WorldWideScience

Sample records for global genome level

  1. Population-level genomics identifies the emergence and global spread of a human transmissible multidrug-resistant nontuberculous mycobacterium

    Science.gov (United States)

    Rodriguez-Rincon, Daniela; Everall, Isobel; Brown, Karen P; Moreno, Pablo; Verma, Deepshikha; Hill, Emily; Drijkoningen, Judith; Gilligan, Peter; Esther, Charles R; Noone, Peadar G; Giddings, Olivia; Bell, Scott C.; Thomson, Rachel; Wainwright, Claire E.; Coulter, Chris; Pandey, Sushil; Wood, Michelle E; Stockwell, Rebecca E; Ramsay, Kay A; Sherrard, Laura J; Kidd, Timothy J; Jabbour, Nassib; Johnson, Graham R; Knibbs, Luke D; Morawska, Lidia; Sly, Peter D; Jones, Andrew; Bilton, Diana; Laurenson, Ian; Ruddy, Michael; Bourke, Stephen; Bowler, Ian CJW; Chapman, Stephen J; Clayton, Andrew; Cullen, Mairi; Daniels, Thomas; Dempsey, Owen; Denton, Miles; Desai, Maya; Drew, Richard J; Edenborough, Frank; Evans, Jason; Folb, Jonathan; Humphrey, Helen; Isalska, Barbara; Jensen-Fangel, Søren; Jönsson, Bodil; Jones, Andrew M.; Katzenstein, Terese L; Lillebaek, Troels; MacGregor, Gordon; Mayell, Sarah; Millar, Michael; Modha, Deborah; Nash, Edward F; O’Brien, Christopher; O’Brien, Deirdre; Ohri, Chandra; Pao, Caroline S; Peckham, Daniel; Perrin, Felicity; Perry, Audrey; Pressler, Tania; Prtak, Laura; Qvist, Tavs; Robb, Ali; Rodgers, Helen; Schaffer, Kirsten; Shafi, Nadia; van Ingen, Jakko; Walshaw, Martin; Watson, Danie; West, Noreen; Whitehouse, Joanna; Haworth, Charles S; Harris, Simon R; Ordway, Diane; Parkhill, Julian; Floto, R. Andres

    2016-01-01

    Lung infections with Mycobacterium abscessus, a species of multidrug resistant nontuberculous mycobacteria, are emerging as an important global threat to individuals with cystic fibrosis (CF) where they accelerate inflammatory lung damage leading to increased morbidity and mortality. Previously, M. abscessus was thought to be independently acquired by susceptible individuals from the environment. However, using whole genome analysis of a global collection of clinical isolates, we show that the majority of M. abscessus infections are acquired through transmission, potentially via fomites and aerosols, of recently emerged dominant circulating clones that have spread globally. We demonstrate that these clones are associated with worse clinical outcomes, show increased virulence in cell-based and mouse infection models, and thus represent an urgent international infection challenge. PMID:27846606

  2. Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response

    Directory of Open Access Journals (Sweden)

    Chong Kang

    2009-09-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are endogenous small RNAs having large-scale regulatory effects on plant development and stress responses. Extensive studies of miRNAs have only been performed in a few model plants. Although miRNAs are proved to be involved in plant cold stress responses, little is known for winter-habit monocots. Brachypodium distachyon, with close evolutionary relationship to cool-season cereals, has recently emerged as a novel model plant. There are few reports of Brachypodium miRNAs. Results High-throughput sequencing and whole-genome-wide data mining led to the identification of 27 conserved miRNAs, as well as 129 predicted miRNAs in Brachypodium. For multiple-member conserved miRNA families, their sizes in Brachypodium were much smaller than those in rice and Populus. The genome organization of miR395 family in Brachypodium was quite different from that in rice. The expression of 3 conserved miRNAs and 25 predicted miRNAs showed significant changes in response to cold stress. Among these miRNAs, some were cold-induced and some were cold-suppressed, but all the conserved miRNAs were up-regulated under cold stress condition. Conclusion Our results suggest that Brachypodium miRNAs are composed of a set of conserved miRNAs and a large proportion of non-conserved miRNAs with low expression levels. Both kinds of miRNAs were involved in cold stress response, but all the conserved miRNAs were up-regulated, implying an important role for cold-induced miRNAs. The different size and genome organization of miRNA families in Brachypodium and rice suggest that the frequency of duplication events or the selection pressure on duplicated miRNAs are different between these two closely related plant species.

  3. Global physical activity levels

    DEFF Research Database (Denmark)

    Hallal, Pedro C; Andersen, Lars Bo; Bull, Fiona C

    2012-01-01

    To implement effective non-communicable disease prevention programmes, policy makers need data for physical activity levels and trends. In this report, we describe physical activity levels worldwide with data for adults (15 years or older) from 122 countries and for adolescents (13-15-years......-income countries. The proportion of 13-15-year-olds doing fewer than 60 min of physical activity of moderate to vigorous intensity per day is 80·3% (80·1-80·5); boys are more active than are girls. Continued improvement in monitoring of physical activity would help to guide development of policies and programmes......-old) from 105 countries. Worldwide, 31·1% (95% CI 30·9-31·2) of adults are physically inactive, with proportions ranging from 17·0% (16·8-17·2) in southeast Asia to about 43% in the Americas and the eastern Mediterranean. Inactivity rises with age, is higher in women than in men, and is increased in high...

  4. Global organization of a positive-strand RNA virus genome.

    Directory of Open Access Journals (Sweden)

    Baodong Wu

    Full Text Available The genomes of plus-strand RNA viruses contain many regulatory sequences and structures that direct different viral processes. The traditional view of these RNA elements are as local structures present in non-coding regions. However, this view is changing due to the discovery of regulatory elements in coding regions and functional long-range intra-genomic base pairing interactions. The ∼4.8 kb long RNA genome of the tombusvirus tomato bushy stunt virus (TBSV contains these types of structural features, including six different functional long-distance interactions. We hypothesized that to achieve these multiple interactions this viral genome must utilize a large-scale organizational strategy and, accordingly, we sought to assess the global conformation of the entire TBSV genome. Atomic force micrographs of the genome indicated a mostly condensed structure composed of interconnected protrusions extending from a central hub. This configuration was consistent with the genomic secondary structure model generated using high-throughput selective 2'-hydroxyl acylation analysed by primer extension (i.e. SHAPE, which predicted different sized RNA domains originating from a central region. Known RNA elements were identified in both domain and inter-domain regions, and novel structural features were predicted and functionally confirmed. Interestingly, only two of the six long-range interactions known to form were present in the structural model. However, for those interactions that did not form, complementary partner sequences were positioned relatively close to each other in the structure, suggesting that the secondary structure level of viral genome structure could provide a basic scaffold for the formation of different long-range interactions. The higher-order structural model for the TBSV RNA genome provides a snapshot of the complex framework that allows multiple functional components to operate in concert within a confined context.

  5. The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes

    KAUST Repository

    Bracken-Grissom, Heather; Collins, Allen G.; Collins, Timothy; Crandall, Keith; Distel, Daniel; Dunn, Casey; Giribet, Gonzalo; Haddock, Steven; Knowlton, Nancy; Martindale, Mark; Medina, Monica; Messing, Charles; O'Brien, Stephen J.; Paulay, Gustav; Putnam, Nicolas; Ravasi, Timothy; Rouse, Greg W.; Ryan, Joseph F.; Schulze, Anja; Worheide, Gert; Adamska, Maja; Bailly, Xavier; Breinholt, Jesse; Browne, William E.; Diaz, M. Christina; Evans, Nathaniel; Flot, Jean-Francois; Fogarty, Nicole; Johnston, Matthew; Kamel, Bishoy; Kawahara, Akito Y.; Laberge, Tammy; Lavrov, Dennis; Michonneau, Francois; Moroz, Leonid L.; Oakley, Todd; Osborne, Karen; Pomponi, Shirley A.; Rhodes, Adelaide; Rodriguez-Lanetty, Mauricio; Santos, Scott R.; Satoh, Nori; Thacker, Robert W.; Van de Peer, Yves; Voolstra, Christian R.; Welch, David Mark; Winston, Judith; Zhou, Xin

    2013-01-01

    Over 95% of all metazoan (animal) species comprise the invertebrates, but very few genomes from these organisms have been sequenced. We have, therefore, formed a Global Invertebrate Genomics Alliance (GIGA). Our intent is to build a collaborative

  6. The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes

    KAUST Repository

    Bracken-Grissom, Heather

    2013-12-12

    Over 95% of all metazoan (animal) species comprise the invertebrates, but very few genomes from these organisms have been sequenced. We have, therefore, formed a Global Invertebrate Genomics Alliance (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.g., species selection, sample collection and storage, sequence assembly, annotation, analytical tools) associated with genome/transcriptome sequencing across a large taxonomic spectrum. We aim to promote standards that will facilitate comparative approaches to invertebrate genomics and collaborations across the international scientific community. Candidate study taxa include species from Porifera, Ctenophora, Cnidaria, Placozoa, Mollusca, Arthropoda, Echinodermata, Annelida, Bryozoa, and Platyhelminthes, among others. GIGA will target 7000 noninsect/nonnematode species, with an emphasis on marine taxa because of the unrivaled phyletic diversity in the oceans. Priorities for selecting invertebrates for sequencing will include, but are not restricted to, their phylogenetic placement; relevance to organismal, ecological, and conservation research; and their importance to fisheries and human health. We highlight benefits of sequencing both whole genomes (DNA) and transcriptomes and also suggest policies for genomic-level data access and sharing based on transparency and inclusiveness. The GIGA Web site () has been launched to facilitate this collaborative venture.

  7. Genomics and Global Justice: toward global agri-genomics critizenship, Genomics, Policy and Society

    NARCIS (Netherlands)

    Korthals, M.J.J.A.A.

    2010-01-01

    Searching for the specific contribution of the life sciences to global justice in agriculture and food, one is faced with six global problems that haunt the world today. These are: population growth (9.2 billion by 2050); the gap between poor and rich peoples; hunger and obesity; increasing

  8. Global Implementation of Genomic Medicine: We Are Not Alone

    Science.gov (United States)

    Manolio, Teri A.; Abramowicz, Marc; Al-Mulla, Fahd; Anderson, Warwick; Balling, Rudi; Berger, Adam C.; Bleyl, Steven; Chakravarti, Aravinda; Chantratita, Wasun; Chisholm, Rex L.; Dissanayake, Vajira H. W.; Dunn, Michael; Dzau, Victor J.; Han, Bok-Ghee; Hubbard, Tim; Kolbe, Anne; Korf, Bruce; Kubo, Michiaki; Lasko, Paul; Leego, Erkki; Mahasirimongkol, Surakameth; Majumdar, Partha P.; Matthijs, Gert; McLeod, Howard L.; Metspalu, Andres; Meulien, Pierre; Miyano, Satoru; Naparstek, Yaakov; O’Rourke, P. Pearl; Patrinos, George P.; Rehm, Heidi L.; Relling, Mary V.; Rennert, Gad; Rodriguez, Laura Lyman; Roden, Dan M.; Shuldiner, Alan R.; Sinha, Sukdev; Tan, Patrick; Ulfendahl, Mats; Ward, Robyn; Williams, Marc S.; Wong, John E.L.; Green, Eric D.; Ginsburg, Geoffrey S.

    2016-01-01

    Advances in high-throughput genomic technologies coupled with a growing number of genomic results potentially useful in clinical care have led to ground-breaking genomic medicine implementation programs in various nations. Many of these innovative programs capitalize on unique local capabilities arising from the structure of their health care systems or their cultural or political milieu, as well as from unusual burdens of disease or risk alleles. Many such programs are being conducted in relative isolation and might benefit from sharing of approaches and lessons learned in other nations. The National Human Genome Research Institute recently brought together 25 of these groups from around the world to describe and compare projects, examine the current state of implementation and desired near-term capabilities, and identify opportunities for collaboration to promote the responsible implementation of genomic medicine. The wide variety of nascent programs in diverse settings demonstrates that implementation of genomic medicine is expanding globally in varied and highly innovative ways. Opportunities for collaboration abound in the areas of evidence generation, health information technology, education, workforce development, pharmacogenomics, and policy and regulatory issues. Several international organizations that are already facilitating effective research collaborations should engage to ensure implementation proceeds collaboratively without potentially wasteful duplication. Efforts to coalesce these groups around concrete but compelling signature projects, such as global eradication of genetically-mediated drug reactions or developing a truly global genomic variant data resource across a wide number of ethnicities, would accelerate appropriate implementation of genomics to improve clinical care world-wide. PMID:26041702

  9. Genomics innovation: transforming healthcare, business, and the global economy.

    Science.gov (United States)

    Jimenez-Sanchez, Gerardo

    2015-12-01

    The genomics revolution has generated an unprecedented number of assets to propel innovation. Initial availability of genomics-based applications show a significant potential to contribute addressing global challenges, such as human health, food security, alternative sources of energies, and environmental sustainability. In the last years, most developed and emerging nations have established bioeconomy agendas where genomics plays a major role to meet their local needs. Genomic medicine is one of the most visible areas where genomics innovation is likely to contribute to a more individualized, predictive, and preventive medical practice. Examples in agriculture, dairy and beef, fishery, aquaculture, and forests industries include the effective selection of genetic variants associated to traits of economic value. Some, in addition to producing more and better foods, already represent an important increase in revenues to their respective industries. It is reasonable to predict that genomics applications will lead to a paradigm shift in our ability to ease significant health, economic, and social burdens. However, to successfully benefit from genomics innovations, it is imperative to address a number of hurdles related to generating robust scientific evidence, developing lower-cost sequencing technologies, effective bioinformatics, as well as sensitive ethical, economical, environmental, legal, and social aspects associated with the development and use of genomics innovations.

  10. Large-scale integration of small molecule-induced genome-wide transcriptional responses, Kinome-wide binding affinities and cell-growth inhibition profiles reveal global trends characterizing systems-level drug action

    Directory of Open Access Journals (Sweden)

    Dusica eVidovic

    2014-09-01

    Full Text Available The Library of Integrated Network-based Cellular Signatures (LINCS project is a large-scale coordinated effort to build a comprehensive systems biology reference resource. The goals of the program include the generation of a very large multidimensional data matrix and informatics and computational tools to integrate, analyze, and make the data readily accessible. LINCS data include genome-wide transcriptional signatures, biochemical protein binding profiles, cellular phenotypic response profiles and various other datasets for a wide range of cell model systems and molecular and genetic perturbations. Here we present a partial survey of this data facilitated by data standards and in particular a robust compound standardization workflow; we integrated several types of LINCS signatures and analyzed the results with a focus on mechanism of action and chemical compounds. We illustrate how kinase targets can be related to disease models and relevant drugs. We identified some fundamental trends that appear to link Kinome binding profiles and transcriptional signatures to chemical information and biochemical binding profiles to transcriptional responses independent of chemical similarity. To fill gaps in the datasets we developed and applied predictive models. The results can be interpreted at the systems level as demonstrated based on a large number of signaling pathways. We can identify clear global relationships, suggesting robustness of cellular responses to chemical perturbation. Overall, the results suggest that chemical similarity is a useful measure at the systems level, which would support phenotypic drug optimization efforts. With this study we demonstrate the potential of such integrated analysis approaches and suggest prioritizing further experiments to fill the gaps in the current data.

  11. Global biogeography of Prochlorococcus genome diversity in the surface ocean.

    Science.gov (United States)

    Kent, Alyssa G; Dupont, Chris L; Yooseph, Shibu; Martiny, Adam C

    2016-08-01

    Prochlorococcus, the smallest known photosynthetic bacterium, is abundant in the ocean's surface layer despite large variation in environmental conditions. There are several genetically divergent lineages within Prochlorococcus and superimposed on this phylogenetic diversity is extensive gene gain and loss. The environmental role in shaping the global ocean distribution of genome diversity in Prochlorococcus is largely unknown, particularly in a framework that considers the vertical and lateral mechanisms of evolution. Here we show that Prochlorococcus field populations from a global circumnavigation harbor extensive genome diversity across the surface ocean, but this diversity is not randomly distributed. We observed a significant correspondence between phylogenetic and gene content diversity, including regional differences in both phylogenetic composition and gene content that were related to environmental factors. Several gene families were strongly associated with specific regions and environmental factors, including the identification of a set of genes related to lower nutrient and temperature regions. Metagenomic assemblies of natural Prochlorococcus genomes reinforced this association by providing linkage of genes across genomic backbones. Overall, our results show that the phylogeography in Prochlorococcus taxonomy is echoed in its genome content. Thus environmental variation shapes the functional capabilities and associated ecosystem role of the globally abundant Prochlorococcus.

  12. Pan genome of the phytoplankton Emiliania underpins its global distribution.

    Science.gov (United States)

    Read, Betsy A; Kegel, Jessica; Klute, Mary J; Kuo, Alan; Lefebvre, Stephane C; Maumus, Florian; Mayer, Christoph; Miller, John; Monier, Adam; Salamov, Asaf; Young, Jeremy; Aguilar, Maria; Claverie, Jean-Michel; Frickenhaus, Stephan; Gonzalez, Karina; Herman, Emily K; Lin, Yao-Cheng; Napier, Johnathan; Ogata, Hiroyuki; Sarno, Analissa F; Shmutz, Jeremy; Schroeder, Declan; de Vargas, Colomban; Verret, Frederic; von Dassow, Peter; Valentin, Klaus; Van de Peer, Yves; Wheeler, Glen; Dacks, Joel B; Delwiche, Charles F; Dyhrman, Sonya T; Glöckner, Gernot; John, Uwe; Richards, Thomas; Worden, Alexandra Z; Zhang, Xiaoyu; Grigoriev, Igor V

    2013-07-11

    Coccolithophores have influenced the global climate for over 200 million years. These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems. They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space. Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean. Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.

  13. The Global Genome Biodiversity Network (GGBN) Data Standard specification

    Science.gov (United States)

    Droege, G.; Barker, K.; Seberg, O.; Coddington, J.; Benson, E.; Berendsohn, W. G.; Bunk, B.; Butler, C.; Cawsey, E. M.; Deck, J.; Döring, M.; Flemons, P.; Gemeinholzer, B.; Güntsch, A.; Hollowell, T.; Kelbert, P.; Kostadinov, I.; Kottmann, R.; Lawlor, R. T.; Lyal, C.; Mackenzie-Dodds, J.; Meyer, C.; Mulcahy, D.; Nussbeck, S. Y.; O'Tuama, É.; Orrell, T.; Petersen, G.; Robertson, T.; Söhngen, C.; Whitacre, J.; Wieczorek, J.; Yilmaz, P.; Zetzsche, H.; Zhang, Y.; Zhou, X.

    2016-01-01

    Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs to be concise and consistent in today’s ever-increasing bioinformatic era, for complementary data aggregators to easily map databases to one another. In order to facilitate exchange of information on genomic samples and their derived data, the Global Genome Biodiversity Network (GGBN) Data Standard is intended to provide a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way. The new data standard presented here build upon existing standards commonly used within the community extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard will reveal and democratize the hidden contents of biodiversity biobanks, for the convenience of everyone in the wider biobanking community. Technical tools exist for data providers to easily map their databases to the standard. Database URL: http://terms.tdwg.org/wiki/GGBN_Data_Standard PMID:27694206

  14. Pan Genome of the Phytoplankton Emiliania Underpins its Global Distribution

    Energy Technology Data Exchange (ETDEWEB)

    Read, Betsy A. [California State Univ. (CalState), San Marcos, CA (United States); Kegel, Jessica [Alfred Wegener Inst. for Polar and Marine Research, Bremerhaven (Germany); Klute, Mary J. [Univ. of Alberta, Edmonton, AB (Canada); Kuo, Alan [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Lefebvre, Stephane C. [J. Craig Venter Inst., San Diego, CA (United States); Maumus, Florian [National Institute of Agricultural Research, Versailles (France); Mayer, Christoph [Alexander Koenig Research Museum, Bonn (Germany); Ruhr Univ., Bochum (Germany); Miller, John [Univ. of Maryland, College Park, MD (United States); Monier, Adam [Monterey Bay Aquarium Research Inst., Moss Landing, CA (United States); Salamov, Asaf [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Young, Jeremy [Univ. College London (United Kingdom); Aguilar, Maria [Univ. of Alberta, Edmonton, AB (Canada); Claverie, Jean-Michel [Aix-Marseille Univ. (France); Frickenhaus, Stephan [Alfred Wegener Inst. for Polar and Marine Research, Bremerhaven (Germany); Univ. of Bremerhaven (Germany); Gonzalez, Karina [Harvard Medical School, Boston, MA (United States); Herman, Emily K. [Univ. of Alberta, Edmonton, AB (Canada); Lin, Yao-Cheng [Ghent Univ. (Belgium); Napier, Johnathan [Rothamstead Research, Harpenden (United Kingdom); Ogata, Hiroyuki [Aix-Marseille Univ. (France); Sarno, Analissa F. [California State Univ. (CalState), San Marcos, CA (United States); Schmutz, Jeremy [USDOE Joint Genome Inst., Walnut Creek, CA (United States); HudsonAlpha Genome Sequencing Center, Huntsville, AL (United States); Schroeder, Declan [Marine Biological Association of the UK, Plymouth (United Kingdom); de Vargas, Columban [CNRS. Univ. Pierre and Marie Curie (France).; Verret, Frederic [Univ. of Essex, Colchester (United Kingdom); von Dassow, Peter [Pontifical Catholic University of Chile, Santiago (Chile); Valentin, Klaus [Alfred Wegener Inst. for Polar and Marine Research, Bremerhaven (Germany); Van de Peer, Yves [Ghent Univ. (Belgium); Wheeler, Glen [Marine Biological Association of the UK, Plymouth (United Kingdom); Plymouth Marine Lab. (United Kingdom); Annotation Consortium, Emiliania huxleyi; Dacks, Joel B. [Univ. of Alberta, Edmonton, AB (Canada); Delwiche, Charles F. [Univ. of Maryland, College Park, MD (United States); Dyhrman, Sonya T. [Woods Hole Oceanographic Inst., MA (United States); Columbia Univ., Palisades, NY (United States); Glockner, Gernot [Univ. of Cologne (Germany); John, Uwe [Alfred Wegener Inst. for Polar and Marine Research, Bremerhaven (Germany); Richards, Thomas [National History Museum, London (United Kingdom); Worden, Alexandra Z. [Monterey Bay Aquarium Research Inst., Moss Landing, CA (United States); Zhang, Xiaoyu [California State Univ. (CalState), San Marcos, CA (United States); Grigoriev, Igor V. [USDOE Joint Genome Inst., Walnut Creek, CA (United States)

    2012-06-18

    Coccolithophores have influenced the global climate for over 200 million years1. These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems2. They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering themvisible fromspace3.Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean4. Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate thatE. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.

  15. Global features of the Alcanivorax borkumensis SK2 genome

    DEFF Research Database (Denmark)

    Reva, Oleg N.; Hallin, Peter Fischer; Willenbrock, Hanni

    2008-01-01

    The global feature of the completely sequenced Alcanivorax borkumensis SK2 type strain chromosome is its symmetry and homogeneity. The origin and terminus of replication are located opposite to each other in the chromosome and are discerned with high signal to noise ratios by maximal oligonucleot......The global feature of the completely sequenced Alcanivorax borkumensis SK2 type strain chromosome is its symmetry and homogeneity. The origin and terminus of replication are located opposite to each other in the chromosome and are discerned with high signal to noise ratios by maximal...... oligonucleotide usage biases on the leading and lagging strand. Genomic DNA structure is rather uniform throughout the chromosome with respect to intrinsic curvature, position preference or base stacking energy. The orthologs and paralogs of A. borkumensis genes with the highest sequence homology were found...

  16. Beyond Our Borders? Public Resistance to Global Genomic Data Sharing.

    Directory of Open Access Journals (Sweden)

    Mary A Majumder

    2016-11-01

    Full Text Available Prospects have never seemed better for a truly global approach to science to improve human health, with leaders of national initiatives laying out their vision of a worldwide network of related projects. An extensive literature addresses obstacles to global genomic data sharing, yet a series of public polls suggests that the scientific community may be overlooking a significant barrier: potential public resistance to data sharing across national borders. In several large United States surveys, university researchers in other countries were deemed the least acceptable group of data users, and a just-completed US survey found a marked increase in privacy and security concerns related to data access by non-US researchers. Furthermore, diminished support for sharing beyond national borders is not unique to the US, although the limited data from outside the US suggest variation across countries as well as demographic groups. Possible sources of resistance include apprehension about privacy and security protections. Strategies for building public support include making the affirmative case for global data sharing, addressing privacy, security, and other legitimate concerns, and investigating public concerns in greater depth.

  17. Global and local level density models

    International Nuclear Information System (INIS)

    Koning, A.J.; Hilaire, S.; Goriely, S.

    2008-01-01

    Four different level density models, three phenomenological and one microscopic, are consistently parameterized using the same set of experimental observables. For each of the phenomenological models, the Constant Temperature Model, the Back-shifted Fermi gas Model and the Generalized Superfluid Model, a version without and with explicit collective enhancement is considered. Moreover, a recently published microscopic combinatorial model is compared with the phenomenological approaches and with the same set of experimental data. For each nuclide for which sufficient experimental data exists, a local level density parameterization is constructed for each model. Next, these local models have helped to construct global level density prescriptions, to be used for cases for which no experimental data exists. Altogether, this yields a collection of level density formulae and parameters that can be used with confidence in nuclear model calculations. To demonstrate this, a large-scale validation with experimental discrete level schemes and experimental cross sections and neutron emission spectra for various different reaction channels has been performed

  18. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

    DEFF Research Database (Denmark)

    Pedersen, Jakob Skou; Valen, Eivind; Velazquez, Amhed Missael Vargas

    2014-01-01

    Epigenetic information is available from contemporary organisms, but is difficult to track back in evolutionary time. Here, we show that genome-wide epigenetic information can be gathered directly from next-generation sequence reads of DNA isolated from ancient remains. Using the genome sequence...... data generated from hair shafts of a 4000-yr-old Paleo-Eskimo belonging to the Saqqaq culture, we generate the first ancient nucleosome map coupled with a genome-wide survey of cytosine methylation levels. The validity of both nucleosome map and methylation levels were confirmed by the recovery...

  19. Exceptionally high levels of recombination across the honey bee genome.

    Science.gov (United States)

    Beye, Martin; Gattermeier, Irene; Hasselmann, Martin; Gempe, Tanja; Schioett, Morten; Baines, John F; Schlipalius, David; Mougel, Florence; Emore, Christine; Rueppell, Olav; Sirviö, Anu; Guzmán-Novoa, Ernesto; Hunt, Greg; Solignac, Michel; Page, Robert E

    2006-11-01

    The first draft of the honey bee genome sequence and improved genetic maps are utilized to analyze a genome displaying 10 times higher levels of recombination (19 cM/Mb) than previously analyzed genomes of higher eukaryotes. The exceptionally high recombination rate is distributed genome-wide, but varies by two orders of magnitude. Analysis of chromosome, sequence, and gene parameters with respect to recombination showed that local recombination rate is associated with distance to the telomere, GC content, and the number of simple repeats as described for low-recombining genomes. Recombination rate does not decrease with chromosome size. On average 5.7 recombination events per chromosome pair per meiosis are found in the honey bee genome. This contrasts with a wide range of taxa that have a uniform recombination frequency of about 1.6 per chromosome pair. The excess of recombination activity does not support a mechanistic role of recombination in stabilizing pairs of homologous chromosome during chromosome pairing. Recombination rate is associated with gene size, suggesting that introns are larger in regions of low recombination and may improve the efficacy of selection in these regions. Very few transposons and no retrotransposons are present in the high-recombining genome. We propose evolutionary explanations for the exceptionally high genome-wide recombination rate.

  20. Measuring the Levels of Ribonucleotides Embedded in Genomic DNA.

    Science.gov (United States)

    Meroni, Alice; Nava, Giulia M; Sertic, Sarah; Plevani, Paolo; Muzi-Falconi, Marco; Lazzaro, Federico

    2018-01-01

    Ribonucleotides (rNTPs) are incorporated into genomic DNA at a relatively high frequency during replication. They have beneficial effects but, if not removed from the chromosomes, increase genomic instability. Here, we describe a fast method to easily estimate the amounts of embedded ribonucleotides into the genome. The protocol described is performed in Saccharomyces cerevisiae and allows us to quantify altered levels of rNMPs due to different mutations in the replicative polymerase ε. However, this protocol can be easily applied to cells derived from any organism.

  1. Global Genome Biodiversity Network: saving a blueprint of the Tree of Life – a botanical perspective

    Science.gov (United States)

    Seberg, O.; Droege, G.; Barker, K.; Coddington, J. A.; Funk, V.; Gostel, M.; Petersen, G.; Smith, P. P.

    2016-01-01

    Background Genomic research depends upon access to DNA or tissue collected and preserved according to high-quality standards. At present, the collections in most natural history museums do not sufficiently address these standards, making them often hard or impossible to use for whole-genome sequencing or transcriptomics. In response to these challenges, natural history museums, herbaria, botanical gardens and other stakeholders have started to build high-quality biodiversity biobanks. Unfortunately, information about these collections remains fragmented, scattered and largely inaccessible. Without a central registry or even an overview of relevant institutions, it is difficult and time-consuming to locate the needed samples. Scope The Global Genome Biodiversity Network (GGBN) was created to fill this vacuum by establishing a one-stop access point for locating samples meeting quality standards for genome-scale applications, while complying with national and international legislations and conventions. Increased accessibility to genomic samples will further genomic research and development, conserve genetic resources, help train the next generation of genome researchers and raise the visibility of biodiversity collections. Additionally, the availability of a data-sharing platform will facilitate identification of gaps in the collections, thereby empowering targeted sampling efforts, increasing the breadth and depth of preservation of genetic diversity. The GGBN is rapidly growing and currently has 41 members. The GGBN covers all branches of the Tree of Life, except humans, but here the focus is on a pilot project with emphasis on ‘harvesting’ the Tree of Life for vascular plant taxa to enable genome-level studies. Conclusion While current efforts are centred on getting the existing samples of all GGBN members online, a pilot project, GGI-Gardens, has been launched as proof of concept. Over the next 6 years GGI-Gardens aims to add to the GGBN high-quality genetic

  2. Amplification of HER2 is a marker for global genomic instability

    Directory of Open Access Journals (Sweden)

    Love Brad

    2008-10-01

    Full Text Available Abstract Background Genomic alterations of the proto-oncogene c-erbB-2 (HER-2/neu are associated with aggressive behavior and poor prognosis in patients with breast cancer. The variable clinical outcomes seen in patients with similar HER2 status, given similar treatments, suggests that the effects of amplification of HER2 can be influenced by other genetic changes. To assess the broader genomic implications of structural changes at the HER2 locus, we investigated relationships between genomic instability and HER2 status in patients with invasive breast cancer. Methods HER2 status was determined using the PathVysion® assay. DNA was extracted after laser microdissection from the 181 paraffin-embedded HER2 amplified (n = 39 or HER2 negative (n = 142 tumor specimens with sufficient tumor available to perform molecular analysis. Allelic imbalance (AI was assessed using a panel of microsatellite markers representing 26 chromosomal regions commonly altered in breast cancer. Student t-tests and partial correlations were used to investigate relationships between genomic instability and HER2 status. Results The frequency of AI was significantly higher (P P Conclusion The poor prognosis associated with HER2 amplification may be attributed to global genomic instability as cells with high frequencies of chromosomal alterations have been associated with increased cellular proliferation and aggressive behavior. In addition, high levels of DNA damage may render tumor cells refractory to treatment. In addition, specific alterations at chromosomes 11q13, 16q22-q24, and 18q21, all of which have been associated with aggressive tumor behavior, may serve as genetic modifiers to HER2 amplification. These data not only improve our understanding of HER in breast pathogenesis but may allow more accurate risk profiles and better treatment options to be developed.

  3. A bibliometric analysis of global research on genome sequencing ...

    African Journals Online (AJOL)

    The results show that disease and protein related researches were the leading research focuses, and comparative genomics and evolution related research had strong potential in the near future. Key words: Genome sequencing, research trend, scientometrics, science citation index expanded (SCI-Expanded), word cluster ...

  4. Variation of global DNA methylation levels with age and in autistic children.

    Science.gov (United States)

    Tsang, Shui-Ying; Ahmad, Tanveer; Mat, Flora W K; Zhao, Cunyou; Xiao, Shifu; Xia, Kun; Xue, Hong

    2016-09-23

    The change in epigenetic signatures, in particular DNA methylation, has been proposed as risk markers for various age-related diseases. However, the course of variation in methylation levels with age, the difference in methylation between genders, and methylation-disease association at the whole genome level is unclear. In the present study, genome-wide methylation levels in DNA extracted from peripheral blood for 2116 healthy Chinese in the 2-97 age range and 280 autistic trios were examined using the fluorescence polarization-based genome-wide DNA methylation quantification method developed by us. Genome-wide or global DNA methylation levels proceeded through multiple phases of variation with age, consisting of a steady increase from age 2 to 25 (r = 0.382) and another rise from age 41 to 55 to reach a peak level of ~80 % (r = 0.265), followed by a sharp decrease to ~40 % in the mid-1970s (age 56 to 75; r = -0.395) and leveling off thereafter. Significant gender effect in methylation levels was observed only for the 41-55 age group in which methylation in females was significantly higher than in males (p = 0.010). In addition, global methylation level was significantly higher in autistic children than in age-matched healthy children (p < 0.001). The multiphasic nature of changes in global methylation levels with age was delineated, and investigation into the factors underlying this profile will be essential to a proper understanding of the aging process. Furthermore, this first report of global hypermethylation in autistic children also illustrates the importance of age-matched controls in characterization of disease-associated variations in DNA methylation.

  5. In vitro analysis of integrated global high-resolution DNA methylation profiling with genomic imbalance and gene expression in osteosarcoma.

    Directory of Open Access Journals (Sweden)

    Bekim Sadikovic

    Full Text Available Genetic and epigenetic changes contribute to deregulation of gene expression and development of human cancer. Changes in DNA methylation are key epigenetic factors regulating gene expression and genomic stability. Recent progress in microarray technologies resulted in developments of high resolution platforms for profiling of genetic, epigenetic and gene expression changes. OS is a pediatric bone tumor with characteristically high level of numerical and structural chromosomal changes. Furthermore, little is known about DNA methylation changes in OS. Our objective was to develop an integrative approach for analysis of high-resolution epigenomic, genomic, and gene expression profiles in order to identify functional epi/genomic differences between OS cell lines and normal human osteoblasts. A combination of Affymetrix Promoter Tilling Arrays for DNA methylation, Agilent array-CGH platform for genomic imbalance and Affymetrix Gene 1.0 platform for gene expression analysis was used. As a result, an integrative high-resolution approach for interrogation of genome-wide tumour-specific changes in DNA methylation was developed. This approach was used to provide the first genomic DNA methylation maps, and to identify and validate genes with aberrant DNA methylation in OS cell lines. This first integrative analysis of global cancer-related changes in DNA methylation, genomic imbalance, and gene expression has provided comprehensive evidence of the cumulative roles of epigenetic and genetic mechanisms in deregulation of gene expression networks.

  6. Subsidiary-level determinants of global initiatives in multinational corporations

    NARCIS (Netherlands)

    Williams, C.

    2009-01-01

    This article examines subsidiary-level factors that promote global initiatives in MNCs. Global initiatives are a key capability of MNCs that domestic firms do not possess, yet there has been little research on how MNCs promote initiatives on a global basis. I draw principally on the knowledge-based

  7. Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping

    DEFF Research Database (Denmark)

    Zhan, Bujie; Fadista, João; Thomsen, Bo

    2011-01-01

    Background Integration of genomic variation with phenotypic information is an effective approach for uncovering genotype-phenotype associations. This requires an accurate identification of the different types of variation in individual genomes. Results We report the integration of the whole genome...... of split-read and read-pair approaches proved to be complementary in finding different signatures. CNVs were identified on the basis of the depth of sequenced reads, and by using SNP and CGH arrays. Conclusions Our results provide high resolution mapping of diverse classes of genomic variation...

  8. A system-level model for the microbial regulatory genome.

    Science.gov (United States)

    Brooks, Aaron N; Reiss, David J; Allard, Antoine; Wu, Wei-Ju; Salvanha, Diego M; Plaisier, Christopher L; Chandrasekaran, Sriram; Pan, Min; Kaur, Amardeep; Baliga, Nitin S

    2014-07-15

    Microbes can tailor transcriptional responses to diverse environmental challenges despite having streamlined genomes and a limited number of regulators. Here, we present data-driven models that capture the dynamic interplay of the environment and genome-encoded regulatory programs of two types of prokaryotes: Escherichia coli (a bacterium) and Halobacterium salinarum (an archaeon). The models reveal how the genome-wide distributions of cis-acting gene regulatory elements and the conditional influences of transcription factors at each of those elements encode programs for eliciting a wide array of environment-specific responses. We demonstrate how these programs partition transcriptional regulation of genes within regulons and operons to re-organize gene-gene functional associations in each environment. The models capture fitness-relevant co-regulation by different transcriptional control mechanisms acting across the entire genome, to define a generalized, system-level organizing principle for prokaryotic gene regulatory networks that goes well beyond existing paradigms of gene regulation. An online resource (http://egrin2.systemsbiology.net) has been developed to facilitate multiscale exploration of conditional gene regulation in the two prokaryotes. © 2014 The Authors. Published under the terms of the CC BY 4.0 license.

  9. Amplification of HER2 is a marker for global genomic instability

    International Nuclear Information System (INIS)

    Ellsworth, Rachel E; Ellsworth, Darrell L; Patney, Heather L; Deyarmin, Brenda; Love, Brad; Hooke, Jeffrey A; Shriver, Craig D

    2008-01-01

    Genomic alterations of the proto-oncogene c-erbB-2 (HER-2/neu) are associated with aggressive behavior and poor prognosis in patients with breast cancer. The variable clinical outcomes seen in patients with similar HER2 status, given similar treatments, suggests that the effects of amplification of HER2 can be influenced by other genetic changes. To assess the broader genomic implications of structural changes at the HER2 locus, we investigated relationships between genomic instability and HER2 status in patients with invasive breast cancer. HER2 status was determined using the PathVysion ® assay. DNA was extracted after laser microdissection from the 181 paraffin-embedded HER2 amplified (n = 39) or HER2 negative (n = 142) tumor specimens with sufficient tumor available to perform molecular analysis. Allelic imbalance (AI) was assessed using a panel of microsatellite markers representing 26 chromosomal regions commonly altered in breast cancer. Student t-tests and partial correlations were used to investigate relationships between genomic instability and HER2 status. The frequency of AI was significantly higher (P < 0.005) in HER2 amplified (27%) compared to HER2 negative tumors (19%). Samples with HER2 amplification showed significantly higher levels of AI (P < 0.05) at chromosomes 11q23, 16q22-q24 and 18q21. Partial correlations including ER status and tumor grade supported associations between HER2 status and alterations at 11q13.1, 16q22-q24 and 18q21. The poor prognosis associated with HER2 amplification may be attributed to global genomic instability as cells with high frequencies of chromosomal alterations have been associated with increased cellular proliferation and aggressive behavior. In addition, high levels of DNA damage may render tumor cells refractory to treatment. In addition, specific alterations at chromosomes 11q13, 16q22-q24, and 18q21, all of which have been associated with aggressive tumor behavior, may serve as genetic modifiers to HER2

  10. Genome and metagenome enabled analyses reveal new insight into the global biogeography and potential urea utilization in marine Thaumarchaeota.

    Science.gov (United States)

    Ahlgren, N.; Parada, A. E.; Fuhrman, J. A.

    2016-02-01

    Marine Thaumarchaea are an abundant, important group of marine microbial communities as they fix carbon, oxidize ammonium, and thus contribute to key N and C cycles in the oceans. From an enrichment culture, we have sequenced the complete genome of a new Thaumarchaeota strain, SPOT01. Analysis of this genome and other Thaumarchaeal genomes contributes new insight into its role in N cycling and clarifies the broader biogeography of marine Thaumarchaeal genera. Phylogenomics of Thaumarchaeota genomes reveal coherent separation into clusters roughly equivalent to the genus level, and SPOT01 represents a new genus of marine Thaumarchaea. Competitive fragment recruitment of globally distributed metagenomes from TARA, Ocean Sampling Day, and those generated from a station off California shows that the SPOT01 genus is often the most abundant genus, especially where total Thaumarchaea are most abundant in the overall community. The SPOT01 genome contains urease genes allowing it to use an alternative form of N. Genomic and metagenomic analysis also reveal that among planktonic genomes and populations, the urease genes in general are more frequently found in members of the SPOT01 genus and another genus dominant in deep waters, thus we predict these two genera contribute most significantly to urea utilization among marine Thaumarchaea. Recruitment also revealed broader biogeographic and ecological patterns of the putative genera. The SPOT01 genus was most abundant at colder temperatures (45 degrees). The genus containing Nitrosopumilus maritimus had the highest temperature range, and the genus containing Candidatus Nitrosopelagicus brevis was typically most abundant at intermediate temperatures and intermediate latitudes ( 35-45 degrees). Together these genome and metagenome enabled analyses provide significant new insight into the ecology and biogeochemical contributions of marine archaea.

  11. Genomic epidemiology of global VIM-producing Enterobacteriaceae.

    Science.gov (United States)

    Matsumura, Yasufumi; Peirano, Gisele; Devinney, Rebekah; Bradford, Patricia A; Motyl, Mary R; Adams, Mark D; Chen, Liang; Kreiswirth, Barry; Pitout, Johann D D

    2017-08-01

    International data on the molecular epidemiology of Enterobacteriaceae with VIM carbapenemases are limited. We performed short read (Illumina) WGS on a global collection of 89 VIM-producing clinical Enterobacteriaceae (2008-14). VIM-producing (11 varieties within 21 different integrons) isolates were mostly obtained from Europe. Certain integrons with bla VIM were specific to a country in different species and clonal complexes (CCs) (In 87 , In 624 , In 916 and In 1323 ), while others had spread globally among various Enterobacteriaceae species (In 110 and In 1209 ). Klebsiella pneumoniae was the most common species ( n  = 45); CC147 from Greece was the most prevalent clone and contained In 590 -like integrons with four different bla VIM s. Enterobacter cloacae complex was the second most common species and mainly consisted of Enterobacter hormaechei ( Enterobacter xiangfangensis , subsp. steigerwaltii and Hoffmann cluster III). CC200 (from Croatia and Turkey), CC114 (Croatia, Greece, Italy and the USA) and CC78 (from Greece, Italy and Spain) containing bla VIM-1 were the most common clones among the E. cloacae complex. This study highlights the importance of surveillance programmes using the latest molecular techniques in providing insight into the characteristics and global distribution of Enterobacteriaceae with bla VIM s. © The Author 2017. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  12. Genome-wide evolutionary dynamics of influenza B viruses on a global scale.

    Directory of Open Access Journals (Sweden)

    Pinky Langat

    2017-12-01

    Full Text Available The global-scale epidemiology and genome-wide evolutionary dynamics of influenza B remain poorly understood compared with influenza A viruses. We compiled a spatio-temporally comprehensive dataset of influenza B viruses, comprising over 2,500 genomes sampled worldwide between 1987 and 2015, including 382 newly-sequenced genomes that fill substantial gaps in previous molecular surveillance studies. Our contributed data increase the number of available influenza B virus genomes in Europe, Africa and Central Asia, improving the global context to study influenza B viruses. We reveal Yamagata-lineage diversity results from co-circulation of two antigenically-distinct groups that also segregate genetically across the entire genome, without evidence of intra-lineage reassortment. In contrast, Victoria-lineage diversity stems from geographic segregation of different genetic clades, with variability in the degree of geographic spread among clades. Differences between the lineages are reflected in their antigenic dynamics, as Yamagata-lineage viruses show alternating dominance between antigenic groups, while Victoria-lineage viruses show antigenic drift of a single lineage. Structural mapping of amino acid substitutions on trunk branches of influenza B gene phylogenies further supports these antigenic differences and highlights two potential mechanisms of adaptation for polymerase activity. Our study provides new insights into the epidemiological and molecular processes shaping influenza B virus evolution globally.

  13. Genome-wide evolutionary dynamics of influenza B viruses on a global scale

    Science.gov (United States)

    Langat, Pinky; Bowden, Thomas A.; Edwards, Stephanie; Gall, Astrid; Rambaut, Andrew; Daniels, Rodney S.; Russell, Colin A.; Pybus, Oliver G.; McCauley, John

    2017-01-01

    The global-scale epidemiology and genome-wide evolutionary dynamics of influenza B remain poorly understood compared with influenza A viruses. We compiled a spatio-temporally comprehensive dataset of influenza B viruses, comprising over 2,500 genomes sampled worldwide between 1987 and 2015, including 382 newly-sequenced genomes that fill substantial gaps in previous molecular surveillance studies. Our contributed data increase the number of available influenza B virus genomes in Europe, Africa and Central Asia, improving the global context to study influenza B viruses. We reveal Yamagata-lineage diversity results from co-circulation of two antigenically-distinct groups that also segregate genetically across the entire genome, without evidence of intra-lineage reassortment. In contrast, Victoria-lineage diversity stems from geographic segregation of different genetic clades, with variability in the degree of geographic spread among clades. Differences between the lineages are reflected in their antigenic dynamics, as Yamagata-lineage viruses show alternating dominance between antigenic groups, while Victoria-lineage viruses show antigenic drift of a single lineage. Structural mapping of amino acid substitutions on trunk branches of influenza B gene phylogenies further supports these antigenic differences and highlights two potential mechanisms of adaptation for polymerase activity. Our study provides new insights into the epidemiological and molecular processes shaping influenza B virus evolution globally. PMID:29284042

  14. Universal global imprints of genome growth and evolution--equivalent length and cumulative mutation density.

    Directory of Open Access Journals (Sweden)

    Hong-Da Chen

    Full Text Available BACKGROUND: Segmental duplication is widely held to be an important mode of genome growth and evolution. Yet how this would affect the global structure of genomes has been little discussed. METHODS/PRINCIPAL FINDINGS: Here, we show that equivalent length, or L(e, a quantity determined by the variance of fluctuating part of the distribution of the k-mer frequencies in a genome, characterizes the latter's global structure. We computed the L(es of 865 complete chromosomes and found that they have nearly universal but (k-dependent values. The differences among the L(e of a chromosome and those of its coding and non-coding parts were found to be slight. CONCLUSIONS: We verified that these non-trivial results are natural consequences of a genome growth model characterized by random segmental duplication and random point mutation, but not of any model whose dominant growth mechanism is not segmental duplication. Our study also indicates that genomes have a nearly universal cumulative "point" mutation density of about 0.73 mutations per site that is compatible with the relatively low mutation rates of (1-5 x 10(-3/site/Mya previously determined by sequence comparison for the human and E. coli genomes.

  15. Integrating genome-based informatics to modernize global disease monitoring, information sharing, and response

    DEFF Research Database (Denmark)

    Aarestrup, Frank Møller; Brown, Eric W; Detter, Chris

    2012-01-01

    The rapid advancement of genome technologies holds great promise for improving the quality and speed of clinical and public health laboratory investigations and for decreasing their cost. The latest generation of genome DNA sequencers can provide highly detailed and robust information on disease...... typing methods to provide point-of-care clinical diagnosis and other essential information for quicker and better treatment of patients. Provided there is free-sharing of information by all clinical and public health laboratories, these genomic tools could spawn a global system of linked databases......-causing microbes, and in the near future these technologies will be suitable for routine use in national, regional, and global public health laboratories. With additional improvements in instrumentation, these next- or third-generation sequencers are likely to replace conventional culture-based and molecular...

  16. Orthogonal stack of global tide gauge sea level data

    Science.gov (United States)

    Trupin, A.; Wahr, J.

    1990-01-01

    Yearly and monthly tide gauge sea level data from around the globe are fitted to numerically generated equilibrium tidal data to search for the 18.6 year lunar tide and 14 month pole tide. Both tides are clearly evident in the results, and their amplitudes and phases are found to be consistent with a global equilibrium response. Global, monthly sea level data from outside the Baltic sea and Gulf of Bothnia are fitted to global atmospheric pressure data to study the response of the ocean to pressure fluctuations. The response is found to be inverted barometer at periods greater than two months. Global averages of tide gauge data, after correcting for the effects of post glacial rebound on individual station records, reveal an increase in sea level over the last 80 years of between 1.1 mm/yr and 1.9 mm/yr.

  17. Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104

    DEFF Research Database (Denmark)

    Leekitcharoenphon, Pimlapas; Hendriksen, Rene S.; Le Hello, Simon

    2016-01-01

    It has been 30 years since the initial emergence and subsequent rapid global spread of multidrug-resistant Salmonella enterica serovar Typhimurium DT104 (MDR DT104). Nonetheless, its origin and transmission route have never been revealed. We used whole-genome sequencing (WGS) and temporally struc...

  18. A future scenario of the global regulatory landscape regarding genome-edited crops

    Science.gov (United States)

    Araki, Motoko

    2017-01-01

    ABSTRACT The global agricultural landscape regarding the commercial cultivation of genetically modified (GM) crops is mosaic. Meanwhile, a new plant breeding technique, genome editing is expected to make genetic engineering-mediated crop breeding more socially acceptable because it can be used to develop crop varieties without introducing transgenes, which have hampered the regulatory review and public acceptance of GM crops. The present study revealed that product- and process-based concepts have been implemented to regulate GM crops in 30 countries. Moreover, this study analyzed the regulatory responses to genome-edited crops in the USA, Argentina, Sweden and New Zealand. The findings suggested that countries will likely be divided in their policies on genome-edited crops: Some will deregulate transgene-free crops, while others will regulate all types of crops that have been modified by genome editing. These implications are discussed from the viewpoint of public acceptance. PMID:27960622

  19. Genome-wide SNP data unveils the globalization of domesticated pigs.

    Science.gov (United States)

    Yang, Bin; Cui, Leilei; Perez-Enciso, Miguel; Traspov, Aleksei; Crooijmans, Richard P M A; Zinovieva, Natalia; Schook, Lawrence B; Archibald, Alan; Gatphayak, Kesinee; Knorr, Christophe; Triantafyllidis, Alex; Alexandri, Panoraia; Semiadi, Gono; Hanotte, Olivier; Dias, Deodália; Dovč, Peter; Uimari, Pekka; Iacolina, Laura; Scandura, Massimo; Groenen, Martien A M; Huang, Lusheng; Megens, Hendrik-Jan

    2017-09-21

    Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection. A deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection. Key events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past

  20. Global change and the measurement of absolute sea-level

    Science.gov (United States)

    Diamante, John M.; Pyle, Thomas E.; Carter, William E.; Scherer, Wolfgang

    To quantify properly the long-term response of sea-level to climate change, land motions must be separated from the apparent or relative sea-level change recorded by conventional tide/sea-level gauges. Here we present a concept for global measurement of the true or “absolute” sea-level change, which combines recent advances in space-based geodetic techniques with plans for a global sea-level network under the World Climate Research Programme (WCRP). Data from initial feasibility tests show that land motion, due to global (plate tectonic), regional (glacial rebound), or local (fluid withdrawal) effects, can probably be measured to ±1cm (on a single measurement basis) by an innovative combination of Very Long Baseline Interferometry (VLBI) and Global Positioning System (GPS) tevhniques. By making repeated observations of position at a number of tide gauges using portable, economical GPS receivers in a differential mode relative to the fewer, more stable, but more expensive VLBI observatories, it will be possible to subtract land motion from the relative sea-level signal. Decadal to century scale trends at the 1-2mm y -1 level will be resolvable in the sea-level and vertical land motion time series within about a decade. Detection of subsidence or uplift at specific gauges will allow correction for land motion or deletion of bad data when computing regional or global, i.e. eustatic, sea-level changes. In addition to their applications in oceanography and climate studies, such data will test models by Peltier and other that relate mantle viscosity and deglaciation history to present rates of crustal subsidence or uplift. If the predicted crustal motions are confirmed, we can also have more confidence in the use of historical tide/sea-level gauge records in retrospective studies of sea-level change related to climate variability on decadal or longer time scales. It is concluded that as few as one-third (about 100) of the total number of tide/sea-level gauges (250

  1. Separating decadal global water cycle variability from sea level rise.

    Science.gov (United States)

    Hamlington, B D; Reager, J T; Lo, M-H; Karnauskas, K B; Leben, R R

    2017-04-20

    Under a warming climate, amplification of the water cycle and changes in precipitation patterns over land are expected to occur, subsequently impacting the terrestrial water balance. On global scales, such changes in terrestrial water storage (TWS) will be reflected in the water contained in the ocean and can manifest as global sea level variations. Naturally occurring climate-driven TWS variability can temporarily obscure the long-term trend in sea level rise, in addition to modulating the impacts of sea level rise through natural periodic undulation in regional and global sea level. The internal variability of the global water cycle, therefore, confounds both the detection and attribution of sea level rise. Here, we use a suite of observations to quantify and map the contribution of TWS variability to sea level variability on decadal timescales. In particular, we find that decadal sea level variability centered in the Pacific Ocean is closely tied to low frequency variability of TWS in key areas across the globe. The unambiguous identification and clean separation of this component of variability is the missing step in uncovering the anthropogenic trend in sea level and understanding the potential for low-frequency modulation of future TWS impacts including flooding and drought.

