuroscience.

    PubMed

    Sarkar, Amar; Harty, Siobhán; Lehto, Soili M; Moeller, Andrew H; Dinan, Timothy G; Dunbar, Robin I M; Cryan, John F; Burnet, Philip W J

    2018-07-01

    Psychology and microbiology make unlikely friends, but the past decade has witnessed striking bidirectional associations between intrinsic gut microbes and the brain, relationships with largely untested psychological implications. Although microbe-brain relationships are receiving a great deal of attention in biomedicine and neuroscience, psychologists have yet to join this journey. Here, we illustrate microbial associations with emotion, cognition, and social behavior. However, despite considerable enthusiasm and potential, technical and conceptual limitations including low statistical power and lack of mechanistic descriptions prevent a nuanced understanding of microbiome-brain-behavior relationships. Our goal is to describe microbial effects in domains of cognitive significance and the associated challenges to stimulate interdisciplinary research on the contribution of this hidden kingdom to psychological processes. Copyright © 2018 Elsevier Ltd. All rights reserved.

  2. Dynamic microbiome evolution in social bees

    PubMed Central

    Kwong, Waldan K.; Medina, Luis A.; Koch, Hauke; Sing, Kong-Wah; Soh, Eunice Jia Yu; Ascher, John S.; Jaffé, Rodolfo; Moran, Nancy A.

    2017-01-01

    The highly social (eusocial) corbiculate bees, comprising the honey bees, bumble bees, and stingless bees, are ubiquitous insect pollinators that fulfill critical roles in ecosystem services and human agriculture. Here, we conduct wide sampling across the phylogeny of these corbiculate bees and reveal a dynamic evolutionary history behind their microbiota, marked by multiple gains and losses of gut associates, the presence of generalist as well as host-specific strains, and patterns of diversification driven, in part, by host ecology (for example, colony size). Across four continents, we found that different host species have distinct gut communities, largely independent of geography or sympatry. Nonetheless, their microbiota has a shared heritage: The emergence of the eusocial corbiculate bees from solitary ancestors appears to coincide with the acquisition of five core gut bacterial lineages, supporting the hypothesis that host sociality facilitates the development and maintenance of specialized microbiomes. PMID:28435856

  3. Temporal Stability of the Human Skin Microbiome.

    PubMed

    Oh, Julia; Byrd, Allyson L; Park, Morgan; Kong, Heidi H; Segre, Julia A

    2016-05-05

    Biogeography and individuality shape the structural and functional composition of the human skin microbiome. To explore these factors' contribution to skin microbial community stability, we generated metagenomic sequence data from longitudinal samples collected over months and years. Analyzing these samples using a multi-kingdom, reference-based approach, we found that despite the skin's exposure to the external environment, its bacterial, fungal, and viral communities were largely stable over time. Site, individuality, and phylogeny were all determinants of stability. Foot sites exhibited the most variability; individuals differed in stability; and transience was a particular characteristic of eukaryotic viruses, which showed little site-specificity in colonization. Strain and single-nucleotide variant-level analysis showed that individuals maintain, rather than reacquire, prevalent microbes from the environment. Longitudinal stability of skin microbial communities generates hypotheses about colonization resistance and empowers clinical studies exploring alterations observed in disease states. Copyright © 2016 Elsevier Inc. All rights reserved.

  4. The microbiome of New World vultures.

    PubMed

    Roggenbuck, Michael; Bærholm Schnell, Ida; Blom, Nikolaj; Bælum, Jacob; Bertelsen, Mads Frost; Sicheritz-Pontén, Thomas; Pontén, Thomas Sicheritz; Sørensen, Søren Johannes; Gilbert, M Thomas P; Graves, Gary R; Hansen, Lars H

    2014-11-25

    Vultures are scavengers that fill a key ecosystem niche, in which they have evolved a remarkable tolerance to bacterial toxins in decaying meat. Here we report the first deep metagenomic analysis of the vulture microbiome. Through face and gut comparisons of 50 vultures representing two species, we demonstrate a remarkably conserved low diversity of gut microbial flora. The gut samples contained an average of 76 operational taxonomic units (OTUs) per specimen, compared with 528 OTUs on the facial skin. Clostridia and Fusobacteria, widely pathogenic to other vertebrates, dominate the vulture's gut microbiota. We reveal a likely faecal-oral-gut route for their origin. DNA of prey species detectable on facial swabs was completely degraded in the gut samples from most vultures, suggesting that the gastrointestinal tracts of vultures are extremely selective. Our findings show a strong adaption of vu