  2. Global tracker for the ALICE high level trigger

    International Nuclear Information System (INIS)

    Vik, Thomas

    2006-01-01

    This thesis deals with two main topics. The first is the implementation and testing of a Kalman filter algorithm in the HLT (High Level Trigger) reconstruction code. This will perform the global tracking in the HLT, that is merging tracklets and hits from the different sub-detectors in the central barrel detector. The second topic is a trigger mode of the HLT which uses the global tracking of particles through the TRD (Transition Radiation Detector), TPC (Time Projection Chamber) and the ITS (Inner Tracking System): The dielectron trigger. Global tracking: The Kalman filter algorithm has been introduced to the HLT tracking scheme. (Author)

  3. Estimating Solar Energy Potential in Buildings on a Global Level

    DEFF Research Database (Denmark)

    Petrichenko, Ksenia

    2015-01-01

    This chapter contributes to the debate around net-zero energy concept from a global perspective. By means of comprehensive modelling, it analyses how much global building energy consumption could be reduced through utilisation of building-integrated solar energy technologies and energy......-efficiency improvements. Valuable insights on the locations and building types, in which it is feasible to achieve a net-zero level of energy performance through solar energy utilisation, are presented in world maps....

  4. The multimillennial sea-level commitment of global warming.

    Science.gov (United States)

    Levermann, Anders; Clark, Peter U; Marzeion, Ben; Milne, Glenn A; Pollard, David; Radic, Valentina; Robinson, Alexander

    2013-08-20

    Global mean sea level has been steadily rising over the last century, is projected to increase by the end of this century, and will continue to rise beyond the year 2100 unless the current global mean temperature trend is reversed. Inertia in the climate and global carbon system, however, causes the global mean temperature to decline slowly even after greenhouse gas emissions have ceased, raising the question of how much sea-level commitment is expected for different levels of global mean temperature increase above preindustrial levels. Although sea-level rise over the last century has been dominated by ocean warming and loss of glaciers, the sensitivity suggested from records of past sea levels indicates important contributions should also be expected from the Greenland and Antarctic Ice Sheets. Uncertainties in the paleo-reconstructions, however, necessitate additional strategies to better constrain the sea-level commitment. Here we combine paleo-evidence with simulations from physical models to estimate the future sea-level commitment on a multimillennial time scale and compute associated regional sea-level patterns. Oceanic thermal expansion and the Antarctic Ice Sheet contribute quasi-linearly, with 0.4 m °C(-1) and 1.2 m °C(-1) of warming, respectively. The saturation of the contribution from glaciers is overcompensated by the nonlinear response of the Greenland Ice Sheet. As a consequence we are committed to a sea-level rise of approximately 2.3 m °C(-1) within the next 2,000 y. Considering the lifetime of anthropogenic greenhouse gases, this imposes the need for fundamental adaptation strategies on multicentennial time scales.

  5. An object model for genome information at all levels of resolution

    Energy Technology Data Exchange (ETDEWEB)

    Honda, S.; Parrott, N.W.; Smith, R.; Lawrence, C.

    1993-12-31

    An object model for genome data at all levels of resolution is described. The model was derived by considering the requirements for representing genome related objects in three application domains: genome maps, large-scale DNA sequencing, and exploring functional information in gene and protein sequences. The methodology used for the object-oriented analysis is also described.

  6. Global insights into acetic acid resistance mechanisms and genetic stability of Acetobacter pasteurianus strains by comparative genomics

    Science.gov (United States)

    Wang, Bin; Shao, Yanchun; Chen, Tao; Chen, Wanping; Chen, Fusheng

    2015-12-01

    Acetobacter pasteurianus (Ap) CICC 20001 and CGMCC 1.41 are two acetic acid bacteria strains that, because of their strong abilities to produce and tolerate high concentrations of acetic acid, have been widely used to brew vinegar in China. To globally understand the fermentation characteristics, acid-tolerant mechanisms and genetic stabilities, their genomes were sequenced. Genomic comparisons with 9 other sequenced Ap strains revealed that their chromosomes were evolutionarily conserved, whereas the plasmids were unique compared with other Ap strains. Analysis of the acid-tolerant metabolic pathway at the genomic level indicated that the metabolism of some amino acids and the known mechanisms of acetic acid tolerance, might collaboratively contribute to acetic acid resistance in Ap strains. The balance of instability factors and stability factors in the genomes of Ap CICC 20001 and CGMCC 1.41 strains might be the basis for their genetic stability, consistent with their stable industrial performances. These observations provide important insights into the acid resistance mechanism and the genetic stability of Ap strains and lay a foundation for future genetic manipulation and engineering of these two strains.

  7. A multistep damage recognition mechanism for global genomic nucleotide excision repair.

    Science.gov (United States)

    Sugasawa, K; Okamoto, T; Shimizu, Y; Masutani, C; Iwai, S; Hanaoka, F

    2001-03-01

    A mammalian nucleotide excision repair (NER) factor, the XPC-HR23B complex, can specifically bind to certain DNA lesions and initiate the cell-free repair reaction. Here we describe a detailed analysis of its binding specificity using various DNA substrates, each containing a single defined lesion. A highly sensitive gel mobility shift assay revealed that XPC-HR23B specifically binds a small bubble structure with or without damaged bases, whereas dual incision takes place only when damage is present in the bubble. This is evidence that damage recognition for NER is accomplished through at least two steps; XPC-HR23B first binds to a site that has a DNA helix distortion, and then the presence of injured bases is verified prior to dual incision. Cyclobutane pyrimidine dimers (CPDs) were hardly recognized by XPC-HR23B, suggesting that additional factors may be required for CPD recognition. Although the presence of mismatched bases opposite a CPD potentiated XPC-HR23B binding, probably due to enhancement of the helix distortion, cell-free excision of such compound lesions was much more efficient than expected from the observed affinity for XPC-HR23B. This also suggests that additional factors and steps are required for the recognition of some types of lesions. A multistep mechanism of this sort may provide a molecular basis for ensuring the high level of damage discrimination that is required for global genomic NER.

  8. Global copy number profiling of cancer genomes | Office of Cancer Genomics

    Science.gov (United States)

    In this article, we introduce a robust and efficient strategy for deriving global and allele-specific copy number alternations (CNA) from cancer whole exome sequencing data based on Log R ratios and B-allele frequencies. Applying the approach to the analysis of over 200 skin cancer samples, we demonstrate its utility for discovering distinct CNA events and for deriving ancillary information such as tumor purity. Availability and implementation: https://github.com/xfwang/CLOSE CONTACT: xuefeng.wang@stonybrook.edu or michael.krauthammer@yale.edu. (Publication Abstract)

  9. Levels of Product Differentiation in the Global Mobile Phones Market

    OpenAIRE

    Andonov, Stanimir

    2006-01-01

    The sixth product level called compliant product is a connecting element between the physical product characteristics and the strategy of the producer company. The article discusses the differentiation among the product offers of companies working in the global markets, as well as the strategies which they use and could use in that respect.

  10. Core Genome Multilocus Sequence Typing for Identification of Globally Distributed Clonal Groups and Differentiation of Outbreak Strains of Listeria monocytogenes.

    Science.gov (United States)

    Chen, Yi; Gonzalez-Escalona, Narjol; Hammack, Thomas S; Allard, Marc W; Strain, Errol A; Brown, Eric W

    2016-10-15

    Many listeriosis outbreaks are caused by a few globally distributed clonal groups, designated clonal complexes or epidemic clones, of Listeria monocytogenes, several of which have been defined by classic multilocus sequence typing (MLST) schemes targeting 6 to 8 housekeeping or virulence genes. We have developed and evaluated core genome MLST (cgMLST) schemes and applied them to isolates from multiple clonal groups, including those associated with 39 listeriosis outbreaks. The cgMLST clusters were congruent with MLST-defined clonal groups, which had various degrees of diversity at the whole-genome level. Notably, cgMLST could distinguish among outbreak strains and epidemiologically unrelated strains of the same clonal group, which could not be achieved using classic MLST schemes. The precise selection of cgMLST gene targets may not be critical for the general identification of clonal groups and outbreak strains. cgMLST analyses further identified outbreak strains, including those associated with recent outbreaks linked to contaminated French-style cheese, Hispanic-style cheese, stone fruit, caramel apple, ice cream, and packaged leafy green salad, as belonging to major clonal groups. We further developed lineage-specific cgMLST schemes, which can include accessory genes when core genomes do not possess sufficient diversity, and this provided additional resolution over species-specific cgMLST. Analyses of isolates from different common-source listeriosis outbreaks revealed various degrees of diversity, indicating that the numbers of allelic differences should always be combined with cgMLST clustering and epidemiological evidence to define a listeriosis outbreak. Classic multilocus sequence typing (MLST) schemes targeting internal fragments of 6 to 8 genes that define clonal complexes or epidemic clones have been widely employed to study L. monocytogenes biodiversity and its relation to pathogenicity potential and epidemiology. We demonstrated that core genome MLST

  11. Global mapping of nonseismic sea level oscillations at tsunami timescales.

    Science.gov (United States)

    Vilibić, Ivica; Šepić, Jadranka

    2017-01-18

    Present investigations of sea level extremes are based on hourly data measured at coastal tide gauges. The use of hourly data restricts existing global and regional analyses to periods larger than 2 h. However, a number of processes occur at minute timescales, of which the most ruinous are tsunamis. Meteotsunamis, hazardous nonseismic waves that occur at tsunami timescales over limited regions, may also locally dominate sea level extremes. Here, we show that nonseismic sea level oscillations at tsunami timescales (sea level extremes, up to 50% in low-tidal basins. The intensity of these oscillations is zonally correlated with mid-tropospheric winds at the 99% significance level, with the variance doubling from the tropics and subtropics to the mid-latitudes. Specific atmospheric patterns are found during strong events at selected locations in the World Ocean, indicating a globally predominant generation mechanism. Our analysis suggests that these oscillations should be considered in sea level hazard assessment studies. Establishing a strong correlation between nonseismic sea level oscillations at tsunami timescales and atmospheric synoptic patterns would allow for forecasting of nonseismic sea level oscillations for operational use, as well as hindcasting and projection of their effects under past, present and future climates.

  12. Stability of XIST repression in relation to genomic imprinting following global genome demethylation in a human cell line

    International Nuclear Information System (INIS)

    Araújo, E.S.S. de; Vasques, L.R.; Stabellini, R.; Krepischi, A.C.V.; Pereira, L.V.

    2014-01-01

    DNA methylation is essential in X chromosome inactivation and genomic imprinting, maintaining repression of XIST in the active X chromosome and monoallelic repression of imprinted genes. Disruption of the DNA methyltransferase genes DNMT1 and DNMT3B in the HCT116 cell line (DKO cells) leads to global DNA hypomethylation and biallelic expression of the imprinted gene IGF2 but does not lead to reactivation of XIST expression, suggesting that XIST repression is due to a more stable epigenetic mark than imprinting. To test this hypothesis, we induced acute hypomethylation in HCT116 cells by 5-aza-2′-deoxycytidine (5-aza-CdR) treatment (HCT116-5-aza-CdR) and compared that to DKO cells, evaluating DNA methylation by microarray and monitoring the expression of XIST and imprinted genes IGF2, H19, and PEG10. Whereas imprinted genes showed biallelic expression in HCT116-5-aza-CdR and DKO cells, the XIST locus was hypomethylated and weakly expressed only under acute hypomethylation conditions, indicating the importance of XIST repression in the active X to cell survival. Given that DNMT3A is the only active DNMT in DKO cells, it may be responsible for ensuring the repression of XIST in those cells. Taken together, our data suggest that XIST repression is more tightly controlled than genomic imprinting and, at least in part, is due to DNMT3A

  13. Stability of XIST repression in relation to genomic imprinting following global genome demethylation in a human cell line

    Energy Technology Data Exchange (ETDEWEB)

    Araújo, E.S.S. de [Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP (Brazil); Centro Internacional de Pesquisa, A.C. Camargo Cancer Center, São Paulo, SP (Brazil); Vasques, L.R. [Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP (Brazil); Stabellini, R.; Krepischi, A.C.V. [Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP (Brazil); Centro Internacional de Pesquisa, A.C. Camargo Cancer Center, São Paulo, SP (Brazil); Pereira, L.V. [Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP (Brazil)

    2014-10-17

    DNA methylation is essential in X chromosome inactivation and genomic imprinting, maintaining repression of XIST in the active X chromosome and monoallelic repression of imprinted genes. Disruption of the DNA methyltransferase genes DNMT1 and DNMT3B in the HCT116 cell line (DKO cells) leads to global DNA hypomethylation and biallelic expression of the imprinted gene IGF2 but does not lead to reactivation of XIST expression, suggesting that XIST repression is due to a more stable epigenetic mark than imprinting. To test this hypothesis, we induced acute hypomethylation in HCT116 cells by 5-aza-2′-deoxycytidine (5-aza-CdR) treatment (HCT116-5-aza-CdR) and compared that to DKO cells, evaluating DNA methylation by microarray and monitoring the expression of XIST and imprinted genes IGF2, H19, and PEG10. Whereas imprinted genes showed biallelic expression in HCT116-5-aza-CdR and DKO cells, the XIST locus was hypomethylated and weakly expressed only under acute hypomethylation conditions, indicating the importance of XIST repression in the active X to cell survival. Given that DNMT3A is the only active DNMT in DKO cells, it may be responsible for ensuring the repression of XIST in those cells. Taken together, our data suggest that XIST repression is more tightly controlled than genomic imprinting and, at least in part, is due to DNMT3A.

  14. Global Gene Expression Profiling of Human Genome Following Exposure to Sarin and Soman

    International Nuclear Information System (INIS)

    Gopalakrishnakone, P.; Pachiappan, A.; Srinivasan, K. N.; Loke, W. K.; Lee, F. K.

    2007-01-01

    Toxicogenomics merges genomics with toxicology is a rapidly expanding field on the assumption that the transcriptional responses of cells to different toxic exposure are sufficiently distinct robust and reproducible to discriminate toxin from different families/classes which can be called as 'fingerprints' or 'Atlases'. In this study chemical weapons sarin was studied in a time and dose dependent manner after exposure to human neuroblastoma cell line. (Sarin or GB) exerts its effect through inhibition of acetylcholinesterase activity and induction of delayed neurotoxicity in a dose [EC 50 50 ppm, (around 372.4 μM)] and time-dependent manner. The effect and/or the mechanism of single or repeated exposures to GB, however, are less clear and yet to be explored at cellular level. The present study aims to scrutinize, the global gene expression profile following sarin toxicity in neuronal cells using Affymetrix-GeneChips. A tim-course study on the effect of a single (3 or 24h) or repeated (24 or 48h) doses of sarin (5ppm) on SHSY5Y cells was carried out. Using GeneSpring (PCA) analysis, 550 genes whose expression was significantly (p less than 0.01) altered by at least 2.5-fold, were selected. The results indicate that the low-level single dose exposure do not always parallel acute toxicity, but can cause a reversible down-regulation of genes and a range of anti-cholinesterase effects. In contrast, repeated doses produced persistent irreversible down-regulation of genes related to neurodegenerative mechanism at 48h. Real-time PCR and western blot analysis confirmed the reduced expression of presenilin 1 (TMP21), 2 and dopa.decarboxylase (DDC) mRNA and proteins. Besides providing an in vitro experimental model for studies on the neuropathophysiology and brain cells this investigation indicate possible mechanisms by which sarin could mediate neuro-degeneration. A comparison will be made with similar study with soman. (author)

  15. Switching between global and local levels: the level repetition effect and its hemispheric asymmetry

    Science.gov (United States)

    Kéïta, Luc; Bedoin, Nathalie; Burack, Jacob A.; Lepore, Franco

    2014-01-01

    The global level of hierarchical stimuli (Navon’s stimuli) is typically processed quicker and better than the local level; further differential hemispheric dominance is described for local (left hemisphere, LH) and global (right hemisphere, RH) processing. However, neuroimaging and behavioral data indicate that stimulus category (letter or object) could modulate the hemispheric asymmetry for the local level processing. Besides, when the targets are unpredictably displayed at the global or local level, the participant has to switch between levels, and the magnitude of the switch cost increases with the number of repeated-level trials preceding the switch. The hemispheric asymmetries associated with level switching is an unresolved issue. LH areas may be involved in carrying over the target level information in case of level repetition. These areas may also largely participate in the processing of level-changed trials. Here we hypothesized that RH areas underly the inhibitory mechanism performed on the irrelevant level, as one of the components of the level switching process. In an experiment using a within-subject design, hierarchical stimuli were briefly presented either to the right or to the left visual field. 32 adults were instructed to identify the target at the global or local level. We assessed a possible RH dominance for the non-target level inhibition by varying the attentional demands through the manipulation of level repetitions (two or gour repeated-level trials before the switch). The behavioral data confirmed a LH specialization only for the local level processing of letter-based stimuli, and detrimental effect of increased level repetitions before a switch. Further, data provides evidence for a RH advantage in inhibiting the non-target level. Taken together, the data supports the notion of the existence of multiple mechanisms underlying level-switch effects. PMID:24723903

  16. INTEGRATED MECHANISMS FOR APROACHING PRIORITY ENVIRONMENTAL ISSUES AT GLOBAL LEVEL

    Directory of Open Access Journals (Sweden)

    iLDIKO iOAN

    2011-03-01

    Full Text Available Integrated mechanisms for approaching priority environmentalissues at global level. At global level, there are considered priorityenvironmental issues two interdependent processes that are essential for thesupport the processes that provide living conditions and wellbeing for the entirehumankind: climate change and loss of biodiversity. Payments of ecosystemservices became already well-known and applied economic instruments, althoughthere are still many uncertainties in the knowledge of eco-economic interdependencies.The paper discusses these aspects in the first part highlighting advantagesand disadvantages, while in the second part there is analyzed an integratedprogram of the United Nations, which was designed for making progress towardboth climate change, and loss of biodiversity. The REDD program – Reduction ofEmissions from Deforestation and forest Degradation – is addressed to developingcountries and it started in 2008. Based on assessment reports we will try toformulate a number of conclusions regarding the program’s effectiveness.

  17. The Level-1 Global Muon Trigger for the CMS Experiment

    OpenAIRE

    Sakulin, H; Taurok, Anton

    2003-01-01

    The three independent Level-1 muon trigger systems in CMS deliver up to 16 muon candidates per bunch crossing, each described by transverse momentum, direction, charge and quality. The Global Muon Trigger combines these measurements in order to find the best four muon candidates in the entire detector and attaches bits from the calorimeter trigger to denote calorimetric isolation and confirmation. A single-board logic design is presented: via a special front panel and a custom back plane more...

  18. Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey

    Directory of Open Access Journals (Sweden)

    Varala Kranthi

    2007-05-01

    Full Text Available Abstract Background Extensive computational and database tools are available to mine genomic and genetic databases for model organisms, but little genomic data is available for many species of ecological or agricultural significance, especially those with large genomes. Genome surveys using conventional sequencing techniques are powerful, particularly for detecting sequences present in many copies per genome. However these methods are time-consuming and have potential drawbacks. High throughput 454 sequencing provides an alternative method by which much information can be gained quickly and cheaply from high-coverage surveys of genomic DNA. Results We sequenced 78 million base-pairs of randomly sheared soybean DNA which passed our quality criteria. Computational analysis of the survey sequences provided global information on the abundant repetitive sequences in soybean. The sequence was used to determine the copy number across regions of large genomic clones or contigs and discover higher-order structures within satellite repeats. We have created an annotated, online database of sequences present in multiple copies in the soybean genome. The low bias of pyrosequencing against repeat sequences is demonstrated by the overall composition of the survey data, which matches well with past estimates of repetitive DNA content obtained by DNA re-association kinetics (Cot analysis. Conclusion This approach provides a potential aid to conventional or shotgun genome assembly, by allowing rapid assessment of copy number in any clone or clone-end sequence. In addition, we show that partial sequencing can provide access to partial protein-coding sequences.

  19. Unique features of a global human ectoparasite identified through sequencing of the bed bug genome.

    Science.gov (United States)

    Benoit, Joshua B; Adelman, Zach N; Reinhardt, Klaus; Dolan, Amanda; Poelchau, Monica; Jennings, Emily C; Szuter, Elise M; Hagan, Richard W; Gujar, Hemant; Shukla, Jayendra Nath; Zhu, Fang; Mohan, M; Nelson, David R; Rosendale, Andrew J; Derst, Christian; Resnik, Valentina; Wernig, Sebastian; Menegazzi, Pamela; Wegener, Christian; Peschel, Nicolai; Hendershot, Jacob M; Blenau, Wolfgang; Predel, Reinhard; Johnston, Paul R; Ioannidis, Panagiotis; Waterhouse, Robert M; Nauen, Ralf; Schorn, Corinna; Ott, Mark-Christoph; Maiwald, Frank; Johnston, J Spencer; Gondhalekar, Ameya D; Scharf, Michael E; Peterson, Brittany F; Raje, Kapil R; Hottel, Benjamin A; Armisén, David; Crumière, Antonin Jean Johan; Refki, Peter Nagui; Santos, Maria Emilia; Sghaier, Essia; Viala, Sèverine; Khila, Abderrahman; Ahn, Seung-Joon; Childers, Christopher; Lee, Chien-Yueh; Lin, Han; Hughes, Daniel S T; Duncan, Elizabeth J; Murali, Shwetha C; Qu, Jiaxin; Dugan, Shannon; Lee, Sandra L; Chao, Hsu; Dinh, Huyen; Han, Yi; Doddapaneni, Harshavardhan; Worley, Kim C; Muzny, Donna M; Wheeler, David; Panfilio, Kristen A; Vargas Jentzsch, Iris M; Vargo, Edward L; Booth, Warren; Friedrich, Markus; Weirauch, Matthew T; Anderson, Michelle A E; Jones, Jeffery W; Mittapalli, Omprakash; Zhao, Chaoyang; Zhou, Jing-Jiang; Evans, Jay D; Attardo, Geoffrey M; Robertson, Hugh M; Zdobnov, Evgeny M; Ribeiro, Jose M C; Gibbs, Richard A; Werren, John H; Palli, Subba R; Schal, Coby; Richards, Stephen

    2016-02-02

    The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host-symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human-bed bug and symbiont-bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite.

  20. Unique features of a global human ectoparasite identified through sequencing of the bed bug genome

    Science.gov (United States)

    Benoit, Joshua B.; Adelman, Zach N.; Reinhardt, Klaus; Dolan, Amanda; Poelchau, Monica; Jennings, Emily C.; Szuter, Elise M.; Hagan, Richard W.; Gujar, Hemant; Shukla, Jayendra Nath; Zhu, Fang; Mohan, M.; Nelson, David R.; Rosendale, Andrew J.; Derst, Christian; Resnik, Valentina; Wernig, Sebastian; Menegazzi, Pamela; Wegener, Christian; Peschel, Nicolai; Hendershot, Jacob M.; Blenau, Wolfgang; Predel, Reinhard; Johnston, Paul R.; Ioannidis, Panagiotis; Waterhouse, Robert M.; Nauen, Ralf; Schorn, Corinna; Ott, Mark-Christoph; Maiwald, Frank; Johnston, J. Spencer; Gondhalekar, Ameya D.; Scharf, Michael E.; Peterson, Brittany F.; Raje, Kapil R.; Hottel, Benjamin A.; Armisén, David; Crumière, Antonin Jean Johan; Refki, Peter Nagui; Santos, Maria Emilia; Sghaier, Essia; Viala, Sèverine; Khila, Abderrahman; Ahn, Seung-Joon; Childers, Christopher; Lee, Chien-Yueh; Lin, Han; Hughes, Daniel S. T.; Duncan, Elizabeth J.; Murali, Shwetha C.; Qu, Jiaxin; Dugan, Shannon; Lee, Sandra L.; Chao, Hsu; Dinh, Huyen; Han, Yi; Doddapaneni, Harshavardhan; Worley, Kim C.; Muzny, Donna M.; Wheeler, David; Panfilio, Kristen A.; Vargas Jentzsch, Iris M.; Vargo, Edward L.; Booth, Warren; Friedrich, Markus; Weirauch, Matthew T.; Anderson, Michelle A. E.; Jones, Jeffery W.; Mittapalli, Omprakash; Zhao, Chaoyang; Zhou, Jing-Jiang; Evans, Jay D.; Attardo, Geoffrey M.; Robertson, Hugh M.; Zdobnov, Evgeny M.; Ribeiro, Jose M. C.; Gibbs, Richard A.; Werren, John H.; Palli, Subba R.; Schal, Coby; Richards, Stephen

    2016-01-01

    The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host–symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human–bed bug and symbiont–bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite. PMID:26836814

  1. Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species.

    Science.gov (United States)

    Teeling, Emma C; Vernes, Sonja C; Dávalos, Liliana M; Ray, David A; Gilbert, M Thomas P; Myers, Eugene

    2018-02-15

    Bats are unique among mammals, possessing some of the rarest mammalian adaptations, including true self-powered flight, laryngeal echolocation, exceptional longevity, unique immunity, contracted genomes, and vocal learning. They provide key ecosystem services, pollinating tropical plants, dispersing seeds, and controlling insect pest populations, thus driving healthy ecosystems. They account for more than 20% of all living mammalian diversity, and their crown-group evolutionary history dates back to the Eocene. Despite their great numbers and diversity, many species are threatened and endangered. Here we announce Bat1K, an initiative to sequence the genomes of all living bat species (n∼1,300) to chromosome-level assembly. The Bat1K genome consortium unites bat biologists (>148 members as of writing), computational scientists, conservation organizations, genome technologists, and any interested individuals committed to a better understanding of the genetic and evolutionary mechanisms that underlie the unique adaptations of bats. Our aim is to catalog the unique genetic diversity present in all living bats to better understand the molecular basis of their unique adaptations; uncover their evolutionary history; link genotype with phenotype; and ultimately better understand, promote, and conserve bats. Here we review the unique adaptations of bats and highlight how chromosome-level genome assemblies can uncover the molecular basis of these traits. We present a novel sequencing and assembly strategy and review the striking societal and scientific benefits that will result from the Bat1K initiative.

  2. Sea level oscillations over minute timescales: a global perspective

    Science.gov (United States)

    Vilibic, Ivica; Sepic, Jadranka

    2016-04-01

    Sea level oscillations occurring over minutes to a few hours are an important contributor to sea level extremes, and a knowledge on their behaviour is essential for proper quantification of coastal marine hazards. Tsunamis, meteotsunamis, infra-gravity waves and harbour oscillations may even dominate sea level extremes in certain areas and thus pose a great danger for humans and coastal infrastructure. Aside for tsunamis, which are, due to their enormous impact to the coastlines, a well-researched phenomena, the importance of other high-frequency oscillations to the sea level extremes is still underrated, as no systematic long-term measurements have been carried out at a minute timescales. Recently, Intergovernmental Oceanographic Commission (IOC) established Sea Level Monitoring Facility portal (http://www.ioc-sealevelmonitoring.org), making 1-min sea level data publicly available for several hundred tide gauge sites in the World Ocean. Thereafter, a global assessment of oscillations over tsunami timescales become possible; however, the portal contains raw sea level data only, being unchecked for spikes, shifts, drifts and other malfunctions of instruments. We present a quality assessment of these data, estimates of sea level variances and contributions of high-frequency processes to the extremes throughout the World Ocean. This is accompanied with assessment of atmospheric conditions and processes which generate intense high-frequency oscillations.

  3. Low levels of LTR retrotransposon deletion by ectopic recombination in the gigantic genomes of salamanders.

    Science.gov (United States)

    Frahry, Matthew Blake; Sun, Cheng; Chong, Rebecca A; Mueller, Rachel Lockridge

    2015-02-01

    Across the tree of life, species vary dramatically in nuclear genome size. Mutations that add or remove sequences from genomes-insertions or deletions, or indels-are the ultimate source of this variation. Differences in the tempo and mode of insertion and deletion across taxa have been proposed to contribute to evolutionary diversity in genome size. Among vertebrates, most of the largest genomes are found within the salamanders, an amphibian clade with genome sizes ranging from ~14 to ~120 Gb. Salamander genomes have been shown to experience slower rates of DNA loss through small (i.e., genomes. However, no studies have addressed DNA loss from salamander genomes resulting from larger deletions. Here, we focus on one type of large deletion-ectopic-recombination-mediated removal of LTR retrotransposon sequences. In ectopic recombination, double-strand breaks are repaired using a "wrong" (i.e., ectopic, or non-allelic) template sequence-typically another locus of similar sequence. When breaks occur within the LTR portions of LTR retrotransposons, ectopic-recombination-mediated repair can produce deletions that remove the internal transposon sequence and the equivalent of one of the two LTR sequences. These deletions leave a signature in the genome-a solo LTR sequence. We compared levels of solo LTRs in the genomes of four salamander species with levels present in five vertebrates with smaller genomes. Our results demonstrate that salamanders have low levels of solo LTRs, suggesting that ectopic-recombination-mediated deletion of LTR retrotransposons occurs more slowly than in other vertebrates with smaller genomes.

  4. Diversity and Genome Analysis of Australian and Global Oilseed Brassica napus L. Germplasm Using Transcriptomics and Whole Genome Re-sequencing

    Directory of Open Access Journals (Sweden)

    M. Michelle Malmberg

    2018-04-01

    Full Text Available Intensive breeding of Brassica napus has resulted in relatively low diversity, such that B. napus would benefit from germplasm improvement schemes that sustain diversity. As such, samples representative of global germplasm pools need to be assessed for existing population structure, diversity and linkage disequilibrium (LD. Complexity reduction genotyping-by-sequencing (GBS methods, including GBS-transcriptomics (GBS-t, enable cost-effective screening of a large number of samples, while whole genome re-sequencing (WGR delivers the ability to generate large numbers of unbiased genomic single nucleotide polymorphisms (SNPs, and identify structural variants (SVs. Furthermore, the development of genomic tools based on whole genomes representative of global oilseed diversity and orientated by the reference genome has substantial industry relevance and will be highly beneficial for canola breeding. As recent studies have focused on European and Chinese varieties, a global diversity panel as well as a substantial number of Australian spring types were included in this study. Focusing on industry relevance, 633 varieties were initially genotyped using GBS-t to examine population structure using 61,037 SNPs. Subsequently, 149 samples representative of global diversity were selected for WGR and both data sets used for a side-by-side evaluation of diversity and LD. The WGR data was further used to develop genomic resources consisting of a list of 4,029,750 high-confidence SNPs annotated using SnpEff, and SVs in the form of 10,976 deletions and 2,556 insertions. These resources form the basis of a reliable and repeatable system allowing greater integration between canola genomics studies, with a strong focus on breeding germplasm and industry applicability.

  5. Genetic and genomic interactions of animals with different ploidy levels.

    Science.gov (United States)

    Bogart, J P; Bi, K

    2013-01-01

    Polyploid animals have independently evolved from diploids in diverse taxa across the tree of life. We review a few polyploid animal species or biotypes where recently developed molecular and cytogenetic methods have significantly improved our understanding of their genetics, reproduction and evolution. Mitochondrial sequences that target the maternal ancestor of a polyploid show that polyploids may have single (e.g. unisexual salamanders in the genus Ambystoma) or multiple (e.g. parthenogenetic polyploid lizards in the genus Aspidoscelis) origins. Microsatellites are nuclear markers that can be used to analyze genetic recombinations, reproductive modes (e.g. Ambystoma) and recombination events (e.g. polyploid frogs such as Pelophylax esculentus). Hom(e)ologous chromosomes and rare intergenomic exchanges in allopolyploids have been distinguished by applying genome-specific fluorescent probes to chromosome spreads. Polyploids arise, and are maintained, through perturbations of the 'normal' meiotic program that would include pre-meiotic chromosome replication and genomic integrity of homologs. When possible, asexual, unisexual and bisexual polyploid species or biotypes interact with diploid relatives, and genes are passed from diploid to polyploid gene pools, which increase genetic diversity and ultimately evolutionary flexibility in the polyploid. When diploid relatives do not exist, polyploids can interact with another polyploid (e.g. species of African Clawed Frogs in the genus Xenopus). Some polyploid fish (e.g. salmonids) and frogs (Xenopus) represent independent lineages whose ancestors experienced whole genome duplication events. Some tetraploid frogs (P. esculentus) and fish (Squaliusalburnoides) may be in the process of becoming independent species, but diploid and triploid forms of these 'species' continue to genetically interact with the comparatively few tetraploid populations. Genetic and genomic interaction between polyploids and diploids is a complex

  6. Low level genome mistranslations deregulate the transcriptome and translatome and generate proteotoxic stress in yeast

    Directory of Open Access Journals (Sweden)

    Paredes João A

    2012-06-01

    Full Text Available Abstract Background Organisms use highly accurate molecular processes to transcribe their genes and a variety of mRNA quality control and ribosome proofreading mechanisms to maintain intact the fidelity of genetic information flow. Despite this, low level gene translational errors induced by mutations and environmental factors cause neurodegeneration and premature death in mice and mitochondrial disorders in humans. Paradoxically, such errors can generate advantageous phenotypic diversity in fungi and bacteria through poorly understood molecular processes. Results In order to clarify the biological relevance of gene translational errors we have engineered codon misreading in yeast and used profiling of total and polysome-associated mRNAs, molecular and biochemical tools to characterize the recombinant cells. We demonstrate here that gene translational errors, which have negligible impact on yeast growth rate down-regulate protein synthesis, activate the unfolded protein response and environmental stress response pathways, and down-regulate chaperones linked to ribosomes. Conclusions We provide the first global view of transcriptional and post-transcriptional responses to global gene translational errors and we postulate that they cause gradual cell degeneration through synergistic effects of overloading protein quality control systems and deregulation of protein synthesis, but generate adaptive phenotypes in unicellular organisms through activation of stress cross-protection. We conclude that these genome wide gene translational infidelities can be degenerative or adaptive depending on cellular context and physiological condition.

  7. The mitochondrial genome of Phallusia mammillata and Phallusia fumigata (Tunicata, Ascidiacea: high genome plasticity at intra-genus level

    Directory of Open Access Journals (Sweden)

    Pesole Graziano

    2007-08-01

    Full Text Available Abstract Background Within Chordata, the subphyla Vertebrata and Cephalochordata (lancelets are characterized by a remarkable stability of the mitochondrial (mt genome, with constancy of gene content and almost invariant gene order, whereas the limited mitochondrial data on the subphylum Tunicata suggest frequent and extensive gene rearrangements, observed also within ascidians of the same genus. Results To confirm this evolutionary trend and to better understand the evolutionary dynamics of the mitochondrial genome in Tunicata Ascidiacea, we have sequenced and characterized the complete mt genome of two congeneric ascidian species, Phallusia mammillata and Phallusia fumigata (Phlebobranchiata, Ascidiidae. The two mtDNAs are surprisingly rearranged, both with respect to one another and relative to those of other tunicates and chordates, with gene rearrangements affecting both protein-coding and tRNA genes. The new data highlight the extraordinary variability of ascidian mt genome in base composition, tRNA secondary structure, tRNA gene content, and non-coding regions (number, size, sequence and location. Indeed, both Phallusia genomes lack the trnD gene, show loss/acquisition of DHU-arm in two tRNAs, and have a G+C content two-fold higher than other ascidians. Moreover, the mt genome of P. fumigata presents two identical copies of trnI, an extra tRNA gene with uncertain amino acid specificity, and four almost identical sequence regions. In addition, a truncated cytochrome b, lacking a C-terminal tail that commonly protrudes into the mt matrix, has been identified as a new mt feature probably shared by all tunicates. Conclusion The frequent occurrence of major gene order rearrangements in ascidians both at high taxonomic level and within the same genus makes this taxon an excellent model to study the mechanisms of gene rearrangement, and renders the mt genome an invaluable phylogenetic marker to investigate molecular biodiversity and speciation

  8. Dynamics of the youth travel market on a global level

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    Timea DEMETER

    2015-06-01

    Full Text Available The segment of young tourists has been considered a niche market and was treated as a branch of the tourism industry. In the past 10 years, however, its market value has began to increase significantly bringing real benefits to the companies adapting to this segment by developing appropriate strategies and policies. Therefore, the aim of this project is to analyse the dynamics of the youth travel market, on a global level, taking into consideration the international youth arrivals, youth accommodation units and the behavioural habits of young tourists, serving as a starting point in the strategy development process.

  9. Global Sourcing, Technology, and Factor Intensity: Firm-level Relationships

    OpenAIRE

    TOMIURA Eiichi

    2007-01-01

    This paper empirically examines how technology and capital intensity are related with the firm's global sourcing decision. Firm-level data are derived from a survey covering all manufacturing industries in Japan without any firm-size threshold. Firms are disaggregated by their make-or-buy decision (in-house or outsourcing) and by their choice of sourcing location (offshore or domestic). Capital-intensive or R&D-intensive firms tend to source in-house from their FDI affiliates rather than outs...

  10. Global Changes in Drought Conditions Under Different Levels of Warming

    Science.gov (United States)

    Naumann, G.; Alfieri, L.; Wyser, K.; Mentaschi, L.; Betts, R. A.; Carrao, H.; Spinoni, J.; Vogt, J.; Feyen, L.

    2018-04-01

    Higher evaporative demands and more frequent and persistent dry spells associated with rising temperatures suggest that drought conditions could worsen in many regions of the world. In this study, we assess how drought conditions may develop across the globe for 1.5, 2, and 3°C warming compared to preindustrial temperatures. Results show that two thirds of global population will experience a progressive increase in drought conditions with warming. For drying areas, drought durations are projected to rise at rapidly increasing rates with warming, averaged globally from 2.0 month/°C below 1.5°C to 4.2 month/°C when approaching 3°C. Drought magnitudes could double for 30% of global landmass under stringent mitigation. If contemporary warming rates continue, water supply-demand deficits could become fivefold in size for most of Africa, Australia, southern Europe, southern and central states of the United States, Central America, the Caribbean, north-west China, and parts of Southern America. In approximately 20% of the global land surface, drought magnitude will halve with warming of 1.5°C and higher levels, mainly most land areas north of latitude 55°N, but also parts of South America and Eastern and South-eastern Asia. A progressive and significant increase in frequency of droughts is projected with warming in the Mediterranean basin, most of Africa, West and Southern Asia, Central America, and Oceania, where droughts are projected to happen 5 to 10 times more frequent even under ambitious mitigation targets and current 100-year events could occur every two to five years under 3°C of warming.

  11. The prognostic significance of whole blood global and specific DNA methylation levels in gastric adenocarcinoma.

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    Mansour S Al-Moundhri

    Full Text Available BACKGROUND: Epigenetics, particularly DNA methylation, has recently been elucidated as important in gastric cancer (GC initiation and progression. We investigated the clinical and prognostic importance of whole blood global and site-specific DNA methylation in GC. METHODS: Genomic DNA was extracted from the peripheral blood of 105 Omani GC patients at diagnosis. DNA methylation was quantified by pyrosequencing of global DNA and specific gene promoter regions at 5 CpG sites for CDH1, 7 CpG sites for p16, 4 CpG sites for p53, and 3 CpG sites for RUNX3. DNA methylation levels in patients were categorized into low, medium, and high tertiles. Associations between methylation level category and clinicopathological features were evaluated using χ(2 tests. Survival analyses were carried out using the Kaplan-Meier method and log rank test. A backward conditional Cox proportional hazards regression model was used to identify independent predictors of survival. RESULTS: Older GC patients had increased methylation levels at specific CpG sites within the CDH1, p53, and RUNX-3 promoters. Male gender was significantly associated with reduced global and increased site-specific DNA methylation levels in CDH1, p16, and p53 promoters. Global DNA low methylation level was associated with better survival on univariate analysis. Patients with high and medium methylation vs. low methylation levels across p16 promoter CpG sites, site 2 in particular, had better survival. Multivariate analysis showed that global DNA hypermethylation was a significant independent predictor of worse survival (hazard ratio (HR = 2.0, 95% CI: 1.1-3.8; p = 0.02 and high methylation mean values across p16 promoter sites 1-7 were associated with better survival with HR of 0.3 (95% CI, 0.1-0.8; p = 0.02 respectively. CONCLUSIONS: Analysis of global and site-specific DNA methylation in peripheral blood by pyrosequencing provides quantitative DNA methylation values that may serve as important

  12. Precise mean sea level measurements using the Global Positioning System

    Science.gov (United States)

    Kelecy, Thomas M.; Born, George H.; Parke, Michael E.; Rocken, Christian

    1994-01-01

    This paper describes the results of a sea level measurement test conducted off La Jolla, California, in November of 1991. The purpose of this test was to determine accurate sea level measurements using a Global Positioning System (GPS) equipped buoy. These measurements were intended to be used as the sea level component for calibration of the ERS 1 satellite altimeter. Measurements were collected on November 25 and 28 when the ERS 1 satellite overflew the calibration area. Two different types of buoys were used. A waverider design was used on November 25 and a spar design on November 28. This provided the opportunity to examine how dynamic effects of the measurement platform might affect the sea level accuracy. The two buoys were deployed at locations approximately 1.2 km apart and about 15 km west of a reference GPS receiver located on the rooftop of the Institute of Geophysics and Planetary Physics at the Scripps Institute of Oceanography. GPS solutions were computed for 45 minutes on each day and used to produce two sea level time series. An estimate of the mean sea level at both locations was computed by subtracting tide gage data collected at the Scripps Pier from the GPS-determined sea level measurements and then filtering out the high-frequency components due to waves and buoy dynamics. In both cases the GPS estimate differed from Rapp's mean altimetric surface by 0.06 m. Thus, the gradient in the GPS measurements matched the gradient in Rapp's surface. These results suggest that accurate sea level can be determined using GPS on widely differing platforms as long as care is taken to determine the height of the GPS antenna phase center above water level. Application areas include measurement of absolute sea level, of temporal variations in sea level, and of sea level gradients (dominantly the geoid). Specific applications would include ocean altimeter calibration, monitoring of sea level in remote regions, and regional experiments requiring spatial and

  13. Global MLST of Salmonella Typhi Revisited in Post-Genomic Era: Genetic conservation, Population Structure and Comparative genomics of rare sequence types

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    Kien-Pong eYap

    2016-03-01

    Full Text Available Typhoid fever, caused by Salmonella enterica serovar Typhi, remains an important public health burden in Southeast Asia and other endemic countries. Various genotyping methods have been applied to study the genetic variations of this human-restricted pathogen. Multilocus Sequence Typing (MLST is one of the widely accepted methods, and recently, there is a growing interest in the re-application of MLST in the post-genomic era. In this study, we provide the global MLST distribution of S. Typhi utilizing both publicly available 1,826 S. Typhi genome sequences in addition to performing conventional MLST on S. Typhi strains isolated from various endemic regions spanning over a century. Our global MLST analysis confirms the predominance of two sequence types (ST1 and ST2 co-existing in the endemic regions. Interestingly, S. Typhi strains with ST8 are currently confined within the African continent. Comparative genomic analyses of ST8 and other rare STs with genomes of ST1/ST2 revealed unique mutations in important virulence genes such as flhB, sipC and tviD that may explain the variations that differentiate between seemingly successful (widespread and unsuccessful (poor dissemination S. Typhi populations. Large scale whole-genome phylogeny demonstrated evidence of phylogeographical structuring and showed that ST8 may have diverged from the earlier ancestral population of ST1 and ST2, which later lost some of its fitness advantages, leading to poor worldwide dissemination. In response to the unprecedented increase in genomic data, this study demonstrates and highlights the utility of large-scale genome-based MLST as a quick and effective approach to narrow the scope of in-depth comparative genomic analysis and consequently provide new insights into the fine scale of pathogen evolution and population structure.

  14. The mitochondrial genome of Frankliniella intonsa: insights into the evolution of mitochondrial genomes at lower taxonomic levels in Thysanoptera.

    Science.gov (United States)

    Yan, Dankan; Tang, Yunxia; Hu, Min; Liu, Fengquan; Zhang, Dongfang; Fan, Jiaqin

    2014-10-01

    Thrips is an ideal group for studying the evolution of mitochondrial (mt) genomes in the genus and family due to independent rearrangements within this order. The complete sequence of the mitochondrial DNA (mtDNA) of the flower thrips Frankliniella intonsa has been completed and annotated in this study. The circular genome is 15,215bp in length with an A+T content of 75.9% and contains the typical 37 genes and it has triplicate putative control regions. Nucleotide composition is A+T biased, and the majority of the protein-coding genes present opposite CG skew which is reflected by the nucleotide composition, codon and amino acid usage. Although the known thrips have massive gene rearrangements, it showed no reversal of strand asymmetry. Gene rearrangements have been found in the lower taxonomic levels of thrips. Three tRNA genes were translocated in the genus Frankliniella and eight tRNA genes in the family Thripidae. Although the gene arrangements of mt genomes of all three thrips species differ massively from the ancestral insect, they are all very similar to each other, indicating that there was a large rearrangement somewhere before the most recent common ancestor of these three species and very little genomic evolution or rearrangements after then. The extremely similar sequences among the CRs suggest that they are ongoing concerted evolution. Analyses of the up and downstream sequence of CRs reveal that the CR2 is actually the ancestral CR. The three CRs are in the same spot in each of the three thrips mt genomes which have the identical inverted genes. These characteristics might be obtained from the most recent common ancestor of this three thrips. Above observations suggest that the mt genomes of the three thrips keep a single massive rearrangement from the common ancestor and have low evolutionary rates among them. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. Base-By-Base: single nucleotide-level analysis of whole viral genome alignments.

    Science.gov (United States)

    Brodie, Ryan; Smith, Alex J; Roper, Rachel L; Tcherepanov, Vasily; Upton, Chris

    2004-07-14

    With ever increasing numbers of closely related virus genomes being sequenced, it has become desirable to be able to compare two genomes at a level more detailed than gene content because two strains of an organism may share the same set of predicted genes but still differ in their pathogenicity profiles. For example, detailed comparison of multiple isolates of the smallpox virus genome (each approximately 200 kb, with 200 genes) is not feasible without new bioinformatics tools. A software package, Base-By-Base, has been developed that provides visualization tools to enable researchers to 1) rapidly identify and correct alignment errors in large, multiple genome alignments; and 2) generate tabular and graphical output of differences between the genomes at the nucleotide level. Base-By-Base uses detailed annotation information about the aligned genomes and can list each predicted gene with nucleotide differences, display whether variations occur within promoter regions or coding regions and whether these changes result in amino acid substitutions. Base-By-Base can connect to our mySQL database (Virus Orthologous Clusters; VOCs) to retrieve detailed annotation information about the aligned genomes or use information from text files. Base-By-Base enables users to quickly and easily compare large viral genomes; it highlights small differences that may be responsible for important phenotypic differences such as virulence. It is available via the Internet using Java Web Start and runs on Macintosh, PC and Linux operating systems with the Java 1.4 virtual machine.

  16. Genome size evolution at the speciation level: the cryptic species complex Brachionus plicatilis (Rotifera).

    Science.gov (United States)

    Stelzer, Claus-Peter; Riss, Simone; Stadler, Peter

    2011-04-07

    Studies on genome size variation in animals are rarely done at lower taxonomic levels, e.g., slightly above/below the species level. Yet, such variation might provide important clues on the tempo and mode of genome size evolution. In this study we used the flow-cytometry method to study the evolution of genome size in the rotifer Brachionus plicatilis, a cryptic species complex consisting of at least 14 closely related species. We found an unexpectedly high variation in this species complex, with genome sizes ranging approximately seven-fold (haploid '1C' genome sizes: 0.056-0.416 pg). Most of this variation (67%) could be ascribed to the major clades of the species complex, i.e. clades that are well separated according to most species definitions. However, we also found substantial variation (32%) at lower taxonomic levels--within and among genealogical species--and, interestingly, among species pairs that are not completely reproductively isolated. In one genealogical species, called B. 'Austria', we found greatly enlarged genome sizes that could roughly be approximated as multiples of the genomes of its closest relatives, which suggests that whole-genome duplications have occurred early during separation of this lineage. Overall, genome size was significantly correlated to egg size and body size, even though the latter became non-significant after controlling for phylogenetic non-independence. Our study suggests that substantial genome size variation can build up early during speciation, potentially even among isolated populations. An alternative, but not mutually exclusive interpretation might be that reproductive isolation tends to build up unusually slow in this species complex.

  17. Genome size evolution at the speciation level: The cryptic species complex Brachionus plicatilis (Rotifera

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    Riss Simone

    2011-04-01

    Full Text Available Abstract Background Studies on genome size variation in animals are rarely done at lower taxonomic levels, e.g., slightly above/below the species level. Yet, such variation might provide important clues on the tempo and mode of genome size evolution. In this study we used the flow-cytometry method to study the evolution of genome size in the rotifer Brachionus plicatilis, a cryptic species complex consisting of at least 14 closely related species. Results We found an unexpectedly high variation in this species complex, with genome sizes ranging approximately seven-fold (haploid '1C' genome sizes: 0.056-0.416 pg. Most of this variation (67% could be ascribed to the major clades of the species complex, i.e. clades that are well separated according to most species definitions. However, we also found substantial variation (32% at lower taxonomic levels - within and among genealogical species - and, interestingly, among species pairs that are not completely reproductively isolated. In one genealogical species, called B. 'Austria', we found greatly enlarged genome sizes that could roughly be approximated as multiples of the genomes of its closest relatives, which suggests that whole-genome duplications have occurred early during separation of this lineage. Overall, genome size was significantly correlated to egg size and body size, even though the latter became non-significant after controlling for phylogenetic non-independence. Conclusions Our study suggests that substantial genome size variation can build up early during speciation, potentially even among isolated populations. An alternative, but not mutually exclusive interpretation might be that reproductive isolation tends to build up unusually slow in this species complex.

  18. Measuring progress of the global sea level observing system

    Science.gov (United States)

    Woodworth, Philip L.; Aarup, Thorkild; Merrifield, Mark; Mitchum, Gary T.; Le Provost, Christian

    Sea level is such a fundamental parameter in the sciences of oceanography geophysics, and climate change, that in the mid-1980s, the Intergovernmental Oceanographic Commission (IOC) established the Global Sea Level Observing System (GLOSS). GLOSS was to improve the quantity and quality of data provided to the Permanent Service for Mean Sea Level (PSMSL), and thereby, data for input to studies of long-term sea level change by the Intergovernmental Panel on Climate Change (IPCC). It would also provide the key data needed for international programs, such as the World Ocean Circulation Experiment (WOCE) and later, the Climate Variability and Predictability Programme (CLIVAR).GLOSS is now one of the main observation components of the Joint Technical Commission for Oceanography and Marine Meteorology (JCOMM) of IOC and the World Meteorological Organization (WMO). Progress and deficiencies in GLOSS were presented in July to the 22nd IOC Assembly at UNESCO in Paris and are contained in the GLOSS Assessment Report (GAR) [IOC, 2003a].

  19. The population genomics of begomoviruses: global scale population structure and gene flow

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    Prasanna HC

    2010-09-01

    Full Text Available Abstract Background The rapidly growing availability of diverse full genome sequences from across the world is increasing the feasibility of studying the large-scale population processes that underly observable pattern of virus diversity. In particular, characterizing the genetic structure of virus populations could potentially reveal much about how factors such as geographical distributions, host ranges and gene flow between populations combine to produce the discontinuous patterns of genetic diversity that we perceive as distinct virus species. Among the richest and most diverse full genome datasets that are available is that for the dicotyledonous plant infecting genus, Begomovirus, in the Family Geminiviridae. The begomoviruses all share the same whitefly vector, are highly recombinogenic and are distributed throughout tropical and subtropical regions where they seriously threaten the food security of the world's poorest people. Results We focus here on using a model-based population genetic approach to identify the genetically distinct sub-populations within the global begomovirus meta-population. We demonstrate the existence of at least seven major sub-populations that can further be sub-divided into as many as thirty four significantly differentiated and genetically cohesive minor sub-populations. Using the population structure framework revealed in the present study, we further explored the extent of gene flow and recombination between genetic populations. Conclusions Although geographical barriers are apparently the most significant underlying cause of the seven major population sub-divisions, within the framework of these sub-divisions, we explore patterns of gene flow to reveal that both host range differences and genetic barriers to recombination have probably been major contributors to the minor population sub-divisions that we have identified. We believe that the global Begomovirus population structure revealed here could

  20. Global challenges of graduate level Ayurvedic education: A survey

    Science.gov (United States)

    Patwardhan, Kishor; Gehlot, Sangeeta; Singh, Girish; Rathore, H.C.S.

    2010-01-01

    In the present day scenario, Ayurveda is globally being perceived in several contradictory ways. Poor quality of Ayurveda graduates produced as a result of poorly structured and poorly regulated education system is at least one of the important factors responsible for this scenario. The present study was carried out to evaluate the ‘Global challenges of graduate level Ayurvedic education’ and is based on the responses of Ayurvedic students and Ayurvedic teachers from various educational institutions of India to a methodically validated questionnaire. As the study indicates, the poor standard of Ayurvedic education in India is definitely a cause of concern. The curriculum of Bachelor of Ayurvedic Medicine and Surgery (BAMS) course of studies is required to be reviewed and restructured. The syllabi are required to be updated with certain relevant topics like laws governing the intellectual property rights, basic procedures of standardization of medicinal products, fundamental methods of evaluating the toxicity of the medicinal products, essentials of healthcare management and the basics of cultivation and marketing of medicinal plants. Furthermore, the study suggests that the Ayurvedic academicians are required to be trained in standard methods of research and documentation skills, and the educational institutions are required to be encouraged to contribute their share in building up the evidence base for Ayurveda in the form of quality education and research. PMID:20532099

  1. Whole-genome sequencing identifies genomic heterogeneity at a nucleotide and chromosomal level in bladder cancer

    Science.gov (United States)

    Morrison, Carl D.; Liu, Pengyuan; Woloszynska-Read, Anna; Zhang, Jianmin; Luo, Wei; Qin, Maochun; Bshara, Wiam; Conroy, Jeffrey M.; Sabatini, Linda; Vedell, Peter; Xiong, Donghai; Liu, Song; Wang, Jianmin; Shen, He; Li, Yinwei; Omilian, Angela R.; Hill, Annette; Head, Karen; Guru, Khurshid; Kunnev, Dimiter; Leach, Robert; Eng, Kevin H.; Darlak, Christopher; Hoeflich, Christopher; Veeranki, Srividya; Glenn, Sean; You, Ming; Pruitt, Steven C.; Johnson, Candace S.; Trump, Donald L.

    2014-01-01

    Using complete genome analysis, we sequenced five bladder tumors accrued from patients with muscle-invasive transitional cell carcinoma of the urinary bladder (TCC-UB) and identified a spectrum of genomic aberrations. In three tumors, complex genotype changes were noted. All three had tumor protein p53 mutations and a relatively large number of single-nucleotide variants (SNVs; average of 11.2 per megabase), structural variants (SVs; average of 46), or both. This group was best characterized by chromothripsis and the presence of subclonal populations of neoplastic cells or intratumoral mutational heterogeneity. Here, we provide evidence that the process of chromothripsis in TCC-UB is mediated by nonhomologous end-joining using kilobase, rather than megabase, fragments of DNA, which we refer to as “stitchers,” to repair this process. We postulate that a potential unifying theme among tumors with the more complex genotype group is a defective replication–licensing complex. A second group (two bladder tumors) had no chromothripsis, and a simpler genotype, WT tumor protein p53, had relatively few SNVs (average of 5.9 per megabase) and only a single SV. There was no evidence of a subclonal population of neoplastic cells. In this group, we used a preclinical model of bladder carcinoma cell lines to study a unique SV (translocation and amplification) of the gene glutamate receptor ionotropic N-methyl D-aspertate as a potential new therapeutic target in bladder cancer. PMID:24469795

  2. Presence of Corporate Frauds at a Global Level

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    Vranješ Svjetlana

    2017-06-01

    Full Text Available The legislative bodies of the countries, members of the accounting and auditing profession, various associations have taken a number of preventive measures and mechanisms for combating corporate criminal activities and financial frauds, but unfortunately, the fact is that even today they often happen in both undeveloped and the most developed market economies. It is therefore essential to pay significant attention to corporate criminal activity and financial frauds that are happening in the business world. The aim of this paper is to show the presence of different forms of corporate criminal activity at a global level, and to display a conceptual framework of criminal activity and motives for their doing. Concluding remarks of this paper provide guidelines for further research and recommendations on how to improve the mechanisms for preventing and detecting criminal activity.

  3. The future for the Global Sea Level Observing System (GLOSS) Sea Level Data Rescue

    Science.gov (United States)

    Bradshaw, Elizabeth; Matthews, Andrew; Rickards, Lesley; Aarup, Thorkild

    2016-04-01

    Historical sea level data are rare and unrepeatable measurements with a number of applications in climate studies (sea level rise), oceanography (ocean currents, tides, surges), geodesy (national datum), geophysics and geology (coastal land movements) and other disciplines. However, long-term time series are concentrated in the northern hemisphere and there are no records at the Permanent Service for Mean Sea Level (PSMSL) global data bank longer than 100 years in the Arctic, Africa, South America or Antarctica. Data archaeology activities will help fill in the gaps in the global dataset and improve global sea level reconstruction. The Global Sea Level Observing System (GLOSS) is an international programme conducted under the auspices of the WMO-IOC Joint Technical Commission for Oceanography and Marine Meteorology. It was set up in 1985 to collect long-term tide gauge observations and to develop systems and standards "for ocean monitoring and flood warning purposes". At the GLOSS-GE-XIV Meeting in 2015, GLOSS agreed on a number of action items to be developed in the next two years. These were: 1. To explore mareogram digitisation applications, including NUNIEAU (more information available at: http://www.mediterranee.cerema.fr/logiciel-de-numerisation-des-enregistrements-r57.html) and other recent developments in scanning/digitisation software, such as IEDRO's Weather Wizards program, to see if they could be used via a browser. 2. To publicise sea level data archaeology and rescue by: • maintaining and regularly updating the Sea Level Data Archaeology page on the GLOSS website • strengthening links to the GLOSS data centres and data rescue organisations e.g. linking to IEDRO, ACRE, RDA • restarting the sea level data rescue blog with monthly posts. 3. Investigate sources of funding for data archaeology and rescue projects. 4. Propose "Guidelines" for rescuing sea level data. These action items will aid the discovery, scanning, digitising and quality control

  4. Global-genome Nucleotide Excision Repair Controlled by Ubiquitin/Sumo Modifiers

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    Peter eRuethemann

    2016-04-01

    Full Text Available Global-genome nucleotide excision repair (GG-NER prevents genome instability by excising a wide range of structurally unrelated DNA base adducts and crosslinks induced by chemical carcinogens, ultraviolet (UV radiation or intracellular metabolic by-products. As a versatile damage sensor, xeroderma pigmentosum group C (XPC protein initiates this generic defense reaction by locating the damage and recruiting the subunits of a large lesion demarcation complex that, in turn, triggers the excision of aberrant DNA by endonucleases. In the very special case of a DNA repair response to UV radiation, the function of this XPC initiator is tightly controlled by the dual action of cullin-type CRL4DDB2 and sumo-targeted RNF111 ubiquitin ligases. This twofold protein ubiquitination system promotes GG-NER reactions by spatially and temporally regulating the interaction of XPC protein with damaged DNA across the nucleosome landscape of chromatin. In the absence of either CRL4DDB2 or RNF111, the DNA excision repair of UV lesions is inefficient, indicating that these two ubiquitin ligases play a critical role in mitigating the adverse biological effects of UV light in the exposed skin.

  5. An Integrative Bioinformatics Framework for Genome-scale Multiple Level Network Reconstruction of Rice

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    Liu Lili

    2013-06-01

    Full Text Available Understanding how metabolic reactions translate the genome of an organism into its phenotype is a grand challenge in biology. Genome-wide association studies (GWAS statistically connect genotypes to phenotypes, without any recourse to known molecular interactions, whereas a molecular mechanistic description ties gene function to phenotype through gene regulatory networks (GRNs, protein-protein interactions (PPIs and molecular pathways. Integration of different regulatory information levels of an organism is expected to provide a good way for mapping genotypes to phenotypes. However, the lack of curated metabolic model of rice is blocking the exploration of genome-scale multi-level network reconstruction. Here, we have merged GRNs, PPIs and genome-scale metabolic networks (GSMNs approaches into a single framework for rice via omics’ regulatory information reconstruction and integration. Firstly, we reconstructed a genome-scale metabolic model, containing 4,462 function genes, 2,986 metabolites involved in 3,316 reactions, and compartmentalized into ten subcellular locations. Furthermore, 90,358 pairs of protein-protein interactions, 662,936 pairs of gene regulations and 1,763 microRNA-target interactions were integrated into the metabolic model. Eventually, a database was developped for systematically storing and retrieving the genome-scale multi-level network of rice. This provides a reference for understanding genotype-phenotype relationship of rice, and for analysis of its molecular regulatory network.

  6. Global estimates of high-level brain drain and deficit.

    Science.gov (United States)

    Ioannidis, John P A

    2004-06-01

    Brain drain, the international migration of scientists in search of better opportunities, has been a long-standing concern, but quantitative measurements are uncommon and limited to specific countries or disciplines. We need to understand brain drain at a global level and estimate the extent to which scientists born in countries with low opportunities never realize their potential. Data on 1523 of the most highly cited scientists for 1981-1999 are analyzed. Overall, 31.9% of these scientists did not reside in the country where they were born (range 18.1-54.6% across 21 different scientific fields). There was great variability across developed countries in the proportions of foreign-born resident scientists and emigrating scientists. Countries without a critical mass of native scientists lost most scientists to migration. This loss occurred in both developed and developing countries. Adjusting for population and using the U.S. as reference, the number of highly cited native-born scientists was at least 75% of the expected number in only 8 countries other than the U.S. It is estimated that approximately 94% of the expected top scientists worldwide have not been able to materialize themselves due to various adverse conditions. Scientific deficit is only likely to help perpetuate these adverse conditions.

  7. Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments

    Directory of Open Access Journals (Sweden)

    Tcherepanov Vasily

    2004-07-01

    Full Text Available Abstract Background With ever increasing numbers of closely related virus genomes being sequenced, it has become desirable to be able to compare two genomes at a level more detailed than gene content because two strains of an organism may share the same set of predicted genes but still differ in their pathogenicity profiles. For example, detailed comparison of multiple isolates of the smallpox virus genome (each approximately 200 kb, with 200 genes is not feasible without new bioinformatics tools. Results A software package, Base-By-Base, has been developed that provides visualization tools to enable researchers to 1 rapidly identify and correct alignment errors in large, multiple genome alignments; and 2 generate tabular and graphical output of differences between the genomes at the nucleotide level. Base-By-Base uses detailed annotation information about the aligned genomes and can list each predicted gene with nucleotide differences, display whether variations occur within promoter regions or coding regions and whether these changes result in amino acid substitutions. Base-By-Base can connect to our mySQL database (Virus Orthologous Clusters; VOCs to retrieve detailed annotation information about the aligned genomes or use information from text files. Conclusion Base-By-Base enables users to quickly and easily compare large viral genomes; it highlights small differences that may be responsible for important phenotypic differences such as virulence. It is available via the Internet using Java Web Start and runs on Macintosh, PC and Linux operating systems with the Java 1.4 virtual machine.

  8. Reassessment of 20th century global mean sea level rise

    Science.gov (United States)

    Dangendorf, Sönke; Marcos, Marta; Wöppelmann, Guy; Conrad, Clinton P.; Frederikse, Thomas; Riva, Riccardo

    2017-01-01

    The rate at which global mean sea level (GMSL) rose during the 20th century is uncertain, with little consensus between various reconstructions that indicate rates of rise ranging from 1.3 to 2 mm⋅y−1. Here we present a 20th-century GMSL reconstruction computed using an area-weighting technique for averaging tide gauge records that both incorporates up-to-date observations of vertical land motion (VLM) and corrections for local geoid changes resulting from ice melting and terrestrial freshwater storage and allows for the identification of possible differences compared with earlier attempts. Our reconstructed GMSL trend of 1.1 ± 0.3 mm⋅y−1 (1σ) before 1990 falls below previous estimates, whereas our estimate of 3.1 ± 1.4 mm⋅y−1 from 1993 to 2012 is consistent with independent estimates from satellite altimetry, leading to overall acceleration larger than previously suggested. This feature is geographically dominated by the Indian Ocean–Southern Pacific region, marking a transition from lower-than-average rates before 1990 toward unprecedented high rates in recent decades. We demonstrate that VLM corrections, area weighting, and our use of a common reference datum for tide gauges may explain the lower rates compared with earlier GMSL estimates in approximately equal proportion. The trends and multidecadal variability of our GMSL curve also compare well to the sum of individual contributions obtained from historical outputs of the Coupled Model Intercomparison Project Phase 5. This, in turn, increases our confidence in process-based projections presented in the Fifth Assessment Report of the Intergovernmental Panel on Climate Change. PMID:28533403

  9. Downscaling drivers of global environmental change: Enabling use of global SRES scenarios at the national and grid levels

    NARCIS (Netherlands)

    van Vuuren, D.P.; Lucas, P.L.; Hilderink, H.

    2007-01-01

    Global environmental change scenarios typically distinguish between about 10–20 global regions. However, various studies need scenario information at a higher level of spatial detail. This paper presents a set of algorithms that aim to fill this gap by providing downscaled scenario data for

  10. Genomes

    National Research Council Canada - National Science Library

    Brown, T. A. (Terence A.)

    2002-01-01

    ... of genome expression and replication processes, and transcriptomics and proteomics. This text is richly illustrated with clear, easy-to-follow, full color diagrams, which are downloadable from the book's website...

  11. Status of research on Drosophila ananassae at global level

    Indian Academy of Sciences (India)

    Extensive research work on D. ananassae has been done by numerous researchers per- taining to .... sae has been most extensively utilized for various kinds of studies at global .... ananassae for quantitative and qualitative analyses of acces-.

  12. Elucidating the triplicated ancestral genome structure of radish based on chromosome-level comparison with the Brassica genomes.

    Science.gov (United States)

    Jeong, Young-Min; Kim, Namshin; Ahn, Byung Ohg; Oh, Mijin; Chung, Won-Hyong; Chung, Hee; Jeong, Seongmun; Lim, Ki-Byung; Hwang, Yoon-Jung; Kim, Goon-Bo; Baek, Seunghoon; Choi, Sang-Bong; Hyung, Dae-Jin; Lee, Seung-Won; Sohn, Seong-Han; Kwon, Soo-Jin; Jin, Mina; Seol, Young-Joo; Chae, Won Byoung; Choi, Keun Jin; Park, Beom-Seok; Yu, Hee-Ju; Mun, Jeong-Hwan

    2016-07-01

    This study presents a chromosome-scale draft genome sequence of radish that is assembled into nine chromosomal pseudomolecules. A comprehensive comparative genome analysis with the Brassica genomes provides genomic evidences on the evolution of the mesohexaploid radish genome. Radish (Raphanus sativus L.) is an agronomically important root vegetable crop and its origin and phylogenetic position in the tribe Brassiceae is controversial. Here we present a comprehensive analysis of the radish genome based on the chromosome sequences of R. sativus cv. WK10039. The radish genome was sequenced and assembled into 426.2 Mb spanning >98 % of the gene space, of which 344.0 Mb were integrated into nine chromosome pseudomolecules. Approximately 36 % of the genome was repetitive sequences and 46,514 protein-coding genes were predicted and annotated. Comparative mapping of the tPCK-like ancestral genome revealed that the radish genome has intermediate characteristics between the Brassica A/C and B genomes in the triplicated segments, suggesting an internal origin from the genus Brassica. The evolutionary characteristics shared between radish and other Brassica species provided genomic evidences that the current form of nine chromosomes in radish was rearranged from the chromosomes of hexaploid progenitor. Overall, this study provides a chromosome-scale draft genome sequence of radish as well as novel insight into evolution of the mesohexaploid genomes in the tribe Brassiceae.

  13. Comparative Sex Chromosome Genomics in Snakes: Differentiation, Evolutionary Strata, and Lack of Global Dosage Compensation

    Science.gov (United States)

    Zektser, Yulia; Mahajan, Shivani; Bachtrog, Doris

    2013-01-01

    Snakes exhibit genetic sex determination, with female heterogametic sex chromosomes (ZZ males, ZW females). Extensive cytogenetic work has suggested that the level of sex chromosome heteromorphism varies among species, with Boidae having entirely homomorphic sex chromosomes, Viperidae having completely heteromorphic sex chromosomes, and Colubridae showing partial differentiation. Here, we take a genomic approach to compare sex chromosome differentiation in these three snake families. We identify homomorphic sex chromosomes in boas (Boidae), but completely heteromorphic sex chromosomes in both garter snakes (Colubridae) and pygmy rattlesnake (Viperidae). Detection of W-linked gametologs enables us to establish the presence of evolutionary strata on garter and pygmy rattlesnake sex chromosomes where recombination was abolished at different time points. Sequence analysis shows that all strata are shared between pygmy rattlesnake and garter snake, i.e., recombination was abolished between the sex chromosomes before the two lineages diverged. The sex-biased transmission of the Z and its hemizygosity in females can impact patterns of molecular evolution, and we show that rates of evolution for Z-linked genes are increased relative to their pseudoautosomal homologs, both at synonymous and amino acid sites (even after controlling for mutational biases). This demonstrates that mutation rates are male-biased in snakes (male-driven evolution), but also supports faster-Z evolution due to differential selective effects on the Z. Finally, we perform a transcriptome analysis in boa and pygmy rattlesnake to establish baseline levels of sex-biased expression in homomorphic sex chromosomes, and show that heteromorphic ZW chromosomes in rattlesnakes lack chromosome-wide dosage compensation. Our study provides the first full scale overview of the evolution of snake sex chromosomes at the genomic level, thus greatly expanding our knowledge of reptilian and vertebrate sex chromosomes

  14. Global DNA methylation synergistically regulates the nuclear and mitochondrial genomes in glioblastoma cells.

    Science.gov (United States)

    Sun, Xin; Johnson, Jacqueline; St John, Justin C

    2018-05-02

    Replication of mitochondrial DNA is strictly regulated during differentiation and development allowing each cell type to acquire its required mtDNA copy number to meet its specific needs for energy. Undifferentiated cells establish the mtDNA set point, which provides low numbers of mtDNA copy but sufficient template for replication once cells commit to specific lineages. However, cancer cells, such as those from the human glioblastoma multiforme cell line, HSR-GBM1, cannot complete differentiation as they fail to enforce the mtDNA set point and are trapped in a 'pseudo-differentiated' state. Global DNA methylation is likely to be a major contributing factor, as DNA demethylation treatments promote differentiation of HSR-GBM1 cells. To determine the relationship between DNA methylation and mtDNA copy number in cancer cells, we applied whole genome MeDIP-Seq and RNA-Seq to HSR-GBM1 cells and following their treatment with the DNA demethylation agents 5-azacytidine and vitamin C. We identified key methylated regions modulated by the DNA demethylation agents that also induced synchronous changes to mtDNA copy number and nuclear gene expression. Our findings highlight the control exerted by DNA methylation on the expression of key genes, the regulation of mtDNA copy number and establishment of the mtDNA set point, which collectively contribute to tumorigenesis.

  15. A genome-wide association study reveals variants in ARL15 that influence adiponectin levels

    NARCIS (Netherlands)

    J.B. Richards (Brent); D. Waterworth (Dawn); S. O'Rahilly (Stephen); M.-F. Hivert (Marie-France); R.J.F. Loos (Ruth); J.R.B. Perry (John); T. Tanaka (Toshiko); N.J. Timpson (Nicholas); R.K. Semple (Robert); N. Soranzo (Nicole); K. Song (Kijoung); N. Rocha (Nuno); E. Grundberg (Elin); J. Dupuis (Josée); J.C. Florez (Jose); C. Langenberg (Claudia); I. Prokopenko (Inga); R. Saxena (Richa); R. Sladek (Rob); Y.S. Aulchenko (Yurii); D.M. Evans (David); G. Waeber (Gérard); M.S. Burnett; N. Sattar (Naveed); J. Devaney (Joseph); C. Willenborg (Christina); A. Hingorani (Aroon); J.C.M. Witteman (Jacqueline); P. Vollenweider (Peter); B. Glaser (Beate); C. Hengstenberg (Christian); L. Ferrucci (Luigi); D. Melzer (David); K. Stark (Klaus); J. Deanfield (John); J. Winogradow (Janina); M. Grassl (Martina); A.S. Hall (Alistair); J.M. Egan (Josephine); J.R. Thompson (John); S.L. Ricketts (Sally); I.R. König (Inke); W. Reinhard (Wibke); S.M. Grundy (Scott); H.E. Wichmann (Heinz Erich); P. Barter (Phil); R. Mahley (Robert); Y.A. Kesaniemi (Antero); D.J. Rader (Daniel); M.P. Reilly (Muredach); S.E. Epstein (Stephen); A.F.R. Stewart (Alexandre); P. Tikka-Kleemola (Päivi); H. Schunkert (Heribert); K.A. Burling (Keith); J. Erdmann (Jeanette); P. Deloukas (Panagiotis); T. Pastinen (Tomi); N.J. Samani (Nilesh); R. McPherson (Ruth); G.D. Smith; T.M. Frayling (Timothy); N.J. Wareham (Nick); J.B. Meigs (James); V. Mooser (Vincent); T.D. Spector (Timothy)

    2009-01-01

    textabstractThe adipocyte-derived protein adiponectin is highly heritable and inversely associated with risk of type 2 diabetes mellitus (T2D) and coronary heart disease (CHD). We meta-analyzed 3 genome-wide association studies for circulating adiponectin levels (n = 8,531) and sought validation of

  16. Association mapping of agro-morphological characters among the global collection of finger millet genotypes using genomic SSR markers.

    Science.gov (United States)

    Kalyana Babu, B; Agrawal, P K; Pandey, Dinesh; Jaiswal, J P; Kumar, Anil

    2014-08-01

    Identification of alleles responsible for various agro-morphological characters is a major concern to further improve the finger millet germplasm. Forty-six genomic SSRs were used for genetic analysis and population structure analysis of a global collection of 190 finger millet genotypes and fifteen agro-morphological characters were evaluated. The overall results showed that Asian genotypes were smaller in height, smaller flag leaf length, less basal tiller number, early flowering and early maturity nature, small ear head length, and smaller in length of longest finger. The 46 SSRs yielded 90 scorable alleles and the polymorphism information content values varied from 0.292 to 0.703 at an average of 0.442. The gene diversity was in the range of 0.355 to 0.750 with an average value of 0.528. The 46 genomic SSR loci grouped the 190 finger millet genotypes into two major clusters based on their geographical origin by the both phylogenetic clustering and population structure analysis by STRUCTURE software. Association mapping of QTLs for 15 agro-morphological characters with 46 genomic SSRs resulted in identification of five markers were linked to QTLs of four traits at a significant threshold (P) level of ≤ 0.01 and ≤ 0.001. The QTL for basal tiller number was strongly associated with the locus UGEP81 at a P value of 0.001 by explaining the phenotypic variance (R (2)) of 10.8%. The QTL for days to 50% flowering was linked by two SSR loci UGEP77 and UGEP90, explained 10 and 8.7% of R (2) respectively at a P value of 0.01. The SSR marker, FM9 found to have strong association to two agro-morphological traits, flag leaf width (P-0.001, R(2)-14.1 %) and plant height (P-0.001, R(2)-11.2%). The markers linked to the QTLs for above agro-morphological characters found in the present study can be further used for cloning of the full length gene, fine mapping and their further use in the marker assisted breeding programmes for introgression of alleles into locally well

  17. Global Metabolic Reconstruction and Metabolic Gene Evolution in the Cattle Genome

    Science.gov (United States)

    Kim, Woonsu; Park, Hyesun; Seo, Seongwon

    2016-01-01

    The sequence of cattle genome provided a valuable opportunity to systematically link genetic and metabolic traits of cattle. The objectives of this study were 1) to reconstruct genome-scale cattle-specific metabolic pathways based on the most recent and updated cattle genome build and 2) to identify duplicated metabolic genes in the cattle genome for better understanding of metabolic adaptations in cattle. A bioinformatic pipeline of an organism for amalgamating genomic annotations from multiple sources was updated. Using this, an amalgamated cattle genome database based on UMD_3.1, was created. The amalgamated cattle genome database is composed of a total of 33,292 genes: 19,123 consensus genes between NCBI and Ensembl databases, 8,410 and 5,493 genes only found in NCBI or Ensembl, respectively, and 266 genes from NCBI scaffolds. A metabolic reconstruction of the cattle genome and cattle pathway genome database (PGDB) was also developed using Pathway Tools, followed by an intensive manual curation. The manual curation filled or revised 68 pathway holes, deleted 36 metabolic pathways, and added 23 metabolic pathways. Consequently, the curated cattle PGDB contains 304 metabolic pathways, 2,460 reactions including 2,371 enzymatic reactions, and 4,012 enzymes. Furthermore, this study identified eight duplicated genes in 12 metabolic pathways in the cattle genome compared to human and mouse. Some of these duplicated genes are related with specific hormone biosynthesis and detoxifications. The updated genome-scale metabolic reconstruction is a useful tool for understanding biology and metabolic characteristics in cattle. There has been significant improvements in the quality of cattle genome annotations and the MetaCyc database. The duplicated metabolic genes in the cattle genome compared to human and mouse implies evolutionary changes in the cattle genome and provides a useful information for further research on understanding metabolic adaptations of cattle. PMID

  18. Individuals with Asperger's disorder exhibit difficulty in switching attention from a local level to a global level.

    Science.gov (United States)

    Katagiri, Masatoshi; Kasai, Tetsuko; Kamio, Yoko; Murohashi, Harumitsu

    2013-02-01

    The purpose of the present study was to determine whether individuals with Asperger's disorder exhibit difficulty in switching attention from a local level to a global level. Eleven participants with Asperger's disorder and 11 age- and gender-matched healthy controls performed a level-repetition switching task using Navon-type hierarchical stimuli. In both groups, level-repetition was beneficial at both levels. Furthermore, individuals with Asperger's disorder exhibited difficulty in switching attention from a local level to a global level compared to control individuals. These findings suggested that there is a problem with the inhibitory mechanism that influences the output of enhanced local visual processing in Asperger's disorder.

  19. Genome-wide meta-analysis uncovers novel loci influencing circulating leptin levels

    DEFF Research Database (Denmark)

    Kilpeläinen, Tuomas O; Carli, Jayne F Martin; Skowronski, Alicja A

    2016-01-01

    . Therefore, we performed a genome-wide association study (GWAS) of circulating leptin levels from 32,161 individuals and followed up loci reaching PFTO....... Although the association of the FTO obesity locus with leptin levels is abolished by adjustment for BMI, associations of the four other loci are independent of adiposity. The GCKR locus was found associated with multiple metabolic traits in previous GWAS and the CCNL1 locus with birth weight. Knockdown...

  20. Higher levels of depression are associated with reduced global bias in visual processing.

    Science.gov (United States)

    de Fockert, Jan W; Cooper, Andrew

    2014-04-01

    Negative moods have been associated with a tendency to prioritise local details in visual processing. The current study investigated the relation between depression and visual processing using the Navon task, a standard task of local and global processing. In the Navon task, global stimuli are presented that are made up of many local parts, and the participants are instructed to report the identity of either a global or a local target shape. Participants with a low self-reported level of depression showed evidence of the expected global processing bias, and were significantly faster at responding to the global, compared with the local level. By contrast, no such difference was observed in participants with high levels of depression. The reduction of the global bias associated with high levels of depression was only observed in the overall speed of responses to global (versus local) targets, and not in the level of interference produced by the global (versus local) distractors. These results are in line with recent findings of a dissociation between local/global processing bias and interference from local/global distractors, and support the claim that depression is associated with a reduction in the tendency to prioritise global-level processing.

  1. Core Genome Multilocus Sequence Typing for Identification of Globally Distributed Clonal Groups and Differentiation of Outbreak Strains of Listeria monocytogenes

    OpenAIRE

    Chen, Yi; Gonzalez-Escalona, Narjol; Hammack, Thomas S.; Allard, Marc W.; Strain, Errol A.; Brown, Eric W.

    2016-01-01

    ABSTRACT Many listeriosis outbreaks are caused by a few globally distributed clonal groups, designated clonal complexes or epidemic clones, of Listeria monocytogenes, several of which have been defined by classic multilocus sequence typing (MLST) schemes targeting 6 to 8 housekeeping or virulence genes. We have developed and evaluated core genome MLST (cgMLST) schemes and applied them to isolates from multiple clonal groups, including those associated with 39 listeriosis outbreaks. The cgMLST...

  2. UNEARTHING GLOBAL FINANCIAL INCLUSION LEVELS AND ANALYSIS OF FINANCIAL INCLUSION AS A MEDIATING FACTOR IN GLOBAL HUMAN DEVELOPMENT

    Directory of Open Access Journals (Sweden)

    Roshny Unnikrishnan

    2015-04-01

    Full Text Available This study is a result of the author’s inquisition to unearth the current values of Global Financial Inclusion and its relationship with economic growth measured by Gross Domestic product(GDP and human development measured by United Nations Human Development Index (HDI. The Financial Inclusion (FI levels are measured using Index for Financial Inclusion .The relationship between GDP and HDI with FI as mediator, using multiple regression, is validated on a global level based on data of 162 countries for the year 2011. An overall global mediation analysis is undertaken to establish Financial Inclusion as a mediating factor and partial mediation on human development is validated. The study is valid and unique in the global context of income inequality prevailing in developed, developing and underdeveloped countries as it validates the argument that an impressive GDP performance does not ensure equity in economic growth.

  3. Genomic ancestry and education level independently influence abdominal fat distributions in a Brazilian admixed population.

    Science.gov (United States)

    França, Giovanny Vinícius Araújo de; De Lucia Rolfe, Emanuella; Horta, Bernardo Lessa; Gigante, Denise Petrucci; Yudkin, John S; Ong, Ken K; Victora, Cesar Gomes

    2017-01-01

    We aimed to identify the independent associations of genomic ancestry and education level with abdominal fat distributions in the 1982 Pelotas birth cohort study, Brazil. In 2,890 participants (1,409 men and 1,481 women), genomic ancestry was assessed using genotype data on 370,539 genome-wide variants to quantify ancestral proportions in each individual. Years of completed education was used to indicate socio-economic position. Visceral fat depth and subcutaneous abdominal fat thickness were measured by ultrasound at age 29-31y; these measures were adjusted for BMI to indicate abdominal fat distributions. Linear regression models were performed, separately by sex. Admixture was observed between European (median proportion 85.3), African (6.6), and Native American (6.3) ancestries, with a strong inverse correlation between the African and European ancestry scores (ρ = -0.93; pabdominal fat distributions in men (both P = 0.001), and inversely associated with subcutaneous abdominal fat distribution in women (p = 0.009). Independent of genomic ancestry, higher education level was associated with lower visceral fat, but higher subcutaneous fat, in both men and women (all pabdominal fat distribution in adults. African ancestry appeared to lower abdominal fat distributions, particularly in men.

  4. Global levels of radiation exposure: Latest international findings

    International Nuclear Information System (INIS)

    Gonzalez, A.J.

    1993-01-01

    The radiation exposure of the world's population has recently been reviewed by the United Nations Scientific Committee on the Effects of Atomic Radiation (UNSCEAR). UNSCEAR has reconfirmed that the normal operation of all peaceful nuclear installations contributes insignificantly to the global exposure to radiation. Even taking into account all the nuclear accidents to date (including Chernobyl), the additional exposure would be equivalent to only about 20 days of natural exposure. Military uses of nuclear energy have committed the world to most of the radiation exposure caused by human activities

  5. Arthropod phylogenetics in light of three novel millipede (myriapoda: diplopoda) mitochondrial genomes with comments on the appropriateness of mitochondrial genome sequence data for inferring deep level relationships.

    Science.gov (United States)

    Brewer, Michael S; Swafford, Lynn; Spruill, Chad L; Bond, Jason E

    2013-01-01

    Arthropods are the most diverse group of eukaryotic organisms, but their phylogenetic relationships are poorly understood. Herein, we describe three mitochondrial genomes representing orders of millipedes for which complete genomes had not been characterized. Newly sequenced genomes are combined with existing data to characterize the protein coding regions of myriapods and to attempt to reconstruct the evolutionary relationships within the Myriapoda and Arthropoda. The newly sequenced genomes are similar to previously characterized millipede sequences in terms of synteny and length. Unique translocations occurred within the newly sequenced taxa, including one half of the Appalachioria falcifera genome, which is inverted with respect to other millipede genomes. Across myriapods, amino acid conservation levels are highly dependent on the gene region. Additionally, individual loci varied in the level of amino acid conservation. Overall, most gene regions showed low levels of conservation at many sites. Attempts to reconstruct the evolutionary relationships suffered from questionable relationships and low support values. Analyses of phylogenetic informativeness show the lack of signal deep in the trees (i.e., genes evolve too quickly). As a result, the myriapod tree resembles previously published results but lacks convincing support, and, within the arthropod tree, well established groups were recovered as polyphyletic. The novel genome sequences described herein provide useful genomic information concerning millipede groups that had not been investigated. Taken together with existing sequences, the variety of compositions and evolution of myriapod mitochondrial genomes are shown to be more complex than previously thought. Unfortunately, the use of mitochondrial protein-coding regions in deep arthropod phylogenetics appears problematic, a result consistent with previously published studies. Lack of phylogenetic signal renders the resulting tree topologies as suspect

  6. Arthropod phylogenetics in light of three novel millipede (myriapoda: diplopoda mitochondrial genomes with comments on the appropriateness of mitochondrial genome sequence data for inferring deep level relationships.

    Directory of Open Access Journals (Sweden)

    Michael S Brewer

    Full Text Available BACKGROUND: Arthropods are the most diverse group of eukaryotic organisms, but their phylogenetic relationships are poorly understood. Herein, we describe three mitochondrial genomes representing orders of millipedes for which complete genomes had not been characterized. Newly sequenced genomes are combined with existing data to characterize the protein coding regions of myriapods and to attempt to reconstruct the evolutionary relationships within the Myriapoda and Arthropoda. RESULTS: The newly sequenced genomes are similar to previously characterized millipede sequences in terms of synteny and length. Unique translocations occurred within the newly sequenced taxa, including one half of the Appalachioria falcifera genome, which is inverted with respect to other millipede genomes. Across myriapods, amino acid conservation levels are highly dependent on the gene region. Additionally, individual loci varied in the level of amino acid conservation. Overall, most gene regions showed low levels of conservation at many sites. Attempts to reconstruct the evolutionary relationships suffered from questionable relationships and low support values. Analyses of phylogenetic informativeness show the lack of signal deep in the trees (i.e., genes evolve too quickly. As a result, the myriapod tree resembles previously published results but lacks convincing support, and, within the arthropod tree, well established groups were recovered as polyphyletic. CONCLUSIONS: The novel genome sequences described herein provide useful genomic information concerning millipede groups that had not been investigated. Taken together with existing sequences, the variety of compositions and evolution of myriapod mitochondrial genomes are shown to be more complex than previously thought. Unfortunately, the use of mitochondrial protein-coding regions in deep arthropod phylogenetics appears problematic, a result consistent with previously published studies. Lack of phylogenetic

  7. Changes in extreme regional sea level under global warming

    NARCIS (Netherlands)

    Brunnabend, S. E.; Dijkstra, H. A.; Kliphuis, Michael; Bal, Henri E.; Seinstra, Frank J.; van Werkhoven, Ben; Maassen, J.; van Meersbergen, Maarten

    2017-01-01

    An important contribution to future changes in regional sea level extremes is due to the changes in intrinsic ocean variability, in particular ocean eddies. Here, we study a scenario of future dynamic sea level (DSL) extremes using a high-resolution version of the Parallel Ocean Program and

  8. Individuals with Asperger's Disorder Exhibit Difficulty in Switching Attention from a Local Level to a Global Level

    Science.gov (United States)

    Katagiri, Masatoshi; Kasai, Tetsuko; Kamio, Yoko; Murohashi, Harumitsu

    2013-01-01

    The purpose of the present study was to determine whether individuals with Asperger's disorder exhibit difficulty in switching attention from a local level to a global level. Eleven participants with Asperger's disorder and 11 age- and gender-matched healthy controls performed a level-repetition switching task using Navon-type hierarchical…

  9. Age-Related Change in Shifting Attention between Global and Local Levels of Hierarchical Stimuli

    Science.gov (United States)

    Huizinga, Mariette; Burack, Jacob A.; Van der Molen, Maurits W.

    2010-01-01

    The focus of this study was the developmental pattern of the ability to shift attention between global and local levels of hierarchical stimuli. Children aged 7 years and 11 years and 21-year-old adults were administered a task (two experiments) that allowed for the examination of 1) the direction of attention to global or local stimulus levels;…

  10. Genome-level comparisons provide insight into the phylogeny and metabolic diversity of species within the genus Lactococcus.

    Science.gov (United States)

    Yu, Jie; Song, Yuqin; Ren, Yan; Qing, Yanting; Liu, Wenjun; Sun, Zhihong

    2017-11-03

    The genomic diversity of different species within the genus Lactococcus and the relationships between genomic differentiation and environmental factors remain unclear. In this study, type isolates of ten Lactococcus species/subspecies were sequenced to assess their genomic characteristics, metabolic diversity, and phylogenetic relationships. The total genome sizes varied between 1.99 (Lactococcus plantarum) and 2.46 megabases (Mb; L. lactis subsp. lactis), and the G + C content ranged from 34.81 (L. lactis subsp. hordniae) to 39.67% (L. raffinolactis) with an average value of 37.02%. Analysis of genome dynamics indicated that the genus Lactococcus has an open pan-genome, while the core genome size decreased with sequential addition at the genus and species group levels. A phylogenetic dendrogram based on the concatenated amino acid sequences of 643 core genes was largely consistent with the phylogenetic tree obtained by 16S ribosomal RNA (rRNA) genes, but it provided a more robust phylogenetic resolution than the 16S rRNA gene-based analysis. Comparative genomics indicated that species in the genus Lactococcus had high degrees of diversity in genome size, gene content, and carbohydrate metabolism. This may be important for the specific adaptations that allow different Lactococcus species to survive in different environments. These results provide a quantitative basis for understanding the genomic and metabolic diversity within the genus Lactococcus, laying the foundation for future studies on taxonomy and functional genomics.

  11. Individuals with Asperger’s Disorder Exhibit Difficulty in Switching Attention from a Local Level to a Global Level

    OpenAIRE

    Katagiri, Masatoshi; Kasai, Tetsuko; Kamio, Yoko; Murohashi, Harumitsu

    2013-01-01

    The purpose of the present study was to determine whether individuals with Asperger’s disorder exhibit difficulty in switching attention from a local level to a global level. Eleven participants with Asperger’s disorder and 11 age- and gendermatched healthy controls performed a level-repetition switching task using Navontype hierarchical stimuli. In both groups, level-repetition was beneficial at both levels. Furthermore, individuals with Asperger’s disorder exhibited difficulty in switchi...

  12. DNA sequence explains seemingly disordered methylation levels in partially methylated domains of Mammalian genomes.

    Directory of Open Access Journals (Sweden)

    Dimos Gaidatzis

    2014-02-01

    Full Text Available For the most part metazoan genomes are highly methylated and harbor only small regions with low or absent methylation. In contrast, partially methylated domains (PMDs, recently discovered in a variety of cell lines and tissues, do not fit this paradigm as they show partial methylation for large portions (20%-40% of the genome. While in PMDs methylation levels are reduced on average, we found that at single CpG resolution, they show extensive variability along the genome outside of CpG islands and DNase I hypersensitive sites (DHS. Methylation levels range from 0% to 100% in a roughly uniform fashion with only little similarity between neighboring CpGs. A comparison of various PMD-containing methylomes showed that these seemingly disordered states of methylation are strongly conserved across cell types for virtually every PMD. Comparative sequence analysis suggests that DNA sequence is a major determinant of these methylation states. This is further substantiated by a purely sequence based model which can predict 31% (R(2 of the variation in methylation. The model revealed CpG density as the main driving feature promoting methylation, opposite to what has been shown for CpG islands, followed by various dinucleotides immediately flanking the CpG and a minor contribution from sequence preferences reflecting nucleosome positioning. Taken together we provide a reinterpretation for the nucleotide-specific methylation levels observed in PMDs, demonstrate their conservation across tissues and suggest that they are mainly determined by specific DNA sequence features.

  13. The genome of Diuraphis noxia, a global aphid pest of small grains.

    Science.gov (United States)

    Nicholson, Scott J; Nickerson, Michael L; Dean, Michael; Song, Yan; Hoyt, Peter R; Rhee, Hwanseok; Kim, Changhoon; Puterka, Gary J

    2015-06-05

    The Russian wheat aphid, Diuraphis noxia Kurdjumov, is one of the most important pests of small grains throughout the temperate regions of the world. This phytotoxic aphid causes severe systemic damage symptoms in wheat, barley, and other small grains as a direct result of the salivary proteins it injects into the plant while feeding. We sequenced and de novo assembled the genome of D. noxia Biotype 2, the strain most virulent to resistance genes in wheat. The assembled genomic scaffolds span 393 MB, equivalent to 93% of its 421 MB genome, and contains 19,097 genes. D. noxia has the most AT-rich insect genome sequenced to date (70.9%), with a bimodal CpG(O/E) distribution and a complete set of methylation related genes. The D. noxia genome displays a widespread, extensive reduction in the number of genes per ortholog group, including defensive, detoxification, chemosensory, and sugar transporter groups in comparison to the Acyrthosiphon pisum genome, including a 65% reduction in chemoreceptor genes. Thirty of 34 known D. noxia salivary genes were found in this assembly. These genes exhibited less homology with those salivary genes commonly expressed in insect saliva, such as glucose dehydrogenase and trehalase, yet greater conservation among genes that are expressed in D. noxia saliva but not detected in the saliva of other insects. Genes involved in insecticide activity and endosymbiont-derived genes were also found, as well as genes involved in virus transmission, although D. noxia is not a viral vector. This genome is the second sequenced aphid genome, and the first of a phytotoxic insect. D. noxia's reduced gene content of may reflect the influence of phytotoxic feeding in shaping the D. noxia genome, and in turn in broadening its host range. The presence of methylation-related genes, including cytosine methylation, is consistent with other parthenogenetic and polyphenic insects. The D. noxia genome will provide an important contrast to the A. pisum genome and

  14. Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in Staphylococcus aureus.

    Science.gov (United States)

    Carroll, Ronan K; Weiss, Andy; Broach, William H; Wiemels, Richard E; Mogen, Austin B; Rice, Kelly C; Shaw, Lindsey N

    2016-02-09

    In Staphylococcus aureus, hundreds of small regulatory or small RNAs (sRNAs) have been identified, yet this class of molecule remains poorly understood and severely understudied. sRNA genes are typically absent from genome annotation files, and as a consequence, their existence is often overlooked, particularly in global transcriptomic studies. To facilitate improved detection and analysis of sRNAs in S. aureus, we generated updated GenBank files for three commonly used S. aureus strains (MRSA252, NCTC 8325, and USA300), in which we added annotations for >260 previously identified sRNAs. These files, the first to include genome-wide annotation of sRNAs in S. aureus, were then used as a foundation to identify novel sRNAs in the community-associated methicillin-resistant strain USA300. This analysis led to the discovery of 39 previously unidentified sRNAs. Investigating the genomic loci of the newly identified sRNAs revealed a surprising degree of inconsistency in genome annotation in S. aureus, which may be hindering the analysis and functional exploration of these elements. Finally, using our newly created annotation files as a reference, we perform a global analysis of sRNA gene expression in S. aureus and demonstrate that the newly identified tsr25 is the most highly upregulated sRNA in human serum. This study provides an invaluable resource to the S. aureus research community in the form of our newly generated annotation files, while at the same time presenting the first examination of differential sRNA expression in pathophysiologically relevant conditions. Despite a large number of studies identifying regulatory or small RNA (sRNA) genes in Staphylococcus aureus, their annotation is notably lacking in available genome files. In addition to this, there has been a considerable lack of cross-referencing in the wealth of studies identifying these elements, often leading to the same sRNA being identified multiple times and bearing multiple names. In this work

  15. Global Anthropogenic Phosphorus Loads to Fresh Water, Grey Water Footprint and Water Pollution Levels: A High-Resolution Global Study

    Science.gov (United States)

    Mekonnen, M. M.; Hoekstra, A. Y. Y.

    2014-12-01

    We estimated anthropogenic phosphorus (P) loads to freshwater, globally at a spatial resolution level of 5 by 5 arc minute. The global anthropogenic P load to freshwater systems from both diffuse and point sources in the period 2002-2010 was 1.5 million tonnes per year. China contributed about 30% to this global anthropogenic P load. India was the second largest contributor (8%), followed by the USA (7%), Spain and Brazil each contributing 6% to the total. The domestic sector contributed the largest share (54%) to this total followed by agriculture (38%) and industry (8%). Among the crops, production of cereals had the largest contribution to the P loads (32%), followed by fruits, vegetables, and oil crops, each contributing about 15% to the total. We also calculated the resultant grey water footprints, and relate the grey water footprints per river basin to runoff to calculate the P-related water pollution level (WPL) per catchment.

  16. Contributing to Tumor Molecular Characterization Projects with a Global Impact | Office of Cancer Genomics

    Science.gov (United States)

    My name is Nicholas Griner and I am the Scientific Program Manager for the Cancer Genome Characterization Initiative (CGCI) in the Office of Cancer Genomics (OCG). Until recently, I spent most of my scientific career working in a cancer research laboratory. In my postdoctoral training, my research focused on identifying novel pathways that contribute to both prostate and breast cancers and studying proteins within these pathways that may be targeted with cancer drugs.

  17. A compromised yeast RNA polymerase II enhances UV sensitivity in the absence of global genome nucleotide excision repair.

    Science.gov (United States)

    Wong, J M; Ingles, C J

    2001-02-01

    Nucleotide excision repair is the major pathway responsible for removing UV-induced DNA damage, and is therefore essential for cell survival following exposure to UV radiation. In this report, we have assessed the contributions of some components of the RNA polymerase II (Pol II) transcription machinery to UV resistance in Saccharomyces cerevisiae. Deletion of the gene encoding the Pol II elongation factor TFIIS (SII) resulted in enhanced UV sensitivity, but only in the absence of global genome repair dependent on the RAD7 and RAD16 genes, a result seen previously with deletions of RAD26 and RAD28, yeast homologs of the human Cockayne syndrome genes CSB and CSA, respectively. A RAD7/16-dependent reduction in survival after UV irradiation was also seen in the presence of mutations in RNA Pol II that confer a defect in its response to SII, as well as with other mutations which reside in regions of the largest subunit of Pol II not involved in SII interactions. Indeed, an increase in UV sensitivity was achieved by simply decreasing the steadystate level of RNA Pol II. Truncation of the C-terminal domain and other RNA Pol II mutations conferred sensitivity to the ribonucleotide reductase inhibitor hydroxyurea and induction of RNR1 and RNR2 mRNAs after UV irradiation was attenuated in these mutant cells. That UV sensitivity can be a consequence of mutations in the RNA Pol II machinery in yeast cells suggests that alterations in transcriptional programs could underlie some of the pathophysiological defects seen in the human disease Cockayne syndrome.

  18. Global Sourcing: Evidence from Spanish Firm-level Data

    DEFF Research Database (Denmark)

    Kohler, Wilhelm; Smolka, Marcel

    2012-01-01

    We investigate the link between productivity of firms and their sourcing behavior. Following Antràs and Helpman (2004) we distinguish between domestic and foreign sourcing, as well as between outsourcing and vertical integration. A firm's choice is driven by a hold-up problem caused by lack of en...... of enforceable contracts. We use Spanish firm-level data to examine the productivity premia associated with the different sourcing strategies....

  19. All the World's a Stage: Facilitating Discovery Science and Improved Cancer Care through the Global Alliance for Genomics and Health.

    Science.gov (United States)

    Lawler, Mark; Siu, Lillian L; Rehm, Heidi L; Chanock, Stephen J; Alterovitz, Gil; Burn, John; Calvo, Fabien; Lacombe, Denis; Teh, Bin Tean; North, Kathryn N; Sawyers, Charles L

    2015-11-01

    The recent explosion of genetic and clinical data generated from tumor genome analysis presents an unparalleled opportunity to enhance our understanding of cancer, but this opportunity is compromised by the reluctance of many in the scientific community to share datasets and the lack of interoperability between different data platforms. The Global Alliance for Genomics and Health is addressing these barriers and challenges through a cooperative framework that encourages "team science" and responsible data sharing, complemented by the development of a series of application program interfaces that link different data platforms, thus breaking down traditional silos and liberating the data to enable new discoveries and ultimately benefit patients. ©2015 American Association for Cancer Research.

  20. Sea Level Data Archaeology for the Global Sea Level Observing System (GLOSS)

    Science.gov (United States)

    Bradshaw, Elizabeth; Matthews, Andy; Rickards, Lesley; Jevrejeva, Svetlana

    2015-04-01

    The Global Sea Level Observing System (GLOSS) was set up in 1985 to collect long term tide gauge observations and has carried out a number of data archaeology activities over the past decade, including sending member organisations questionnaires to report on their repositories. The GLOSS Group of Experts (GLOSS GE) is looking to future developments in sea level data archaeology and will provide its user community with guidance on finding, digitising, quality controlling and distributing historic records. Many records may not be held in organisational archives and may instead by in national libraries, archives and other collections. GLOSS will promote a Citizen Science approach to discovering long term records by providing tools for volunteers to report data. Tide gauge data come in two different formats, charts and hand-written ledgers. Charts are paper analogue records generated by the mechanical instrument driving a pen trace. Several GLOSS members have developed software to automatically digitise these charts and the various methods were reported in a paper on automated techniques for the digitization of archived mareograms, delivered to the GLOSS GE 13th meeting. GLOSS is creating a repository of software for scanning analogue charts. NUNIEAU is the only publically available software for digitising tide gauge charts but other organisations have developed their own tide gauge digitising software that is available internally. There are several other freely available software packages that convert image data to numerical values. GLOSS could coordinate a comparison study of the various different digitising software programs by: Sending the same charts to each organisation and asking everyone to digitise them using their own procedures Comparing the digitised data Providing recommendations to the GLOSS community The other major form of analogue sea level data is handwritten ledgers, which are usually observations of high and low waters, but sometimes contain higher

  1. Interaction of a common painkiller piroxicam and copper-piroxicam with chromatin causes structural alterations accompanied by modulation at the epigenomic/genomic level.

    Science.gov (United States)

    Goswami, Sathi; Sanyal, Sulagna; Chakraborty, Payal; Das, Chandrima; Sarkar, Munna

    2017-08-01

    NSAIDs are the most common class of painkillers and anti-inflammatory agents. They also show other functions like chemoprevention and chemosuppression for which they act at the protein but not at the genome level since they are mostly anions at physiological pH, which prohibit their approach to the poly-anionic DNA. Complexing the drugs with bioactive metal obliterate their negative charge and allow them to bind to the DNA, thereby, opening the possibility of genome level interaction. To test this hypothesis, we present the interaction of a traditional NSAID, Piroxicam and its copper complex with core histone and chromatin. Spectroscopy, DLS, and SEM studies were applied to see the effect of the interaction on the structure of histone/chromatin. This was coupled with MTT assay, immunoblot analysis, confocal microscopy, micro array analysis and qRT-PCR. The interaction of Piroxicam and its copper complex with histone/chromatin results in structural alterations. Such structural alterations can have different biological manifestations, but to test our hypothesis, we have focused only on the accompanied modulations at the epigenomic/genomic level. The complex, showed alteration of key epigenetic signatures implicated in transcription in the global context, although Piroxicam caused no significant changes. We have correlated such alterations caused by the complex with the changes in global gene expression and validated the candidate gene expression alterations. Our results provide the proof of concept that DNA binding ability of the copper complexes of a traditional NSAID, opens up the possibility of modulations at the epigenomic/genomic level. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Photobiomodulation effects on mRNA levels from genomic and chromosome stabilization genes in injured muscle.

    Science.gov (United States)

    da Silva Neto Trajano, Larissa Alexsandra; Trajano, Eduardo Tavares Lima; da Silva Sergio, Luiz Philippe; Teixeira, Adilson Fonseca; Mencalha, Andre Luiz; Stumbo, Ana Carolina; de Souza da Fonseca, Adenilson

    2018-04-26

    Muscle injuries are the most prevalent type of injury in sports. A great number of athletes have relapsed in muscle injuries not being treated properly. Photobiomodulation therapy is an inexpensive and safe technique with many benefits in muscle injury treatment. However, little has been explored about the infrared laser effects on DNA and telomeres in muscle injuries. Thus, the aim of this study was to evaluate photobiomodulation effects on mRNA relative levels from genes related to telomere and genomic stabilization in injured muscle. Wistar male rats were randomly divided into six groups: control, laser 25 mW, laser 75 mW, injury, injury laser 25 mW, and injury laser 75 mW. Photobiomodulation was performed with 904 nm, 3 J/cm 2 at 25 or 75 mW. Cryoinjury was induced by two applications of a metal probe cooled in liquid nitrogen directly on the tibialis anterior muscle. After euthanasia, skeletal muscle samples were withdrawn and total RNA extracted for evaluation of mRNA levels from genomic (ATM and p53) and chromosome stabilization (TRF1 and TRF2) genes by real-time quantitative polymerization chain reaction. Data show that photobiomodulation reduces the mRNA levels from ATM and p53, as well reduces mRNA levels from TRF1 and TRF2 at 25 and 75 mW in injured skeletal muscle. In conclusion, photobiomodulation alters mRNA relative levels from genes related to genomic and telomere stabilization in injured skeletal muscle.

  3. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

    Directory of Open Access Journals (Sweden)

    Cronn Richard

    2009-12-01

    Full Text Available Abstract Background Molecular evolutionary studies share the common goal of elucidating historical relationships, and the common challenge of adequately sampling taxa and characters. Particularly at low taxonomic levels, recent divergence, rapid radiations, and conservative genome evolution yield limited sequence variation, and dense taxon sampling is often desirable. Recent advances in massively parallel sequencing make it possible to rapidly obtain large amounts of sequence data, and multiplexing makes extensive sampling of megabase sequences feasible. Is it possible to efficiently apply massively parallel sequencing to increase phylogenetic resolution at low taxonomic levels? Results We reconstruct the infrageneric phylogeny of Pinus from 37 nearly-complete chloroplast genomes (average 109 kilobases each of an approximately 120 kilobase genome generated using multiplexed massively parallel sequencing. 30/33 ingroup nodes resolved with ≥ 95% bootstrap support; this is a substantial improvement relative to prior studies, and shows massively parallel sequencing-based strategies can produce sufficient high quality sequence to reach support levels originally proposed for the phylogenetic bootstrap. Resampling simulations show that at least the entire plastome is necessary to fully resolve Pinus, particularly in rapidly radiating clades. Meta-analysis of 99 published infrageneric phylogenies shows that whole plastome analysis should provide similar gains across a range of plant genera. A disproportionate amount of phylogenetic information resides in two loci (ycf1, ycf2, highlighting their unusual evolutionary properties. Conclusion Plastome sequencing is now an efficient option for increasing phylogenetic resolution at lower taxonomic levels in plant phylogenetic and population genetic analyses. With continuing improvements in sequencing capacity, the strategies herein should revolutionize efforts requiring dense taxon and character sampling

  4. Thermosteric contribution of warming oceans to the global sea level variations

    OpenAIRE

    Bâki Iz H.

    2016-01-01

    Thermosteric contribution of warming oceans to the global sea level variations during the last century was evaluated at globally distributed 27 tide gauge stations with records over 80 years. The assessment was made using a recently proposed lagged model inclusive of a sea level trend, long and decadal periodicities, and lagged sea surface temperature measurements. The new model solutions revealed that almost all the long period periodic sea level changes experienced a...

  5. Evaluating model simulations of 20th century sea-level rise. Part 1: global mean sea-level change

    NARCIS (Netherlands)

    Slangen, A.B.A.; Meyssignac, B.; Agosta, C.; Champollion, N.; Church, J.A.; Fettweis, X.; Ligtenberg, S.R.M.; Marzeion, B.; Melet, A.; Palmer, M.D.; Richter, K.; Roberts, C.D.; Spada, G.

    2017-01-01

    Sea level change is one of the major consequences of climate change and is projected to affect coastal communities around the world. Here, global mean sea level (GMSL) change estimated by 12 climate models from phase 5 of the World Climate Research Programme’s Climate Model Intercomparison Project

  6. The Not-So-Global Blood Oxygen Level-Dependent Signal.

    Science.gov (United States)

    Billings, Jacob; Keilholz, Shella

    2018-04-01

    Global signal regression is a controversial processing step for resting-state functional magnetic resonance imaging, partly because the source of the global blood oxygen level-dependent (BOLD) signal remains unclear. On the one hand, nuisance factors such as motion can readily introduce coherent BOLD changes across the whole brain. On the other hand, the global signal has been linked to neural activity and vigilance levels, suggesting that it contains important neurophysiological information and should not be discarded. Any widespread pattern of coordinated activity is likely to contribute appreciably to the global signal. Such patterns may include large-scale quasiperiodic spatiotemporal patterns, known also to be tied to performance on vigilance tasks. This uncertainty surrounding the separability of the global BOLD signal from concurrent neurological processes motivated an examination of the global BOLD signal's spatial distribution. The results clarify that although the global signal collects information from all tissue classes, a diverse subset of the BOLD signal's independent components contribute the most to the global signal. Further, the timing of each network's contribution to the global signal is not consistent across volunteers, confirming the independence of a constituent process that comprises the global signal.

  7. The Genomes of All Angiosperms: A Call for a Coordinated Global Census

    Directory of Open Access Journals (Sweden)

    David W. Galbraith

    2011-01-01

    Full Text Available Recent advances in biological instrumentation and associated experimental technologies now permit an unprecedented efficiency and scale for the acquisition of genomic data, at ever-decreasing costs. Further advances, with accompanying decreases in cost, are expected in the very near term. It now becomes appropriate to discuss the best uses of these technologies in the context of the angiosperms. This white paper proposes a complete genomic census of the approximately 500,000 species of flowering plants, outlines the goals of this census and their value, and provides a road map towards achieving these goals in a timely manner.

  8. Association of postmenopausal endogenous sex hormones with global methylation level of leukocyte DNA among Japanese women

    Directory of Open Access Journals (Sweden)

    Iwasaki Motoki

    2012-07-01

    Full Text Available Abstract Background Although global hypomethylation of leukocyte DNA has been associated with an increased risk of several sites of cancer, including breast cancer, determinants of global methylation level among healthy individuals remain largely unexplored. Here, we examined whether postmenopausal endogenous sex hormones were associated with the global methylation level of leukocyte DNA. Methods A cross-sectional study was conducted using the control group of a breast cancer case–control study in Nagano, Japan. Subjects were postmenopausal women aged 55 years or over who provided blood samples. We measured global methylation level of peripheral blood leukocyte DNA by luminometric methylation assay; estradiol, estrone, androstenedione, dehydroepiandrosterone sulfate, testosterone and free testosterone by radioimmunoassay; bioavailable estradiol by the ammonium sulfate precipitation method; and sex-hormone binding globulin by immunoradiometric assay. A linear trend of association between methylation and hormone levels was evaluated by regression coefficients in a multivariable liner regression model. A total of 185 women were included in the analyses. Results Mean global methylation level (standard deviation was 70.3% (3.1 and range was from 60.3% to 79.2%. Global methylation level decreased 0.27% per quartile category for estradiol and 0.39% per quartile category for estrone while it increased 0.41% per quartile category for bioavailable estradiol. However, we found no statistically significant association of any sex hormone level measured in the present study with global methylation level of leukocyte DNA. Conclusions Our findings suggest that endogenous sex hormones are not major determinants of the global methylation level of leukocyte DNA.

  9. Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications.

    Science.gov (United States)

    Christen, Matthias; Del Medico, Luca; Christen, Heinz; Christen, Beat

    2017-01-01

    Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs. Without the need for specialized computing skills, biologists can submit their DNA designs to a fully automated pipeline that generates the optimal retrosynthetic route for higher-order DNA assembly. To test the algorithm, we partitioned a 783 kb Caulobacter crescentus genome design. We validated the partitioning strategy by assembling a 20 kb test segment encompassing a difficult to synthesize DNA sequence. Successful assembly from 1 kb subblocks into the 20 kb segment highlights the effectiveness of the Genome Partitioner for reducing synthesis costs and timelines for higher-order DNA assembly. The Genome Partitioner is broadly applicable to translate DNA designs into ready to order sequences that can be assembled with standardized protocols, thus offering new opportunities to harness the diversity of microbial genomes for synthetic biology applications. The Genome Partitioner web tool can be accessed at https://christenlab.ethz.ch/GenomePartitioner.

  10. Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications.

    Directory of Open Access Journals (Sweden)

    Matthias Christen

    Full Text Available Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs. Without the need for specialized computing skills, biologists can submit their DNA designs to a fully automated pipeline that generates the optimal retrosynthetic route for higher-order DNA assembly. To test the algorithm, we partitioned a 783 kb Caulobacter crescentus genome design. We validated the partitioning strategy by assembling a 20 kb test segment encompassing a difficult to synthesize DNA sequence. Successful assembly from 1 kb subblocks into the 20 kb segment highlights the effectiveness of the Genome Partitioner for reducing synthesis costs and timelines for higher-order DNA assembly. The Genome Partitioner is broadly applicable to translate DNA designs into ready to order sequences that can be assembled with standardized protocols, thus offering new opportunities to harness the diversity of microbial genomes for synthetic biology applications. The Genome Partitioner web tool can be accessed at https://christenlab.ethz.ch/GenomePartitioner.

  11. Global Fire Emissions Indicators, Country-Level Tabular Data: 1997-2015

    Data.gov (United States)

    National Aeronautics and Space Administration — The Global Fire Emissions Indicators, Country-Level Tabular Data: 1997-2015 contains country tabulations from 1997 to 2015 for the total area burned (hectares) and...

  12. GHRSST Level 4 AVHRR_AMSR_OI Global Blended Sea Surface Temperature Analysis (GDS version 1)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A Group for High Resolution Sea Surface Temperature (GHRSST) global Level 4 sea surface temperature analysis produced daily on a 0.25 degree grid at the NOAA...

  13. GHRSST Level 4 MW_OI Global Foundation Sea Surface Temperature analysis (GDS version 2)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A Group for High Resolution Sea Surface Temperature (GHRSST) global Level 4 sea surface temperature analysis produced daily on a 0.25 degree grid at Remote Sensing...

  14. High density, genome-wide markers and intra-specific replication yield an unprecedented phylogenetic reconstruction of a globally significant, speciose lineage of Eucalyptus.

    Science.gov (United States)

    Jones, Rebecca C; Nicolle, Dean; Steane, Dorothy A; Vaillancourt, René E; Potts, Brad M

    2016-12-01

    We used genome-wide markers and an unprecedented scale of sampling to construct a phylogeny for a globally significant Eucalyptus lineage that has been impacted by hybridisation, recent radiation and morphological convergence. Our approach, using 3109 DArT markers distributed throughout the genome and 540 samples covering 185 terminal taxa in sections Maidenaria, Exsertaria, Latoangulatae and related smaller sections, with multiple geographically widespread samples per terminal taxon, produced a phylogeny that largely matched the morphological treatment of sections, though sections Exsertaria and Latoangulatae were polyphyletic. At lower levels there were numerous inconsistencies between the morphological treatment and the molecular phylogeny, and taxa within the three main sections were generally not monophyletic at the series (at least 62% polyphyly) or species (at least 52% polyphyly) level. Some of the discrepancies appear to be the result of morphological convergence or misclassifications, and we propose some taxonomic reassessments to address this. However, many inconsistencies appear to be the products of incomplete speciation and/or hybridisation. Our analysis represents a significant advance on previous phylogenies of these important eucalypt sections (which have mainly used single samples to represent each species), thus providing a robust phylogenetic framework for evolutionary and ecological studies. Copyright © 2016 Elsevier Inc. All rights reserved.

  15. Nucleotide excision repair : complexes and complexities : a study of global genome repair in human cells

    NARCIS (Netherlands)

    Volker, Marcel

    2006-01-01

    Of all exogenous agents that damage genomic DNA and hence threaten its integrity, the ultraviolet B (UVB) component of sunlight is highly relevant because of its abundance. UVB induces predominantly cyclobutane pyrimidine dimers and 6-4 photoproducts. In humans, these photolesions are repaired by

  16. Genome-Wide Tuning of Protein Expression Levels to Rapidly Engineer Microbial Traits.

    Science.gov (United States)

    Freed, Emily F; Winkler, James D; Weiss, Sophie J; Garst, Andrew D; Mutalik, Vivek K; Arkin, Adam P; Knight, Rob; Gill, Ryan T

    2015-11-20

    The reliable engineering of biological systems requires quantitative mapping of predictable and context-independent expression over a broad range of protein expression levels. However, current techniques for modifying expression levels are cumbersome and are not amenable to high-throughput approaches. Here we present major improvements to current techniques through the design and construction of E. coli genome-wide libraries using synthetic DNA cassettes that can tune expression over a ∼10(4) range. The cassettes also contain molecular barcodes that are optimized for next-generation sequencing, enabling rapid and quantitative tracking of alleles that have the highest fitness advantage. We show these libraries can be used to determine which genes and expression levels confer greater fitness to E. coli under different growth conditions.

  17. Genomic Analysis of the Emergence and Rapid Global Dissemination of the Clonal Group 258 Klebsiella pneumoniae Pandemic.

    Directory of Open Access Journals (Sweden)

    Jolene R Bowers

    Full Text Available Multidrug-resistant Klebsiella pneumoniae producing the KPC carbapenemase have rapidly spread throughout the world, causing severe healthcare-associated infections with limited antimicrobial treatment options. Dissemination of KPC-producing K. pneumoniae is largely attributed to expansion of a single dominant strain, ST258. In this study, we explore phylogenetic relationships and evolution within ST258 and its clonal group, CG258, using whole genome sequence analysis of 167 isolates from 20 countries collected over 17 years. Our results show a common ST258 ancestor emerged from its diverse parental clonal group around 1995 and likely acquired blaKPC prior to dissemination. Over the past two decades, ST258 has remained highly clonal despite diversity in accessory elements and divergence in the capsule polysaccharide synthesis locus. Apart from the large recombination event that gave rise to ST258, few mutations set it apart from its clonal group. However, one mutation occurs in a global transcription regulator. Characterization of outer membrane protein sequences revealed a profile in ST258 that includes a truncated OmpK35 and modified OmpK37. Our work illuminates potential genomic contributors to the pathogenic success of ST258, helps us better understand the global dissemination of this strain, and identifies genetic markers unique to ST258.

  18. Functional architecture and global properties of the Corynebacterium glutamicum regulatory network: Novel insights from a dataset with a high genomic coverage.

    Science.gov (United States)

    Freyre-González, Julio A; Tauch, Andreas

    2017-09-10

    Corynebacterium glutamicum is a Gram-positive, anaerobic, rod-shaped soil bacterium able to grow on a diversity of carbon sources like sugars and organic acids. It is a biotechnological relevant organism because of its highly efficient ability to biosynthesize amino acids, such as l-glutamic acid and l-lysine. Here, we reconstructed the most complete C. glutamicum regulatory network to date and comprehensively analyzed its global organizational properties, systems-level features and functional architecture. Our analyses show the tremendous power of Abasy Atlas to study the functional organization of regulatory networks. We created two models of the C. glutamicum regulatory network: all-evidences (containing both weak and strong supported interactions, genomic coverage=73%) and strongly-supported (only accounting for strongly supported evidences, genomic coverage=71%). Using state-of-the-art methodologies, we prove that power-law behaviors truly govern the connectivity and clustering coefficient distributions. We found a non-previously reported circuit motif that we named complex feed-forward motif. We highlighted the importance of feedback loops for the functional architecture, beyond whether they are statistically over-represented or not in the network. We show that the previously reported top-down approach is inadequate to infer the hierarchy governing a regulatory network because feedback bridges different hierarchical layers, and the top-down approach disregards the presence of intermodular genes shaping the integration layer. Our findings all together further support a diamond-shaped, three-layered hierarchy exhibiting some feedback between processing and coordination layers, which is shaped by four classes of systems-level elements: global regulators, locally autonomous modules, basal machinery and intermodular genes. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Evolution of global contribution in multi-level threshold public goods games with insurance compensation

    Science.gov (United States)

    Du, Jinming; Tang, Lixin

    2018-01-01

    Understanding voluntary contribution in threshold public goods games has important practical implications. To improve contributions and provision frequency, free-rider problem and assurance problem should be solved. Insurance could play a significant, but largely unrecognized, role in facilitating a contribution to provision of public goods through providing insurance compensation against the losses. In this paper, we study how insurance compensation mechanism affects individuals’ decision-making under risk environments. We propose a multi-level threshold public goods game model where two kinds of public goods games (local and global) are considered. Particularly, the global public goods game involves a threshold, which is related to the safety of all the players. We theoretically probe the evolution of contributions of different levels and free-riders, and focus on the influence of the insurance on the global contribution. We explore, in both the cases, the scenarios that only global contributors could buy insurance and all the players could. It is found that with greater insurance compensation, especially under high collective risks, players are more likely to contribute globally when only global contributors are insured. On the other hand, global contribution could be promoted if a premium discount is given to global contributors when everyone buys insurance.

  20. Banking biological collections: data warehousing, data mining, and data dilemmas in genomics and global health policy.

    Science.gov (United States)

    Blatt, R J R

    2000-01-01

    While DNA databases may offer the opportunity to (1) assess population-based prevalence of specific genes and variants, (2) simplify the search for molecular markers, (3) improve targeted drug discovery and development for disease management, (4) refine strategies for disease prevention, and (5) provide the data necessary for evidence-based decision-making, serious scientific and social questions remain. Whether samples are identified, coded, or anonymous, biological banking raises profound ethical and legal issues pertaining to access, informed consent, privacy and confidentiality of genomic information, civil liberties, patenting, and proprietary rights. This paper provides an overview of key policy issues and questions pertaining to biological banking, with a focus on developments in specimen collection, transnational distribution, and public health and academic-industry research alliances. It highlights the challenges posed by the commercialization of genomics, and proposes the need for harmonization of biological banking policies.

  1. A genome-wide association study reveals variants in ARL15 that influence adiponectin levels.

    Directory of Open Access Journals (Sweden)

    J Brent Richards

    2009-12-01

    Full Text Available The adipocyte-derived protein adiponectin is highly heritable and inversely associated with risk of type 2 diabetes mellitus (T2D and coronary heart disease (CHD. We meta-analyzed 3 genome-wide association studies for circulating adiponectin levels (n = 8,531 and sought validation of the lead single nucleotide polymorphisms (SNPs in 5 additional cohorts (n = 6,202. Five SNPs were genome-wide significant in their relationship with adiponectin (P< or =5x10(-8. We then tested whether these 5 SNPs were associated with risk of T2D and CHD using a Bonferroni-corrected threshold of P< or =0.011 to declare statistical significance for these disease associations. SNPs at the adiponectin-encoding ADIPOQ locus demonstrated the strongest associations with adiponectin levels (P-combined = 9.2x10(-19 for lead SNP, rs266717, n = 14,733. A novel variant in the ARL15 (ADP-ribosylation factor-like 15 gene was associated with lower circulating levels of adiponectin (rs4311394-G, P-combined = 2.9x10(-8, n = 14,733. This same risk allele at ARL15 was also associated with a higher risk of CHD (odds ratio [OR] = 1.12, P = 8.5x10(-6, n = 22,421 more nominally, an increased risk of T2D (OR = 1.11, P = 3.2x10(-3, n = 10,128, and several metabolic traits. Expression studies in humans indicated that ARL15 is well-expressed in skeletal muscle. These findings identify a novel protein, ARL15, which influences circulating adiponectin levels and may impact upon CHD risk.

  2. Quantification of trace-level DNA by real-time whole genome amplification.

    Science.gov (United States)

    Kang, Min-Jung; Yu, Hannah; Kim, Sook-Kyung; Park, Sang-Ryoul; Yang, Inchul

    2011-01-01

    Quantification of trace amounts of DNA is a challenge in analytical applications where the concentration of a target DNA is very low or only limited amounts of samples are available for analysis. PCR-based methods including real-time PCR are highly sensitive and widely used for quantification of low-level DNA samples. However, ordinary PCR methods require at least one copy of a specific gene sequence for amplification and may not work for a sub-genomic amount of DNA. We suggest a real-time whole genome amplification method adopting the degenerate oligonucleotide primed PCR (DOP-PCR) for quantification of sub-genomic amounts of DNA. This approach enabled quantification of sub-picogram amounts of DNA independently of their sequences. When the method was applied to the human placental DNA of which amount was accurately determined by inductively coupled plasma-optical emission spectroscopy (ICP-OES), an accurate and stable quantification capability for DNA samples ranging from 80 fg to 8 ng was obtained. In blind tests of laboratory-prepared DNA samples, measurement accuracies of 7.4%, -2.1%, and -13.9% with analytical precisions around 15% were achieved for 400-pg, 4-pg, and 400-fg DNA samples, respectively. A similar quantification capability was also observed for other DNA species from calf, E. coli, and lambda phage. Therefore, when provided with an appropriate standard DNA, the suggested real-time DOP-PCR method can be used as a universal method for quantification of trace amounts of DNA.

  3. A genome-wide association study identifies rs2000999 as a strong genetic determinant of circulating haptoglobin levels.

    Directory of Open Access Journals (Sweden)

    Philippe Froguel

    Full Text Available Haptoglobin is an acute phase inflammatory marker. Its main function is to bind hemoglobin released from erythrocytes to aid its elimination, and thereby haptoglobin prevents the generation of reactive oxygen species in the blood. Haptoglobin levels have been repeatedly associated with a variety of inflammation-linked infectious and non-infectious diseases, including malaria, tuberculosis, human immunodeficiency virus, hepatitis C, diabetes, carotid atherosclerosis, and acute myocardial infarction. However, a comprehensive genetic assessment of the inter-individual variability of circulating haptoglobin levels has not been conducted so far.We used a genome-wide association study initially conducted in 631 French children followed by a replication in three additional European sample sets and we identified a common single nucleotide polymorphism (SNP, rs2000999 located in the Haptoglobin gene (HP as a strong genetic predictor of circulating Haptoglobin levels (P(overall = 8.1 × 10(-59, explaining 45.4% of its genetic variability (11.8% of Hp global variance. The functional relevance of rs2000999 was further demonstrated by its specific association with HP mRNA levels (β = 0.23 ± 0.08, P = 0.007. Finally, SNP rs2000999 was associated with decreased total and low-density lipoprotein cholesterol in 8,789 European children (P(total cholesterol = 0.002 and P(LDL = 0.0008.Given the central position of haptoglobin in many inflammation-related metabolic pathways, the relevance of rs2000999 genotyping when evaluating haptoglobin concentration should be further investigated in order to improve its diagnostic/therapeutic and/or prevention impact.

  4. International cooperative initiatives in global climate governance: Raising the ambition level or delegitimizing the UNFCCC?

    NARCIS (Netherlands)

    Widerberg, O.E.; Pattberg, P.H.

    2015-01-01

    To close the gap between existing country pledges and the necessary ambition level to limit anthropogenic climate change to not more than 2°C average global temperature increase above pre-industrial levels, decision makers from both the public and private domain have started to explore a number of

  5. Statistical analysis of global surface air temperature and sea level using cointegration methods

    DEFF Research Database (Denmark)

    Schmith, Torben; Johansen, Søren; Thejll, Peter

    Global sea levels are rising which is widely understood as a consequence of thermal expansion and melting of glaciers and land-based ice caps. Due to physically-based models being unable to simulate observed sea level trends, semi-empirical models have been applied as an alternative for projecting...... of future sea levels. There is in this, however, potential pitfalls due to the trending nature of the time series. We apply a statistical method called cointegration analysis to observed global sea level and surface air temperature, capable of handling such peculiarities. We find a relationship between sea...... level and temperature and find that temperature causally depends on the sea level, which can be understood as a consequence of the large heat capacity of the ocean. We further find that the warming episode in the 1940s is exceptional in the sense that sea level and warming deviates from the expected...

  6. Nature vs. nurture in human sociality: multi-level genomic analyses of social conformity.

    Science.gov (United States)

    Chen, Biqing; Zhu, Zijian; Wang, Yingying; Ding, Xiaohu; Guo, Xiaobo; He, Mingguang; Fang, Wan; Zhou, Qin; Zhou, Shanbi; Lei, Han; Huang, Ailong; Chen, Tingmei; Ni, Dongsheng; Gu, Yuping; Liu, Jianing; Rao, Yi

    2018-05-01

    Social conformity is fundamental to human societies and has been studied for more than six decades, but our understanding of its mechanisms remains limited. Individual differences in conformity have been attributed to social and cultural environmental influences, but not to genes. Here we demonstrate a genetic contribution to conformity after analyzing 1,140 twins and single-nucleotide polymorphism (SNP)-based studies of 2,130 young adults. A two-step genome-wide association study (GWAS) revealed replicable associations in 9 genomic loci, and a meta-analysis of three GWAS with a sample size of ~2,600 further confirmed one locus, corresponding to the NAV3 (Neuron Navigator 3) gene which encodes a protein important for axon outgrowth and guidance. Further multi-level (haplotype, gene, pathway) GWAS strongly associated genes including NAV3, PTPRD (protein tyrosine phosphatase receptor type D), ARL10 (ADP ribosylation factor-like GTPase 10), and CTNND2 (catenin delta 2), with conformity. Magnetic resonance imaging of 64 subjects shows correlation of activation or structural features of brain regions with the SNPs of these genes, supporting their functional significance. Our results suggest potential moderate genetic influence on conformity, implicate several specific genetic elements in conformity and will facilitate further research on cellular and molecular mechanisms underlying human conformity.

  7. Global sea level variations from altimetry, GRACE and Argo data over 2005–2014

    Directory of Open Access Journals (Sweden)

    Wei Feng

    2015-07-01

    Full Text Available Total sea level variations (SLVs are caused by two major components: steric variations due to thermal expansion of seawater, and mass-induced variations due to mass exchange between ocean and land. In this study, the global SLV and its steric and mass components were estimated by satellite altimetry, Argo float data and the Gravity Recovery and Climate Experiment (GRACE data over 2005–2014. Space gravimetry observations from GRACE suggested that two-thirds of the global mean sea level rise rate observed by altimetry (i.e., 3.1 ± 0.3 mm/a from 2005 to 2014 could be explained by an increase in ocean mass. Furthermore, the global mean sea level was observed to drop significantly during the 2010/2011 La Niña event, which may be attributed to the decline of ocean mass and steric SLV. Since early 2011, the global mean sea level began to rise rapidly, which was attributed to an increase in ocean mass. The findings in this study suggested that the global mean sea-level budget was closed from 2005 to 2014 based on altimetry, GRACE, and Argo data.

  8. C-RAF function at the genome-wide transcriptome level: A systematic view.

    Science.gov (United States)

    Huang, Ying; Zhang, Xin-Yu; An, Su; Yang, Yang; Liu, Ying; Hao, Qian; Guo, Xiao-Xi; Xu, Tian-Rui

    2018-05-20

    C-RAF was the first member of the RAF kinase family to be discovered. Since its discovery, C-RAF has been found to regulate many fundamental cell processes, such as cell proliferation, cell death, and metabolism. However, the majority of these functions are achieved through interactions with different proteins; the genes regulated by C-RAF in its active or inactive state remain unclear. In the work, we used RNA-seq analysis to study the global transcriptomes of C-RAF bearing or C-RAF knockout cells in quiescent or EGF activated states. We identified 3353 genes that are promoted or suppressed by C-RAF. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that these genes are involved in drug addiction, cardiomyopathy, autoimmunity, and regulation of cell metabolism. Our results provide a panoramic view of C-RAF function, including known and novel functions, and have revealed potential targets for elucidating the role of C-RAF. Copyright © 2018 Elsevier B.V. All rights reserved.

  9. Improvement of Global and Regional Mean Sea Level Trends Derived from all Altimetry Missions.

    Science.gov (United States)

    Ablain, Michael; Benveniste, Jérôme; Faugere, Yannice; Larnicol, Gilles; Cazenave, Anny; Johannessen, Johnny A.; Stammer, Detlef; Timms, Gary

    2012-07-01

    The global mean sea level (GMSL) has been calculated on a continual basis since January 1993 using data from satellite altimetry missions. The global mean sea level (MSL) deduced from TOPEX/Poseidon, Jason-1 and Jason-2 is increasing with a global trend of 3.2 mm from 1993 to 2010 applying the post glacial rebound (MSL Aviso website http://www.jason.oceanobs.com/msl). Besides, the regional sea level trends bring out an inhomogeneous repartition of the ocean elevation with local MSL slopes ranging from +/- 8 mm/year. A study published in 2009 [Ablain et al., 2009] has shown that the global MSL trend uncertainty was estimated at +/-0.6 mm/year with a confidence interval of 90%. The main sources of errors at global and regional scales are due to the orbit calculation and the wet troposphere correction. But others sea-level components have also a significant impact on the long-term stability of MSL as for instance the stability of instrumental parameters and the atmospheric corrections. Thanks to recent studies performed in Sea Level Essential Climate Variable Project in the frame of the Climate Change Initiative, an ESA Programme, in addition to activities performed within the SALP/CNES, strong improvements have been provided for the estimation of the global and regional MSL trends. In this paper, we propose to describe them; they concern the orbit calculation thanks to new gravity fields, the atmospheric corrections thanks to ERA-interim reanalyses, the wet troposphere corrections thanks to the stability improvement, and also empirical corrections allowing us to link regional time series together better. These improvements are described at global and regional scale for all the altimetry missions.

  10. A tiling microarray for global analysis of chloroplast genome expression in cucumber and other plants

    Directory of Open Access Journals (Sweden)

    Pląder Wojciech

    2011-09-01

    Full Text Available Abstract Plastids are small organelles equipped with their own genomes (plastomes. Although these organelles are involved in numerous plant metabolic pathways, current knowledge about the transcriptional activity of plastomes is limited. To solve this problem, we constructed a plastid tiling microarray (PlasTi-microarray consisting of 1629 oligonucleotide probes. The oligonucleotides were designed based on the cucumber chloroplast genomic sequence and targeted both strands of the plastome in a non-contiguous arrangement. Up to 4 specific probes were designed for each gene/exon, and the intergenic regions were covered regularly, with 70-nt intervals. We also developed a protocol for direct chemical labeling and hybridization of as little as 2 micrograms of chloroplast RNA. We used this protocol for profiling the expression of the cucumber chloroplast plastome on the PlasTi-microarray. Owing to the high sequence similarity of plant plastomes, the newly constructed microarray can be used to study plants other than cucumber. Comparative hybridization of chloroplast transcriptomes from cucumber, Arabidopsis, tomato and spinach showed that the PlasTi-microarray is highly versatile.

  11. Statistical analysis of global surface temperature and sea level using cointegration methods

    DEFF Research Database (Denmark)

    Schmidt, Torben; Johansen, Søren; Thejll, Peter

    2012-01-01

    Global sea levels are rising which is widely understood as a consequence of thermal expansion and melting of glaciers and land-based ice caps. Due to the lack of representation of ice-sheet dynamics in present-day physically-based climate models being unable to simulate observed sea level trends......, semi-empirical models have been applied as an alternative for projecting of future sea levels. There is in this, however, potential pitfalls due to the trending nature of the time series. We apply a statistical method called cointegration analysis to observed global sea level and land-ocean surface air...... temperature, capable of handling such peculiarities. We find a relationship between sea level and temperature and find that temperature causally depends on the sea level, which can be understood as a consequence of the large heat capacity of the ocean. We further find that the warming episode in the 1940s...

  12. Local adaptation at the transcriptome level in brown trout: evidence from early life history temperature genomic reaction norms.

    Directory of Open Access Journals (Sweden)

    Kristian Meier

    Full Text Available Local adaptation and its underlying molecular basis has long been a key focus in evolutionary biology. There has recently been increased interest in the evolutionary role of plasticity and the molecular mechanisms underlying local adaptation. Using transcriptome analysis, we assessed differences in gene expression profiles for three brown trout (Salmo trutta populations, one resident and two anadromous, experiencing different temperature regimes in the wild. The study was based on an F2 generation raised in a common garden setting. A previous study of the F1 generation revealed different reaction norms and significantly higher QST than FST among populations for two early life-history traits. In the present study we investigated if genomic reaction norm patterns were also present at the transcriptome level. Eggs from the three populations were incubated at two temperatures (5 and 8 degrees C representing conditions encountered in the local environments. Global gene expression for fry at the stage of first feeding was analysed using a 32k cDNA microarray. The results revealed differences in gene expression between populations and temperatures and population × temperature interactions, the latter indicating locally adapted reaction norms. Moreover, the reaction norms paralleled those observed previously at early life-history traits. We identified 90 cDNA clones among the genes with an interaction effect that were differently expressed between the ecologically divergent populations. These included genes involved in immune- and stress response. We observed less plasticity in the resident as compared to the anadromous populations, possibly reflecting that the degree of environmental heterogeneity encountered by individuals throughout their life cycle will select for variable level of phenotypic plasticity at the transcriptome level. Our study demonstrates the usefulness of transcriptome approaches to identify genes with different temperature reaction

  13. Genome sequencing - the ultimate answer to global real time genotyping and surveillance?

    DEFF Research Database (Denmark)

    Hendriksen, Rene S.

    2013-01-01

    organised to discuss the possibility of using WGS as diagnostic tool on a global scale. These meetings were attended by scientists and policy makers from around the world. The general conclusion of these meetings was that the technology exists and that the spread in the application should be linked...

  14. Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into emergence and spread of multidrug resistance

    Science.gov (United States)

    Manson, Abigail L.; Cohen, Keira A.; Abeel, Thomas; Desjardins, Christopher A.; Armstrong, Derek T.; Barry, Clifton E.; Brand, Jeannette; Chapman, Sinéad B.; Cho, Sang-Nae; Gabrielian, Andrei; Gomez, James; Jodals, Andreea M.; Joloba, Moses; Jureen, Pontus; Lee, Jong Seok; Malinga, Lesibana; Maiga, Mamoudou; Nordenberg, Dale; Noroc, Ecaterina; Romancenco, Elena; Salazar, Alex; Ssengooba, Willy; Velayati, A. A.; Winglee, Kathryn; Zalutskaya, Aksana; Via, Laura E.; Cassell, Gail H.; Dorman, Susan E.; Ellner, Jerrold; Farnia, Parissa; Galagan, James E.; Rosenthal, Alex; Crudu, Valeriu; Homorodean, Daniela; Hsueh, Po-Ren; Narayanan, Sujatha; Pym, Alexander S.; Skrahina, Alena; Swaminathan, Soumya; Van der Walt, Martie; Alland, David; Bishai, William R.; Cohen, Ted; Hoffner, Sven; Birren, Bruce W.; Earl, Ashlee M.

    2017-01-01

    Multidrug-resistant tuberculosis (MDR-TB), caused by drug resistant strains of Mycobacterium tuberculosis, is an increasingly serious problem worldwide. In this study, we examined a dataset of 5,310 M. tuberculosis whole genome sequences from five continents. Despite great diversity with respect to geographic point of isolation, genetic background and drug resistance, patterns of drug resistance emergence were conserved globally. We have identified harbinger mutations that often precede MDR. In particular, the katG S315T mutation, conferring resistance to isoniazid, overwhelmingly arose before rifampicin resistance across all lineages, geographic regions, and time periods. Molecular diagnostics that include markers for rifampicin resistance alone will be insufficient to identify pre-MDR strains. Incorporating knowledge of pre-MDR polymorphisms, particularly katG S315, into molecular diagnostics will enable targeted treatment of patients with pre-MDR-TB to prevent further development of MDR-TB. PMID:28092681

  15. Noiseonomics: the relationship between ambient noise levels in the sea and global economic trends.

    Science.gov (United States)

    Frisk, George V

    2012-01-01

    In recent years, the topic of noise in the sea and its effects on marine mammals has attracted considerable attention from both the scientific community and the general public. Since marine mammals rely heavily on acoustics as a primary means of communicating, navigating, and foraging in the ocean, any change in their acoustic environment may have an impact on their behavior. Specifically, a growing body of literature suggests that low-frequency, ambient noise levels in the open ocean increased approximately 3.3 dB per decade during the period 1950-2007. Here we show that this increase can be attributed primarily to commercial shipping activity, which in turn, can be linked to global economic growth. As a corollary, we conclude that ambient noise levels can be directly related to global economic conditions. We provide experimental evidence supporting this theory and discuss its implications for predicting future noise levels based on global economic trends.

  16. Functional Genomics and Phylogenetic Evidence Suggest Genus-Wide Cobalamin Production by the Globally Distributed Marine Nitrogen Fixer Trichodesmium.

    Science.gov (United States)

    Walworth, Nathan G; Lee, Michael D; Suffridge, Christopher; Qu, Pingping; Fu, Fei-Xue; Saito, Mak A; Webb, Eric A; Sañudo-Wilhelmy, Sergio A; Hutchins, David A

    2018-01-01

    Only select prokaryotes can biosynthesize vitamin B 12 (i.e., cobalamins), but these organic co-enzymes are required by all microbial life and can be vanishingly scarce across extensive ocean biomes. Although global ocean genome data suggest cyanobacteria to be a major euphotic source of cobalamins, recent studies have highlighted that >95% of cyanobacteria can only produce a cobalamin analog, pseudo-B 12 , due to the absence of the BluB protein that synthesizes the α ligand 5,6-dimethylbenzimidizole (DMB) required to biosynthesize cobalamins. Pseudo-B 12 is substantially less bioavailable to eukaryotic algae, as only certain taxa can intracellularly remodel it to one of the cobalamins. Here we present phylogenetic, metagenomic, transcriptomic, proteomic, and chemical analyses providing multiple lines of evidence that the nitrogen-fixing cyanobacterium Trichodesmium transcribes and translates the biosynthetic, cobalamin-requiring BluB enzyme. Phylogenetic evidence suggests that the Trichodesmium DMB biosynthesis gene, bluB , is of ancient origin, which could have aided in its ecological differentiation from other nitrogen-fixing cyanobacteria. Additionally, orthologue analyses reveal two genes encoding iron-dependent B 12 biosynthetic enzymes (cbiX and isiB), suggesting that iron availability may be linked not only to new nitrogen supplies from nitrogen fixation, but also to B 12 inputs by Trichodesmium . These analyses suggest that Trichodesmium contains the genus-wide genomic potential for a previously unrecognized role as a source of cobalamins, which may prove to considerably impact marine biogeochemical cycles.

  17. Forecasting the Global Mean Sea Level, a Continuous-Time State-Space Approach

    DEFF Research Database (Denmark)

    Boldrini, Lorenzo

    In this paper we propose a continuous-time, Gaussian, linear, state-space system to model the relation between global mean sea level (GMSL) and the global mean temperature (GMT), with the aim of making long-term projections for the GMSL. We provide a justification for the model specification based......) and the temperature reconstruction from Hansen et al. (2010). We compare the forecasting performance of the proposed specification to the procedures developed in Rahmstorf (2007b) and Vermeer and Rahmstorf (2009). Finally, we compute projections for the sea-level rise conditional on the 21st century SRES temperature...

  18. Globalization

    Directory of Open Access Journals (Sweden)

    Tulio Rosembuj

    2006-12-01

    Full Text Available There is no singular globalization, nor is the result of an individual agent. We could start by saying that global action has different angles and subjects who perform it are different, as well as its objectives. The global is an invisible invasion of materials and immediate effects.

  19. Globalization

    OpenAIRE

    Tulio Rosembuj

    2006-01-01

    There is no singular globalization, nor is the result of an individual agent. We could start by saying that global action has different angles and subjects who perform it are different, as well as its objectives. The global is an invisible invasion of materials and immediate effects.

  20. The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

    Science.gov (United States)

    Reddy, T.B.K.; Thomas, Alex D.; Stamatis, Dimitri; Bertsch, Jon; Isbandi, Michelle; Jansson, Jakob; Mallajosyula, Jyothi; Pagani, Ioanna; Lobos, Elizabeth A.; Kyrpides, Nikos C.

    2015-01-01

    The Genomes OnLine Database (GOLD; http://www.genomesonline.org) is a comprehensive online resource to catalog and monitor genetic studies worldwide. GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata. Here we report version 5 (v.5) of the database. The newly designed database schema and web user interface supports several new features including the implementation of a four level (meta)genome project classification system and a simplified intuitive web interface to access reports and launch search tools. The database currently hosts information for about 19 200 studies, 56 000 Biosamples, 56 000 sequencing projects and 39 400 analysis projects. More than just a catalog of worldwide genome projects, GOLD is a manually curated, quality-controlled metadata warehouse. The problems encountered in integrating disparate and varying quality data into GOLD are briefly highlighted. GOLD fully supports and follows the Genomic Standards Consortium (GSC) Minimum Information standards. PMID:25348402

  1. The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

    Energy Technology Data Exchange (ETDEWEB)

    Reddy, Tatiparthi B. K. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Thomas, Alex D. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Stamatis, Dimitri [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Bertsch, Jon [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Isbandi, Michelle [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Jansson, Jakob [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Mallajosyula, Jyothi [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Pagani, Ioanna [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lobos, Elizabeth A. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Kyrpides, Nikos C. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)

    2014-10-27

    The Genomes OnLine Database (GOLD; http://www.genomesonline.org) is a comprehensive online resource to catalog and monitor genetic studies worldwide. GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata. Within this paper, we report version 5 (v.5) of the database. The newly designed database schema and web user interface supports several new features including the implementation of a four level (meta)genome project classification system and a simplified intuitive web interface to access reports and launch search tools. The database currently hosts information for about 19 200 studies, 56 000 Biosamples, 56 000 sequencing projects and 39 400 analysis projects. More than just a catalog of worldwide genome projects, GOLD is a manually curated, quality-controlled metadata warehouse. The problems encountered in integrating disparate and varying quality data into GOLD are briefly highlighted. Lastly, GOLD fully supports and follows the Genomic Standards Consortium (GSC) Minimum Information standards.

  2. A new method to estimate global mass transport and its implication for sea level rise

    Science.gov (United States)

    Yi, S.; Heki, K.

    2017-12-01

    Estimates of changes in global land mass by using GRACE observations can be achieved by two methods, a mascon method and a forward modeling method. However, results from these two methods show inconsistent secular trend. Sea level budget can be adopted to validate the consistency among observations of sea level rise by altimetry, steric change by the Argo project, and mass change by GRACE. Mascon products from JPL, GSFC and CSR are compared here, we find that all these three products cannot achieve a reconciled sea level budget, while this problem can be solved by a new forward modeling method. We further investigate the origin of this difference, and speculate that it is caused by the signal leakage from the ocean mass. Generally, it is well recognized that land signals leak into oceans, but it also happens the other way around. We stress the importance of correction of leakage from the ocean in the estimation of global land masses. Based on a reconciled sea level budget, we confirmed that global sea level rise has been accelerating significantly over 2005-2015, as a result of the ongoing global temperature increase.

  3. Visualization and measurement of ATP levels in living cells replicating hepatitis C virus genome RNA.

    Directory of Open Access Journals (Sweden)

    Tomomi Ando

    Full Text Available Adenosine 5'-triphosphate (ATP is the primary energy currency of all living organisms and participates in a variety of cellular processes. Although ATP requirements during viral lifecycles have been examined in a number of studies, a method by which ATP production can be monitored in real-time, and by which ATP can be quantified in individual cells and subcellular compartments, is lacking, thereby hindering studies aimed at elucidating the precise mechanisms by which viral replication energized by ATP is controlled. In this study, we investigated the fluctuation and distribution of ATP in cells during RNA replication of the hepatitis C virus (HCV, a member of the Flaviviridae family. We demonstrated that cells involved in viral RNA replication actively consumed ATP, thereby reducing cytoplasmic ATP levels. Subsequently, a method to measure ATP levels at putative subcellular sites of HCV RNA replication in living cells was developed by introducing a recently-established Förster resonance energy transfer (FRET-based ATP indicator, called ATeam, into the NS5A coding region of the HCV replicon. Using this method, we were able to observe the formation of ATP-enriched dot-like structures, which co-localize with non-structural viral proteins, within the cytoplasm of HCV-replicating cells but not in non-replicating cells. The obtained FRET signals allowed us to estimate ATP concentrations within HCV replicating cells as ∼5 mM at possible replicating sites and ∼1 mM at peripheral sites that did not appear to be involved in HCV replication. In contrast, cytoplasmic ATP levels in non-replicating Huh-7 cells were estimated as ∼2 mM. To our knowledge, this is the first study to demonstrate changes in ATP concentration within cells during replication of the HCV genome and increased ATP levels at distinct sites within replicating cells. ATeam may be a powerful tool for the study of energy metabolism during replication of the viral genome.

  4. Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis.

    Science.gov (United States)

    Wyrsch, Ethan R; Roy Chowdhury, Piklu; Chapman, Toni A; Charles, Ian G; Hammond, Jeffrey M; Djordjevic, Steven P

    2016-01-01

    Contamination of waste effluent from hospitals and intensive food animal production with antimicrobial residues is an immense global problem. Antimicrobial residues exert selection pressures that influence the acquisition of antimicrobial resistance and virulence genes in diverse microbial populations. Despite these concerns there is only a limited understanding of how antimicrobial residues contribute to the global problem of antimicrobial resistance. Furthermore, rapid detection of emerging bacterial pathogens and strains with resistance to more than one antibiotic class remains a challenge. A comprehensive, sequence-based genomic epidemiological surveillance model that captures essential microbial metadata is needed, both to improve surveillance for antimicrobial resistance and to monitor pathogen evolution. Escherichia coli is an important pathogen causing both intestinal [intestinal pathogenic E. coli (IPEC)] and extraintestinal [extraintestinal pathogenic E. coli (ExPEC)] disease in humans and food animals. ExPEC are the most frequently isolated Gram negative pathogen affecting human health, linked to food production practices and are often resistant to multiple antibiotics. Cattle are a known reservoir of IPEC but they are not recognized as a source of ExPEC that impact human or animal health. In contrast, poultry are a recognized source of multiple antibiotic resistant ExPEC, while swine have received comparatively less attention in this regard. Here, we review what is known about ExPEC in swine and how pig production contributes to the problem of antibiotic resistance.

  5. Regional growth management policies: Toward reducing global warming at state and local levels

    International Nuclear Information System (INIS)

    Purdie, J.

    1995-01-01

    State and local governments in the United States are accepting mandates to coordinate legislated land use and growth management planning with vigorous environmental protection and resource conservation. These mandates, implemented or planned in states with populations totaling over 100 million, will directly impact growth patterns and ultimately affect the level of atmospheric gases and particulates generated within their borders. This paper addresses the issues of growth management and land use planning at the local, state and regional levels and identifies areas impacting global warming. A review of existing systems will be presented, and recommendations will be made to improve monitoring of growth management mechanisms and organizational structures with the goal of global atmospheric improvement. The issues discussed include urban sprawl, transportation, and growth patterns as managed by policies also designed to protect environments and provide for sustainable growth. Areas for improved coordination between jurisdictions to ease global warming will also be examined

  6. Changes in yields and their variability at different levels of global warming

    Science.gov (United States)

    Childers, Katelin

    2015-04-01

    An assessment of climate change impacts at different levels of global warming is crucial to inform the political discussion about mitigation targets as well as for the inclusion of climate change impacts in Integrated Assessment Models (IAMs) that generally only provide global mean temperature change as an indicator of climate change. While there is a well-established framework for the scalability of regional temperature and precipitation changes with global mean temperature change we provide an assessment of the extent to which impacts such as crop yield changes can also be described in terms of global mean temperature changes without accounting for the specific underlying emissions scenario. Based on multi-crop-model simulations of the four major cereal crops (maize, rice, soy, and wheat) on a 0.5 x 0.5 degree global grid generated within ISI-MIP, we show the average spatial patterns of projected crop yield changes at one half degree warming steps. We find that emissions scenario dependence is a minor component of the overall variance of projected yield changes at different levels of global warming. Furthermore, scenario dependence can be reduced by accounting for the direct effects of CO2 fertilization in each global climate model (GCM)/impact model combination through an inclusion of the global atmospheric CO2 concentration as a second predictor. The choice of GCM output used to force the crop model simulations accounts for a slightly larger portion of the total yield variance, but the greatest contributor to variance in both global and regional crop yields and at all levels of warming, is the inter-crop-model spread. The unique multi impact model ensemble available with ISI-MIP data also indicates that the overall variability of crop yields is projected to increase in conjunction with increasing global mean temperature. This result is consistent throughout the ensemble of impact models and across many world regions. Such a hike in yield volatility could have

  7. Past and future contribution of global groundwater depletion to sea-level rise

    NARCIS (Netherlands)

    Wada, Y.; Beek, L.P.H. van; Sperna Weiland, F.C.; Chao, B.; Wu, Y.-H.; Bierkens, M.F.P.

    2012-01-01

    Recent studies suggest the increasing contribution of groundwater depletion to global sea-level rise. Groundwater depletion has more than doubled during the last decades, primarily due to increase in water demand, while the increase in water impoundments behind dams has been tapering off since

  8. The decrease of CO2 emission intensity is decarbonization at national and global levels

    International Nuclear Information System (INIS)

    Sun, J.W.

    2005-01-01

    This viewpoint proposes the definition: 'Decarbonization refers to a decrease of CO 2 emission intensity in a trend'. This viewpoint then argues that an analysis of decarbonization at national and global levels based on that definition would lead to the correct calculation of decarbonization

  9. University-Level Teaching of Anthropogenic Global Climate Change (AGCC) via Student Inquiry

    Science.gov (United States)

    Bush, Drew; Sieber, Renee; Seiler, Gale; Chandler, Mark

    2017-01-01

    This paper reviews university-level efforts to improve understanding of anthropogenic global climate change (AGCC) through curricula that enable student scientific inquiry. We examined 152 refereed publications and proceedings from academic conferences and selected 26 cases of inquiry learning that overcome specific challenges to AGCC teaching.…

  10. Modelling of local/global architectures for second level trigger at the LHC experiment

    International Nuclear Information System (INIS)

    Hajduk, Z.; Iwanski, W.; Korecyl, K.; Strong, J.

    1994-01-01

    Different architectures of the second level triggering system for experiments on LHC have been simulated. The basic scheme was local/global system with distributed computing power. As a tool the authors have used the object-oriented MODSIM II language

  11. Global dimensions for Lie groups at level k and their conformally exceptional quantum subgroups

    CERN Document Server

    Coquereaux, Robert

    2010-01-01

    We obtain formulae giving global dimensions for fusion categories defined by Lie groups G at level k and for the associated module-categories obtained via conformal embeddings. The results can be expressed in terms of Lie quantum superfactorials of type G. The later are related, for the type Ar, to the quantum Barnes function.

  12. Tools for Genomic and Transcriptomic Analysis of Microbes at Single-Cell Level

    Directory of Open Access Journals (Sweden)

    Zixi Chen

    2017-09-01

    Full Text Available Microbiologists traditionally study population rather than individual cells, as it is generally assumed that the status of individual cells will be similar to that observed in the population. However, the recent studies have shown that the individual behavior of each single cell could be quite different from that of the whole population, suggesting the importance of extending traditional microbiology studies to single-cell level. With recent technological advances, such as flow cytometry, next-generation sequencing (NGS, and microspectroscopy, single-cell microbiology has greatly enhanced the understanding of individuality and heterogeneity of microbes in many biological systems. Notably, the application of multiple ‘omics’ in single-cell analysis has shed light on how individual cells perceive, respond, and adapt to the environment, how heterogeneity arises under external stress and finally determines the fate of the whole population, and how microbes survive under natural conditions. As single-cell analysis involves no axenic cultivation of target microorganism, it has also been demonstrated as a valuable tool for dissecting the microbial ‘dark matter.’ In this review, current state-of-the-art tools and methods for genomic and transcriptomic analysis of microbes at single-cell level were critically summarized, including single-cell isolation methods and experimental strategies of single-cell analysis with NGS. In addition, perspectives on the future trends of technology development in the field of single-cell analysis was also presented.

  13. Globalization

    OpenAIRE

    Andru?cã Maria Carmen

    2013-01-01

    The field of globalization has highlighted an interdependence implied by a more harmonious understanding determined by the daily interaction between nations through the inducement of peace and the management of streamlining and the effectiveness of the global economy. For the functioning of the globalization, the developing countries that can be helped by the developed ones must be involved. The international community can contribute to the institution of the development environment of the gl...

  14. Improvement of global and regional mean sea level derived from satellite altimetry multi missions

    Science.gov (United States)

    Ablain, M.; Faugere, Y.; Larnicol, G.; Picot, N.; Cazenave, A.; Benveniste, J.

    2012-04-01

    With the satellite altimetry missions, the global mean sea level (GMSL) has been calculated on a continual basis since January 1993. 'Verification' phases, during which the satellites follow each other in close succession (Topex/Poseidon--Jason-1, then Jason-1--Jason-2), help to link up these different missions by precisely determining any bias between them. Envisat, ERS-1 and ERS-2 are also used, after being adjusted on these reference missions, in order to compute Mean Sea Level at high latitudes (higher than 66°N and S), and also to improve spatial resolution by combining all these missions together. The global mean sea level (MSL) deduced from TOPEX/Poseidon, Jason-1 and Jason-2 provide a global rate of 3.2 mm from 1993 to 2010 applying the post glacial rebound (MSL aviso website http://www.jason.oceanobs.com/msl). Besides, the regional sea level trends bring out an inhomogeneous repartition of the ocean elevation with local MSL slopes ranging from + 8 mm/yr to - 8 mm/year. A study published in 2009 [Ablain et al., 2009] has shown that the global MSL trend unceratainty was estimated at +/-0.6 mm/year with a confidence interval of 90%. The main sources of errors at global and regional scales are due to the orbit calculation and the wet troposphere correction. But others sea-level components have also a significant impact on the long-term stability of MSL as for instance the stability of instrumental parameters and the atmospheric corrections. Thanks to recent studies performed in the frame of the SALP project (supported by CNES) and Sea-level Climate Change Initiative project (supported by ESA), strong improvements have been provided for the estimation of the global and regional MSL trends. In this paper, we propose to describe them; they concern the orbit calculation thanks to new gravity fields, the atmospheric corrections thanks to ERA-interim reanalyses, the wet troposphere corrections thanks to the stability improvement, and also empirical corrections

  15. Autism and increased paternal age related changes in global levels of gene expression regulation.

    Directory of Open Access Journals (Sweden)

    Mark D Alter

    2011-02-01

    Full Text Available A causal role of mutations in multiple general transcription factors in neurodevelopmental disorders including autism suggested that alterations in global levels of gene expression regulation might also relate to disease risk in sporadic cases of autism. This premise can be tested by evaluating for changes in the overall distribution of gene expression levels. For instance, in mice, variability in hippocampal-dependent behaviors was associated with variability in the pattern of the overall distribution of gene expression levels, as assessed by variance in the distribution of gene expression levels in the hippocampus. We hypothesized that a similar change in variance might be found in children with autism. Gene expression microarrays covering greater than 47,000 unique RNA transcripts were done on RNA from peripheral blood lymphocytes (PBL of children with autism (n = 82 and controls (n = 64. Variance in the distribution of gene expression levels from each microarray was compared between groups of children. Also tested was whether a risk factor for autism, increased paternal age, was associated with variance. A decrease in the variance in the distribution of gene expression levels in PBL was associated with the diagnosis of autism and a risk factor for autism, increased paternal age. Traditional approaches to microarray analysis of gene expression suggested a possible mechanism for decreased variance in gene expression. Gene expression pathways involved in transcriptional regulation were down-regulated in the blood of children with autism and children of older fathers. Thus, results from global and gene specific approaches to studying microarray data were complimentary and supported the hypothesis that alterations at the global level of gene expression regulation are related to autism and increased paternal age. Global regulation of transcription, thus, represents a possible point of convergence for multiple etiologies of autism and other

  16. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

    Science.gov (United States)

    Matthew Parks; Richard Cronn; Aaron Liston

    2009-01-01

    We reconstruct the infrageneric phylogeny of Pinus from 37 nearly-complete chloroplast genomes (average 109 kilobases each of an approximately 120 kilobase genome) generated using multiplexed massively parallel sequencing. We found that 30/33 ingroup nodes resolved wlth > 95-percent bootstrap support; this is a substantial improvement relative...

  17. New evidence for "far-field" Holocene sea level oscillations and links to global climate records

    Science.gov (United States)

    Leonard, N. D.; Welsh, K. J.; Clark, T. R.; Feng, Y.-x.; Pandolfi, J. M.; Zhao, J.-x.

    2018-04-01

    Rising sea level in the coming century is of significant concern, yet predicting relative sea level change in response to eustatic sea level variability is complex. Potential analogues are provided by the recent geological past but, until recently, many sea level reconstructions have been limited to millennial scale interpretations due to age uncertainties and paucity in proxy derived records. Here we present a sea level history for the tectonically stable "far-field" Great Barrier Reef, Australia, derived from 94 high precision uranium-thorium dates of sub-fossil coral microatolls. Our results provide evidence for at least two periods of relative sea level instability during the Holocene. These sea level oscillations are broadly synchronous with Indo-Pacific negative sea surface temperature anomalies, rapid global cooling events and glacial advances. We propose that the pace and magnitude of these oscillations are suggestive of eustatic/thermosteric processes operating in conjunction with regional climatic controls.

  18. The global coastline dataset: the observed relation between erosion and sea-level rise

    Science.gov (United States)

    Donchyts, G.; Baart, F.; Luijendijk, A.; Hagenaars, G.

    2017-12-01

    Erosion of sandy coasts is considered one of the key risks of sea-level rise. Because sandy coastlines of the world are often highly populated, erosive coastline trends result in risk to populations and infrastructure. Most of our understanding of the relation between sea-level rise and coastal erosion is based on local or regional observations and generalizations of numerical and physical experiments. Until recently there was no reliable global scale assessment of the location of sandy coasts and their rate of erosion and accretion. Here we present the global coastline dataset that covers erosion indicators on a local scale with global coverage. The dataset uses our global coastline transects grid defined with an alongshore spacing of 250 m and a cross shore length extending 1 km seaward and 1 km landward. This grid matches up with pre-existing local grids where available. We present the latest results on validation of coastal-erosion trends (based on optical satellites) and classification of sandy versus non-sandy coasts. We show the relation between sea-level rise (based both on tide-gauges and multi-mission satellite altimetry) and observed erosion trends over the last decades, taking into account broken-coastline trends (for example due to nourishments).An interactive web application presents the publicly-accessible results using a backend based on Google Earth Engine. It allows both researchers and stakeholders to use objective estimates of coastline trends, particularly when authoritative sources are not available.

  19. A heuristic evaluation of long-term global sea level acceleration

    Science.gov (United States)

    Spada, Giorgio; Olivieri, Marco; Galassi, Gaia

    2015-05-01

    In view of the scientific and social implications, the global mean sea level rise (GMSLR) and its possible causes and future trend have been a challenge for so long. For the twentieth century, reconstructions generally indicate a rate of GMSLR in the range of 1.5 to 2.0 mm yr-1. However, the existence of nonlinear trends is still debated, and current estimates of the secular acceleration are subject to ample uncertainties. Here we use various GMSLR estimates published on scholarly journals since the 1940s for a heuristic assessment of global sea level acceleration. The approach, alternative to sea level reconstructions, is based on simple statistical methods and exploits the principles of meta-analysis. Our results point to a global sea level acceleration of 0.54 ± 0.27 mm/yr/century (1σ) between 1898 and 1975. This supports independent estimates and suggests that a sea level acceleration since the early 1900s is more likely than currently believed.

  20. Terpene metabolic engineering via nuclear or chloroplast genomes profoundly and globally impacts off-target pathways through metabolite signalling.

    Science.gov (United States)

    Pasoreck, Elise K; Su, Jin; Silverman, Ian M; Gosai, Sager J; Gregory, Brian D; Yuan, Joshua S; Daniell, Henry

    2016-09-01

    The impact of metabolic engineering on nontarget pathways and outcomes of metabolic engineering from different genomes are poorly understood questions. Therefore, squalene biosynthesis genes FARNESYL DIPHOSPHATE SYNTHASE (FPS) and SQUALENE SYNTHASE (SQS) were engineered via the Nicotiana tabacum chloroplast (C), nuclear (N) or both (CN) genomes to promote squalene biosynthesis. SQS levels were ~4300-fold higher in C and CN lines than in N, but all accumulated ~150-fold higher squalene due to substrate or storage limitations. Abnormal leaf and flower phenotypes, including lower pollen production and reduced fertility, were observed regardless of the compartment or level of transgene expression. Substantial changes in metabolomes of all lines were observed: levels of 65-120 unrelated metabolites, including the toxic alkaloid nicotine, changed by as much as 32-fold. Profound effects of transgenesis on nontarget gene expression included changes in the abundance of 19 076 transcripts by up to 2000-fold in CN; 7784 transcripts by up to 1400-fold in N; and 5224 transcripts by as much as 2200-fold in C. Transporter-related transcripts were induced, and cell cycle-associated transcripts were disproportionally repressed in all three lines. Transcriptome changes were validated by qRT-PCR. The mechanism underlying these large changes likely involves metabolite-mediated anterograde and/or retrograde signalling irrespective of the level of transgene expression or end product, due to imbalance of metabolic pools, offering new insight into both anticipated and unanticipated consequences of metabolic engineering. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  1. Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels

    DEFF Research Database (Denmark)

    Van Leeuwen, Elisabeth M.; Karssen, Lennart C.; Deelen, Joris

    2015-01-01

    created by the Genome of the Netherlands Project and perform association testing with blood lipid levels. We report the discovery of five novel associations at four loci (P value -4), including a rare missense variant in ABCA6 (rs77542162, p.Cys1359Arg, frequency 0.034), which is predicted...

  2. Universal features in the genome-level evolution of protein domains.

    Science.gov (United States)

    Cosentino Lagomarsino, Marco; Sellerio, Alessandro L; Heijning, Philip D; Bassetti, Bruno

    2009-01-01

    Protein domains can be used to study proteome evolution at a coarse scale. In particular, they are found on genomes with notable statistical distributions. It is known that the distribution of domains with a given topology follows a power law. We focus on a further aspect: these distributions, and the number of distinct topologies, follow collective trends, or scaling laws, depending on the total number of domains only, and not on genome-specific features. We present a stochastic duplication/innovation model, in the class of the so-called 'Chinese restaurant processes', that explains this observation with two universal parameters, representing a minimal number of domains and the relative weight of innovation to duplication. Furthermore, we study a model variant where new topologies are related to occurrence in genomic data, accounting for fold specificity. Both models have general quantitative agreement with data from hundreds of genomes, which indicates that the domains of a genome are built with a combination of specificity and robust self-organizing phenomena. The latter are related to the basic evolutionary 'moves' of duplication and innovation, and give rise to the observed scaling laws, a priori of the specific evolutionary history of a genome. We interpret this as the concurrent effect of neutral and selective drives, which increase duplication and decrease innovation in larger and more complex genomes. The validity of our model would imply that the empirical observation of a small number of folds in nature may be a consequence of their evolution.

  3. DNA micro array analysis of yeast global genome expression in response to ELF-MF exposure

    International Nuclear Information System (INIS)

    Shimizu, K.; Yamamoto, T.; Ishibashi, T.; Kyoh, B.

    2002-01-01

    There is wide spread public concern over the possible health risk of ELF-MF. Electromagnetic fields may produce a variety of effects in several biological systems, including the elevation of cancer risk and reduction of cell growth. Epidemiological studies have shown weak correlations between the exposure to ELF and the incidence of several cancers, but negative studies have also been reported. Moreover, there are some reports that basic biological events such as the cell cycle and DNA replication were affected by exposure to MF. However, to date the molecular mechanism of the MF effect on living organism is not clear. In this study, we used yeast DNA micro array to examine the transcriptional profile of all genes in response to ELF-MF. A few years ago it was difficult to carry out a global gene expression study to identify important genes regarding ELF-MF, however, today DNA micro arrays allow gene regulation in response to high density ELF-MF exposure. Thus we used micro array to analyze changes in mRNA abundance during ELF-MF exposure

  4. Evaluation of Global Genomic DNA Methylation in Human Whole Blood by Capillary Electrophoresis UV Detection

    Directory of Open Access Journals (Sweden)

    Angelo Zinellu

    2017-01-01

    Full Text Available Alterations in global DNA methylation are implicated in various pathophysiological processes. The development of simple and quick, yet robust, methods to assess DNA methylation is required to facilitate its measurement and interpretation in clinical practice. We describe a highly sensitive and reproducible capillary electrophoresis method with UV detection for the separation and detection of cytosine and methylcytosine, after formic acid hydrolysis of DNA extracted from human whole blood. Hydrolysed samples were dried and resuspended with water and directly injected into the capillary without sample derivatization procedures. The use of a run buffer containing 50 mmol/L BIS-TRIS propane (BTP phosphate buffer at pH 3.25 and 60 mmol/L sodium acetate buffer at pH 3.60 (4 : 1, v/v allowed full analyte identification within 11 min. Precision tests indicated an elevated reproducibility with an interassay CV of 1.98% when starting from 2 μg of the extracted DNA. The method was successfully tested by measuring the DNA methylation degree both in healthy volunteers and in reference calf thymus DNA.

  5. Global levels of histone modifications in peripheral blood mononuclear cells of subjects with exposure to nickel.

    Science.gov (United States)

    Arita, Adriana; Niu, Jingping; Qu, Qingshan; Zhao, Najuan; Ruan, Ye; Nadas, Arthur; Chervona, Yana; Wu, Fen; Sun, Hong; Hayes, Richard B; Costa, Max

    2012-02-01

    Occupational exposure to nickel (Ni) is associated with an increased risk for lung and nasal cancers. Ni compounds exhibit weak mutagenic activity, cause gene amplification, and disrupt cellular epigenetic homeostasis. However, the Ni-induced changes in global histone modification levels have only been tested in vitro. This study was conducted in a Chinese population to determine whether occupational exposure to Ni is associated with alterations of global histone modification levels and to evaluate the inter- and intraindividual variance of global histone modification levels. Forty-five subjects with occupational exposure to Ni and 75 referents were recruited. Urinary Ni and global H3K4 trimethylation, H3K9 acetylation, and H3K9 dimethylation levels were measured in peripheral blood mononuclear cells (PBMCs) of subjects. H3K4me3 was elevated in Ni-exposed subjects (0.25% ± 0.11%) compared with referents (0.15% ± 0.04%; p = 0.0004), and H3K9me2 was decreased (Ni-exposed subjects, 0.11% ± 0.05%; referents, 0.15% ± 0.04%; p = 0.003). H3K4me3 was positively (r = 0.4, p = 0.0008) and H3K9ac was negatively (r = 0.1, p = 0.01) associated with urinary Ni. Interindividual variances of H3K4me3, H3K9ac, and H3K9me2 were larger compared with intraindividual variance in both exposure test groups, resulting in reliability coefficients (an estimate of consistency of a set of measurements) of 0.60, 0.67, and 0.79 for H3K4me3, H3K9ac, and H3K9me2, respectively, for Ni-exposed subjects and of 0.75, 0.74, and 0.97, respectively, for referent subjects. The results of this study indicate that occupational exposure to Ni is associated with alterations of global histone modification levels and that measurements of global levels of histone modifications are relatively stable over time in human PBMCs.

  6. Attention to local and global levels of hierarchical Navon figures affects rapid scene categorization.

    Science.gov (United States)

    Brand, John; Johnson, Aaron P

    2014-01-01

    In four experiments, we investigated how attention to local and global levels of hierarchical Navon figures affected the selection of diagnostic spatial scale information used in scene categorization. We explored this issue by asking observers to classify hybrid images (i.e., images that contain low spatial frequency (LSF) content of one image, and high spatial frequency (HSF) content from a second image) immediately following global and local Navon tasks. Hybrid images can be classified according to either their LSF, or HSF content; thus, making them ideal for investigating diagnostic spatial scale preference. Although observers were sensitive to both spatial scales (Experiment 1), they overwhelmingly preferred to classify hybrids based on LSF content (Experiment 2). In Experiment 3, we demonstrated that LSF based hybrid categorization was faster following global Navon tasks, suggesting that LSF processing associated with global Navon tasks primed the selection of LSFs in hybrid images. In Experiment 4, replicating Experiment 3 but suppressing the LSF information in Navon letters by contrast balancing the stimuli examined this hypothesis. Similar to Experiment 3, observers preferred to classify hybrids based on LSF content; however and in contrast, LSF based hybrid categorization was slower following global than local Navon tasks.

  7. Attention to local and global levels of hierarchical Navon figures affects rapid scene categorization

    Science.gov (United States)

    Brand, John; Johnson, Aaron P.

    2014-01-01

    In four experiments, we investigated how attention to local and global levels of hierarchical Navon figures affected the selection of diagnostic spatial scale information used in scene categorization. We explored this issue by asking observers to classify hybrid images (i.e., images that contain low spatial frequency (LSF) content of one image, and high spatial frequency (HSF) content from a second image) immediately following global and local Navon tasks. Hybrid images can be classified according to either their LSF, or HSF content; thus, making them ideal for investigating diagnostic spatial scale preference. Although observers were sensitive to both spatial scales (Experiment 1), they overwhelmingly preferred to classify hybrids based on LSF content (Experiment 2). In Experiment 3, we demonstrated that LSF based hybrid categorization was faster following global Navon tasks, suggesting that LSF processing associated with global Navon tasks primed the selection of LSFs in hybrid images. In Experiment 4, replicating Experiment 3 but suppressing the LSF information in Navon letters by contrast balancing the stimuli examined this hypothesis. Similar to Experiment 3, observers preferred to classify hybrids based on LSF content; however and in contrast, LSF based hybrid categorization was slower following global than local Navon tasks. PMID:25520675

  8. Genome-level homology and phylogeny of Shewanella (Gammaproteobacteria: lteromonadales: Shewanellaceae

    Directory of Open Access Journals (Sweden)

    Dikow Rebecca B

    2011-05-01

    Full Text Available Abstract Background The explosion in availability of whole genome data provides the opportunity to build phylogenetic hypotheses based on these data as well as the ability to learn more about the genomes themselves. The biological history of genes and genomes can be investigated based on the taxomonic history provided by the phylogeny. A phylogenetic hypothesis based on complete genome data is presented for the genus Shewanella (Gammaproteobacteria: Alteromonadales: Shewanellaceae. Nineteen taxa from Shewanella (16 species and 3 additional strains of one species as well as three outgroup species representing the genera Aeromonas (Gammaproteobacteria: Aeromonadales: Aeromonadaceae, Alteromonas (Gammaproteobacteria: Alteromonadales: Alteromonadaceae and Colwellia (Gammaproteobacteria: Alteromonadales: Colwelliaceae are included for a total of 22 taxa. Results Putatively homologous regions were found across unannotated genomes and tested with a phylogenetic analysis. Two genome-wide data-sets are considered, one including only those genomic regions for which all taxa are represented, which included 3,361,015 aligned nucleotide base-pairs (bp and a second that additionally includes those regions present in only subsets of taxa, which totaled 12,456,624 aligned bp. Alignment columns in these large data-sets were then randomly sampled to create smaller data-sets. After the phylogenetic hypothesis was generated, genome annotations were projected onto the DNA sequence alignment to compare the historical hypothesis generated by the phylogeny with the functional hypothesis posited by annotation. Conclusions Individual phylogenetic analyses of the 243 locally co-linear genome regions all failed to recover the genome topology, but the smaller data-sets that were random samplings of the large concatenated alignments all produced the genome topology. It is shown that there is not a single orthologous copy of 16S rRNA across the taxon sampling included in this

  9. Changes in crop yields and their variability at different levels of global warming

    Science.gov (United States)

    Ostberg, Sebastian; Schewe, Jacob; Childers, Katelin; Frieler, Katja

    2018-05-01

    An assessment of climate change impacts at different levels of global warming is crucial to inform the policy discussion about mitigation targets, as well as for the economic evaluation of climate change impacts. Integrated assessment models often use global mean temperature change (ΔGMT) as a sole measure of climate change and, therefore, need to describe impacts as a function of ΔGMT. There is already a well-established framework for the scalability of regional temperature and precipitation changes with ΔGMT. It is less clear to what extent more complex biological or physiological impacts such as crop yield changes can also be described in terms of ΔGMT, even though such impacts may often be more directly relevant for human livelihoods than changes in the physical climate. Here we show that crop yield projections can indeed be described in terms of ΔGMT to a large extent, allowing for a fast estimation of crop yield changes for emissions scenarios not originally covered by climate and crop model projections. We use an ensemble of global gridded crop model simulations for the four major staple crops to show that the scenario dependence is a minor component of the overall variance of projected yield changes at different levels of ΔGMT. In contrast, the variance is dominated by the spread across crop models. Varying CO2 concentrations are shown to explain only a minor component of crop yield variability at different levels of global warming. In addition, we find that the variability in crop yields is expected to increase with increasing warming in many world regions. We provide, for each crop model, geographical patterns of mean yield changes that allow for a simplified description of yield changes under arbitrary pathways of global mean temperature and CO2 changes, without the need for additional climate and crop model simulations.

  10. Visual arts training is linked to flexible attention to local and global levels of visual stimuli.

    Science.gov (United States)

    Chamberlain, Rebecca; Wagemans, Johan

    2015-10-01

    Observational drawing skill has been shown to be associated with the ability to focus on local visual details. It is unclear whether superior performance in local processing is indicative of the ability to attend to, and flexibly switch between, local and global levels of visual stimuli. It is also unknown whether these attentional enhancements remain specific to observational drawing skill or are a product of a wide range of artistic activities. The current study aimed to address these questions by testing if flexible visual processing predicts artistic group membership and observational drawing skill in a sample of first-year bachelor's degree art students (n=23) and non-art students (n=23). A pattern of local and global visual processing enhancements was found in relation to artistic group membership and drawing skill, with local processing ability found to be specifically related to individual differences in drawing skill. Enhanced global processing and more fluent switching between local and global levels of hierarchical stimuli predicted both drawing skill and artistic group membership, suggesting that these are beneficial attentional mechanisms for art-making in a range of domains. These findings support a top-down attentional model of artistic expertise and shed light on the domain specific and domain-general attentional enhancements induced by proficiency in the visual arts. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Resource base influences genome-wide DNA methylation levels in wild baboons (Papio cynocephalus)

    Science.gov (United States)

    Lea, Amanda J.; Altmann, Jeanne; Alberts, Susan C.; Tung, Jenny

    2015-01-01

    Variation in resource availability commonly exerts strong effects on fitness-related traits in wild animals. However, we know little about the molecular mechanisms that mediate these effects, or about their persistence over time. To address these questions, we profiled genome-wide whole blood DNA methylation levels in two sets of wild baboons: (i) ‘wild-feeding’ baboons that foraged naturally in a savanna environment and (ii) ‘Lodge’ baboons that had ready access to spatially concentrated human food scraps, resulting in high feeding efficiency and low daily travel distances. We identified 1,014 sites (0.20% of sites tested) that were differentially methylated between wild-feeding and Lodge baboons, providing the first evidence that resource availability shapes the epigenome in a wild mammal. Differentially methylated sites tended to occur in contiguous stretches (i.e., in differentially methylated regions or DMRs), in promoters and enhancers, and near metabolism-related genes, supporting their functional importance in gene regulation. In agreement, reporter assay experiments confirmed that methylation at the largest identified DMR, located in the promoter of a key glycolysis-related gene, was sufficient to causally drive changes in gene expression. Intriguingly, all dispersing males carried a consistent epigenetic signature of their membership in a wild-feeding group, regardless of whether males dispersed into or out of this group as adults. Together, our findings support a role for DNA methylation in mediating ecological effects on phenotypic traits in the wild, and emphasize the dynamic environmental sensitivity of DNA methylation levels across the life course. PMID:26508127

  12. Evolution of sociality in spiders leads to depleted genomic diversity at both population and species levels.

    Science.gov (United States)

    Settepani, V; Schou, M F; Greve, M; Grinsted, L; Bechsgaard, J; Bilde, T

    2017-08-01

    Across several animal taxa, the evolution of sociality involves a suite of characteristics, a "social syndrome," that includes cooperative breeding, reproductive skew, primary female-biased sex ratio, and the transition from outcrossing to inbreeding mating system, factors that are expected to reduce effective population size (Ne). This social syndrome may be favoured by short-term benefits but come with long-term costs, because the reduction in Ne amplifies loss of genetic diversity by genetic drift, ultimately restricting the potential of populations to respond to environmental change. To investigate the consequences of this social life form on genetic diversity, we used a comparative RAD-sequencing approach to estimate genomewide diversity in spider species that differ in level of sociality, reproductive skew and mating system. We analysed multiple populations of three independent sister-species pairs of social inbreeding and subsocial outcrossing Stegodyphus spiders, and a subsocial outgroup. Heterozygosity and within-population diversity were sixfold to 10-fold lower in social compared to subsocial species, and demographic modelling revealed a tenfold reduction in Ne of social populations. Species-wide genetic diversity depends on population divergence and the viability of genetic lineages. Population genomic patterns were consistent with high lineage turnover, which homogenizes the genetic structure that builds up between inbreeding populations, ultimately depleting genetic diversity at the species level. Indeed, species-wide genetic diversity of social species was 5-8 times lower than that of subsocial species. The repeated evolution of species with this social syndrome is associated with severe loss of genomewide diversity, likely to limit their evolutionary potential. © 2017 John Wiley & Sons Ltd.

  13. Discovery of global genomic re-organization based on comparison of two newly sequenced rice mitochondrial genomes with cytoplasmic male sterility-related genes

    Directory of Open Access Journals (Sweden)

    Yamada Mari

    2010-03-01

    Full Text Available Abstract Background Plant mitochondrial genomes are known for their complexity, and there is abundant evidence demonstrating that this organelle is important for plant sexual reproduction. Cytoplasmic male sterility (CMS is a phenomenon caused by incompatibility between the nucleus and mitochondria that has been discovered in various plant species. As the exact sequence of steps leading to CMS has not yet been revealed, efforts should be made to elucidate the factors underlying the mechanism of this important trait for crop breeding. Results Two CMS mitochondrial genomes, LD-CMS, derived from Oryza sativa L. ssp. indica (434,735 bp, and CW-CMS, derived from Oryza rufipogon Griff. (559,045 bp, were newly sequenced in this study. Compared to the previously sequenced Nipponbare (Oryza sativa L. ssp. japonica mitochondrial genome, the presence of 54 out of 56 protein-encoding genes (including pseudo-genes, 22 tRNA genes (including pseudo-tRNAs, and three rRNA genes was conserved. Two other genes were not present in the CW-CMS mitochondrial genome, and one of them was present as part of the newly identified chimeric ORF, CW-orf307. At least 12 genomic recombination events were predicted between the LD-CMS mitochondrial genome and Nipponbare, and 15 between the CW-CMS genome and Nipponbare, and novel genetic structures were formed by these genomic rearrangements in the two CMS lines. At least one of the genomic rearrangements was completely unique to each CMS line and not present in 69 rice cultivars or 9 accessions of O. rufipogon. Conclusion Our results demonstrate novel mitochondrial genomic rearrangements that are unique in CMS cytoplasm, and one of the genes that is unique in the CW mitochondrial genome, CW-orf307, appeared to be the candidate most likely responsible for the CW-CMS event. Genomic rearrangements were dynamic in the CMS lines in comparison with those of rice cultivars, suggesting that 'death' and possible 'birth' processes of the

  14. Genome-health nutrigenomics and nutrigenetics: nutritional requirements or 'nutriomes' for chromosomal stability and telomere maintenance at the individual level.

    Science.gov (United States)

    Bull, Caroline; Fenech, Michael

    2008-05-01

    It is becoming increasingly evident that (a) risk for developmental and degenerative disease increases with more DNA damage, which in turn is dependent on nutritional status, and (b) the optimal concentration of micronutrients for prevention of genome damage is also dependent on genetic polymorphisms that alter the function of genes involved directly or indirectly in the uptake and metabolism of micronutrients required for DNA repair and DNA replication. The development of dietary patterns, functional foods and supplements that are designed to improve genome-health maintenance in individuals with specific genetic backgrounds may provide an important contribution to an optimum health strategy based on the diagnosis and individualised nutritional prevention of genome damage, i.e. genome health clinics. The present review summarises some of the recent knowledge relating to micronutrients that are associated with chromosomal stability and provides some initial insights into the likely nutritional factors that may be expected to have an impact on the maintenance of telomeres. It is evident that developing effective strategies for defining nutrient doses and combinations or 'nutriomes' for genome-health maintenance at the individual level is essential for further progress in this research field.

  15. Enrichment and genome sequence of the group I.1a ammonia-oxidizing Archaeon "Ca. Nitrosotenuis uzonensis" representing a clade globally distributed in thermal habitats.

    Directory of Open Access Journals (Sweden)

    Elena V Lebedeva

    Full Text Available The discovery of ammonia-oxidizing archaea (AOA of the phylum Thaumarchaeota and the high abundance of archaeal ammonia monooxygenase subunit A encoding gene sequences in many environments have extended our perception of nitrifying microbial communities. Moreover, AOA are the only aerobic ammonia oxidizers known to be active in geothermal environments. Molecular data indicate that in many globally distributed terrestrial high-temperature habits a thaumarchaeotal lineage within the Nitrosopumilus cluster (also called "marine" group I.1a thrives, but these microbes have neither been isolated from these systems nor functionally characterized in situ yet. In this study, we report on the enrichment and genomic characterization of a representative of this lineage from a thermal spring in Kamchatka. This thaumarchaeote, provisionally classified as "Candidatus Nitrosotenuis uzonensis", is a moderately thermophilic, non-halophilic, chemolithoautotrophic ammonia oxidizer. The nearly complete genome sequence (assembled into a single scaffold of this AOA confirmed the presence of the typical thaumarchaeotal pathways for ammonia oxidation and carbon fixation, and indicated its ability to produce coenzyme F420 and to chemotactically react to its environment. Interestingly, like members of the genus Nitrosoarchaeum, "Candidatus N. uzonensis" also possesses a putative artubulin-encoding gene. Genome comparisons to related AOA with available genome sequences confirmed that the newly cultured AOA has an average nucleotide identity far below the species threshold and revealed a substantial degree of genomic plasticity with unique genomic regions in "Ca. N. uzonensis", which potentially include genetic determinants of ecological niche differentiation.

  16. Enrichment and genome sequence of the group I.1a ammonia-oxidizing Archaeon "Ca. Nitrosotenuis uzonensis" representing a clade globally distributed in thermal habitats.

    Science.gov (United States)

    Lebedeva, Elena V; Hatzenpichler, Roland; Pelletier, Eric; Schuster, Nathalie; Hauzmayer, Sandra; Bulaev, Aleksandr; Grigor'eva, Nadezhda V; Galushko, Alexander; Schmid, Markus; Palatinszky, Marton; Le Paslier, Denis; Daims, Holger; Wagner, Michael

    2013-01-01

    The discovery of ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota and the high abundance of archaeal ammonia monooxygenase subunit A encoding gene sequences in many environments have extended our perception of nitrifying microbial communities. Moreover, AOA are the only aerobic ammonia oxidizers known to be active in geothermal environments. Molecular data indicate that in many globally distributed terrestrial high-temperature habits a thaumarchaeotal lineage within the Nitrosopumilus cluster (also called "marine" group I.1a) thrives, but these microbes have neither been isolated from these systems nor functionally characterized in situ yet. In this study, we report on the enrichment and genomic characterization of a representative of this lineage from a thermal spring in Kamchatka. This thaumarchaeote, provisionally classified as "Candidatus Nitrosotenuis uzonensis", is a moderately thermophilic, non-halophilic, chemolithoautotrophic ammonia oxidizer. The nearly complete genome sequence (assembled into a single scaffold) of this AOA confirmed the presence of the typical thaumarchaeotal pathways for ammonia oxidation and carbon fixation, and indicated its ability to produce coenzyme F420 and to chemotactically react to its environment. Interestingly, like members of the genus Nitrosoarchaeum, "Candidatus N. uzonensis" also possesses a putative artubulin-encoding gene. Genome comparisons to related AOA with available genome sequences confirmed that the newly cultured AOA has an average nucleotide identity far below the species threshold and revealed a substantial degree of genomic plasticity with unique genomic regions in "Ca. N. uzonensis", which potentially include genetic determinants of ecological niche differentiation.

  17. Implementation and synchronisation of the First Level Global Trigger for the CMS experiment at LHC

    International Nuclear Information System (INIS)

    Taurok, A.; Bergauer, H.; Padrta, M.

    2001-01-01

    The hardware implementation of the First Level Global Trigger for the Compact Muon Solenoid experiment at the CERN Large Hadron Collider is described. Special emphasis is given to the algorithm logic and the synchronisation procedure. Up to 128 different trigger algorithms are calculated in parallel by the Global Trigger (GT) for every beam crossing taking place at 25 ns intervals. Already, at the first trigger level the GT is able to select complex topological event configurations by performing fast calculations. The electronics is based on VME and relies completely on Field Programmable Gate Arrays (FPGA) technology. The electronic circuits are optimised for speed by exploiting, to a great extent, the small look-up tables provided in the FPGA chips

  18. Global Strategy Implementation at the Business Unit Level: Operational Capabilities and Administrative Mechanisms

    OpenAIRE

    Kendall Roth; David M Schweiger; Allen J Morrison

    1991-01-01

    The study examines the impact of internationally strategy on organizational design and the influence of the organizational design on effectiveness at the business unit level. The empirical findings are based on survey responses from eighty-two business units competing in global industries. The findings are supportive of the contingency notion which suggests that business unit effectiveness is a function of the fit between the international strategy and the organizational design.© 1991 JIBS. J...

  19. Global climate targets and future consumption level: an evaluation of the required GHG intensity

    International Nuclear Information System (INIS)

    Girod, Bastien; Van Vuuren, Detlef Peter; Hertwich, Edgar G

    2013-01-01

    Discussion and analysis on international climate policy often focuses on the rather abstract level of total national and regional greenhouse gas (GHG) emissions. At some point, however, emission reductions need to be translated to consumption level. In this article, we evaluate the implications of the strictest IPCC representative concentration pathway for key consumption categories (food, travel, shelter, goods, services). We use IPAT style identities to account for possible growth in global consumption levels and indicate the required change in GHG emission intensity for each category (i.e. GHG emission per calorie, person kilometer, square meter, kilogram, US dollar). The proposed concept provides guidance for product developers, consumers and policymakers. To reach the 2 °C climate target (2.1 tCO 2 -eq. per capita in 2050), the GHG emission intensity of consumption has to be reduced by a factor of 5 in 2050. The climate targets on consumption level allow discussion of the feasibility of this climate target at product and consumption level. In most consumption categories products in line with this climate target are available. For animal food and air travel, reaching the GHG intensity targets with product modifications alone will be challenging and therefore structural changes in consumption patterns might be needed. The concept opens up possibilities for further research on potential solutions on the consumption and product level to global climate mitigation. (letter)

  20. Global Knowledge Futures: Articulating the Emergence of a New Meta-level Field

    Directory of Open Access Journals (Sweden)

    Jennifer M. Gidley

    2013-06-01

    Full Text Available In this paper I articulate a new meta-level field of studies that I call global knowledge futures—a field through which other emerging transdisciplinary fields can be integrated to cohere knowledge at a higher level. I contrast this with the current dominant knowledge paradigm of the global knowledge economy with its fragmentation, commodification and instrumentalism based on neoliberal knowledge capitalism. I take a big-picture, macrohistorical lens to the new thinking and new knowledge patterns that are emerging within the evolution of consciousness discourse. I explore three discourses: postformal studies, integral studies and planetary studies—using a fourth discourse, futures studies, to provide a macro-temporal framing. By extending the meta-fields of postformal, integral and planetary studies into a prospective future dimension, I locate areas of development where these leading-edge discourses can be brought into closer dialogue with each other. In this meeting point of four boundary-spanning discourses I identify the new meta-level field of global knowledge futures, grounded in human thinking capacities, such as creativity, imagination, dialogue and collaboration.

  1. Impaired global, and compensatory local, biological motion processing in people with high levels of autistic traits.

    Science.gov (United States)

    van Boxtel, Jeroen J A; Lu, Hongjing

    2013-01-01

    People with Autism Spectrum Disorder (ASD) are hypothesized to have poor high-level processing but superior low-level processing, causing impaired social recognition, and a focus on non-social stimulus contingencies. Biological motion perception provides an ideal domain to investigate exactly how ASD modulates the interaction between low and high-level processing, because it involves multiple processing stages, and carries many important social cues. We investigated individual differences among typically developing observers in biological motion processing, and whether such individual differences associate with the number of autistic traits. In Experiment 1, we found that individuals with fewer autistic traits were automatically and involuntarily attracted to global biological motion information, whereas individuals with more autistic traits did not show this pre-attentional distraction. We employed an action adaptation paradigm in the second study to show that individuals with more autistic traits were able to compensate for deficits in global processing with an increased involvement in local processing. Our findings can be interpreted within a predictive coding framework, which characterizes the functional relationship between local and global processing stages, and explains how these stages contribute to the perceptual difficulties associated with ASD.

  2. Impaired global, and compensatory local, biological motion processing in people with high levels of autistic traits

    Directory of Open Access Journals (Sweden)

    Jeroen J A Van Boxtel

    2013-04-01

    Full Text Available People with Autism Spectrum Disorder (ASD are hypothesized to have poor high-level processing but superior low-level processing, causing impaired social recognition, and a focus on non-social stimulus contingencies. Biological motion perception provides an ideal domain to investigate exactly how ASD modulates the interaction between low and high-level processing, because it involves multiple processing stages, and carries many important social cues. We investigated individual differences among typically developing observers in biological motion processing, and whether such individual differences associate with the number of autistic traits. In Experiment 1, we found that individuals with fewer autistic traits were automatically and involuntarily attracted to global biological motion information, whereas individuals with more autistic traits did not show this pre-attentional distraction. We employed an action adaptation paradigm in the second study to show that individuals with more autistic traits were able to compensate for deficits in global processing with an increased involvement in local processing. Our findings can be interpreted within a predictive coding framework, which characterizes the functional relationship between local and global processing stages, and explains how these stages contribute to the perceptual difficulties associated with ASD.

  3. Evaluation of the Global Mean Sea Level Budget between 1993 and 2014

    DEFF Research Database (Denmark)

    Chambers, Don P.; Cazenave, Anny; Champollion, Nicolas

    2017-01-01

    Evaluating global mean sea level (GMSL) in terms of its components—mass and steric—is useful for both quantifying the accuracy of the measurements and understanding the processes that contribute to GMSL rise. In this paper, we review the GMSL budget over two periods—1993 to 2014 and 2005 to 2014......—using multiple data sets of both total GMSL and the components (mass and steric). In addition to comparing linear trends, we also compare the level of agreement of the time series. For the longer period (1993–2014), we find closure in terms of the long-term trend but not for year-to-year variations...

  4. Sleep deprivation and activation of morning levels of cellular and genomic markers of inflammation.

    Science.gov (United States)

    Irwin, Michael R; Wang, Minge; Campomayor, Capella O; Collado-Hidalgo, Alicia; Cole, Steve

    2006-09-18

    Inflammation is associated with increased risk of cardiovascular disorders, arthritis, diabetes mellitus, and mortality. The effects of sleep loss on the cellular and genomic mechanisms that contribute to inflammatory cytokine activity are not known. In 30 healthy adults, monocyte intracellular proinflammatory cytokine production was repeatedly assessed during the day across 3 baseline periods and after partial sleep deprivation (awake from 11 pm to 3 am). We analyzed the impact of sleep loss on transcription of proinflammatory cytokine genes and used DNA microarray analyses to characterize candidate transcription-control pathways that might mediate the effects of sleep loss on leukocyte gene expression. In the morning after a night of sleep loss, monocyte production of interleukin 6 and tumor necrosis factor alpha was significantly greater compared with morning levels following uninterrupted sleep. In addition, sleep loss induced a more than 3-fold increase in transcription of interleukin 6 messenger RNA and a 2-fold increase in tumor necrosis factor alpha messenger RNA. Bioinformatics analyses suggested that the inflammatory response was mediated by the nuclear factor kappaB inflammatory signaling system as well as through classic hormone and growth factor response pathways. Sleep loss induces a functional alteration of the monocyte proinflammatory cytokine response. A modest amount of sleep loss also alters molecular processes that drive cellular immune activation and induce inflammatory cytokines; mapping the dynamics of sleep loss on molecular signaling pathways has implications for understanding the role of sleep in altering immune cell physiologic characteristics. Interventions that target sleep might constitute new strategies to constrain inflammation with effects on inflammatory disease risk.

  5. From Multilatina to Global Latina: Unveiling the corporate-level international strategy choices of Grupo Nutresa

    Directory of Open Access Journals (Sweden)

    MARIA A DE VILLA

    Full Text Available Research on Multilatinas has underexplored multinationals from Colombia and their corporate-level international strategy choices to develop into Global Latinas. Building on interviews, documents, and archival data about Grupo Nutresa -Colombia's most international firm in manufactured goods-, this study unveils and discusses this firm's corporate-level international strategy choices between 1960 and 2014. A prevailing notion is that most multinationals from Latin America continue to target international operations to focus mainly on their home region through an export, multidomestic or transnational corporate-level international strategy. In contrast, data show that Grupo Nutresa chose to evolve through a sequential approach from an export to a transnational corporate-level international strategy while its international operations were able to transcend its home region to reach North America, Asia, Europe, Africa, and Oceania. These results add to international business research on emergent market multinational companies (EMNCs from Latin America by unveiling the corporate-level international strategy choices of a Colombian origin Multilatina that transformed into a Global Latina.

  6. The impact of future sea-level rise on the global tides

    Science.gov (United States)

    Pickering, M. D.; Horsburgh, K. J.; Blundell, J. R.; Hirschi, J. J.-M.; Nicholls, R. J.; Verlaan, M.; Wells, N. C.

    2017-06-01

    Tides are a key component in coastal extreme water levels. Possible changes in the tides caused by mean sea-level rise (SLR) are therefore of importance in the analysis of coastal flooding, as well as many other applications. We investigate the effect of future SLR on the tides globally using a fully global forward tidal model: OTISmpi. Statistical comparisons of the modelled and observed tidal solutions demonstrate the skill of the refined model setup with no reliance on data assimilation. We simulate the response of the four primary tidal constituents to various SLR scenarios. Particular attention is paid to future changes at the largest 136 coastal cities, where changes in water level would have the greatest impact. Spatially uniform SLR scenarios ranging from 0.5 to 10 m with fixed coastlines show that the tidal amplitudes in shelf seas globally respond strongly to SLR with spatially coherent areas of increase and decrease. Changes in the M2 and S2 constituents occur globally in most shelf seas, whereas changes in K1 and O1 are confined to Asian shelves. With higher SLR tidal changes are often not proportional to the SLR imposed and larger portions of mean high water (MHW) changes are above proportional. Changes in MHW exceed ±10% of the SLR at 10% of coastal cities. SLR scenarios allowing for coastal recession tend increasingly to result in a reduction in tidal range. The fact that the fixed and recession shoreline scenarios result mainly in changes of opposing sign is explained by the effect of the perturbations on the natural period of oscillation of the basin. Our results suggest that coastal management strategies could influence the sign of the tidal amplitude change. The effect of a spatially varying SLR, in this case fingerprints of the initial elastic response to ice mass loss, modestly alters the tidal response with the largest differences at high latitudes.

  7. Globalization

    DEFF Research Database (Denmark)

    Plum, Maja

    Globalization is often referred to as external to education - a state of affair facing the modern curriculum with numerous challenges. In this paper it is examined as internal to curriculum; analysed as a problematization in a Foucaultian sense. That is, as a complex of attentions, worries, ways...... of reasoning, producing curricular variables. The analysis is made through an example of early childhood curriculum in Danish Pre-school, and the way the curricular variable of the pre-school child comes into being through globalization as a problematization, carried forth by the comparative practices of PISA...

  8. Globalization

    OpenAIRE

    F. Gerard Adams

    2008-01-01

    The rapid globalization of the world economy is causing fundamental changes in patterns of trade and finance. Some economists have argued that globalization has arrived and that the world is “flat†. While the geographic scope of markets has increased, the author argues that new patterns of trade and finance are a result of the discrepancies between “old†countries and “new†. As the differences are gradually wiped out, particularly if knowledge and technology spread worldwide, the t...

  9. Characterizing the Global Impact of P2P Overlays on the AS-Level Underlay

    Science.gov (United States)

    Rasti, Amir Hassan; Rejaie, Reza; Willinger, Walter

    This paper examines the problem of characterizing and assessing the global impact of the load imposed by a Peer-to-Peer (P2P) overlay on the AS-level underlay. In particular, we capture Gnutella snapshots for four consecutive years, obtain the corresponding AS-level topology snapshots of the Internet and infer the AS-paths associated with each overlay connection. Assuming a simple model of overlay traffic, we analyze the observed load imposed by these Gnutella snapshots on the AS-level underlay using metrics that characterize the load seen on individual AS-paths and by the transit ASes, illustrate the churn among the top transit ASes during this 4-year period, and describe the propagation of traffic within the AS-level hierarchy.

  10. Physical mapping of a large plant genome using global high-information-content-fingerprinting: the distal region of the wheat ancestor Aegilops tauschii chromosome 3DS

    Directory of Open Access Journals (Sweden)

    You Frank M

    2010-06-01

    Triticeae genome. This study demonstrates that global fingerprinting of the large plant genomes is a viable strategy for generating physical maps. Physical maps allow the description of the co-linearity between wheat and grass genomes and provide a powerful tool for positional cloning of new genes.

  11. Genetic and epigenetic alterations induced by different levels of rye genome integration in wheat recipient.

    Science.gov (United States)

    Zheng, X L; Zhou, J P; Zang, L L; Tang, A T; Liu, D Q; Deng, K J; Zhang, Y

    2016-06-17

    The narrow genetic variation present in common wheat (Triticum aestivum) varieties has greatly restricted the improvement of crop yield in modern breeding systems. Alien addition lines have proven to be an effective means to broaden the genetic diversity of common wheat. Wheat-rye addition lines, which are the direct bridge materials for wheat improvement, have been wildly used to produce new wheat cultivars carrying alien rye germplasm. In this study, we investigated the genetic and epigenetic alterations in two sets of wheat-rye disomic addition lines (1R-7R) and the corresponding triticales. We used expressed sequence tag-simple sequence repeat, amplified fragment length polymorphism, and methylation-sensitive amplification polymorphism analyses to analyze the effects of the introduction of alien chromosomes (either the entire genome or sub-genome) to wheat genetic background. We found obvious and diversiform variations in the genomic primary structure, as well as alterations in the extent and pattern of the genomic DNA methylation of the recipient. Meanwhile, these results also showed that introduction of different rye chromosomes could induce different genetic and epigenetic alterations in its recipient, and the genetic background of the parents is an important factor for genomic and epigenetic variation induced by alien chromosome addition.

  12. Global and Country-Level Fragility to Major Disruptions in Crop Production

    Science.gov (United States)

    Puma, M. J.; Wada, Y.; Chon, S. Y.; Cook, B. I.; Nordbotten, J. M.

    2016-12-01

    New food polices are needed to mitigate vulnerabilities in the global food system to unexpected and severe production losses. The starting point for developing such policies is the ability to quantify the potential range of food and economic losses associated with major food-production shocks. Although individual major shock events are unpredictable, it is possible to quantify the relative vulnerabilities of the global food system as a whole and of individual countries within the system to production shocks. Here we combine a scale for food disruptions, which links the magnitude for a production shock with the corresponding short-term food and economic losses for that event (analogous to the well-known Richter magnitude scale for earthquakes), with country-level food system metrics. We demonstrate the value of our approach using the recent El Niño event of 2015-2016. Ultimately, these metrics can be used as part of efforts to develop national and global level food policies to prepare for and mitigate possible food-supply disruptions.

  13. Sea level and global ice volumes from the Last Glacial Maximum to the Holocene.

    Science.gov (United States)

    Lambeck, Kurt; Rouby, Hélène; Purcell, Anthony; Sun, Yiying; Sambridge, Malcolm

    2014-10-28

    The major cause of sea-level change during ice ages is the exchange of water between ice and ocean and the planet's dynamic response to the changing surface load. Inversion of ∼1,000 observations for the past 35,000 y from localities far from former ice margins has provided new constraints on the fluctuation of ice volume in this interval. Key results are: (i) a rapid final fall in global sea level of ∼40 m in sea level, the main phase of deglaciation occurred from ∼16.5 ka BP to ∼8.2 ka BP at an average rate of rise of 12 m⋅ka(-1) punctuated by periods of greater, particularly at 14.5-14.0 ka BP at ≥40 mm⋅y(-1) (MWP-1A), and lesser, from 12.5 to 11.5 ka BP (Younger Dryas), rates; (iv) no evidence for a global MWP-1B event at ∼11.3 ka BP; and (v) a progressive decrease in the rate of rise from 8.2 ka to ∼2.5 ka BP, after which ocean volumes remained nearly constant until the renewed sea-level rise at 100-150 y ago, with no evidence of oscillations exceeding ∼15-20 cm in time intervals ≥200 y from 6 to 0.15 ka BP.

  14. Global warming and sea level rise. Chikyu Ondanka to kaimen josho

    Energy Technology Data Exchange (ETDEWEB)

    Mimura, N [Ibaraki University, Ibaraki (Japan). Faculty of Engineering

    1993-10-15

    This paper describes the following matters on the problems of global warming and sea level rise. The first evaluation report published by the inter-government panel on climate change (IPCC) in 1990 estimates that, if emission of greenhouse effect gas keeps increasing at the present rate, the air temperature and the average sea level would rise by 3[degree]C and 65 centimeters, respectively by 2100. Global warming would not only result in rise of the sea level, but also accompany changes in strengths and routes of tropical low pressure areas, and precipitation patterns. Downstream areas of large rivers and island countries on coral reefs may have a risk of getting submerged. Countries having coasts developed to high densities (Japan, for example) would be subjected to a high potential effect. An 'East Hemisphere International Conference on Sea Level Rising Problem' was held in Japan in August 1993 as part of the works to prepare the second evaluation report of the IPCC (publication scheduled for 1995). The conference was attended by 24 countries, and 43 study results were reported. 4 figs.

  15. Phosphatase Rtr1 Regulates Global Levels of Serine 5 RNA Polymerase II C-Terminal Domain Phosphorylation and Cotranscriptional Histone Methylation.

    Science.gov (United States)

    Hunter, Gerald O; Fox, Melanie J; Smith-Kinnaman, Whitney R; Gogol, Madelaine; Fleharty, Brian; Mosley, Amber L

    2016-09-01

    In eukaryotes, the C-terminal domain (CTD) of Rpb1 contains a heptapeptide repeat sequence of (Y1S2P3T4S5P6S7)n that undergoes reversible phosphorylation through the opposing action of kinases and phosphatases. Rtr1 is a conserved protein that colocalizes with RNA polymerase II (RNAPII) and has been shown to be important for the transition from elongation to termination during transcription by removing RNAPII CTD serine 5 phosphorylation (Ser5-P) at a selection of target genes. In this study, we show that Rtr1 is a global regulator of the CTD code with deletion of RTR1 causing genome-wide changes in Ser5-P CTD phosphorylation and cotranscriptional histone H3 lysine 36 trimethylation (H3K36me3). Using chromatin immunoprecipitation and high-resolution microarrays, we show that RTR1 deletion results in global changes in RNAPII Ser5-P levels on genes with different lengths and transcription rates consistent with its role as a CTD phosphatase. Although Ser5-P levels increase, the overall occupancy of RNAPII either decreases or stays the same in the absence of RTR1 Additionally, the loss of Rtr1 in vivo leads to increases in H3K36me3 levels genome-wide, while total histone H3 levels remain relatively constant within coding regions. Overall, these findings suggest that Rtr1 regulates H3K36me3 levels through changes in the number of binding sites for the histone methyltransferase Set2, thereby influencing both the CTD and histone codes. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  16. Association between serum organochlorines and global methylation level of leukocyte DNA among Japanese women: a cross-sectional study

    Energy Technology Data Exchange (ETDEWEB)

    Itoh, Hiroaki [Department of Epidemiology and Environmental Health, Juntendo University Faculty of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113–8421 Japan (Japan); Iwasaki, Motoki, E-mail: moiwasak@ncc.go.jp [Epidemiology Division, Research Center for Cancer Prevention and Screening, National Cancer Center, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104–0045 Japan (Japan); Kasuga, Yoshio [Department of Surgery, Nagano Matsushiro General Hospital, 183 Matsushiro, Matsushiro-cho, Nagano City, Nagano Prefecture 381–1231 Japan (Japan); Yokoyama, Shiro; Onuma, Hiroshi [Department of Breast and Thyroid Surgery, Nagano Red Cross Hospital, 5-22-1 Wakasato, Nagano City, Nagano Prefecture 380–8582 Japan (Japan); Nishimura, Hideki [Department of Respiratory Surgery and Breast Surgery, Nagano Municipal Hospital, 1333–1 Tomitake, Nagano City, Nagano Prefecture 381–8551 Japan (Japan); Kusama, Ritsu [Department of Surgery, Hokushin General Hospital, 1-5-63 Nishi, Nakano City, Nagano Prefecture 383–8505 Japan (Japan); Yoshida, Teruhiko [Division of Genetics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104–0045 Japan (Japan); Yokoyama, Kazuhito [Department of Epidemiology and Environmental Health, Juntendo University Faculty of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113–8421 Japan (Japan); Tsugane, Shoichiro [Dierctor Research Center for Cancer Prevention and Screening, National Cancer Center, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104–0045 Japan (Japan)

    2014-08-15

    While the global methylation level of leukocyte DNA may be a suitable biomarker for cancer risk, the level may be influenced by multiple factors, both environmental and host-related, one of which is exposure to environmental pollutants. To date, three epidemiologic studies have examined associations between serum organochlorine levels and global DNA methylation level, but their findings are not fully consistent, and the associations thus require confirmation in other well-characterized populations. We tested the association between organochlorine exposure and the global DNA methylation level of leukocytes in Japanese women. We conducted a cross-sectional study using the control group of a breast cancer case–control study in Japan. Subjects were 403 Japanese women who provided blood samples. Serum polychlorinated biphenyls (PCBs) and nine pesticide-related organochlorines were measured by gas chromatography isotope-dilution high-resolution mass spectrometry. Further, global methylation level of peripheral leukocyte DNA among 399 women was measured by luminometric methylation assay. Linear trends in the association between methylation and quartile levels of organochlorines were evaluated by regression coefficients in a multivariable linear regression model. We found significant inverse associations between the global methylation level in leukocyte DNA and many of the organochlorine levels measured. Global methylation level was significantly decreased by 0.33–0.83% per quartile category for serum o,p′-dichlorodiphenyltrichloroethane (o,p′-DDT), p,p′-DDT, p,p′-dichlorodiphenyldichloroethylene, trans-nonachlor, oxychlordane, hexachlorobenzene, β-hexachlorocyclohexane, PCB17, PCB52/69, PCB74, PCB114, and PCB183. Serum organochlorine levels were inversely associated with the global methylation level of leukocyte DNA in a relatively large sample of Japanese women. - Highlights: • Many serum organochlorine pesticides were inversely associated with the global

  17. Current and future levels of mercury atmospheric pollution on a global scale

    Science.gov (United States)

    Pacyna, Jozef M.; Travnikov, Oleg; De Simone, Francesco; Hedgecock, Ian M.; Sundseth, Kyrre; Pacyna, Elisabeth G.; Steenhuisen, Frits; Pirrone, Nicola; Munthe, John; Kindbom, Karin

    2016-10-01

    An assessment of current and future emissions, air concentrations, and atmospheric deposition of mercury worldwide is presented on the basis of results obtained during the performance of the EU GMOS (Global Mercury Observation System) project. Emission estimates for mercury were prepared with the main goal of applying them in models to assess current (2013) and future (2035) air concentrations and atmospheric deposition of this contaminant. The combustion of fossil fuels (mainly coal) for energy and heat production in power plants and in industrial and residential boilers, as well as artisanal and small-scale gold mining, is one of the major anthropogenic sources of Hg emissions to the atmosphere at present. These sources account for about 37 and 25 % of the total anthropogenic Hg emissions globally, estimated to be about 2000 t. Emissions in Asian countries, particularly in China and India, dominate the total emissions of Hg. The current estimates of mercury emissions from natural processes (primary mercury emissions and re-emissions), including mercury depletion events, were estimated to be 5207 t year-1, which represents nearly 70 % of the global mercury emission budget. Oceans are the most important sources (36 %), followed by biomass burning (9 %). A comparison of the 2035 anthropogenic emissions estimated for three different scenarios with current anthropogenic emissions indicates a reduction of these emissions in 2035 up to 85 % for the best-case scenario. Two global chemical transport models (GLEMOS and ECHMERIT) have been used for the evaluation of future mercury pollution levels considering future emission scenarios. Projections of future changes in mercury deposition on a global scale simulated by these models for three anthropogenic emissions scenarios of 2035 indicate a decrease in up to 50 % deposition in the Northern Hemisphere and up to 35 % in Southern Hemisphere for the best-case scenario. The EU GMOS project has proved to be a very important

  18. Current and future levels of mercury atmospheric pollution on a global scale

    Directory of Open Access Journals (Sweden)

    J. M. Pacyna

    2016-10-01

    Full Text Available An assessment of current and future emissions, air concentrations, and atmospheric deposition of mercury worldwide is presented on the basis of results obtained during the performance of the EU GMOS (Global Mercury Observation System project. Emission estimates for mercury were prepared with the main goal of applying them in models to assess current (2013 and future (2035 air concentrations and atmospheric deposition of this contaminant. The combustion of fossil fuels (mainly coal for energy and heat production in power plants and in industrial and residential boilers, as well as artisanal and small-scale gold mining, is one of the major anthropogenic sources of Hg emissions to the atmosphere at present. These sources account for about 37 and 25 % of the total anthropogenic Hg emissions globally, estimated to be about 2000 t. Emissions in Asian countries, particularly in China and India, dominate the total emissions of Hg. The current estimates of mercury emissions from natural processes (primary mercury emissions and re-emissions, including mercury depletion events, were estimated to be 5207 t year−1, which represents nearly 70 % of the global mercury emission budget. Oceans are the most important sources (36 %, followed by biomass burning (9 %. A comparison of the 2035 anthropogenic emissions estimated for three different scenarios with current anthropogenic emissions indicates a reduction of these emissions in 2035 up to 85 % for the best-case scenario. Two global chemical transport models (GLEMOS and ECHMERIT have been used for the evaluation of future mercury pollution levels considering future emission scenarios. Projections of future changes in mercury deposition on a global scale simulated by these models for three anthropogenic emissions scenarios of 2035 indicate a decrease in up to 50 % deposition in the Northern Hemisphere and up to 35 % in Southern Hemisphere for the best-case scenario. The EU GMOS project has

  19. Assessing the value of the ATL13 inland water level product for the Global Flood Partnership

    Science.gov (United States)

    Schumann, G.; Pappenberger, F.; Bates, P. D.; Neal, J. C.; Jasinski, M. F.

    2015-12-01

    This paper reports on the activities and first results of an our ICESat-2 Early Adopter (EA) project for inland water observations. Our team will assess the value of the ICESat-2 water level product using two flood model use cases, one over the California Bay Delta and one over the Niger Inland Delta. Application of the ALT13 product into routine operations will be ensured via an ALT13 database integrated into the pillar "Global Flood Service and Toolbox" (GFST) of the Global Flood Partnership (GFP). GFP is a cooperation framework between scientific organizations and flood disaster managers worldwide to develop flood observational and modelling infrastructure, leveraging on existing initiatives for better predicting and managing flood disaster impacts and flood risk globally. GFP is hosted as an Expert Working Group by the Global Disaster Alert and Coordination System (GDACS). The objective of this EA project is to make the ICESat-2 water level data available to the international GFP community. The EA team believes that the ALT13 product, after successful demonstration of its value in model calibration/validation and monitoring of large floodplain inundation dynamics, should be made easily accessible to the GFP. The GFST will host data outputs and tools from different flood models and for different applications and regions. All these models can benefit from ALT13 if made available to GFP through GFST. Here, we will introduce both test cases and their model setups and report on first preliminary "capabilities" test runs with the Niger model and ICESat-1 as well as radar altimeter data. Based on our results, we will also reflect on expected capabilities and potential of the ICESat-2 mission for river observations.

  20. Segmental and global lordosis changes with two-level axial lumbar interbody fusion and posterior instrumentation

    Science.gov (United States)

    Melgar, Miguel A; Tobler, William D; Ernst, Robert J; Raley, Thomas J; Anand, Neel; Miller, Larry E; Nasca, Richard J

    2014-01-01

    Background Loss of lumbar lordosis has been reported after lumbar interbody fusion surgery and may portend poor clinical and radiographic outcome. The objective of this research was to measure changes in segmental and global lumbar lordosis in patients treated with presacral axial L4-S1 interbody fusion and posterior instrumentation and to determine if these changes influenced patient outcomes. Methods We performed a retrospective, multi-center review of prospectively collected data in 58 consecutive patients with disabling lumbar pain and radiculopathy unresponsive to nonsurgical treatment who underwent L4-S1 interbody fusion with the AxiaLIF two-level system (Baxano Surgical, Raleigh NC). Main outcomes included back pain severity, Oswestry Disability Index (ODI), Odom's outcome criteria, and fusion status using flexion and extension radiographs and computed tomography scans. Segmental (L4-S1) and global (L1-S1) lumbar lordosis measurements were made using standing lateral radiographs. All patients were followed for at least 24 months (mean: 29 months, range 24-56 months). Results There was no bowel injury, vascular injury, deep infection, neurologic complication or implant failure. Mean back pain severity improved from 7.8±1.7 at baseline to 3.3±2.6 at 2 years (p lordosis, defined as a change in Cobb angle ≤ 5°, was identified in 84% of patients at L4-S1 and 81% of patients at L1-S1. Patients with loss or gain in segmental or global lordosis experienced similar 2-year outcomes versus those with less than a 5° change. Conclusions/Clinical Relevance Two-level axial interbody fusion supplemented with posterior fixation does not alter segmental or global lordosis in most patients. Patients with postoperative change in lordosis greater than 5° have similarly favorable long-term clinical outcomes and fusion rates compared to patients with less than 5° lordosis change. PMID:25694920

  1. Flexible trigger menu implementation on the Global Trigger for the CMS Level-1 trigger upgrade

    Science.gov (United States)

    MATSUSHITA, Takashi; CMS Collaboration

    2017-10-01

    The CMS experiment at the Large Hadron Collider (LHC) has continued to explore physics at the high-energy frontier in 2016. The integrated luminosity delivered by the LHC in 2016 was 41 fb-1 with a peak luminosity of 1.5 × 1034 cm-2s-1 and peak mean pile-up of about 50, all exceeding the initial estimations for 2016. The CMS experiment has upgraded its hardware-based Level-1 trigger system to maintain its performance for new physics searches and precision measurements at high luminosities. The Global Trigger is the final step of the CMS Level-1 trigger and implements a trigger menu, a set of selection requirements applied to the final list of objects from calorimeter and muon triggers, for reducing the 40 MHz collision rate to 100 kHz. The Global Trigger has been upgraded with state-of-the-art FPGA processors on Advanced Mezzanine Cards with optical links running at 10 GHz in a MicroTCA crate. The powerful processing resources of the upgraded system enable implementation of more algorithms at a time than previously possible, allowing CMS to be more flexible in how it handles the available trigger bandwidth. Algorithms for a trigger menu, including topological requirements on multi-objects, can be realised in the Global Trigger using the newly developed trigger menu specification grammar. Analysis-like trigger algorithms can be represented in an intuitive manner and the algorithms are translated to corresponding VHDL code blocks to build a firmware. The grammar can be extended in future as the needs arise. The experience of implementing trigger menus on the upgraded Global Trigger system will be presented.

  2. Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface.

    Science.gov (United States)

    McKenna, Duane D; Scully, Erin D; Pauchet, Yannick; Hoover, Kelli; Kirsch, Roy; Geib, Scott M; Mitchell, Robert F; Waterhouse, Robert M; Ahn, Seung-Joon; Arsala, Deanna; Benoit, Joshua B; Blackmon, Heath; Bledsoe, Tiffany; Bowsher, Julia H; Busch, André; Calla, Bernarda; Chao, Hsu; Childers, Anna K; Childers, Christopher; Clarke, Dave J; Cohen, Lorna; Demuth, Jeffery P; Dinh, Huyen; Doddapaneni, HarshaVardhan; Dolan, Amanda; Duan, Jian J; Dugan, Shannon; Friedrich, Markus; Glastad, Karl M; Goodisman, Michael A D; Haddad, Stephanie; Han, Yi; Hughes, Daniel S T; Ioannidis, Panagiotis; Johnston, J Spencer; Jones, Jeffery W; Kuhn, Leslie A; Lance, David R; Lee, Chien-Yueh; Lee, Sandra L; Lin, Han; Lynch, Jeremy A; Moczek, Armin P; Murali, Shwetha C; Muzny, Donna M; Nelson, David R; Palli, Subba R; Panfilio, Kristen A; Pers, Dan; Poelchau, Monica F; Quan, Honghu; Qu, Jiaxin; Ray, Ann M; Rinehart, Joseph P; Robertson, Hugh M; Roehrdanz, Richard; Rosendale, Andrew J; Shin, Seunggwan; Silva, Christian; Torson, Alex S; Jentzsch, Iris M Vargas; Werren, John H; Worley, Kim C; Yocum, George; Zdobnov, Evgeny M; Gibbs, Richard A; Richards, Stephen

    2016-11-11

    Relatively little is known about the genomic basis and evolution of wood-feeding in beetles. We undertook genome sequencing and annotation, gene expression assays, studies of plant cell wall degrading enzymes, and other functional and comparative studies of the Asian longhorned beetle, Anoplophora glabripennis, a globally significant invasive species capable of inflicting severe feeding damage on many important tree species. Complementary studies of genes encoding enzymes involved in digestion of woody plant tissues or detoxification of plant allelochemicals were undertaken with the genomes of 14 additional insects, including the newly sequenced emerald ash borer and bull-headed dung beetle. The Asian longhorned beetle genome encodes a uniquely diverse arsenal of enzymes that can degrade the main polysaccharide networks in plant cell walls, detoxify plant allelochemicals, and otherwise facilitate feeding on woody plants. It has the metabolic plasticity needed to feed on diverse plant species, contributing to its highly invasive nature. Large expansions of chemosensory genes involved in the reception of pheromones and plant kairomones are consistent with the complexity of chemical cues it uses to find host plants and mates. Amplification and functional divergence of genes associated with specialized feeding on plants, including genes originally obtained via horizontal gene transfer from fungi and bacteria, contributed to the addition, expansion, and enhancement of the metabolic repertoire of the Asian longhorned beetle, certain other phytophagous beetles, and to a lesser degree, other phytophagous insects. Our results thus begin to establish a genomic basis for the evolutionary success of beetles on plants.

  3. MOVE : A Multi-Level Ontology-Based Visualization and Exploration Framework for Genomic Networks

    NARCIS (Netherlands)

    Bosman, D.W.; Blom, E.J.; Ogao, P.J.; Kuipers, O.P.; Roerdink, J.B.T.M.

    2007-01-01

    Among the various research areas that comprise bioinformatics, systems biology is gaining increasing attention. An important goal of systems biology is the unraveling of dynamic interactions between components of living cells (e.g., proteins, genes). These interactions exist among others on genomic,

  4. The levels of yield and purity of genomic DNA from five tomato ...

    African Journals Online (AJOL)

    Isolation of good quality genomic DNA from different plant materials is an important prerequisite for many molecular techniques related to both basic and applied research in the areas of plant molecular biology, crop improvement, biodiversity studies and conservation of genetic materials. Therefore, the need to extract ...

  5. Global-, Regional-, and Country-Level Economic Impacts of Dental Diseases in 2015.

    Science.gov (United States)

    Righolt, A J; Jevdjevic, M; Marcenes, W; Listl, S

    2018-05-01

    Up-to-date information about the economic impact of dental diseases is essential for health care decision makers when seeking to make rational use of available resources. The purpose of this study was to provide up-to-date estimates for dental expenditures (direct costs) and productivity losses (indirect costs) due to dental diseases on the global, regional, and country level. Direct costs of dental diseases were estimated using a previously established systematic approach; indirect costs were estimated using an approach developed by the World Health Organization Commission on Macroeconomics and Health and factoring in 2015 values for gross domestic product and disability-adjusted life years from the Global Burden of Disease Study. The estimated direct costs of dental diseases amounted to $356.80 billion and indirect costs were estimated at $187.61 billion, totaling worldwide costs due to dental diseases of $544.41 billion in 2015. After adjustment for purchasing power parity, the highest levels of per capita dental expenditures were found for High-Income North America, Australasia, Western Europe, High-Income Asia Pacific, and East Asia; the highest levels of per capita productivity losses were found for Western Europe, Australasia, High-Income North America, High-Income Asia Pacific, and Central Europe. Severe tooth loss was found to imply 67% of global productivity losses due to dental diseases, followed by severe periodontitis (21%) and untreated caries (12%). From an economic perspective, improvements in population oral health may be highly beneficial and could contribute to further increases in people's well-being given available resources.

  6. Projected global ground-level ozone impacts on vegetation under different emission and climate scenarios

    Directory of Open Access Journals (Sweden)

    P. Sicard

    2017-10-01

    Full Text Available The impact of ground-level ozone (O3 on vegetation is largely under-investigated at the global scale despite large areas worldwide that are exposed to high surface O3 levels. To explore future potential impacts of O3 on vegetation, we compared historical and projected surface O3 concentrations simulated by six global atmospheric chemistry transport models on the basis of three representative concentration pathways emission scenarios (i.e. RCP2.6, 4.5, 8.5. To assess changes in the potential surface O3 threat to vegetation at the global scale, we used the AOT40 metric. Results point out a significant exceedance of AOT40 in comparison with the recommendations of UNECE for the protection of vegetation. In fact, many areas of the Northern Hemisphere show that AOT40-based critical levels will be exceeded by a factor of at least 10 under RCP8.5. Changes in surface O3 by 2100 worldwide range from about +4–5 ppb in the RCP8.5 scenario to reductions of about 2–10 ppb in the most optimistic scenario, RCP2.6. The risk of O3 injury for vegetation, through the potential O3 impact on photosynthetic assimilation, decreased by 61 and 47 % under RCP2.6 and RCP4.5, respectively, and increased by 70 % under RCP8.5. Key biodiversity areas in southern and northern Asia, central Africa and North America were identified as being at risk from high O3 concentrations.

  7. BIGSdb: Scalable analysis of bacterial genome variation at the population level

    Directory of Open Access Journals (Sweden)

    Maiden Martin CJ

    2010-12-01

    Full Text Available Abstract Background The opportunities for bacterial population genomics that are being realised by the application of parallel nucleotide sequencing require novel bioinformatics platforms. These must be capable of the storage, retrieval, and analysis of linked phenotypic and genotypic information in an accessible, scalable and computationally efficient manner. Results The Bacterial Isolate Genome Sequence Database (BIGSDB is a scalable, open source, web-accessible database system that meets these needs, enabling phenotype and sequence data, which can range from a single sequence read to whole genome data, to be efficiently linked for a limitless number of bacterial specimens. The system builds on the widely used mlstdbNet software, developed for the storage and distribution of multilocus sequence typing (MLST data, and incorporates the capacity to define and identify any number of loci and genetic variants at those loci within the stored nucleotide sequences. These loci can be further organised into 'schemes' for isolate characterisation or for evolutionary or functional analyses. Isolates and loci can be indexed by multiple names and any number of alternative schemes can be accommodated, enabling cross-referencing of different studies and approaches. LIMS functionality of the software enables linkage to and organisation of laboratory samples. The data are easily linked to external databases and fine-grained authentication of access permits multiple users to participate in community annotation by setting up or contributing to different schemes within the database. Some of the applications of BIGSDB are illustrated with the genera Neisseria and Streptococcus. The BIGSDB source code and documentation are available at http://pubmlst.org/software/database/bigsdb/. Conclusions Genomic data can be used to characterise bacterial isolates in many different ways but it can also be efficiently exploited for evolutionary or functional studies. BIGSDB

  8. Category (CAT) IIIb Level 1 Test Plan for Global Positioning System (GPS)

    Science.gov (United States)

    1993-09-01

    applications. CAT 11Tb is defined in Advisory Circular ( AC ) 120-28C [1] as "a precision instrument approach and landing with no decision height (DH), or...2) FAA AC 20-57A (Automatic Landing Systems) [31, AC 120-28C (Criteria for Approval of CAT III Landing Weather Minima) [I] and the FAA tunnel-in...AD-A274 098I I~II l~iiUIRII 11111ilIII2 DOT/FAA/RD-93/21 Category ( CAT ) IIb Level 1 MTR 93W0000102 Research and Test Plan for Global Development

  9. The risk of water scarcity at different levels of global warming

    Science.gov (United States)

    Schewe, Jacob; Sharpe, Simon

    2015-04-01

    Water scarcity is a threat to human well-being and economic development in many countries today. Future climate change is expected to exacerbate the global water crisis by reducing renewable freshwater resources different world regions, many of which are already dry. Studies of future water scarcity often focus on most-likely, or highest-confidence, scenarios. However, multi-model projections of water resources reveal large uncertainty ranges, which are due to different types of processes (climate, hydrology, human) and are therefore not easy to reduce. Thus, central estimates or multi-model mean results may be insufficient to inform policy and management. Here we present an alternative, risk-based approach. We use an ensemble of multiple global climate and hydrological models to quantify the likelihood of crossing a given water scarcity threshold under different levels of global warming. This approach allows assessing the risk associated with any particular, pre-defined threshold (or magnitude of change that must be avoided), regardless of whether it lies in the center or in the tails of the uncertainty distribution. We show applications of this method on the country and river basin scale, illustrate the effects of societal processes on the resulting risk estimates, and discuss the further potential of this approach for research and stakeholder dialogue.

  10. Global agenda, local health: including concepts of health security in preparedness programs at the jurisdictional level.

    Science.gov (United States)

    Eby, Chas

    2014-01-01

    The Global Health Security Agenda's objectives contain components that could help health departments address emerging public health challenges that threaten the population. As part of the agenda, partner countries with advanced public health systems will support the development of infrastructure in stakeholder health departments. To facilitate this process and augment local programs, state and local health departments may want to include concepts of health security in their public health preparedness offices in order to simultaneously build capacity. Health security programs developed by public health departments should complete projects that are closely aligned with the objectives outlined in the global agenda and that facilitate the completion of current preparedness grant requirements. This article identifies objectives and proposes tactical local projects that run parallel to the 9 primary objectives of the Global Health Security Agenda. Executing concurrent projects at the international and local levels in preparedness offices will accelerate the completion of these objectives and help prevent disease epidemics, detect health threats, and respond to public health emergencies. Additionally, future funding tied or related to health security may become more accessible to state and local health departments that have achieved these objectives.

  11. Complete Genome Sequences of Isolates of Enterococcus faecium Sequence Type 117, a Globally Disseminated Multidrug-Resistant Clone

    Science.gov (United States)

    Tedim, Ana P.; Lanza, Val F.; Manrique, Marina; Pareja, Eduardo; Ruiz-Garbajosa, Patricia; Cantón, Rafael; Baquero, Fernando; Tobes, Raquel

    2017-01-01

    ABSTRACT The emergence of nosocomial infections by multidrug-resistant sequence type 117 (ST117) Enterococcus faecium has been reported in several European countries. ST117 has been detected in Spanish hospitals as one of the main causes of bloodstream infections. We analyzed genome variations of ST117 strains isolated in Madrid and describe the first ST117 closed genome sequences. PMID:28360174

  12. Circulating C3 levels predict renal and global outcome in patients with renal vasculitis.

    Science.gov (United States)

    Villacorta, Javier; Diaz-Crespo, Francisco; Acevedo, Mercedes; Cavero, Teresa; Guerrero, Carmen; Praga, Manuel; Fernandez-Juarez, Gema

    2016-11-01

    Several studies have demonstrated the crucial role of complement activation in the pathogenesis of ANCA-associated vasculitis. We aimed to assess the association between baseline serum C3 (sC3) levels and long-term outcomes in patients with renal vasculitis. This retrospective study included 111 patients with renal vasculitis from three hospitals who underwent a renal biopsy between 1997 and 2014. Serum levels of C3 were measured at the onset and the study population was divided into three tertiles according to sC3 concentrations (tertile 1 128 mg/dl). Patients with lower sC3 (tertile 1) were compared with those having higher levels of sC3 (tertile 2 and tertile 3). Histological, clinical, and laboratory data were recorded for analysis. The primary end point was the composite of end-stage renal disease (ESRD) and death from any cause. Lower sC3 levels were associated with a higher need for dialysis and lower response rate to treatment (p = 0.04 and p = 0.007, respectively). Renal and global survival at 1 and 5 years was 53 and 46 % in patients with lower sC3 (tertile 1) compared with 72 and 65 % in patients with higher sC3 (upper two tertiles) (p = 0.04). In a multivariate Cox-regression model, when adjusted by renal function and histopatholologic categories, lower sC3 remained as an independent predictor of ESRD and death (HR, 1.9; 95 % CI, 1.1 to 3.4; p = 0.02). Baseline serum C3 levels have an independent prognostic value in predicting long-term renal and global survival in patients with renal vasculitis.

  13. Statistical characterization of global Sea Surface Salinity for SMOS level 3 and 4 products

    Science.gov (United States)

    Gourrion, J.; Aretxabaleta, A. L.; Ballabrera, J.; Mourre, B.

    2009-04-01

    The Soil Moisture and Ocean Salinity (SMOS) mission of the European Space Agency will soon provide sea surface salinity (SSS) estimates to the scientific community. Because of the numerous geophysical contamination sources and the instrument complexity, the salinity products will have a low signal to noise ratio at level 2 (individual estimates??) that is expected to increase up to mission requirements (0.1 psu) at level 3 (global maps with regular distribution) after spatio-temporal accumulation of the observations. Geostatistical methods such as Optimal Interpolation are being implemented at the level 3/4 production centers to operate this noise reduction step. The methodologies require auxiliary information about SSS statistics that, under Gaussian assumption, consist in the mean field and the covariance of the departures from it. The present study is a contribution to the definition of the best estimates for mean field and covariances to be used in the near-future SMOS level 3 and 4 products. We use complementary information from sparse in-situ observations and imperfect outputs from state-of-art model simulations. Various estimates of the mean field are compared. An alternative is the use of a SSS climatology such as the one provided by the World Ocean Atlas 2005. An historical SSS dataset from the World Ocean Database 2005 is reanalyzed and combined with the recent global observations obtained by the Array for Real-Time Geostrophic Oceanography (ARGO). Regional tendencies in the long-term temporal evolution of the near-surface ocean salinity are evident, suggesting that the use of a SSS climatology to describe the current mean field may introduce biases of magnitude similar to the precision goal. Consequently, a recent SSS dataset may be preferred to define the mean field needed for SMOS level 3 and 4 production. The in-situ observation network allows a global mapping of the low frequency component of the variability, i.e. decadal, interannual and seasonal

  14. Levels-of-processing effects on recollection and familiarity during transient global amnesia and after recovery.

    Science.gov (United States)

    Thoma, Patrizia; Schwarz, Michael; Daum, Irene

    2010-11-01

    The aim of the present study was to investigate the pattern of recollection and familiarity deficits and the modulation of recognition memory performance by the depth of encoding (deep vs. shallow) in transient global amnesia (TGA). Ten patients with TGA and 11 control subjects were assessed during the acute stage and after recovery 7 to 19 days later. Both recollection and familiarity were impaired in the acute stage and showed significant, albeit not complete, recovery by the time of the postacute assessment. The patients did, however, show a significant levels-of-processing effect, which was significantly reduced in acute TGA, but not at follow-up. The significant levels-of-processing effect during acute TGA might be linked to recruitment of the prefrontal cortex. (c) 2010 APA, all rights reserved

  15. Influence Of Aircraft Engine Exhaust Emissions At A Global Level And Preventive Measures

    Directory of Open Access Journals (Sweden)

    Jasna Golubić

    2004-07-01

    Full Text Available The work considers the differences in the aircraft engine exhaustemissions, as well as the impact of the emissions on theenvironment depending on several factors. These include theage of the engine, i. e. technical refinement, engine operating regimesat different thrusts during time periods: takeoff, climb,approach, etc. Also, the exhaust emissions do not have thesame influence on different atmospheric layers. The pollutantsemitted at higher altitudes during cruising have become agreater problem, although the volume of pollutants is smaller,due to the chemical complexity and sensitivity of these layers ascompared to the lower layers of atmosphere. One of the reasonswhy these problems have long remained outside the focus of interestof the environmentalists is that the air transport of goodsand people is performed at high altitudes, so that the pollutionof atmosphere does not present a direct threat to anyone, sincethe environment is being polluted at a global level and thereforeis more difficult to notice at the local level.

  16. A global standard for monitoring coastal wetland vulnerability to accelerated sea-level rise

    Science.gov (United States)

    Webb, Edward L.; Friess, Daniel A.; Krauss, Ken W.; Cahoon, Donald R.; Guntenspergen, Glenn R.; Phelps, Jacob

    2013-01-01

    Sea-level rise threatens coastal salt-marshes and mangrove forests around the world, and a key determinant of coastal wetland vulnerability is whether its surface elevation can keep pace with rising sea level. Globally, a large data gap exists because wetland surface and shallow subsurface processes remain unaccounted for by traditional vulnerability assessments using tide gauges. Moreover, those processes vary substantially across wetlands, so modelling platforms require relevant local data. The low-cost, simple, high-precision rod surface-elevation table–marker horizon (RSET-MH) method fills this critical data gap, can be paired with spatial data sets and modelling and is financially and technically accessible to every country with coastal wetlands. Yet, RSET deployment has been limited to a few regions and purposes. A coordinated expansion of monitoring efforts, including development of regional networks that could support data sharing and collaboration, is crucial to adequately inform coastal climate change adaptation policy at several scales.

  17. Global mean sea-level rise in a world agreed upon in Paris

    Science.gov (United States)

    Bittermann, Klaus; Rahmstorf, Stefan; Kopp, Robert E.; Kemp, Andrew C.

    2017-12-01

    Although the 2015 Paris Agreement seeks to hold global average temperature to ‘well below 2 °C above pre-industrial levels and to pursue efforts to limit the temperature increase to 1.5 °C above pre-industrial levels’, projections of global mean sea-level (GMSL) rise commonly focus on scenarios in which there is a high probability that warming exceeds 1.5 °C. Using a semi-empirical model, we project GMSL changes between now and 2150 CE under a suite of temperature scenarios that satisfy the Paris Agreement temperature targets. The projected magnitude and rate of GMSL rise varies among these low emissions scenarios. Stabilizing temperature at 1.5 °C instead of 2 °C above preindustrial reduces GMSL in 2150 CE by 17 cm (90% credible interval: 14-21 cm) and reduces peak rates of rise by 1.9 mm yr-1 (90% credible interval: 1.4-2.6 mm yr-1). Delaying the year of peak temperature has little long-term influence on GMSL, but does reduce the maximum rate of rise. Stabilizing at 2 °C in 2080 CE rather than 2030 CE reduces the peak rate by 2.7 mm yr-1 (90% credible interval: 2.0-4.0 mm yr-1).

  18. Promoting health equity: WHO health inequality monitoring at global and national levels

    Directory of Open Access Journals (Sweden)

    Ahmad Reza Hosseinpoor

    2015-09-01

    Full Text Available Background: Health equity is a priority in the post-2015 sustainable development agenda and other major health initiatives. The World Health Organization (WHO has a history of promoting actions to achieve equity in health, including efforts to encourage the practice of health inequality monitoring. Health inequality monitoring systems use disaggregated data to identify disadvantaged subgroups within populations and inform equity-oriented health policies, programs, and practices. Objective: This paper provides an overview of a number of recent and current WHO initiatives related to health inequality monitoring at the global and/or national level. Design: We outline the scope, content, and intended uses/application of the following: Health Equity Monitor database and theme page; State of inequality: reproductive, maternal, newborn, and child health report; Handbook on health inequality monitoring: with a focus on low- and middle-income countries; Health inequality monitoring eLearning module; Monitoring health inequality: an essential step for achieving health equity advocacy booklet and accompanying video series; and capacity building workshops conducted in WHO Member States and Regions. Conclusions: The paper concludes by considering how the work of the WHO can be expanded upon to promote the establishment of sustainable and robust inequality monitoring systems across a variety of health topics among Member States and at the global level.

  19. Temperature-driven global sea-level variability in the Common Era

    Science.gov (United States)

    Kopp, Robert E.; Kemp, Andrew C.; Bittermann, Klaus; Horton, Benjamin P.; Donnelly, Jeffrey P.; Gehrels, W. Roland; Hay, Carling C.; Mitrovica, Jerry X.; Morrow, Eric D.; Rahmstorf, Stefan

    2016-01-01

    We assess the relationship between temperature and global sea-level (GSL) variability over the Common Era through a statistical metaanalysis of proxy relative sea-level reconstructions and tide-gauge data. GSL rose at 0.1 ± 0.1 mm/y (2σ) over 0–700 CE. A GSL fall of 0.2 ± 0.2 mm/y over 1000–1400 CE is associated with ∼0.2 °C global mean cooling. A significant GSL acceleration began in the 19th century and yielded a 20th century rise that is extremely likely (probability P≥0.95) faster than during any of the previous 27 centuries. A semiempirical model calibrated against the GSL reconstruction indicates that, in the absence of anthropogenic climate change, it is extremely likely (P=0.95) that 20th century GSL would have risen by less than 51% of the observed 13.8±1.5 cm. The new semiempirical model largely reconciles previous differences between semiempirical 21st century GSL projections and the process model-based projections summarized in the Intergovernmental Panel on Climate Change’s Fifth Assessment Report. PMID:26903659

  20. Promoting health equity: WHO health inequality monitoring at global and national levels.

    Science.gov (United States)

    Hosseinpoor, Ahmad Reza; Bergen, Nicole; Schlotheuber, Anne

    2015-01-01

    Health equity is a priority in the post-2015 sustainable development agenda and other major health initiatives. The World Health Organization (WHO) has a history of promoting actions to achieve equity in health, including efforts to encourage the practice of health inequality monitoring. Health inequality monitoring systems use disaggregated data to identify disadvantaged subgroups within populations and inform equity-oriented health policies, programs, and practices. This paper provides an overview of a number of recent and current WHO initiatives related to health inequality monitoring at the global and/or national level. We outline the scope, content, and intended uses/application of the following: Health Equity Monitor database and theme page; State of inequality: reproductive, maternal, newborn, and child health report; Handbook on health inequality monitoring: with a focus on low- and middle-income countries; Health inequality monitoring eLearning module; Monitoring health inequality: an essential step for achieving health equity advocacy booklet and accompanying video series; and capacity building workshops conducted in WHO Member States and Regions. The paper concludes by considering how the work of the WHO can be expanded upon to promote the establishment of sustainable and robust inequality monitoring systems across a variety of health topics among Member States and at the global level.

  1. Promoting health equity: WHO health inequality monitoring at global and national levels

    Science.gov (United States)

    Hosseinpoor, Ahmad Reza; Bergen, Nicole; Schlotheuber, Anne

    2015-01-01

    Background Health equity is a priority in the post-2015 sustainable development agenda and other major health initiatives. The World Health Organization (WHO) has a history of promoting actions to achieve equity in health, including efforts to encourage the practice of health inequality monitoring. Health inequality monitoring systems use disaggregated data to identify disadvantaged subgroups within populations and inform equity-oriented health policies, programs, and practices. Objective This paper provides an overview of a number of recent and current WHO initiatives related to health inequality monitoring at the global and/or national level. Design We outline the scope, content, and intended uses/application of the following: Health Equity Monitor database and theme page; State of inequality: reproductive, maternal, newborn, and child health report; Handbook on health inequality monitoring: with a focus on low- and middle-income countries; Health inequality monitoring eLearning module; Monitoring health inequality: an essential step for achieving health equity advocacy booklet and accompanying video series; and capacity building workshops conducted in WHO Member States and Regions. Conclusions The paper concludes by considering how the work of the WHO can be expanded upon to promote the establishment of sustainable and robust inequality monitoring systems across a variety of health topics among Member States and at the global level. PMID:26387506

  2. Flexible trigger menu implementation on the Global Trigger for the CMS Level-1 trigger upgrade

    CERN Document Server

    Matsushita, Takashi

    2017-01-01

    The CMS experiment at the Large Hadron Collider (LHC) has continued to explore physics at the high-energy frontier in 2016. The integrated luminosity delivered by the LHC in 2016 was 41~fb$^{-1}$ with a peak luminosity of 1.5 $\\times$ 10$^{34}$ cm$^{-2}$s$^{-1}$ and peak mean pile-up of about 50, all exceeding the initial estimations for 2016. The CMS experiment has upgraded its hardware-based Level-1 trigger system to maintain its performance for new physics searches and precision measurements at high luminosities. The Global Trigger is the final step of the CMS \\mbox{Level-1} trigger and implements a trigger menu, a set of selection requirements applied to the final list of objects from calorimeter and muon triggers, for reducing the 40 MHz collision rate to 100 kHz. The Global Trigger has been upgraded with state-of-the-art FPGA processors on Advanced Mezzanine Cards with optical links running at 10 GHz in a MicroTCA crate. The powerful processing resources of the upgraded system enable implemen...

  3. Comparative Genomic Analysis of Globally Dominant ST131 Clone with Other Epidemiologically Successful Extraintestinal Pathogenic Escherichia coli (ExPEC Lineages

    Directory of Open Access Journals (Sweden)

    Sabiha Shaik

    2017-10-01

    Full Text Available Escherichia coli sequence type 131 (ST131, a pandemic clone responsible for the high incidence of extraintestinal pathogenic E. coli (ExPEC infections, has been known widely for its contribution to the worldwide dissemination of multidrug resistance. Although other ExPEC-associated and extended-spectrum-β-lactamase (ESBL-producing E. coli clones, such as ST38, ST405, and ST648 have been studied widely, no comparative genomic data with respect to other genotypes exist for ST131. In this study, comparative genomic analysis was performed for 99 ST131 E. coli strains with 40 genomes from three other STs, including ST38 (n = 12, ST405 (n = 10, and ST648 (n = 18, and functional studies were performed on five in-house strains corresponding to the four STs. Phylogenomic analysis results from this study corroborated with the sequence type-specific clonality. Results from the genome-wide resistance profiling confirmed that all strains were inherently multidrug resistant. ST131 genomes showed unique virulence profiles, and analysis of mobile genetic elements and their associated methyltransferases (MTases has revealed that several of them were missing from the majority of the non-ST131 strains. Despite the fact that non-ST131 strains lacked few essential genes belonging to the serum resistome, the in-house strains representing all four STs demonstrated similar resistance levels to serum antibactericidal activity. Core genome analysis data revealed that non-ST131 strains usually lacked several ST131-defined genomic coordinates, and a significant number of genes were missing from the core of the ST131 genomes. Data from this study reinforce adaptive diversification of E. coli strains belonging to the ST131 lineage and provide new insights into the molecular mechanisms underlying clonal diversification of the ST131 lineage.

  4. Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Mohan Babu

    2014-02-01

    Full Text Available Large-scale proteomic analyses in Escherichia coli have documented the composition and physical relationships of multiprotein complexes, but not their functional organization into biological pathways and processes. Conversely, genetic interaction (GI screens can provide insights into the biological role(s of individual gene and higher order associations. Combining the information from both approaches should elucidate how complexes and pathways intersect functionally at a systems level. However, such integrative analysis has been hindered due to the lack of relevant GI data. Here we present a systematic, unbiased, and quantitative synthetic genetic array screen in E. coli describing the genetic dependencies and functional cross-talk among over 600,000 digenic mutant combinations. Combining this epistasis information with putative functional modules derived from previous proteomic data and genomic context-based methods revealed unexpected associations, including new components required for the biogenesis of iron-sulphur and ribosome integrity, and the interplay between molecular chaperones and proteases. We find that functionally-linked genes co-conserved among γ-proteobacteria are far more likely to have correlated GI profiles than genes with divergent patterns of evolution. Overall, examining bacterial GIs in the context of protein complexes provides avenues for a deeper mechanistic understanding of core microbial systems.

  5. Dependency of high coastal water level and river discharge at the global scale

    Science.gov (United States)

    Ward, P.; Couasnon, A.; Haigh, I. D.; Muis, S.; Veldkamp, T.; Winsemius, H.; Wahl, T.

    2017-12-01

    It is widely recognized that floods cause huge socioeconomic impacts. From 1980-2013, global flood losses exceeded $1 trillion, with 220,000 fatalities. These impacts are particularly hard felt in low-lying densely populated deltas and estuaries, whose location at the coast-land interface makes them naturally prone to flooding. When river and coastal floods coincide, their impacts in these deltas and estuaries are often worse than when they occur in isolation. Such floods are examples of so-called `compound events'. In this contribution, we present the first global scale analysis of the statistical dependency of high coastal water levels (and the storm surge component alone) and river discharge. We show that there is statistical dependency between these components at more than half of the stations examined. We also show time-lags in the highest correlation between peak discharges and coastal water levels. Finally, we assess the probability of the simultaneous occurrence of design discharge and design coastal water levels, assuming both independence and statistical dependence. For those stations where we identified statistical dependency, the probability is between 1 and 5 times greater, when the dependence structure is accounted for. This information is essential for understanding the likelihood of compound flood events occurring at locations around the world as well as for accurate flood risk assessments and effective flood risk management. The research was carried out by analysing the statistical dependency between observed coastal water levels (and the storm surge component) from GESLA-2 and river discharge using gauged data from GRDC stations all around the world. The dependence structure was examined using copula functions.

  6. Genomic Microdiversity of Bifidobacterium pseudocatenulatum Underlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention

    Directory of Open Access Journals (Sweden)

    Guojun Wu

    2017-02-01

    Full Text Available The genomic basis of the response to dietary intervention of human gut beneficial bacteria remains elusive, which hinders precise manipulation of the microbiota for human health. After receiving a dietary intervention enriched with nondigestible carbohydrates for 105 days, a genetically obese child with Prader-Willi syndrome lost 18.4% of his body weight and showed significant improvement in his bioclinical parameters. We obtained five isolates (C1, C15, C55, C62, and C95 of one of the most abundantly promoted beneficial species, Bifidobacterium pseudocatenulatum, from a postintervention fecal sample. Intriguingly, these five B. pseudocatenulatum strains showed differential responses during the dietary intervention. Two strains were largely unaffected, while the other three were promoted to different extents by the changes in dietary carbohydrate resources. The differential responses of these strains were consistent with their functional clustering based on the COGs (Clusters of Orthologous Groups, including those involved with the ABC-type sugar transport systems, suggesting that the strain-specific genomic variations may have contributed to the niche adaption. Particularly, B. pseudocatenulatum C15, which had the most diverse types and highest gene copy numbers of carbohydrate-active enzymes targeting plant polysaccharides, had the highest abundance after the dietary intervention. These studies show the importance of understanding genomic diversity of specific members of the gut microbiota if precise nutrition approaches are to be realized.

  7. Targeting the right input data to improve crop modeling at global level

    Science.gov (United States)

    Adam, M.; Robertson, R.; Gbegbelegbe, S.; Jones, J. W.; Boote, K. J.; Asseng, S.

    2012-12-01

    Designed for location-specific simulations, the use of crop models at a global level raises important questions. Crop models are originally premised on small unit areas where environmental conditions and management practices are considered homogeneous. Specific information describing soils, climate, management, and crop characteristics are used in the calibration process. However, when scaling up for global application, we rely on information derived from geographical information systems and weather generators. To run crop models at broad, we use a modeling platform that assumes a uniformly generated grid cell as a unit area. Specific weather, specific soil and specific management practices for each crop are represented for each of the cell grids. Studies on the impacts of the uncertainties of weather information and climate change on crop yield at a global level have been carried out (Osborne et al, 2007, Nelson et al., 2010, van Bussel et al, 2011). Detailed information on soils and management practices at global level are very scarce but recognized to be of critical importance (Reidsma et al., 2009). Few attempts to assess the impact of their uncertainties on cropping systems performances can be found. The objectives of this study are (i) to determine sensitivities of a crop model to soil and management practices, inputs most relevant to low input rainfed cropping systems, and (ii) to define hotspots of sensitivity according to the input data. We ran DSSAT v4.5 globally (CERES-CROPSIM) to simulate wheat yields at 45arc-minute resolution. Cultivar parameters were calibrated and validated for different mega-environments (results not shown). The model was run for nitrogen-limited production systems. This setting was chosen as the most representative to simulate actual yield (especially for low-input rainfed agricultural systems) and assumes crop growth to be free of any pest and diseases damages. We conducted a sensitivity analysis on contrasting management

  8. A System of Systems Approach to Integrating Global Sea Level Change Application Programs

    Science.gov (United States)

    Bambachus, M. J.; Foster, R. S.; Powell, C.; Cole, M.

    2005-12-01

    The global sea level change application community has numerous disparate models used to make predications over various regional and temporal scales. These models have typically been focused on limited sets of data and optimized for specific areas or questions of interest. Increasingly, decision makers at the national, international, and local/regional levels require access to these application data models and want to be able to integrate large disparate data sets, with new ubiquitous sensor data, and use these data across models from multiple sources. These requirements will force the Global Sea Level Change application community to take a new system-of-systems approach to their programs. We present a new technical architecture approach to the global sea level change program that provides external access to the vast stores of global sea level change data, provides a collaboration forum for the discussion and visualization of data, and provides a simulation environment to evaluate decisions. This architectural approach will provide the tools to support multi-disciplinary decision making. A conceptual system of systems approach is needed to address questions around the multiple approaches to tracking and predicting Sea Level Change. A systems of systems approach would include (1) a forum of data providers, modelers, and users, (2) a service oriented architecture including interoperable web services with a backbone of Grid computing capability, and (3) discovery and access functionality to the information developed through this structure. Each of these three areas would be clearly designed to maximize communication, data use for decision making and flexibility and extensibility for evolution of technology and requirements. In contemplating a system-of-systems approach, it is important to highlight common understanding and coordination as foundational to success across the multiple systems. The workflow of science in different applications is often conceptually similar

  9. Global projections of extreme sea levels in view of climate change

    Science.gov (United States)

    Vousdoukas, M. I.; Feyen, L.; Voukouvalas, E.; Mentaschi, L.; Verlaan, M.; Jevrejeva, S.; Jackson, L. P.

    2017-12-01

    Global warming is expected to drive increasing extreme sea levels (ESLs) and flood risk along the world's coasts. The present contribution aims to present global ESL projections obtained by combining dynamic simulations of all the major ESL components during the present century, considering the latest CMIP5 projections for RCP4.5 and RCP8.5. Baseline values are obtained combining global re-analyses of tides, waves, and storm surges, including the effects of tropical cyclones. The global average RSLR is projected around 20 and 24 cm by the 2050s under RCP4.5 and RCP8.5, respectively and is projected to reach 46 and 67 cm by the year 2100. The largest increases in MSL are projected along the South Pacific, Australia and West Africa, while the smaller RSLR is projected around East North America, and Europe. Contributions from waves and storm surges show a very weak increasing global trend, which becomes statistically significant only towards the end of the century and under RCP8.5. However, for areas like the East China Sea, Sea of Japan, Alaska, East Bering Sea, as well as the Southern Ocean, climate extremes could increase up to 15%. By the end of this century the 100-year event ESL along the world's coastlines will on average increase by 48 cm for RCP4.5 and 75 cm for RCP8.5. The strongest rise is projected along the Southern Ocean exceeding 1 m under RCP8.5 by the end of the century. Increase exceeding 80 cm is projected for East Asia, West North America, East South America, and the North Indian Ocean. Considering always the business as usual and the year 2100, the lowest increase in ESL100 is projected along the East North America and Europe (below 50 cm). The present findings indicate that, under both RCPs, by the year 2050 the present day 100-year event will occur every 5 years along a large part of the tropics, rendering coastal zones exposed to intermittent flood hazard.

  10. Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations

    KAUST Repository

    Abdallah, Abdallah

    2015-10-21

    Although Bacillus Calmette-Guérin (BCG) vaccines against tuberculosis have been available for more than 90 years, their effectiveness has been hindered by variable protective efficacy and a lack of lasting memory responses. One factor contributing to this variability may be the diversity of the BCG strains that are used around the world, in part from genomic changes accumulated during vaccine production and their resulting differences in gene expression. We have compared the genomes and transcriptomes of a global collection of fourteen of the most widely used BCG strains at single base-pair resolution. We have also used quantitative proteomics to identify key differences in expression of proteins across five representative BCG strains of the four tandem duplication (DU) groups. We provide a comprehensive map of single nucleotide polymorphisms (SNPs), copy number variation and insertions and deletions (indels) across fourteen BCG strains. Genome-wide SNP characterization allowed the construction of a new and robust phylogenic genealogy of BCG strains. Transcriptional and proteomic profiling revealed a metabolic remodeling in BCG strains that may be reflected by altered immunogenicity and possibly vaccine efficacy. Together, these integrated-omic data represent the most comprehensive catalogue of genetic variation across a global collection of BCG strains.

  11. Microbial Culturomics Application for Global Health: Noncontiguous Finished Genome Sequence and Description of Pseudomonas massiliensis Strain CB-1T sp. nov. in Brazil.

    Science.gov (United States)

    Bardet, Lucie; Cimmino, Teresa; Buffet, Clémence; Michelle, Caroline; Rathored, Jaishriram; Tandina, Fatalmoudou; Lagier, Jean-Christophe; Khelaifia, Saber; Abrahão, Jônatas; Raoult, Didier; Rolain, Jean-Marc

    2018-02-01

    Culturomics is a new postgenomics field that explores the microbial diversity of the human gut coupled with taxono-genomic strategy. Culturomics, and the microbiome science more generally, are anticipated to transform global health diagnostics and inform the ways in which gut microbial diversity contributes to human health and disease, and by extension, to personalized medicine. Using culturomics, we report in this study the description of strain CB1 T ( = CSUR P1334 = DSM 29075), a new species isolated from a stool specimen from a 37-year-old Brazilian woman. This description includes phenotypic characteristics and complete genome sequence and annotation. Strain CB1 T is a gram-negative aerobic and motile bacillus, exhibits neither catalase nor oxidase activities, and presents a 98.3% 16S rRNA sequence similarity with Pseudomonas putida. The 4,723,534 bp long genome contains 4239 protein-coding genes and 74 RNA genes, including 15 rRNA genes (5 16S rRNA, 4 23S rRNA, and 6 5S rRNA) and 59 tRNA genes. Strain CB1 T was named Pseudomonas massiliensis sp. nov. and classified into the family Pseudomonadaceae. This study demonstrates the usefulness of microbial culturomics in exploration of human microbiota in diverse geographies and offers new promise for incorporating new omics technologies for innovation in diagnostic medicine and global health.

  12. Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations

    KAUST Repository

    Abdallah, Abdallah; Hill-Cawthorne, Grant A.; Otto, Thomas D.; Coll, Francesc; Guerra-Assunç ã o, José Afonso; Gao, Ge; Naeem, Raeece; Ansari, Hifzur Rahman; Malas, Tareq Majed Yasin; Adroub, Sabir; Verboom, Theo; Ummels, Roy; Zhang, Huoming; Panigrahi, Aswini Kumar; McNerney, Ruth; Brosch, Roland; Clark, Taane G.; Behr, Marcel A.; Bitter, Wilbert; Pain, Arnab

    2015-01-01

    Although Bacillus Calmette-Guérin (BCG) vaccines against tuberculosis have been available for more than 90 years, their effectiveness has been hindered by variable protective efficacy and a lack of lasting memory responses. One factor contributing to this variability may be the diversity of the BCG strains that are used around the world, in part from genomic changes accumulated during vaccine production and their resulting differences in gene expression. We have compared the genomes and transcriptomes of a global collection of fourteen of the most widely used BCG strains at single base-pair resolution. We have also used quantitative proteomics to identify key differences in expression of proteins across five representative BCG strains of the four tandem duplication (DU) groups. We provide a comprehensive map of single nucleotide polymorphisms (SNPs), copy number variation and insertions and deletions (indels) across fourteen BCG strains. Genome-wide SNP characterization allowed the construction of a new and robust phylogenic genealogy of BCG strains. Transcriptional and proteomic profiling revealed a metabolic remodeling in BCG strains that may be reflected by altered immunogenicity and possibly vaccine efficacy. Together, these integrated-omic data represent the most comprehensive catalogue of genetic variation across a global collection of BCG strains.

  13. TEN YEARS AFTER THE GLOBAL CRISES - EXPORTS RECOVERY AT REGIONAL LEVEL IN ROMANIA

    Directory of Open Access Journals (Sweden)

    Artur-Emilian SIMION

    2018-05-01

    Full Text Available After ten years of the global financial crises, which peak in Romania was 2009, the negative impact on exports and imports of Romania are still in place for some Romanian counties. The scale of the impact highlights the strong connections between the national economy and the economy of the other EU countries, which have suffered during the crisis because of falling demand for imports from Romania. The good export recovery is not a favorable thing for those counties who focused theirs exports on primary products, products based on natural resources and low-technology products. These exports lead to the decrease in foreign exchange earnings and implicitly the potential of endogenous growth at the county level, mainly due to deteriorating terms of trade. The paper is focused on Romanian exports recovery analysis, taking into account the impact of world financial crisis, which started in Romania in 2009. A special attention is paid to the recovery of exports at the regional level and to the importance of the structural changes of Romanian export, occurred in 2017 compared to 2008. Also, in this article are analyzed the concentration of exports at county level, the main partners on export, the share of the first 10 partners and evolution of export per capita at the counties level. The trade balance is used to classify the counties in: net exporters (export>import and net importers (import>export.

  14. Does global progress on sanitation really lag behind water? An analysis of global progress on community- and household-level access to safe water and sanitation.

    Science.gov (United States)

    Cumming, Oliver; Elliott, Mark; Overbo, Alycia; Bartram, Jamie

    2014-01-01

    Safe drinking water and sanitation are important determinants of human health and wellbeing and have recently been declared human rights by the international community. Increased access to both were included in the Millennium Development Goals under a single dedicated target for 2015. This target was reached in 2010 for water but sanitation will fall short; however, there is an important difference in the benchmarks used for assessing global access. For drinking water the benchmark is community-level access whilst for sanitation it is household-level access, so a pit latrine shared between households does not count toward the Millennium Development Goal (MDG) target. We estimated global progress for water and sanitation under two scenarios: with equivalent household- and community-level benchmarks. Our results demonstrate that the "sanitation deficit" is apparent only when household-level sanitation access is contrasted with community-level water access. When equivalent benchmarks are used for water and sanitation, the global deficit is as great for water as it is for sanitation, and sanitation progress in the MDG-period (1990-2015) outstrips that in water. As both drinking water and sanitation access yield greater benefits at the household-level than at the community-level, we conclude that any post-2015 goals should consider a household-level benchmark for both.

  15. Comparative genomics reveals diversified CRISPR-Cas systems of globally distributed Microcystis aeruginosa, a freshwater bloom-forming cyanobacterium

    Directory of Open Access Journals (Sweden)

    Chen eYang

    2015-05-01

    Full Text Available Microcystis aeruginosa is one of the most common and dominant bloom-forming cyanobacteria in freshwater lakes around the world. Microcystis cells can produce toxic secondary metabolites, such as microcystins, which are harmful to human health. Two M. aeruginosa strains were isolated from two highly eutrophic lakes in China and their genomes were sequenced. Comparative genomic analysis was performed with the 12 other available M. aeruginosa genomes and closely related unicellular cyanobacterium. Each genome of M. aeruginosa containing at least one clustered regularly interspaced short palindromic repeat (CRISPR locus and total 71 loci were identified, suggesting it is ubiquitous in M. aeruginosa genomes. In addition to the previously reported subtype I-D cas gene sets, three CAS subtypes I-A, III-A and III-B were identified and characterized in this study. Seven types of CRISPR direct repeat have close association with CAS subtype, confirming that different and specific secondary structures of CRISPR repeats are important for the recognition, binding and process of corresponding cas gene sets. Homology search of the CRISPR spacer sequences provides a history of not only resistance to bacteriophages and plasmids known to be associated with M. aeruginosa, but also the ability to target much more exogenous genetic material in the natural environment. These adaptive and heritable defense mechanisms play a vital role in keeping genomic stability and self-maintenance by restriction of horizontal gene transfer. Maintaining genomic stability and modulating genomic plasticity are both important evolutionary strategies for M. aeruginosa in adaptation and survival in various habitats.

  16. Multi-hazard national-level risk assessment in Africa using global approaches

    Science.gov (United States)

    Fraser, Stuart; Jongman, Brenden; Simpson, Alanna; Murnane, Richard

    2016-04-01

    In recent years Sub-Saharan Africa has been characterized by unprecedented opportunity for transformation and sustained growth. However, natural disasters such as droughts, floods, cyclones, earthquakes, landslides, volcanic eruptions and extreme temperatures cause significant economic and human losses, and major development challenges. Quantitative disaster risk assessments are an important basis for governments to understand disaster risk in their country, and to develop effective risk management and risk financing solutions. However, the data-scarce nature of many Sub-Saharan African countries as well as a lack of financing for risk assessments has long prevented detailed analytics. Recent advances in globally applicable disaster risk modelling practices and data availability offer new opportunities. In December 2013 the European Union approved a € 60 million contribution to support the development of an analytical basis for risk financing and to accelerate the effective implementation of a comprehensive disaster risk reduction. The World Bank's Global Facility for Disaster Reduction and Recovery (GFDRR) was selected as the implementing partner of the Program for Result Area 5: the "Africa Disaster Risk Assessment and Financing Program." As part of this effort, the GFDRR is overseeing the production of national-level multi-hazard risk profiles for a range of countries in Sub-Saharan Africa, using a combination of national and global datasets and state-of-the-art hazard and risk assessment methodologies. In this presentation, we will highlight the analytical approach behind these assessments, and show results for the first five countries for which the assessment has been completed (Kenya, Uganda, Senegal, Niger and Ethiopia). The presentation will also demonstrate the visualization of the risk assessments into understandable and visually attractive risk profile documents.

  17. Global cost analysis on adaptation to sea level rise based on RCP/SSP scenarios

    Science.gov (United States)

    Kumano, N.; Tamura, M.; Yotsukuri, M.; Kuwahara, Y.; Yokoki, H.

    2017-12-01

    Low-lying areas are the most vulnerable to sea level rise (SLR) due to climate change in the future. In order to adapt to SLR, it is necessary to decide whether to retreat from vulnerable areas or to install dykes to protect them from inundation. Therefore, cost- analysis of adaptation using coastal dykes is one of the most essential issues in the context of climate change and its countermeasures. However, few studies have globally evaluated the future costs of adaptation in coastal areas. This study tries to globally analyze the cost of adaptation in coastal areas. First, global distributions of projected inundation impacts induced by SLR including astronomical high tide were assessed. Economic damage was estimated on the basis of the econometric relationship between past hydrological disasters, affected population, and per capita GDP using CRED's EM-DAT database. Second, the cost of adaptation was also determined using the cost database and future scenarios. The authors have built a cost database for installed coastal dykes worldwide and applied it to estimating the future cost of adaptation. The unit costs of dyke construction will increase with socio-economic scenario (SSP) such as per capita GDP. Length of vulnerable coastline is calculated by identifying inundation areas using ETOPO1. Future cost was obtained by multiplying the length of vulnerable coastline and the unit cost of dyke construction. Third, the effectiveness of dyke construction was estimated by comparing cases with and without adaptation.As a result, it was found that incremental adaptation cost is lower than economic damage in the cases of SSP1 and SSP3 under RCP scenario, while the cost of adaptation depends on the durability of the coastal dykes.

  18. OMI/Aura Surface Reflectance Climatology Level 3 Global 0.5deg Lat/Lon Grid V003

    Data.gov (United States)

    National Aeronautics and Space Administration — The OMI Earth Surface Reflectance Climatology product, OMLER (Global 0.5deg Lat/Lon grid) which is based on Version 003 Level-1B top of atmosphere upwelling radiance...

  19. GHRSST Level 4 MW_IR_OI Global Foundation Sea Surface Temperature analysis (GDS versions 1 and 2)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A Group for High Resolution Sea Surface Temperature (GHRSST) global Level 4 sea surface temperature analysis produced daily on a 0.81 degree grid at Remote Sensing...

  20. Critical threshold levels of DNA methyltransferase 1 are required to maintain DNA methylation across the genome in human cancer cells.

    Science.gov (United States)

    Cai, Yi; Tsai, Hsing-Chen; Yen, Ray-Whay Chiu; Zhang, Yang W; Kong, Xiangqian; Wang, Wei; Xia, Limin; Baylin, Stephen B

    2017-04-01

    Reversing DNA methylation abnormalities and associated gene silencing, through inhibiting DNA methyltransferases (DNMTs) is an important potential cancer therapy paradigm. Maximizing this potential requires defining precisely how these enzymes maintain genome-wide, cancer-specific DNA methylation. To date, there is incomplete understanding of precisely how the three DNMTs, 1, 3A, and 3B, interact for maintaining DNA methylation abnormalities in cancer. By combining genetic and shRNA depletion strategies, we define not only a dominant role for DNA methyltransferase 1 (DNMT1) but also distinct roles of 3A and 3B in genome-wide DNA methylation maintenance. Lowering DNMT1 below a threshold level is required for maximal loss of DNA methylation at all genomic regions, including gene body and enhancer regions, and for maximally reversing abnormal promoter DNA hypermethylation and associated gene silencing to reexpress key genes. It is difficult to reach this threshold with patient-tolerable doses of current DNMT inhibitors (DNMTIs). We show that new approaches, like decreasing the DNMT targeting protein, UHRF1, can augment the DNA demethylation capacities of existing DNA methylation inhibitors for fully realizing their therapeutic potential. © 2017 Cai et al.; Published by Cold Spring Harbor Laboratory Press.

  1. Microtheories for Spatial Data Infrastructures - Accounting for Diversity of Local Conceptualizations at a Global Level

    Science.gov (United States)

    Duce, Stephanie; Janowicz, Krzysztof

    The categorization of our environment into feature types is an essential prerequisite for cartography, geographic information retrieval, routing applications, spatial decision support systems, and data sharing in general. However, there is no a priori conceptualization of the world and the creation of features and types is an act of cognition. Humans conceptualize their environment based on multiple criteria such as their cultural background, knowledge, motivation, and particularly by space and time. Sharing and making these conceptualizations explicit in a formal, unambiguous way is at the core of semantic interoperability. One way to cope with semantic heterogeneities is by standardization, i.e., by agreeing on a shared conceptualization. This bears the danger of losing local diversity. In contrast, this work proposes the use of microtheories for Spatial Data Infrastructures, such as INSPIRE, to account for the diversity of local conceptualizations while maintaining their semantic interoperability at a global level. We introduce a novel methodology to structure ontologies by spatial and temporal aspects, in our case administrative boundaries, which reflect variations in feature conceptualization. A local, bottom-up approach, based on non-standard inference, is used to compute global feature definitions which are neither too broad nor too specific. Using different conceptualizations of rivers and other geographic feature types, we demonstrate how the present approach can improve the INSPIRE data model and ease its adoption by European member states.

  2. University-Level Teaching of Anthropogenic Global Climate Change (AGCC) via Student Inquiry

    Science.gov (United States)

    Bush, Drew; Sieber, Renee; Seiler, Gale; Chandler, Mark

    2017-01-01

    This paper reviews university-level efforts to improve understanding of anthropogenic global climate change (AGCC) through curricula that enable student scientific inquiry. We examined 152 refereed publications and proceedings from academic conferences and selected 26 cases of inquiry learning that overcome specific challenges to AGCC teaching. This review identifies both the strengths and weaknesses of each of these case studies. It is the first to go beyond examining the impact of specific inquiry instructional approaches to offer a synthesis of cases. We find that inquiry teaching can succeed by concretising scientific processes, providing access to global data and evidence, imparting critical and higher order thinking about AGCC science policy and contextualising learning with places and scientific facts. We recommend educational researchers and scientists collaborate to create and refine curricula that utilise geospatial technologies, climate models and communication technologies to bring students into contact with scientists, climate data and authentic AGCC research processes. Many available science education technologies and curricula also require further research to maximise trade-offs between implementation and training costs and their educational value.

  3. [Sex differences in relationship between creativity and hemispheric information processing in global and local levels].

    Science.gov (United States)

    Razumnikova, O M; Vol'f, N V

    2012-01-01

    Sex differences in creativity related global-local hemispheric selective processing were examined by hierarchical letter presenting in conditions of their perception and comparison. Fifty-six right-handed males and 68 females (aged 17-22 years) participated in the experiments. Originality-imagery was assessed by a computer-based Torrance 'Incomplete Figures' test software. Verbal creativity was valued by original sentence using of three nouns from remote semantic categories. The results show that irrespectively of the sex factor and the type of creative thinking, its originality is provided by high speed of right-hemispheric processes of information selection on the global level and delay in the interhemispheric communication. Relationships between originality of ideas and hemispheric attentional characteristics are presented mostly in men while verbal creative problem solving, and in women while figurative original thinking. Originality of verbal activity in men is more associated with success of selective processes in the left hemisphere, but in women--with selective functions of both hemispheres. Figurative thinking in men is less related to hemispheric characteristics of attention compared with women. Increase of figurative originality in women is accompanied acceleration of processes of selection of the information in the right hemisphere, and also higher efficiency of local attention as well as speeds ofglobal processing in the left hemisphere.

  4. Detection of ST-T Episode Based on the Global Curvature of Isoelectric Level in ECG

    Energy Technology Data Exchange (ETDEWEB)

    Kang, D. W.; Jun, D. G.; Lee, K. J.; Yoon, H. R. [Yonsei University, Seoul (Korea)

    2001-04-01

    This paper describes an automated detection algorithm of ST-T episodes using global curvature which can connect the isoelectric level in ECG and can eliminate not only the slope of ST segment, but also difference of the baseline and global curve. This above method of baseline correction is very faster than classical baseline correction methods. The optimal values of parameters for baseline correction were found as the value having the highest detection rate of ST episode. The features as input of backpropagation Neural Network were extracted from the whole ST segment. The European ST-T database was used as training and test data. Finally, ST elevation, ST depression and normal ST were classified. The average ST episode sensitivity and predictivity were 85.42%, 80.29%, respectively. This result shows the high speed and reliability in ST episode detection. In conclusion, the proposed method showed the possibility in various applications for the Holter system. (author). 17 refs., 5 figs., 4 tabs.

  5. Global warming response options in Brazil's forest sector: comparison of project-level costs and benefits

    International Nuclear Information System (INIS)

    Fearnside, P.M.

    1995-01-01

    A project-level assessment of monetary and carbon costs and benefits for five classes of global warming response options in the forest sector is attempted for typical Brazilian conditions. Options considered are: silvicultural plantations (for pulp, charcoal and sawlogs), sustainable timber management and reduction of deforestation. Comparison of pulpwood and sawlog plantations with the vegetation characteristic of deforested areas indicates of modest carbon benefit. Plantations for charcoal can produce a substantial carbon benefit through fossil fuel substitution, but much of this calculated benefit disappears if discount rates greater than zero are applied to carbon. Sustainable timber management, when compared with existing forest, represents a net carbon loss, accumulation of carbon in wood products being insufficient to compensate for biomass reduction over a 100 year time scale. Reduction of deforestation has great potential as a global warming response option, its per-hectare carbon benefits being approximately four times that of silvicultural plantation establishment for pulp and sawlogs over a 100 year period. The costs of reducing deforestation are difficult to assess, however, due to the importance of government policy changes such as removal of land speculation and land tenure establishment as motives for clearing. Although these changes would not cost money and would have tremendous carbon and other benefits, they have not yet occurred. (Author)

  6. Revisiting the contemporary sea-level budget on global and regional scales.

    Science.gov (United States)

    Rietbroek, Roelof; Brunnabend, Sandra-Esther; Kusche, Jürgen; Schröter, Jens; Dahle, Christoph

    2016-02-09

    Dividing the sea-level budget into contributions from ice sheets and glaciers, the water cycle, steric expansion, and crustal movement is challenging, especially on regional scales. Here, Gravity Recovery And Climate Experiment (GRACE) gravity observations and sea-level anomalies from altimetry are used in a joint inversion, ensuring a consistent decomposition of the global and regional sea-level rise budget. Over the years 2002-2014, we find a global mean steric trend of 1.38 ± 0.16 mm/y, compared with a total trend of 2.74 ± 0.58 mm/y. This is significantly larger than steric trends derived from in situ temperature/salinity profiles and models which range from 0.66 ± 0.2 to 0.94 ± 0.1 mm/y. Mass contributions from ice sheets and glaciers (1.37 ± 0.09 mm/y, accelerating with 0.03 ± 0.02 mm/y(2)) are offset by a negative hydrological component (-0.29 ± 0.26 mm/y). The combined mass rate (1.08 ± 0.3 mm/y) is smaller than previous GRACE estimates (up to 2 mm/y), but it is consistent with the sum of individual contributions (ice sheets, glaciers, and hydrology) found in literature. The altimetric sea-level budget is closed by coestimating a remaining component of 0.22 ± 0.26 mm/y. Well above average sea-level rise is found regionally near the Philippines (14.7 ± 4.39 mm/y) and Indonesia (8.3 ± 4.7 mm/y) which is dominated by steric components (11.2 ± 3.58 mm/y and 6.4 ± 3.18 mm/y, respectively). In contrast, in the central and Eastern part of the Pacific, negative steric trends (down to -2.8 ± 1.53 mm/y) are detected. Significant regional components are found, up to 5.3 ± 2.6 mm/y in the northwest Atlantic, which are likely due to ocean bottom pressure variations.

  7. The global SMOS Level 3 daily soil moisture and brightness temperature maps

    Directory of Open Access Journals (Sweden)

    A. Al Bitar

    2017-06-01

    Full Text Available The objective of this paper is to present the multi-orbit (MO surface soil moisture (SM and angle-binned brightness temperature (TB products for the SMOS (Soil Moisture and Ocean Salinity mission based on a new multi-orbit algorithm. The Level 3 algorithm at CATDS (Centre Aval de Traitement des Données SMOS makes use of MO retrieval to enhance the robustness and quality of SM retrievals. The motivation of the approach is to make use of the longer temporal autocorrelation length of the vegetation optical depth (VOD compared to the corresponding SM autocorrelation in order to enhance the retrievals when an acquisition occurs at the border of the swath. The retrieval algorithm is implemented in a unique operational processor delivering multiple parameters (e.g. SM and VOD using multi-angular dual-polarisation TB from MO. A subsidiary angle-binned TB product is provided. In this study the Level 3 TB V310 product is showcased and compared to SMAP (Soil Moisture Active Passive TB. The Level 3 SM V300 product is compared to the single-orbit (SO retrievals from the Level 2 SM processor from ESA with aligned configuration. The advantages and drawbacks of the Level 3 SM product (L3SM are discussed. The comparison is done on a global scale between the two datasets and on the local scale with respect to in situ data from AMMA-CATCH and USDA ARS Watershed networks. The results obtained from the global analysis show that the MO implementation enhances the number of retrievals: up to 9 % over certain areas. The comparison with the in situ data shows that the increase in the number of retrievals does not come with a decrease in quality, but rather at the expense of an increased time lag in product availability from 6 h to 3.5 days, which can be a limiting factor for applications like flood forecast but reasonable for drought monitoring and climate change studies. The SMOS L3 soil moisture and L3 brightness temperature products are delivered using an

  8. MO-AB-BRA-01: A Global Level Set Based Formulation for Volumetric Modulated Arc Therapy

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, D; Lyu, Q; Ruan, D; O’Connor, D; Low, D; Sheng, K [Department of Radiation Oncology, University of California Los Angeles, Los Angeles, CA (United States)

    2016-06-15

    Purpose: The current clinical Volumetric Modulated Arc Therapy (VMAT) optimization is formulated as a non-convex problem and various greedy heuristics have been employed for an empirical solution, jeopardizing plan consistency and quality. We introduce a novel global direct aperture optimization method for VMAT to overcome these limitations. Methods: The global VMAT (gVMAT) planning was formulated as an optimization problem with an L2-norm fidelity term and an anisotropic total variation term. A level set function was used to describe the aperture shapes and adjacent aperture shapes were penalized to control MLC motion range. An alternating optimization strategy was implemented to solve the fluence intensity and aperture shapes simultaneously. Single arc gVMAT plans, utilizing 180 beams with 2° angular resolution, were generated for a glioblastoma multiforme (GBM), lung (LNG), and 2 head and neck cases—one with 3 PTVs (H&N3PTV) and one with 4 PTVs (H&N4PTV). The plans were compared against the clinical VMAT (cVMAT) plans utilizing two overlapping coplanar arcs. Results: The optimization of the gVMAT plans had converged within 600 iterations. gVMAT reduced the average max and mean OAR dose by 6.59% and 7.45% of the prescription dose. Reductions in max dose and mean dose were as high as 14.5 Gy in the LNG case and 15.3 Gy in the H&N3PTV case. PTV coverages (D95, D98, D99) were within 0.25% of the prescription dose. By globally considering all beams, the gVMAT optimizer allowed some beams to deliver higher intensities, yielding a dose distribution that resembles a static beam IMRT plan with beam orientation optimization. Conclusions: The novel VMAT approach allows for the search of an optimal plan in the global solution space and generates deliverable apertures directly. The single arc VMAT approach fully utilizes the digital linacs’ capability in dose rate and gantry rotation speed modulation. Varian Medical Systems, NIH grant R01CA188300, NIH grant R43CA183390.

  9. Global fishery development patterns are driven by profit but not trophic level.

    Science.gov (United States)

    Sethi, Suresh A; Branch, Trevor A; Watson, Reg

    2010-07-06

    Successful ocean management needs to consider not only fishing impacts but drivers of harvest. Consolidating post-1950 global catch and economic data, we assess which attributes of fisheries are good indicators for fishery development. Surprisingly, year of development and economic value are not correlated with fishery trophic levels. Instead, patterns emerge of profit-driven fishing for attributes related to costs and revenues. Post-1950 fisheries initially developed on shallow ranging species with large catch, high price, and big body size, and then expanded to less desirable species. Revenues expected from developed fisheries declined 95% from 1951 to 1999, and few high catch or valuable fishing opportunities remain. These results highlight the importance of economic attributes of species as leading indicators for harvest-related impacts in ocean ecosystems.

  10. Investigating sea level rise due to global warming in the teaching laboratory using Archimedes’ principle

    International Nuclear Information System (INIS)

    Hughes, Stephen; Pearce, Darren

    2015-01-01

    A teaching laboratory experiment is described that uses Archimedes’ principle to precisely investigate the effect of global warming on the oceans. A large component of sea level rise is due to the increase in the volume of water due to the decrease in water density with increasing temperature. Water close to 0 °C is placed in a beaker and a glass marble hung from an electronic balance immersed in the water. As the water warms, the weight of the marble increases as the water is less buoyant due to the decrease in density. In the experiment performed in this paper a balance with a precision of 0.1 mg was used with a marble 40.0 cm 3 and mass of 99.3 g, yielding water density measurements with an average error of −0.008 ± 0.011%. (paper)

  11. Real Time Global Tests of the ALICE High Level Trigger Data Transport Framework

    CERN Document Server

    Becker, B.; Cicalo J.; Cleymans, C.; de Vaux, G.; Fearick, R.W.; Lindenstruth, V.; Richter, M.; Rorich, D.; Staley, F.; Steinbeck, T.M.; Szostak, A.; Tilsner, H.; Weis, R.; Vilakazi, Z.Z.

    2008-01-01

    The High Level Trigger (HLT) system of the ALICE experiment is an online event filter and trigger system designed for input bandwidths of up to 25 GB/s at event rates of up to 1 kHz. The system is designed as a scalable PC cluster, implementing several hundred nodes. The transport of data in the system is handled by an object-oriented data flow framework operating on the basis of the publisher-subscriber principle, being designed fully pipelined with lowest processing overhead and communication latency in the cluster. In this paper, we report the latest measurements where this framework has been operated on five different sites over a global north-south link extending more than 10,000 km, processing a ``real-time'' data flow.

  12. Greenland and Antarctica Ice Sheet Mass Changes and Effects on Global Sea Level

    DEFF Research Database (Denmark)

    Forsberg, René; Sørensen, Louise Sandberg; Simonsen, Sebastian Bjerregaard

    2017-01-01

    Thirteen years of GRACE data provide an excellent picture of the current mass changes of Greenland and Antarctica, with mass loss in the GRACE period 2002–2015 amounting to 265 ± 25 GT/year for Greenland (including peripheral ice caps), and 95 ± 50 GT/year for Antarctica, corresponding to 0.......72 and 0.26 mm/year average global sea level change. A significant acceleration in mass loss rate is found, especially for Antarctica, while Greenland mass loss, after a corresponding acceleration period, and a record mass loss in the summer of 2012, has seen a slight decrease in short-term mass loss trend....... The yearly mass balance estimates, based on point mass inversion methods, have relatively large errors, both due to uncertainties in the glacial isostatic adjustment processes, especially for Antarctica, leakage from unmodelled ocean mass changes, and (for Greenland) difficulties in separating mass signals...

  13. Component-Level Selection and Qualification for the Global Ecosystem Dynamics Investigation (GEDI) Laser Altimeter Transmitter

    Science.gov (United States)

    Frese, Erich A.; Chiragh, Furqan L.; Switzer, Robert; Vasilyev, Aleksey A.; Thomes, Joe; Coyle, D. Barry; Stysley, Paul R.

    2018-01-01

    Flight quality solid-state lasers require a unique and extensive set of testing and qualification processes, both at the system and component levels to insure the laser's promised performance. As important as the overall laser transmitter design is, the quality and performance of individual subassemblies, optics, and electro-optics dictate the final laser unit's quality. The Global Ecosystem Dynamics Investigation (GEDI) laser transmitters employ all the usual components typical for a diode-pumped, solid-state laser, yet must each go through their own individual process of specification, modeling, performance demonstration, inspection, and destructive testing. These qualification processes and results for the laser crystals, laser diode arrays, electro-optics, and optics, will be reviewed as well as the relevant critical issues encountered, prior to their installation in the GEDI flight laser units.

  14. The challenges of genome-wide interaction studies: lessons to learn from the analysis of HDL blood levels.

    Directory of Open Access Journals (Sweden)

    Elisabeth M van Leeuwen

    Full Text Available Genome-wide association studies (GWAS have revealed 74 single nucleotide polymorphisms (SNPs associated with high-density lipoprotein cholesterol (HDL blood levels. This study is, to our knowledge, the first genome-wide interaction study (GWIS to identify SNP×SNP interactions associated with HDL levels. We performed a GWIS in the Rotterdam Study (RS cohort I (RS-I using the GLIDE tool which leverages the massively parallel computing power of Graphics Processing Units (GPUs to perform linear regression on all genome-wide pairs of SNPs. By performing a meta-analysis together with Rotterdam Study cohorts II and III (RS-II and RS-III, we were able to filter 181 interaction terms with a p-value<1 · 10-8 that replicated in the two independent cohorts. We were not able to replicate any of these interaction term in the AGES, ARIC, CHS, ERF, FHS and NFBC-66 cohorts (Ntotal = 30,011 when adjusting for multiple testing. Our GWIS resulted in the consistent finding of a possible interaction between rs774801 in ARMC8 (ENSG00000114098 and rs12442098 in SPATA8 (ENSG00000185594 being associated with HDL levels. However, p-values do not reach the preset Bonferroni correction of the p-values. Our study suggest that even for highly genetically determined traits such as HDL the sample sizes needed to detect SNP×SNP interactions are large and the 2-step filtering approaches do not yield a solution. Here we present our analysis plan and our reservations concerning GWIS.

  15. Comparative analyses reveal high levels of conserved colinearity between the finger millet and rice genomes.

    Science.gov (United States)

    Srinivasachary; Dida, Mathews M; Gale, Mike D; Devos, Katrien M

    2007-08-01

    Finger millet is an allotetraploid (2n = 4x = 36) grass that belongs to the Chloridoideae subfamily. A comparative analysis has been carried out to determine the relationship of the finger millet genome with that of rice. Six of the nine finger millet homoeologous groups corresponded to a single rice chromosome each. Each of the remaining three finger millet groups were orthologous to two rice chromosomes, and in all the three cases one rice chromosome was inserted into the centromeric region of a second rice chromosome to give the finger millet chromosomal configuration. All observed rearrangements were, among the grasses, unique to finger millet and, possibly, the Chloridoideae subfamily. Gene orders between rice and finger millet were highly conserved, with rearrangements being limited largely to single marker transpositions and small putative inversions encompassing at most three markers. Only some 10% of markers mapped to non-syntenic positions in rice and finger millet and the majority of these were located in the distal 14% of chromosome arms, supporting a possible correlation between recombination and sequence evolution as has previously been observed in wheat. A comparison of the organization of finger millet, Panicoideae and Pooideae genomes relative to rice allowed us to infer putative ancestral chromosome configurations in the grasses.

  16. Contemporary moment of residential architecture at the global level: HOUSING 15

    Directory of Open Access Journals (Sweden)

    Petrović Vladana

    2017-01-01

    Full Text Available 'That architectonic exhibitions are an indispensable and significant part of the history of architecture has been proven by numerous exhibitions dating back from the first decades of the 20th century, the Paris exhibitions (Salon d'Automne, where three manifest exhibition designs by Le Corbusier were presented, promoting a new system of values of the forthcoming modernist movement, then the Berlin exhibitions in the second half of the 20th century (Interbau 1957, IBA 1987 where the Postmodern was promoted, up to the second decade of the 21st century and the Biennial in Venice (La Biennale di Venezia, 2014, whose uniting topic was One Hundred Years of ,Modernity' (prof arch Darko Marušić, quote from the catalogue of the HOUSING 15. HOUSING 15 is an exhibition that was created on the initiative of the Department of Residential Building, Faculty of Civil Engineering and Architecture, University of Nis, in order to present the modern housing architecture at the global level. The exhibition was shown at the BINA 2016 and was followed by a round table discussion upon the topic Contemporary moment of residential architecture at the global level. The idea of the round table was to compare domestic and international experience in this field and draw attention toward the attitude on the present, electronic time considering the development of the residential architecture. The specificity of this exhibition, compared to the other events of a similar nature, is that in addition to architectural design the scientific expert reviews for the selected works are also presented, given by the international scientific and artistic committee of the exhibition. The paper is the summary of the discussion held at the round table, and it presents the potential problems, answers and conclusions relating to residential architecture today from the professional perspective.

  17. Diffuse radiation increases global ecosystem-level water-use efficiency

    Science.gov (United States)

    Moffat, A. M.; Reichstein, M.; Cescatti, A.; Knohl, A.; Zaehle, S.

    2012-12-01

    Current environmental changes lead not only to rising atmospheric CO2 levels and air temperature but also to changes in air pollution and thus the light quality of the solar radiation reaching the land-surface. While rising CO2 levels are thought to enhance photosynthesis and closure of stomata, thus leading to relative water savings, the effect of diffuse radiation on transpiration by plants is less clear. It has been speculated that the stimulation of photosynthesis by increased levels of diffuse light may be counteracted by higher transpiration and consequently water depletion and drought stress. Ultimately, in water co-limited systems, the overall effect of diffuse radiation will depend on the sensitivity of canopy transpiration versus photosynthesis to diffuse light, i.e. whether water-use efficiency changes with relative levels of diffuse light. Our study shows that water-use efficiency increases significantly with higher fractions of diffuse light. It uses the ecosystem-atmosphere gas-exchange observations obtained with the eddy covariance method at 29 flux tower sites. In contrast to previous global studies, the analysis is based directly on measurements of diffuse radiation. Its effect on water-use efficiency was derived by analyzing the multivariate response of carbon and water fluxes to radiation and air humidity using a purely empirical approach based on artificial neural networks. We infer that per unit change of diffuse fraction the water-use efficiency increases up to 40% depending on diffuse fraction levels and ecosystem type. Hence, in regions with increasing diffuse radiation positive effects on primary production are expected even under conditions where water is co-limiting productivity.

  18. Global 5-Hydroxymethylcytosine Levels Are Profoundly Reduced in Multiple Genitourinary Malignancies.

    Directory of Open Access Journals (Sweden)

    Enrico Munari

    Full Text Available Solid tumors are characterized by a plethora of epigenetic changes. In particular, patterns methylation of cytosines at the 5-position (5mC in the context of CpGs are frequently altered in tumors. Recent evidence suggests that 5mC can get converted to 5-hydroxylmethylcytosine (5hmC in an enzymatic process involving ten eleven translocation (TET protein family members, and this process appears to be important in facilitating plasticity of cytosine methylation. Here we evaluated the global levels of 5hmC using a validated immunohistochemical staining method in a large series of clear cell renal cell carcinoma (n = 111, urothelial cell carcinoma (n = 55 and testicular germ cell tumors (n = 84 and matched adjacent benign tissues. Whereas tumor-adjacent benign tissues were mostly characterized by high levels of 5hmC, renal cell carcinoma and urothelial cell carcinoma showed dramatically reduced staining for 5hmC. 5hmC levels were low in both primary tumors and metastases of clear cell renal cell carcinoma and showed no association with disease outcomes. In normal testis, robust 5hmC staining was only observed in stroma and Sertoli cells. Seminoma showed greatly reduced 5hmC immunolabeling, whereas differentiated teratoma, embryonal and yolk sack tumors exhibited high 5hmC levels. The substantial tumor specific loss of 5hmC, particularly in clear cell renal cell carcinoma and urothelial cell carcinoma, suggests that alterations in pathways involved in establishing and maintaining 5hmC levels might be very common in cancer and could potentially be exploited for diagnosis and treatment.

  19. Germs, genomics and global public health: How can advances in genomic sciences be integrated into public health in the developing world to deal with infectious diseases?

    Science.gov (United States)

    Pang, T

    2009-12-01

    Scientific and technological advances derived from the genomics revolution have a central role to play in dealing with continuing infectious disease threats in the developing world caused by emerging and re-emerging pathogens. These techniques, coupled with increasing knowledge of host-pathogen interactions, can assist in the early identification and containment of outbreaks as well as in the development of preventive vaccination and therapeutic interventions, including the urgent need for new antibiotics. However, the effective application of genomics technologies faces key barriers and challenges which occur at three stages: from the research to the products, from the products to individual patients, and, finally, from patients to entire populations. There needs to be an emphasis on research in areas of greatest need, in facilitating the translation of research into interventions and, finally, the effective delivery of such interventions to those in greatest need. Ultimate success will depend on bringing together science, society and policy to develop effective public health implementation strategies to provide health security and health equity for all peoples.

  20. Global Anthropogenic Phosphorus Loads to Freshwater and Associated Grey Water Footprints and Water Pollution Levels: A High-Resolution Global Study

    Science.gov (United States)

    Mekonnen, Mesfin M.; Hoekstra, Arjen Y.

    2018-01-01

    We estimate the global anthropogenic phosphorus (P) loads to freshwater and the associated grey water footprints (GWFs) for the period 2002-2010, at a spatial resolution of 5 × 5 arc min, and compare the GWF per river basin to runoff to assess the P-related water pollution level (WPL). The global anthropogenic P load to freshwater systems from both diffuse and point sources is estimated at 1.5 Tg/yr. More than half of this total load was in Asia, followed by Europe (19%) and Latin America and the Caribbean (13%). The domestic sector contributed 54% to the total, agriculture 38%, and industry 8%. In agriculture, cereals production had the largest contribution to the P load (31%), followed by fruits, vegetables, and oil crops, each contributing 15%. The global total GWF related to anthropogenic P loads is estimated to be 147 × 1012 m3/yr, with China contributing 30%, India 8%, USA 7%, and Spain and Brazil 6% each. The basins with WPL > 1 (where GWF exceeds the basin's assimilation capacity) together cover about 38% of the global land area, 37% of the global river discharge, and provide residence to about 90% of the global population.

  1. Whole genome shotgun sequencing of Indian strains of Streptococcus agalactiae

    Directory of Open Access Journals (Sweden)

    Balaji Veeraraghavan

    2017-12-01

    Full Text Available Group B streptococcus is known as a leading cause of neonatal infections in developing countries. The present study describes the whole genome shotgun sequences of four Group B Streptococcus (GBS isolates. Molecular data on clonality is lacking for GBS in India. The present genome report will add important information on the scarce genome data of GBS and will help in deriving comparative genome studies of GBS isolates at global level. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession numbers NHPL00000000 – NHPO00000000.

  2. Global Climatology of the Coastal Low-Level Wind Jets using different Reanalysis

    Science.gov (United States)

    Lima, Daniela C. A.; Soares, Pedro M. M.; Semedo, Alvaro; Cardoso, Rita M.

    2016-04-01

    Coastal Low-Level Jets (henceforth referred to as "coastal jets" or simply as CLLJ) are low-tropospheric mesoscale wind features, with wind speed maxima confined to the marine atmospheric boundary layer (MABL), typically bellow 1km. Coastal jets occur in the eastern flank of the semi-permanent subtropical mid-latitude high pressure systems, along equatorward eastern boundary currents, due to a large-scale synoptic forcing. The large-scale synoptic forcing behind CLLJ occurrences is a high pressure system over the ocean and a thermal low inland. This results in coastal parallel winds that are the consequence of the geostrophic adjustment. CLLJ are found along the California (California-Oregon) and the Canary (Iberia and Northeastern Africa) currents in the Northern Hemisphere, and along the Peru-Humboldt (Peru-Chile), Benguela (Namibia) and Western Australia (West Australia) currents in the Southern Hemisphere. In the Arabian Sea (Oman CLLJ), the interaction between the high pressure over the Indian Ocean in summer (Summer Indian Monsoon) and the Somali (also known as Findlater) Jet forces a coastal jet wind feature off the southeast coast of Oman. Coastal jets play an important role in the regional climates of the mid-latitude western continental regions. The decrease of the sea surface temperatures (SST) along the coast due to upwelling lowers the evaporation over the ocean and the coast parallel winds prevents the advection of marine air inshore. The feedback processes between the CLLJ and upwelling play a crucial role in the regional climate, namely, promoting aridity since the parallel flow prevents the intrusion of moisture inland, and increasing fish stocks through the transport of rich nutrient cold water from the bottom. In this study, the global coastal low-level wind jets are identified and characterized using an ensemble of three reanalysis, the ECMWF Interim Reanalysis (ERA-Interim), the Japanese 55-year Reanalysis (JRA-55) and the NCEP Climate Forecast

  3. Constraining the Antarctic contribution to global sea-level change: ANDRILL and beyond

    Science.gov (United States)

    Naish, Timothy

    2016-04-01

    Observations, models and paleoclimate reconstructions suggest that Antarctica's marine-based ice sheets behave in an unstable manner with episodes of rapid retreat in response to warming climate. Understanding the processes involved in this "marine ice sheet instability" is key for improving estimates of Antarctic ice sheet contribution to future sea-level rise. Another motivating factor is that far-field sea-level reconstructions and ice sheet models imply global mean sea level (GMSL) was up to 20m and 10m higher, respectively, compared with present day, during the interglacials of the warm Pliocene (~4-3Ma) and Late Pleistocene (at ~400ka and 125ka). This was when atmospheric CO2 was between 280 and 400ppm and global average surface temperatures were 1 to 3°C warmer, suggesting polar ice sheets are highly sensitive to relatively modest increases in climate forcing. Such magnitudes of GMSL rise not only require near complete melt of the Greenland Ice Sheet and the West Antarctic Ice Sheet, but a substantial retreat of marine-based sectors of East Antarctic Ice Sheet. Recent geological drilling initiatives on the continental margin of Antarctica from both ship- (e.g. IODP; International Ocean Discovery Program) and ice-based (e.g. ANDRILL/Antarctic Geological Drilling) platforms have provided evidence supporting retreat of marine-based ice. However, without direct access through the ice sheet to archives preserved within sub-glacial sedimentary basins, the volume and extent of ice sheet retreat during past interglacials cannot be directly constrained. Sediment cores have been successfully recovered from beneath ice shelves by the ANDRILL Program and ice streams by the WISSARD (Whillans Ice Stream Sub-glacial Access Research Drilling) Project. Together with the potential of the new RAID (Rapid Access Ice Drill) initiative, these demonstrate the technological feasibility of accessing the subglacial bed and deeper sedimentary archives. In this talk I will outline the

  4. The influence of global sea level changes on European shale distribution and gas exploration

    Energy Technology Data Exchange (ETDEWEB)

    Turner, P.; Cornelius, C.T.; Clarke, H. [Cuadrilla Resources Ltd., Staffordshire (United Kingdom)

    2010-07-01

    Technological advances in directional drilling and hydraulic fracturing technology have unlocked new supplies of shale gas from reservoirs that were previously considered to be uneconomic. Several companies, both experienced majors and small independents, are currently evaluating the unconventional resource potential of mainland Europe. This paper demonstrated that global sea level changes govern the distribution of marine black shales. The Hallam Curve was used in this study to identify periods of prospective gas shale deposition. In general, these correspond to post-glacial periods of relatively high sea level. Under-filled marginal sedimentary basins are key exploration targets. The geochemical and petrophysical characteristics of the shales deposited under these conditions are often comparable to North American shales, particularly the Barnett Shale which is currently in production. Many orogenic events influence European shales in terms of organic maturity, hydrocarbon generation and fracture generation. The main prospective horizons in ascending stratigraphic sequence are the Alum Shale, Llandovery Shale, Fammenian/Frasnian Shale, Serpukhovian Shale, Toarcian Shale, Kimmeridge Clay and the Tertiary Eocene and Oligocene shales common to central Europe. This paper presented the authors initial exploration strategy, with particular focus on the Lower Palaeozoic of central Europe, the Namurian of northwest England and the Jurassic Posidonia Formation of the Roer Valley Graben in Holland. The potential obstacles to unconventional exploration in Europe include restricted access to surface locations, high water usage, a lack of convenient pipeline infrastructure, strict environmental regulations, a high population density and lack of suitable drilling rigs and well completion equipment. 13 refs., 7 figs.

  5. Global Assessment of the SMAP Level-4 Soil Moisture Product Using Assimilation Diagnostics

    Science.gov (United States)

    Reichle, Rolf; Liu, Qing; De Lannoy, Gabrielle; Crow, Wade; Kimball, John; Koster, Randy; Ardizzone, Joe

    2018-01-01

    The Soil Moisture Active Passive (SMAP) mission Level-4 Soil Moisture (L4_SM) product provides 3-hourly, 9-km resolution, global estimates of surface (0-5 cm) and root-zone (0-100 cm) soil moisture and related land surface variables from 31 March 2015 to present with approx. 2.5-day latency. The ensemble-based L4_SM algorithm assimilates SMAP brightness temperature (Tb) observations into the Catchment land surface model. This study describes the spatially distributed L4_SM analysis and assesses the observation-minus-forecast (O-F) Tb residuals and the soil moisture and temperature analysis increments. Owing to the climatological rescaling of the Tb observations prior to assimilation, the analysis is essentially unbiased, with global mean values of approx. 0.37 K for the O-F Tb residuals and practically zero for the soil moisture and temperature increments. There are, however, modest regional (absolute) biases in the O-F residuals (under approx. 3 K), the soil moisture increments (under approx. 0.01 cu m/cu m), and the surface soil temperature increments (under approx. 1 K). Typical instantaneous values are approx. 6 K for O-F residuals, approx. 0.01 (approx. 0.003) cu m/cu m for surface (root-zone) soil moisture increments, and approx. 0.6 K for surface soil temperature increments. The O-F diagnostics indicate that the actual errors in the system are overestimated in deserts and densely vegetated regions and underestimated in agricultural regions and transition zones between dry and wet climates. The O-F auto-correlations suggest that the SMAP observations are used efficiently in western North America, the Sahel, and Australia, but not in many forested regions and the high northern latitudes. A case study in Australia demonstrates that assimilating SMAP observations successfully corrects short-term errors in the L4_SM rainfall forcing.

  6. The Contribution of Tissue Level Organization to Genomic Stability Following Low Dose/Low Dose Rate Gamma and Proton Irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Cheryl G. Burrell, Ph.D.

    2012-05-14

    The formation of functional tissue units is necessary in maintaining homeostasis within living systems, with individual cells contributing to these functional units through their three-dimensional organization with integrin and adhesion proteins to form a complex extra-cellular matrix (ECM). This is of particular importance in those tissues susceptible to radiation-induced tumor formation, such as epithelial glands. The assembly of epithelial cells of the thyroid is critical to their normal receipt of, and response to, incoming signals. Traditional tissue culture and live animals present significant challenges to radiation exposure and continuous sampling, however, the production of bioreactor-engineered tissues aims to bridge this gap by improve capabilities in continuous sampling from the same functional tissue, thereby increasing the ability to extrapolate changes induced by radiation to animals and humans in vivo. Our study proposes that the level of tissue organization will affect the induction and persistence of low dose radiation-induced genomic instability. Rat thyroid cells, grown in vitro as 3D tissue analogs in bioreactors and as 2D flask grown cultures were exposed to acute low dose (1, 5, 10 and 200 cGy) gamma rays. To assess immediate (6 hours) and delayed (up to 30 days) responses post-irradiation, various biological endpoints were studied including cytogenetic analyses, apoptosis analysis and cell viability/cytotoxicity analyses. Data assessing caspase 3/7 activity levels show that, this activity varies with time post radiation and that, overall, 3D cultures display more genomic instability (as shown by the lower levels of apoptosis over time) when compared to the 2D cultures. Variation in cell viability levels were only observed at the intermediate and late time points post radiation. Extensive analysis of chromosomal aberrations will give further insight on the whether the level of tissue organization influences genomic instability patterns after

  7. Global population genomics and comparisons of selective signatures from two invasions of melon fly, Zeugodacus cucurbitae (Diptera: Tephritidae)

    Science.gov (United States)

    Population genetics is a powerful tool for invasion biology and pest management, from tracing invasion pathways to informing management decisions with inference of population demographics. Genomics greatly increases the resolution of population-scale analyses, yet outside of model species with exten...

  8. Whole Genome and Global Gene Expression Analyses of the Model Mushroom Flammulina velutipes Reveal a High Capacity for Lignocellulose Degradation

    Science.gov (United States)

    Park, Young-Jin; Baek, Jeong Hun; Lee, Seonwook; Kim, Changhoon; Rhee, Hwanseok; Kim, Hyungtae; Seo, Jeong-Sun; Park, Hae-Ran; Yoon, Dae-Eun; Nam, Jae-Young; Kim, Hong-Il; Kim, Jong-Guk; Yoon, Hyeokjun; Kang, Hee-Wan; Cho, Jae-Yong; Song, Eun-Sung; Sung, Gi-Ho; Yoo, Young-Bok; Lee, Chang-Soo; Lee, Byoung-Moo; Kong, Won-Sik

    2014-01-01

    Flammulina velutipes is a fungus with health and medicinal benefits that has been used for consumption and cultivation in East Asia. F. velutipes is also known to degrade lignocellulose and produce ethanol. The overlapping interests of mushroom production and wood bioconversion make F. velutipes an attractive new model for fungal wood related studies. Here, we present the complete sequence of the F. velutipes genome. This is the first sequenced genome for a commercially produced edible mushroom that also degrades wood. The 35.6-Mb genome contained 12,218 predicted protein-encoding genes and 287 tRNA genes assembled into 11 scaffolds corresponding with the 11 chromosomes of strain KACC42780. The 88.4-kb mitochondrial genome contained 35 genes. Well-developed wood degrading machinery with strong potential for lignin degradation (69 auxiliary activities, formerly FOLymes) and carbohydrate degradation (392 CAZymes), along with 58 alcohol dehydrogenase genes were highly expressed in the mycelium, demonstrating the potential application of this organism to bioethanol production. Thus, the newly uncovered wood degrading capacity and sequential nature of this process in F. velutipes, offer interesting possibilities for more detailed studies on either lignin or (hemi-) cellulose degradation in complex wood substrates. The mutual interest in wood degradation by the mushroom industry and (ligno-)cellulose biomass related industries further increase the significance of F. velutipes as a new model. PMID:24714189

  9. Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution.

    Science.gov (United States)

    Ma, Wenxiu; Ay, Ferhat; Lee, Choli; Gulsoy, Gunhan; Deng, Xinxian; Cook, Savannah; Hesson, Jennifer; Cavanaugh, Christopher; Ware, Carol B; Krumm, Anton; Shendure, Jay; Blau, C Anthony; Disteche, Christine M; Noble, William S; Duan, ZhiJun

    2018-06-01

    The folding and three-dimensional (3D) organization of chromatin in the nucleus critically impacts genome function. The past decade has witnessed rapid advances in genomic tools for delineating 3D genome architecture. Among them, chromosome conformation capture (3C)-based methods such as Hi-C are the most widely used techniques for mapping chromatin interactions. However, traditional Hi-C protocols rely on restriction enzymes (REs) to fragment chromatin and are therefore limited in resolution. We recently developed DNase Hi-C for mapping 3D genome organization, which uses DNase I for chromatin fragmentation. DNase Hi-C overcomes RE-related limitations associated with traditional Hi-C methods, leading to improved methodological resolution. Furthermore, combining this method with DNA capture technology provides a high-throughput approach (targeted DNase Hi-C) that allows for mapping fine-scale chromatin architecture at exceptionally high resolution. Hence, targeted DNase Hi-C will be valuable for delineating the physical landscapes of cis-regulatory networks that control gene expression and for characterizing phenotype-associated chromatin 3D signatures. Here, we provide a detailed description of method design and step-by-step working protocols for these two methods. Copyright © 2018 Elsevier Inc. All rights reserved.

  10. Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels

    Science.gov (United States)

    van Leeuwen, Elisabeth M.; Karssen, Lennart C.; Deelen, Joris; Isaacs, Aaron; Medina-Gomez, Carolina; Mbarek, Hamdi; Kanterakis, Alexandros; Trompet, Stella; Postmus, Iris; Verweij, Niek; van Enckevort, David J.; Huffman, Jennifer E.; White, Charles C.; Feitosa, Mary F.; Bartz, Traci M.; Manichaikul, Ani; Joshi, Peter K.; Peloso, Gina M.; Deelen, Patrick; van Dijk, Freerk; Willemsen, Gonneke; de Geus, Eco J.; Milaneschi, Yuri; Penninx, Brenda W.J.H.; Francioli, Laurent C.; Menelaou, Androniki; Pulit, Sara L.; Rivadeneira, Fernando; Hofman, Albert; Oostra, Ben A.; Franco, Oscar H.; Leach, Irene Mateo; Beekman, Marian; de Craen, Anton J.M.; Uh, Hae-Won; Trochet, Holly; Hocking, Lynne J.; Porteous, David J.; Sattar, Naveed; Packard, Chris J.; Buckley, Brendan M.; Brody, Jennifer A.; Bis, Joshua C.; Rotter, Jerome I.; Mychaleckyj, Josyf C.; Campbell, Harry; Duan, Qing; Lange, Leslie A.; Wilson, James F.; Hayward, Caroline; Polasek, Ozren; Vitart, Veronique; Rudan, Igor; Wright, Alan F.; Rich, Stephen S.; Psaty, Bruce M.; Borecki, Ingrid B.; Kearney, Patricia M.; Stott, David J.; Adrienne Cupples, L.; Neerincx, Pieter B.T.; Elbers, Clara C.; Francesco Palamara, Pier; Pe'er, Itsik; Abdellaoui, Abdel; Kloosterman, Wigard P.; van Oven, Mannis; Vermaat, Martijn; Li, Mingkun; Laros, Jeroen F.J.; Stoneking, Mark; de Knijff, Peter; Kayser, Manfred; Veldink, Jan H.; van den Berg, Leonard H.; Byelas, Heorhiy; den Dunnen, Johan T.; Dijkstra, Martijn; Amin, Najaf; Joeri van der Velde, K.; van Setten, Jessica; Kattenberg, Mathijs; van Schaik, Barbera D.C.; Bot, Jan; Nijman, Isaäc J.; Mei, Hailiang; Koval, Vyacheslav; Ye, Kai; Lameijer, Eric-Wubbo; Moed, Matthijs H.; Hehir-Kwa, Jayne Y.; Handsaker, Robert E.; Sunyaev, Shamil R.; Sohail, Mashaal; Hormozdiari, Fereydoun; Marschall, Tobias; Schönhuth, Alexander; Guryev, Victor; Suchiman, H. Eka D.; Wolffenbuttel, Bruce H.; Platteel, Mathieu; Pitts, Steven J.; Potluri, Shobha; Cox, David R.; Li, Qibin; Li, Yingrui; Du, Yuanping; Chen, Ruoyan; Cao, Hongzhi; Li, Ning; Cao, Sujie; Wang, Jun; Bovenberg, Jasper A.; Jukema, J. Wouter; van der Harst, Pim; Sijbrands, Eric J.; Hottenga, Jouke-Jan; Uitterlinden, Andre G.; Swertz, Morris A.; van Ommen, Gert-Jan B.; de Bakker, Paul I.W.; Eline Slagboom, P.; Boomsma, Dorret I.; Wijmenga, Cisca; van Duijn, Cornelia M.

    2015-01-01

    Variants associated with blood lipid levels may be population-specific. To identify low-frequency variants associated with this phenotype, population-specific reference panels may be used. Here we impute nine large Dutch biobanks (~35,000 samples) with the population-specific reference panel created by the Genome of the Netherlands Project and perform association testing with blood lipid levels. We report the discovery of five novel associations at four loci (P value <6.61 × 10−4), including a rare missense variant in ABCA6 (rs77542162, p.Cys1359Arg, frequency 0.034), which is predicted to be deleterious. The frequency of this ABCA6 variant is 3.65-fold increased in the Dutch and its effect (βLDL-C=0.135, βTC=0.140) is estimated to be very similar to those observed for single variants in well-known lipid genes, such as LDLR. PMID:25751400

  11. Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis

    OpenAIRE

    Wyrsch, Ethan R.; Roy Chowdhury, Piklu; Chapman, Toni A.; Charles, Ian G.; Hammond, Jeffrey M.; Djordjevic, Steven P.

    2016-01-01

    Contamination of waste effluent from hospitals and intensive food animal production with antimicrobial residues is an immense global problem. Antimicrobial residues exert selection pressures that influence the acquisition of antimicrobial resistance and virulence genes in diverse microbial populations. Despite these concerns there is only a limited understanding of how antimicrobial residues contribute to the global problem of antimicrobial resistance. Furthermore, rapid detection of emerging...

  12. The Global Dimension of Water Governance: Why the River Basin Approach Is No Longer Sufficient and Why Cooperative Action at Global Level Is Needed

    Directory of Open Access Journals (Sweden)

    Arjen Y. Hoekstra

    2010-12-01

    Full Text Available When water problems extend beyond the borders of local communities, the river basin is generally seen as the most appropriate unit for analysis, planning, and institutional arrangements. In this paper it is argued that addressing water problems at the river basin level is not always sufficient. Many of today’s seemingly local water issues carry a (subcontinental or even global dimension, which urges for a governance approach that comprises institutional arrangements at a level beyond that of the river basin. This paper examines a number of arguments for the thesis that good water governance requires a global approach complementary to the river basin approach. Subsequently, it identifies four major issues to be addressed at global scale: Efficiency, equity, sustainability and security of water supply in a globalised world. Finally, the paper raises the question of what kind of institutional arrangements could be developed to cope with the global dimension of water issues. A few possible directions are explored, ranging from an international protocol on full-cost water pricing and a water label for water-intensive products to the implementation of water footprint quotas and the water-neutral concept.

  13. Engineering and Implementing an Executive-Level Communication Plan in a Global Professional Environment: A Case Study

    Directory of Open Access Journals (Sweden)

    Bridgette Lipman

    2015-06-01

    Full Text Available Communication within organisations in a global environment requires effective internal and strategic planning at the executive level. Previous studies indicate that measurement is a key factor in assessing the needs and success of global communication within an organisation. Survey questions were used to measure satisfaction responses from 650 local and 110 global employees in a technology division of a large manufacturing company. In this case study, employees expressed the need to connect team members through face-to-face meetings, employee webcast meetings, web chat forums, and an updated employee networking site. The findings formed the foundations for recommendations for strategy, objectives, and tactics within the organisation.

  14. Comparing the cariogenic species Streptococcus sobrinus and S. mutans on whole genome level

    Directory of Open Access Journals (Sweden)

    Georg Conrads

    2014-12-01

    Full Text Available Background: Two closely related species of mutans streptococci, namely Streptococcus mutans and Streptococcus sobrinus, are associated with dental caries in humans. Their acidogenic and aciduric capacity is directly associated with the cariogenic potential of these bacteria. To survive acidic and temporarily harsh conditions in the human oral cavity with hundreds of other microbial co-colonizers as competitors, both species have developed numerous mechanisms for adaptation. Objectives: The recently published novel genome information for both species is used to elucidate genetic similarities but especially differences and to discuss the impact on cariogenicity of the corresponding phenotypic properties including adhesion, carbohydrate uptake and fermentation, acid tolerance, signaling by two component systems, competence, and oxidative stress resistance. Conclusions: S. sobrinus can down-regulate the SpaA-mediated adherence to the pellicle. It has a smaller number of two-component signaling systems and bacteriocin-related genes than S. mutans, but all or even more immunity proteins. It lacks the central competence genes comC, comS, and comR. There are more genes coding for glucosyltransferases and a novel energy production pathway formed by lactate oxidase, which is not found in S. mutans. Both species show considerable differences in the regulation of fructan catabolism. However, both S. mutans and S. sobrinus share most of these traits and should therefore be considered as equally virulent with regard to dental caries.

  15. Fully functional global genome repair of (6-4) photoproducts and compromised transcription-coupled repair of cyclobutane pyrimidine dimers in condensed mitotic chromatin

    Energy Technology Data Exchange (ETDEWEB)

    Komura, Jun-ichiro, E-mail: junkom@med.tohoku.ac.jp [Department of Cell Biology, Tohoku University Graduate School of Medicine, Sendai 980-8575 (Japan); Ikehata, Hironobu [Department of Cell Biology, Tohoku University Graduate School of Medicine, Sendai 980-8575 (Japan); Mori, Toshio [Radioisotope Research Center, Nara Medical University, Kashihara, Nara 634-8521 (Japan); Ono, Tetsuya [Department of Cell Biology, Tohoku University Graduate School of Medicine, Sendai 980-8575 (Japan)

    2012-03-10

    During mitosis, chromatin is highly condensed, and activities such as transcription and semiconservative replication do not occur. Consequently, the condensed condition of mitotic chromatin is assumed to inhibit DNA metabolism by impeding the access of DNA-transacting proteins. However, about 40 years ago, several researchers observed unscheduled DNA synthesis in UV-irradiated mitotic chromosomes, suggesting the presence of excision repair. We re-examined this subject by directly measuring the removal of UV-induced DNA lesions by an ELISA and by a Southern-based technique in HeLa cells arrested at mitosis. We observed that the removal of (6-4) photoproducts from the overall genome in mitotic cells was as efficient as in interphase cells. This suggests that global genome repair of (6-4) photoproducts is fully functional during mitosis, and that the DNA in mitotic chromatin is accessible to proteins involved in this mode of DNA repair. Nevertheless, not all modes of DNA repair seem fully functional during mitosis. We also observed that the removal of cyclobutane pyrimidine dimers from the dihydrofolate reductase and c-MYC genes in mitotic cells was very slow. This suggests that transcription-coupled repair of cyclobutane pyrimidine dimers is compromised or non-functional during mitosis, which is probably the consequence of mitotic transcriptional repression. -- Highlights: Black-Right-Pointing-Pointer Global genome repair of (6-4) photoproducts is fully active in mitotic cells. Black-Right-Pointing-Pointer DNA in condensed mitotic chromatin does not seem inaccessible or inert. Black-Right-Pointing-Pointer Mitotic transcriptional repression may impair transcription-coupled repair.

  16. Fully functional global genome repair of (6-4) photoproducts and compromised transcription-coupled repair of cyclobutane pyrimidine dimers in condensed mitotic chromatin

    International Nuclear Information System (INIS)

    Komura, Jun-ichiro; Ikehata, Hironobu; Mori, Toshio; Ono, Tetsuya

    2012-01-01

    During mitosis, chromatin is highly condensed, and activities such as transcription and semiconservative replication do not occur. Consequently, the condensed condition of mitotic chromatin is assumed to inhibit DNA metabolism by impeding the access of DNA-transacting proteins. However, about 40 years ago, several researchers observed unscheduled DNA synthesis in UV-irradiated mitotic chromosomes, suggesting the presence of excision repair. We re-examined this subject by directly measuring the removal of UV-induced DNA lesions by an ELISA and by a Southern-based technique in HeLa cells arrested at mitosis. We observed that the removal of (6-4) photoproducts from the overall genome in mitotic cells was as efficient as in interphase cells. This suggests that global genome repair of (6-4) photoproducts is fully functional during mitosis, and that the DNA in mitotic chromatin is accessible to proteins involved in this mode of DNA repair. Nevertheless, not all modes of DNA repair seem fully functional during mitosis. We also observed that the removal of cyclobutane pyrimidine dimers from the dihydrofolate reductase and c-MYC genes in mitotic cells was very slow. This suggests that transcription-coupled repair of cyclobutane pyrimidine dimers is compromised or non-functional during mitosis, which is probably the consequence of mitotic transcriptional repression. -- Highlights: ► Global genome repair of (6-4) photoproducts is fully active in mitotic cells. ► DNA in condensed mitotic chromatin does not seem inaccessible or inert. ► Mitotic transcriptional repression may impair transcription-coupled repair.

  17. The Global Survey Method Applied to Ground-level Cosmic Ray Measurements

    Science.gov (United States)

    Belov, A.; Eroshenko, E.; Yanke, V.; Oleneva, V.; Abunin, A.; Abunina, M.; Papaioannou, A.; Mavromichalaki, H.

    2018-04-01

    The global survey method (GSM) technique unites simultaneous ground-level observations of cosmic rays in different locations and allows us to obtain the main characteristics of cosmic-ray variations outside of the atmosphere and magnetosphere of Earth. This technique has been developed and applied in numerous studies over many years by the Institute of Terrestrial Magnetism, Ionosphere and Radiowave Propagation (IZMIRAN). We here describe the IZMIRAN version of the GSM in detail. With this technique, the hourly data of the world-wide neutron-monitor network from July 1957 until December 2016 were processed, and further processing is enabled upon the receipt of new data. The result is a database of homogeneous and continuous hourly characteristics of the density variations (an isotropic part of the intensity) and the 3D vector of the cosmic-ray anisotropy. It includes all of the effects that could be identified in galactic cosmic-ray variations that were caused by large-scale disturbances of the interplanetary medium in more than 50 years. These results in turn became the basis for a database on Forbush effects and interplanetary disturbances. This database allows correlating various space-environment parameters (the characteristics of the Sun, the solar wind, et cetera) with cosmic-ray parameters and studying their interrelations. We also present features of the coupling coefficients for different neutron monitors that enable us to make a connection from ground-level measurements to primary cosmic-ray variations outside the atmosphere and the magnetosphere. We discuss the strengths and weaknesses of the current version of the GSM as well as further possible developments and improvements. The method developed allows us to minimize the problems of the neutron-monitor network, which are typical for experimental physics, and to considerably enhance its advantages.

  18. Global DNA Methylation in the Chestnut Blight Fungus Cryphonectria parasitica and Genome-Wide Changes in DNA Methylation Accompanied with Sectorization

    Directory of Open Access Journals (Sweden)

    Kum-Kang So

    2018-02-01

    Full Text Available Mutation in CpBck1, an ortholog of the cell wall integrity mitogen-activated protein kinase kinase kinase (MAPKKK of Saccharomyces cerevisiae, in the chestnut blight fungus Cryphonectria parasitica resulted in a sporadic sectorization as culture proceeded. The progeny from the sectored area maintained the characteristics of the sector, showing a massive morphogenetic change, including robust mycelial growth without differentiation. Epigenetic changes were investigated as the genetic mechanism underlying this sectorization. Quantification of DNA methylation and whole-genome bisulfite sequencing revealed genome-wide DNA methylation of the wild-type at each nucleotide level and changes in DNA methylation of the sectored progeny. Compared to the wild-type, the sectored progeny exhibited marked genome-wide DNA hypomethylation but increased methylation sites. Expression analysis of two DNA methyltransferases, including two representative types of DNA methyltransferase (DNMTase, demonstrated that both were significantly down-regulated in the sectored progeny. However, functional analysis using mutant phenotypes of corresponding DNMTases demonstrated that a mutant of CpDmt1, an ortholog of RID of Neurospora crassa, resulted in the sectored phenotype but the CpDmt2 mutant did not, suggesting that the genetic basis of fungal sectorization is more complex. The present study revealed that a mutation in a signaling pathway component resulted in sectorization accompanied with changes in genome-wide DNA methylation, which suggests that this signal transduction pathway is important for epigenetic control of sectorization via regulation of genes involved in DNA methylation.

  19. Global, regional, and national levels of maternal mortality, 1990-2015: a systematic analysis for the Global Burden of Disease Study 2015

    OpenAIRE

    GBD Maternal Mortality Collaborators

    2016-01-01

    BACKGROUND: In transitioning from the Millennium Development Goal to the Sustainable Development Goal era, it is imperative to comprehensively assess progress toward reducing maternal mortality to identify areas of success, remaining challenges, and frame policy discussions. We aimed to quantify maternal mortality throughout the world by underlying cause and age from 1990 to 2015. METHODS: We estimated maternal mortality at the global, regional, and national levels from 1990 to 2015 for ages ...

  20. Correlation of microRNA levels during hypoxia with predicted target mRNAs through genome-wide microarray analysis

    Directory of Open Access Journals (Sweden)

    Page Grier P

    2009-03-01

    Full Text Available Abstract Background Low levels of oxygen in tissues, seen in situations such as chronic lung disease, necrotic tumors, and high altitude exposures, initiate a signaling pathway that results in active transcription of genes possessing a hypoxia response element (HRE. The aim of this study was to investigate whether a change in miRNA expression following hypoxia could account for changes in the cellular transcriptome based on currently available miRNA target prediction tools. Methods To identify changes induced by hypoxia, we conducted mRNA- and miRNA-array-based experiments in HT29 cells, and performed comparative analysis of the resulting data sets based on multiple target prediction algorithms. To date, few studies have investigated an environmental perturbation for effects on genome-wide miRNA levels, or their consequent influence on mRNA output. Results Comparison of miRNAs with predicted mRNA targets indicated a lower level of concordance than expected. We did, however, find preliminary evidence of combinatorial regulation of mRNA expression by miRNA. Conclusion Target prediction programs and expression profiling techniques do not yet adequately represent the complexity of miRNA-mediated gene repression, and new methods may be required to better elucidate these pathways. Our data suggest the physiologic impact of miRNAs on cellular transcription results from a multifaceted network of miRNA and mRNA relationships, working together in an interconnected system and in context of hundreds of RNA species. The methods described here for comparative analysis of cellular miRNA and mRNA will be useful for understanding genome wide regulatory responsiveness and refining miRNA predictive algorithms.

  1. IGESS: a statistical approach to integrating individual-level genotype data and summary statistics in genome-wide association studies.

    Science.gov (United States)

    Dai, Mingwei; Ming, Jingsi; Cai, Mingxuan; Liu, Jin; Yang, Can; Wan, Xiang; Xu, Zongben

    2017-09-15

    Results from genome-wide association studies (GWAS) suggest that a complex phenotype is often affected by many variants with small effects, known as 'polygenicity'. Tens of thousands of samples are often required to ensure statistical power of identifying these variants with small effects. However, it is often the case that a research group can only get approval for the access to individual-level genotype data with a limited sample size (e.g. a few hundreds or thousands). Meanwhile, summary statistics generated using single-variant-based analysis are becoming publicly available. The sample sizes associated with the summary statistics datasets are usually quite large. How to make the most efficient use of existing abundant data resources largely remains an open question. In this study, we propose a statistical approach, IGESS, to increasing statistical power of identifying risk variants and improving accuracy of risk prediction by i ntegrating individual level ge notype data and s ummary s tatistics. An efficient algorithm based on variational inference is developed to handle the genome-wide analysis. Through comprehensive simulation studies, we demonstrated the advantages of IGESS over the methods which take either individual-level data or summary statistics data as input. We applied IGESS to perform integrative analysis of Crohns Disease from WTCCC and summary statistics from other studies. IGESS was able to significantly increase the statistical power of identifying risk variants and improve the risk prediction accuracy from 63.2% ( ±0.4% ) to 69.4% ( ±0.1% ) using about 240 000 variants. The IGESS software is available at https://github.com/daviddaigithub/IGESS . zbxu@xjtu.edu.cn or xwan@comp.hkbu.edu.hk or eeyang@hkbu.edu.hk. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  2. Global brain blood-oxygen level responses to autonomic challenges in obstructive sleep apnea.

    Directory of Open Access Journals (Sweden)

    Paul M Macey

    Full Text Available Obstructive sleep apnea (OSA is accompanied by brain injury, perhaps resulting from apnea-related hypoxia or periods of impaired cerebral perfusion. Perfusion changes can be determined indirectly by evaluation of cerebral blood volume and oxygenation alterations, which can be measured rapidly and non-invasively with the global blood oxygen level dependent (BOLD signal, a magnetic resonance imaging procedure. We assessed acute BOLD responses in OSA subjects to pressor challenges that elicit cerebral blood flow changes, using a two-group comparative design with healthy subjects as a reference. We separately assessed female and male patterns, since OSA characteristics and brain injury differ between sexes. We studied 94 subjects, 37 with newly-diagnosed, untreated OSA (6 female (age mean ± std: 52.1±8.1 yrs; apnea/hypopnea index [AHI]: 27.7±15.6 events/hr and 31 male 54.3±8.4 yrs; AHI: 37.4±19.6 events/hr, and 20 female (age 50.5±8.1 yrs and 37 male (age 45.6±9.2 yrs healthy control subjects. We measured brain BOLD responses every 2 s while subjects underwent cold pressor, hand grip, and Valsalva maneuver challenges. The global BOLD signal rapidly changed after the first 2 s of each challenge, and differed in magnitude between groups to two challenges (cold pressor, hand grip, but not to the Valsalva maneuver (repeated measures ANOVA, p<0.05. OSA females showed greater differences from males in response magnitude and pattern, relative to healthy counterparts. Cold pressor BOLD signal increases (mean ± adjusted standard error at the 8 s peak were: OSA 0.14±0.08% vs. Control 0.31±0.06%, and hand grip at 6 s were: OSA 0.08±0.03% vs. Control at 0.30±0.02%. These findings, indicative of reduced cerebral blood flow changes to autonomic challenges in OSA, complement earlier reports of altered resting blood flow and reduced cerebral artery responsiveness. Females are more affected than males, an outcome which may contribute to the sex

  3. State - Level Regulation's Effectiveness in Addressing Global Climate Change and Promoting Solar Energy Deployment

    Science.gov (United States)

    Peterman, Carla Joy

    Paper 1, Local Solutions to Global Problems: Climate Change Policies and Regulatory Jurisdiction, considers the efficacy of various types of environmental regulations when they are applied locally to pollutants whose damages extend beyond the jurisdiction of the local regulators. Local regulations of a global pollutant may be ineffective if producers and consumers can avoid them by transacting outside the reach of the local regulator. In many cases, this may involve the physical relocation of the economic activity, a problem often referred to as "leakage." This paper highlights another way in which local policies can be circumvented: through the shuffling of who buys from whom. The paper maintains that the problems of reshuffling are exacerbated when the options for compliance with the regulations are more flexible. Numerical analyses is presented demonstrating that several proposed policies to limit greenhouse gas emissions from the California electricity sector may have very little effect on carbon emissions if they are applied only within that state. Paper 1 concludes that although local subsidies for energy efficiency, renewable electricity, and transportation biofuels constitute attempts to pick technology winners, they may be the only mechanisms that local jurisdictions, acting alone, have at their disposal to address climate change. Paper 2, Pass-Through of Solar PV Incentives to Consumers: The Early Years of California's Solar PV Incentives, examines the pass through of incentives to California solar PV system owners. The full post-subsidy price consumers pay for solar power is a key metric of the success of solar PV incentive programs and of overall PV market performance. This study examines the early years of California's most recent wave of distributed solar PV incentives (2000-2008) to determine the pass-through of incentives. Examination of this period is both intellectually and pragmatically important due to the high level of incentives provided and

  4. Variations in the G6PC2/ABCB11 genomic region are associated with fasting glucose levels

    DEFF Research Database (Denmark)

    Chen, Wei-Min; Erdos, Michael R; Jackson, Anne U

    2008-01-01

    Identifying the genetic variants that regulate fasting glucose concentrations may further our understanding of the pathogenesis of diabetes. We therefore investigated the association of fasting glucose levels with SNPs in 2 genome-wide scans including a total of 5,088 nondiabetic individuals from...... Finland and Sardinia. We found a significant association between the SNP rs563694 and fasting glucose concentrations (P = 3.5 x 10(-7)). This association was further investigated in an additional 18,436 nondiabetic individuals of mixed European descent from 7 different studies. The combined P value...... for association in these follow-up samples was 6.9 x 10(-26), and combining results from all studies resulted in an overall P value for association of 6.4 x 10(-33). Across these studies, fasting glucose concentrations increased 0.01-0.16 mM with each copy of the major allele, accounting for approximately 1...

  5. [Analysis of genomic DNA methylation level in radish under cadmium stress by methylation-sensitive amplified polymorphism technique].

    Science.gov (United States)

    Yang, Jin-Lan; Liu, Li-Wang; Gong, Yi-Qin; Huang, Dan-Qiong; Wang, Feng; He, Ling-Li

    2007-06-01

    The level of cytosine methylation induced by cadmium in radish (Raphanus sativus L.) genome was analysed using the technique of methylation-sensitive amplified polymorphism (MSAP). The MSAP ratios in radish seedling exposed to cadmium chloride at the concentration of 50, 250 and 500 mg/L were 37%, 43% and 51%, respectively, and the control was 34%; the full methylation levels (C(m)CGG in double strands) were at 23%, 25% and 27%, respectively, while the control was 22%. The level of increase in MSAP and full methylation indicated that de novo methylation occurred in some 5'-CCGG sites under Cd stress. There was significant positive correlation between increase of total DNA methylation level and CdCl(2) concentration. Four types of MSAP patterns: de novo methylation, de-methylation, atypical pattern and no changes of methylation pattern were identified among CdCl(2) treatments and the control. DNA methylation alteration in plants treated with CdCl(2) was mainly through de novo methylation.

  6. The integration of object levels and their content: a theory of global/local processing and related hemispheric differences.

    Science.gov (United States)

    Hübner, Ronald; Volberg, Gregor

    2005-06-01

    This article presents and tests the authors' integration hypothesis of global/local processing, which proposes that at early stages of processing, the identities of global and local units of a hierarchical stimulus are represented separately from information about their respective levels and that, therefore, identity and level information have to be integrated at later stages. It further states that the cerebral hemispheres differ in their capacities for these binding processes. Three experiments are reported in which the integration hypothesis was tested. Participants had to identify a letter at a prespecified level with the viewing duration restricted by a mask. False reporting of the letter at the nontarget level was predicted to occur more often when the integration of identity and level could fail. This was the case. Moreover, visual-field effects occurred, as expected. Finally, a multinomial model was constructed and fitted to the data. ((c) 2005 APA, all rights reserved).

  7. Detecting anthropogenic footprints in regional and global sea level rise since 1900

    Science.gov (United States)

    Dangendorf, S.; Marcos, M.; Piecuch, C. G.; Jensen, J.

    2015-12-01

    While there is scientific consensus that global and local mean sea level (GMSL and LMSL) is rising since the late 19th century, it remains unclear how much of this rise is due to natural variability or anthropogenic forcing. Distinguishing both contributions requires an extensive knowledge about the persistence of natural high and low stands in GMSL and LMSL. This is challenging, since observational time series represent the superposition of various processes with different spectral properties. Here we provide a probabilistic upper range of long-term persistent natural GMSL/LMSL variability (P=0.99), which in turn determines the minimum/maximum anthropogenic contribution since 1900. To account for different spectral characteristics of various contributing processes, we separate LMSL (corrected for vertical land motion) into a slowly varying volumetric (mass and density changes) and a more rapidly changing atmospheric component. Based on a combination of spectral analyses of tide gauge records, barotropic and baroclinic ocean models and numerical Monte-Carlo experiments, we find that in records where transient atmospheric processes dominate the spectra, the persistence of natural volumetric changes tends to be underestimated. If each component is assessed separately, natural centennial trends are locally up to ~1.0 mm/yr larger than in case of an integrated assessment, therefore erroneously enhancing the significance of anthropogenic footprints. The GMSL, however, remains unaffected by such biases. On the basis of a model assessment of the separate components, we conclude that it is virtually certain (P=0.99) that at least 45% of the observed increase in GMSL is of anthropogenic origin.

  8. Regions of mid-level human visual cortex sensitive to the global coherence of local image patches.

    Science.gov (United States)

    Mannion, Damien J; Kersten, Daniel J; Olman, Cheryl A

    2014-08-01

    The global structural arrangement and spatial layout of the visual environment must be derived from the integration of local signals represented in the lower tiers of the visual system. This interaction between the spatially local and global properties of visual stimulation underlies many of our visual capacities, and how this is achieved in the brain is a central question for visual and cognitive neuroscience. Here, we examine the sensitivity of regions of the posterior human brain to the global coordination of spatially displaced naturalistic image patches. We presented observers with image patches in two circular apertures to the left and right of central fixation, with the patches drawn from either the same (coherent condition) or different (noncoherent condition) extended image. Using fMRI at 7T (n = 5), we find that global coherence affected signal amplitude in regions of dorsal mid-level cortex. Furthermore, we find that extensive regions of mid-level visual cortex contained information in their local activity pattern that could discriminate coherent and noncoherent stimuli. These findings indicate that the global coordination of local naturalistic image information has important consequences for the processing in human mid-level visual cortex.

  9. Global Intersection of Long Non-Coding RNAs with Processed and Unprocessed Pseudogenes in the Human Genome

    Directory of Open Access Journals (Sweden)

    Michael John Milligan

    2016-03-01

    Full Text Available Pseudogenes are abundant in the human genome and had long been thought of purely as nonfunctional gene fossils. Recent observations point to a role for pseudogenes in regulating genes transcriptionally and post-transcriptionally in human cells. To computationally interrogate the network space of integrated pseudogene and long non-coding RNA regulation in the human transcriptome, we developed and implemented an algorithm to identify all long non-coding RNA (lncRNA transcripts that overlap the genomic spans, and specifically the exons, of any human pseudogenes in either sense or antisense orientation. As inputs to our algorithm, we imported three public repositories of pseudogenes: GENCODE v17 (processed and unprocessed, Ensembl 72; Retroposed Pseudogenes V5 (processed only and Yale Pseudo60 (processed and unprocessed, Ensembl 60; two public lncRNA catalogs: Broad Institute, GENCODE v17; NCBI annotated piRNAs; and NHGRI clinical variants. The data sets were retrieved from the UCSC Genome Database using the UCSC Table Browser. We identified 2277 loci containing exon-to-exon overlaps between pseudogenes, both processed and unprocessed, and long non-coding RNA genes. Of these loci we identified 1167 with Genbank EST and full-length cDNA support providing direct evidence of transcription on one or both strands with exon-to-exon overlaps. The analysis converged on 313 pseudogene-lncRNA exon-to-exon overlaps that were bidirectionally supported by both full-length cDNAs and ESTs. In the process of identifying transcribed pseudogenes, we generated a comprehensive, positionally non-redundant encyclopedia of human pseudogenes, drawing upon multiple, and formerly disparate public pseudogene repositories. Collectively, these observations suggest that pseudogenes are pervasively transcribed on both strands and are common drivers of gene regulation.

  10. Global, regional, and national consumption levels of dietary fats and oils in 1990 and 2010

    DEFF Research Database (Denmark)

    Micha, Renata; Khatibzadeh, Shahab; Shi, Peilin

    2014-01-01

    at older ages. Intakes were similar by sex. Between 1990 and 2010, global saturated fat, dietary cholesterol, and trans fat intakes remained stable, while omega 6, seafood omega 3, and plant omega 3 fat intakes each increased. CONCLUSIONS: These novel global data on dietary fats and oils identify dramatic......OBJECTIVES: To quantify global consumption of key dietary fats and oils by country, age, and sex in 1990 and 2010. DESIGN: Data were identified, obtained, and assessed among adults in 16 age- and sex-specific groups from dietary surveys worldwide on saturated, omega 6, seafood omega 3, plant omega....../day (228 mg/day) for dietary cholesterol; 5 to 3,886 mg/day (163 mg/day) for seafood omega 3; and plant omega 3. Countries representing 52.4% of the global population had national mean intakes for omega 6 fat ≥ 5%E; corresponding proportions meeting optimal intakes...

  11. GHRSST Level 2P USA NAVOCEANO AVHRR17 Global SST:1

    Data.gov (United States)

    National Aeronautics and Space Administration — Multi-Channel SST retreivals generated in real-time from NOAA-17 AVHRR Global Area Coverage data. Used operationally in Navy oceanographic analyses and forecasts.

  12. GHRSST Level 2P USA NAVOCEANO AVHRR METOP-A Global SST:1

    Data.gov (United States)

    National Aeronautics and Space Administration — Multi-Channel SST retreivals generated in real-time from METOP-A AVHRR Global Area Coverage data. Used operationally in Navy oceanographic analyses and forecasts.

  13. GHRSST Level 2P USA NAVOCEANO AVHRR18 Global SST:1

    Data.gov (United States)

    National Aeronautics and Space Administration — Multi-Channel SST retreivals generated in real-time from NOAA-18 AVHRR Global Area Coverage data. Used operationally in Navy oceanographic analyses and forecasts.

  14. The Influence of Global Macroeconomic Factors on Stock Values: A Sector Level Analysis

    OpenAIRE

    Şerife Özlen

    2014-01-01

    Investors and policy makers should carefully analyze stock returns and their possible relationships with microeconomic and macroeconomic factors in both local and global arena. Since the markets are increasingly becoming global, the outcomes may be more important for international factors. Therefore, this study aims to identify the relationship between selected international macroeconomic variables (FTSE-100 England market index, GDAX Germany market index, NYSE Composite market index, Gold pr...

  15. Global Systems-Level Analysis of Hfq and SmpB Deletion Mutants in Salmonella: Implications for Virulence and Global Protein Translation

    Energy Technology Data Exchange (ETDEWEB)

    Ansong, Charles; Yoon, Hyunjin; Porwollik, Steffen; Mottaz-Brewer, Heather; Petritis, Brianne O.; Jaitly, Navdeep; Adkins, Joshua N.; Mcclelland, Michael; Heffron, Fred; Smith, Richard D.

    2009-03-11

    In recent years the profound importance of sRNA-mediated translational/post-transcriptional regulation has been increasingly appreciated. However, the global role played by translational regulation in control of gene expression has never been elucidated in any organism for the simple reason that global proteomics methods required to accurately characterize post-transcriptional processes and the knowledge of translational control mechanisms have only become available within the last few years. The proteins Hfq and SmpB are essential for the biological activity of a range of regulatory sRNAs and thus provide a means to identify potential targets of sRNA regulation. We performed a sample-matched global proteomics and transcriptional analysis to examine the role of Hfq and SmpB in global protein translation and virulence using the Salmonella typhimurium model system. Samples were analyzed from bacteria grown under four different conditions; two laboratory conditions and two that are thought to mimic the intracellular environment. We show that mutants of hfq and smpB directly or indirectly modulate at least 20% and 4% of all Salmonella proteins, respectively, with limited correlation between transcription and protein expression. This is the first report suggesting that SmpB could be a general translational regulator. The broad spectrum of proteins modulated by Hfq was also surprising including central metabolism, LPS biosynthesis, two-component regulatory systems, quorum sensing, SP1-TTSS, oxidative stress, fatty acid metabolism, nucleoside and nucleotide metabolism, envelope stress, aminoacyl-tRNA synthetases, amino acid biosynthesis, peptide transport, and motility.. The extent of global regulation of translation by Hfq is unexpected, with profound effects in all stages of Salmonella’s life cycle. Our results represent the first global systems-level analysis of translational regulation; the elucidated potential targets of sRNA regulation from our analysis will

  16. Abortion incidence between 1990 and 2014: global, regional, and subregional levels and trends

    Science.gov (United States)

    Sedgh, Gilda; Bearak, Jonathan; Singh, Susheela; Bankole, Akinrinola; Popinchalk, Anna; Ganatra, Bela; Rossier, Clémentine; Gerdts, Caitlin; Tunçalp, Özge; Johnson, Brooke Ronald; Johnston, Heidi Bart; Alkema, Leontine

    2017-01-01

    Summary Background Information about the incidence of induced abortion is needed to motivate and inform efforts to help women avoid unintended pregnancies and to monitor progress toward that end. We estimate subregional, regional, and global levels and trends in abortion incidence for 1990 to 2014, and abortion rates in subgroups of women. We use the results to estimate the proportion of pregnancies that end in abortion and examine whether abortion rates vary in countries grouped by the legal status of abortion. Methods We requested abortion data from government agencies and compiled data from international sources and nationally representative studies. With data for 1069 country-years, we estimated incidence using a Bayesian hierarchical time series model whereby the overall abortion rate is a function of the modelled rates in subgroups of women of reproductive age defined by their marital status and contraceptive need and use, and the sizes of these subgroups. Findings We estimated that 35 abortions (90% uncertainty interval [UI] 33 to 44) occurred annually per 1000 women aged 15–44 years worldwide in 2010–14, which was 5 points less than 40 (39–48) in 1990–94 (90% UI for decline −11 to 0). Because of population growth, the annual number of abortions worldwide increased by 5·9 million (90% UI −1·3 to 15·4), from 50·4 million in 1990–94 (48·6 to 59·9) to 56·3 million (52·4 to 70·0) in 2010–14. In the developed world, the abortion rate declined 19 points (–26 to −14), from 46 (41 to 59) to 27 (24 to 37). In the developing world, we found a non-significant 2 point decline (90% UI −9 to 4) in the rate from 39 (37 to 47) to 37 (34 to 46). Some 25% (90% UI 23 to 29) of pregnancies ended in abortion in 2010–14. Globally, 73% (90% UI 59 to 82) of abortions were obtained by married women in 2010–14 compared with 27% (18 to 41) obtained by unmarried women. We did not observe an association between the abortion rates for 2010–14 and the

  17. The logic of DNA replication in double-stranded DNA viruses: insights from global analysis of viral genomes.

    Science.gov (United States)

    Kazlauskas, Darius; Krupovic, Mart; Venclovas, Česlovas

    2016-06-02

    Genomic DNA replication is a complex process that involves multiple proteins. Cellular DNA replication systems are broadly classified into only two types, bacterial and archaeo-eukaryotic. In contrast, double-stranded (ds) DNA viruses feature a much broader diversity of DNA replication machineries. Viruses differ greatly in both completeness and composition of their sets of DNA replication proteins. In this study, we explored whether there are common patterns underlying this extreme diversity. We identified and analyzed all major functional groups of DNA replication proteins in all available proteomes of dsDNA viruses. Our results show that some proteins are common to viruses infecting all domains of life and likely represent components of the ancestral core set. These include B-family polymerases, SF3 helicases, archaeo-eukaryotic primases, clamps and clamp loaders of the archaeo-eukaryotic type, RNase H and ATP-dependent DNA ligases. We also discovered a clear correlation between genome size and self-sufficiency of viral DNA replication, the unanticipated dominance of replicative helicases and pervasive functional associations among certain groups of DNA replication proteins. Altogether, our results provide a comprehensive view on the diversity and evolution of replication systems in the DNA virome and uncover fundamental principles underlying the orchestration of viral DNA replication. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Are sea-level-rise trends along the coasts of the north Indian Ocean consistent with global estimates?

    Digital Repository Service at National Institute of Oceanography (India)

    Unnikrishnan, A.S.; Shankar, D.

    yielded sea-level-rise estimates between 1.06–1.75 mm/ yrear-1 , with a regional average of 1.29 mm yr-1, when corrected for global isostatic adjustment (GIA) using model data, with a regional average of 1.29 mm-1.. These estimates are consistent...

  19. An improved empirical dynamic control system model of global mean sea level rise and surface temperature change

    Science.gov (United States)

    Wu, Qing; Luu, Quang-Hung; Tkalich, Pavel; Chen, Ge

    2018-04-01

    Having great impacts on human lives, global warming and associated sea level rise are believed to be strongly linked to anthropogenic causes. Statistical approach offers a simple and yet conceptually verifiable combination of remotely connected climate variables and indices, including sea level and surface temperature. We propose an improved statistical reconstruction model based on the empirical dynamic control system by taking into account the climate variability and deriving parameters from Monte Carlo cross-validation random experiments. For the historic data from 1880 to 2001, we yielded higher correlation results compared to those from other dynamic empirical models. The averaged root mean square errors are reduced in both reconstructed fields, namely, the global mean surface temperature (by 24-37%) and the global mean sea level (by 5-25%). Our model is also more robust as it notably diminished the unstable problem associated with varying initial values. Such results suggest that the model not only enhances significantly the global mean reconstructions of temperature and sea level but also may have a potential to improve future projections.

  20. Site-level evaluation of satellite-based global terrestrial gross primary production and net primary production monitoring.

    Science.gov (United States)

    David P. Turner; William D. Ritts; Warren B. Cohen; Thomas K. Maeirsperger; Stith T. Gower; Al A. Kirschbaum; Steve W. Runnings; Maosheng Zhaos; Steven C. Wofsy; Allison L. Dunn; Beverly E. Law; John L. Campbell; Walter C. Oechel; Hyo Jung Kwon; Tilden P. Meyers; Eric E. Small; Shirley A. Kurc; John A. Gamon

    2005-01-01

    Operational monitoring of global terrestrial gross primary production (GPP) and net primary production (NPP) is now underway using imagery from the satellite-borne Moderate Resolution Imaging Spectroradiometer (MODIS) sensor. Evaluation of MODIS GPP and NPP products will require site-level studies across a range of biomes, with close attention to numerous scaling...

  1. PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance.

    NARCIS (Netherlands)

    Nadon, Celine; Van Walle, Ivo; Gerner-Smidt, Peter; Campos, Josefina; Chinen, Isabel; Concepcion-Acevedo, Jeniffer; Gilpin, Brent; Smith, Anthony M; Man Kam, Kai; Perez, Enrique; Trees, Eija; Kubota, Kristy; Takkinen, Johanna; Nielsen, Eva Møller; Carleton, Heather

    2017-01-01

    PulseNet International is a global network dedicated to laboratory-based surveillance for food-borne diseases. The network comprises the national and regional laboratory networks of Africa, Asia Pacific, Canada, Europe, Latin America and the Caribbean, the Middle East, and the United States. The

  2. A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic

    DEFF Research Database (Denmark)

    Holden, Matthew T G; Hsu, Li-Yang; Kurt, Kevin

    2013-01-01

    The widespread use of antibiotics in association with high-density clinical care has driven the emergence of drug-resistant bacteria that are adapted to thrive in hospitalized patients. Of particular concern are globally disseminated methicillin-resistant Staphylococcus aureus (MRSA) clones that ...

  3. Global co-existence of two evolutionary lineages of parvovirus B19 1a, different in genome-wide synonymous positions.

    Directory of Open Access Journals (Sweden)

    Marijke W A Molenaar-de Backer

    Full Text Available Parvovirus B19 (B19V can cause infection in humans. To date, three genotypes of B19V, with subtypes, are known, of which genotype 1a is the most prevalent genotype in the Western world. We sequenced the genome of B19V strains of 65 asymptomatic, recently infected Dutch blood donors, to investigate the spatio-temporal distribution of B19V strains, in the years 2003-2009. The sequences were compared to B19V sequences from Dutch patients with fifth disease, and to global B19V sequences as available from GenBank. All Dutch B19V strains belonged to genotype 1a. Phylogenetic analysis of the strains from Dutch blood donors showed that two groups of genotype 1a co-exist. A clear-cut division into the two groups was also found among the B19V strains from Dutch patients, and among the B19V sequences in GenBank. The two groups of genotype 1a co-exist around the world and do not appear to differ in their ability to cause disease. Strikingly, the two groups of B19V predominantly differ in synonymous mutations, distributed throughout the entire genome of B19V. We propose to call the two groups of B19V genotype 1a respectively subtype 1a1 and 1a2.

  4. The genome-wide identification and transcriptional levels of DNA methyltransferases and demethylases in globe artichoke.

    Science.gov (United States)

    Gianoglio, Silvia; Moglia, Andrea; Acquadro, Alberto; Comino, Cinzia; Portis, Ezio

    2017-01-01

    Changes to the cytosine methylation status of DNA, driven by the activity of C5 methyltransferases (C5-MTases) and demethylases, exert an important influence over development, transposon movement, gene expression and imprinting. Three groups of C5-MTase enzymes have been identified in plants, namely MET (methyltransferase 1), CMT (chromomethyltransferases) and DRM (domains rearranged methyltransferases). Here the repertoire of genes encoding C5-MTase and demethylase by the globe artichoke (Cynara cardunculus var. scolymus) is described, based on sequence homology, a phylogenetic analysis and a characterization of their functional domains. A total of ten genes encoding C5-MTase (one MET, five CMTs and four DRMs) and five demethylases was identified. An analysis of their predicted product's protein structure suggested an extensive level of conservation has been retained by the C5-MTases. Transcriptional profiling based on quantitative real time PCR revealed a number of differences between the genes encoding maintenance and de novo methyltransferases, sometimes in a tissue- or development-dependent manner, which implied a degree of functional specialization.

  5. The genome-wide identification and transcriptional levels of DNA methyltransferases and demethylases in globe artichoke.

    Directory of Open Access Journals (Sweden)

    Silvia Gianoglio

    Full Text Available Changes to the cytosine methylation status of DNA, driven by the activity of C5 methyltransferases (C5-MTases and demethylases, exert an important influence over development, transposon movement, gene expression and imprinting. Three groups of C5-MTase enzymes have been identified in plants, namely MET (methyltransferase 1, CMT (chromomethyltransferases and DRM (domains rearranged methyltransferases. Here the repertoire of genes encoding C5-MTase and demethylase by the globe artichoke (Cynara cardunculus var. scolymus is described, based on sequence homology, a phylogenetic analysis and a characterization of their functional domains. A total of ten genes encoding C5-MTase (one MET, five CMTs and four DRMs and five demethylases was identified. An analysis of their predicted product's protein structure suggested an extensive level of conservation has been retained by the C5-MTases. Transcriptional profiling based on quantitative real time PCR revealed a number of differences between the genes encoding maintenance and de novo methyltransferases, sometimes in a tissue- or development-dependent manner, which implied a degree of functional specialization.

  6. A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues.

    Directory of Open Access Journals (Sweden)

    Athma A Pai

    2011-02-01

    Full Text Available The modification of DNA by methylation is an important epigenetic mechanism that affects the spatial and temporal regulation of gene expression. Methylation patterns have been described in many contexts within and across a range of species. However, the extent to which changes in methylation might underlie inter-species differences in gene regulation, in particular between humans and other primates, has not yet been studied. To this end, we studied DNA methylation patterns in livers, hearts, and kidneys from multiple humans and chimpanzees, using tissue samples for which genome-wide gene expression data were also available. Using the multi-species gene expression and methylation data for 7,723 genes, we were able to study the role of promoter DNA methylation in the evolution of gene regulation across tissues and species. We found that inter-tissue methylation patterns are often conserved between humans and chimpanzees. However, we also found a large number of gene expression differences between species that might be explained, at least in part, by corresponding differences in methylation levels. In particular, we estimate that, in the tissues we studied, inter-species differences in promoter methylation might underlie as much as 12%-18% of differences in gene expression levels between humans and chimpanzees.

  7. Comparative Genomics Revealed Genetic Diversity and Species/Strain-Level Differences in Carbohydrate Metabolism of Three Probiotic Bifidobacterial Species

    Directory of Open Access Journals (Sweden)

    Toshitaka Odamaki

    2015-01-01

    Full Text Available Strains of Bifidobacterium longum, Bifidobacterium breve, and Bifidobacterium animalis are widely used as probiotics in the food industry. Although numerous studies have revealed the properties and functionality of these strains, it is uncertain whether these characteristics are species common or strain specific. To address this issue, we performed a comparative genomic analysis of 49 strains belonging to these three bifidobacterial species to describe their genetic diversity and to evaluate species-level differences. There were 166 common clusters between strains of B. breve and B. longum, whereas there were nine common clusters between strains of B. animalis and B. longum and four common clusters between strains of B. animalis and B. breve. Further analysis focused on carbohydrate metabolism revealed the existence of certain strain-dependent genes, such as those encoding enzymes for host glycan utilisation or certain membrane transporters, and many genes commonly distributed at the species level, as was previously reported in studies with limited strains. As B. longum and B. breve are human-residential bifidobacteria (HRB, whereas B. animalis is a non-HRB species, several of the differences in these species’ gene distributions might be the result of their adaptations to the nutrient environment. This information may aid both in selecting probiotic candidates and in understanding their potential function as probiotics.

  8. Global Production Networks and International Inequality: Making a Case for a Meso-Level Turn in Macro-Comparative Sociology

    Directory of Open Access Journals (Sweden)

    Mathew Mahutga

    2015-08-01

    Full Text Available In this article, I extend recent macro-comparative empirical research on the developmental implications of global production networks. I draw from theories of commodity/value chains, global production networks and economic sociology to identify three contending theoretical perspectives for exactly how the developmental returns to network participants should be distributed-cooperation, exploitation and differential gains-and derive testable hypotheses for each. Adding to recent empirical advances for measuring the average network position of firms at the country level, I evaluate these hypotheses by way of dynamic panel regression models of hourly wage rates in the garment and transportation equipment industries. The results suggest that macro-sociological theories linking underdevelopment to the structure of the world-economy, as well as theories of the distribution of the gains from network participation, miss important variation at the industry level. Cooperation provides a poor account of the distribution of the gains from network participation. Instead, both industries appear to distribute the gains from network participation differentially across network participants. However, the extent of this inequality increases, and the garment industry transitions to exploitation, when global production networks become entrenched organizational logics. Variation in the distribution of the returns to network participation is explicable only by accounting for production-network governance as it varies across industries and over time. I conclude by highlighting the analytical utility to macro-comparative sociology of a turn toward the mesa-level of global industries.

  9. Climate technology transfer at the local, national and global levels: analyzing the relationships between multi-level structures

    NARCIS (Netherlands)

    Tessema Abissa, Fisseha; Tessema Abissa, Fisseha

    2014-01-01

    This thesis examines the relationships between multi-leveled decision structures for climate technology transfer through an analysis of top-down macro-policy and bottom-up micro-implementation. It examines how international climate technology transfer policy under the UNFCCC filters down to the

  10. Current and future levels of mercury atmospheric pollution on a global scale

    NARCIS (Netherlands)

    Pacyna, J. M.; Travnikov, O.; De Simone, F.; Hedgecock, I. M.; Sundseth, K.; Pacyna, E. G.; Steenhuisen, F.; Pirrone, N.; Munthe, J.; Kindbom, K.

    2016-01-01

    An assessment of current and future emissions, air concentrations, and atmospheric deposition of mercury worldwide is presented on the basis of results obtained during the performance of the EU GMOS (Global Mercury Observation System) project. Emission estimates for mercury were prepared with the

  11. Current and future levels of mercury atmospheric pollution on global scale

    NARCIS (Netherlands)

    Pacyna, Jozef M.; Travnikov, Oleg; De Simone, Francesco; Hedgecock, Ian M.; Sundseth, Kyrre; Pacyna, Elisabeth G.; Steenhuisen, Frits; Pirrone, Nicola; Munthe, John; Kindbom, Karin

    2016-01-01

    An assessment of current and future emissions, air concentrations and atmospheric deposition of mercury world-wide are presented on the basis of results obtained during the performance of the EU GMOS (Global Mercury Observation System) project. Emission estimates for mercury were prepared with the

  12. Limits to global groundwater consumption : Effects on groundwater levels and river low flows

    NARCIS (Netherlands)

    de Graaf, I.E.M.

    2016-01-01

    Freshwater is essential for human existence. With increasing global population and economic growth, freshwater demands almost tripled over the past decades and are expected to rise further. During dry periods, when water in rivers and lakes is scarce and cannot meet human water demands, people often

  13. Global gray water footprint and water pollution levels related to anthropogenic nitrogen loads to fresh water

    NARCIS (Netherlands)

    Mekonnen, Mesfin; Hoekstra, Arjen Ysbert

    2015-01-01

    This is the first global assessment of nitrogen-related water pollution in river basins with a specification of the pollution by economic sector, and by crop for the agricultural sector. At a spatial resolution of 5 by 5 arc minute, we estimate anthropogenic nitrogen (N) loads to freshwater,

  14. A New Global Coastal Database for Impact and Vulnerability Analysis to Sea-Level Rise

    NARCIS (Netherlands)

    Vafeidis, A.T.; Nicholls, R.J.; McFadden, L.; Tol, R.S.J.; Hinkel, J.; Spencer, T.; Grashoff, P.S.; Boot, G.; Klein, R.J.T.

    2008-01-01

    A new global coastal database has been developed within the context of the DINAS-COAST project. The database covers the world's coasts, excluding Antarctica, and includes information on more than 80 physical, ecological, and socioeconomic parameters of the coastal zone. The database provides the

  15. Extending Theorisations of the Global Teacher: Care Work, Gender, and Street-Level Policies

    Science.gov (United States)

    Robert, Sarah A.

    2016-01-01

    This article is concerned with teachers' negotiation of global transitions premised on improving educational opportunity with implications for professionalism. The study blends sociology of gender, work, and organisations and gender policy analysis to theorise teachers' policy negotiations. I explore how 20 Argentine teachers mediate 3 programmes'…

  16. Employer Expectations of Accounting Undergraduates' Entry-Level Knowledge and Skills in Global Financial Reporting

    Science.gov (United States)

    Jones, Christopher G.; Vedd, Rishma; Yoon, Sung Wook

    2008-01-01

    The globalization of business has led to the adoption of International Financial Reporting Standards (IFRS) around the world. Recently, the Securities and Exchange Commission issued a roadmap for IFRS implementation starting in 2014, with earlier adoption permitted. Yet according to recent surveys, few U.S. universities have a strategy in place to…

  17. The global burden of child burn injuries in light of country level economic development and income inequality.

    Science.gov (United States)

    Sengoelge, Mathilde; El-Khatib, Ziad; Laflamme, Lucie

    2017-06-01

    Child burn mortality differs widely between regions and is closely related to material deprivation, but reports on their global distribution are few. Investigating their country level distribution in light of economic level and income inequality will help assess the potential for macro-level improvements. We extracted data for child burn mortality from the Global Burden of Disease study 2013 and combined data into 1-14 years to calculate rates at country, region and income levels. We also compiled potential lives saved. Then we examined the relationship between country level gross domestic product per capita from the World Bank and income inequality (Gini Index) from the Standardized World Income Inequality Database and child burn mortality using Spearman coefficient correlations. Worldwide, the burden of child burn deaths is 2.5 per 100,000 across 103 countries with the largest burden in Sub-Saharan Africa (4.5 per 100,000). Thirty-four thousand lives could be saved yearly if all countries in the world had the same rates as the best performing group of high-income countries; the majority in low-income countries. There was a negative graded association between economic level and child burns for all countries aggregated and at regional level, but no consistent pattern existed for income inequality at regional level. The burden of child burn mortality varies by region and income level with prevention efforts needed most urgently in middle-income countries and Sub-Saharan Africa. Investment in safe living conditions and access to medical care are paramount to achieving further reductions in the global burden of preventable child burn deaths.

  18. The global burden of child burn injuries in light of country level economic development and income inequality

    Directory of Open Access Journals (Sweden)

    Mathilde Sengoelge

    2017-06-01

    Full Text Available Child burn mortality differs widely between regions and is closely related to material deprivation, but reports on their global distribution are few. Investigating their country level distribution in light of economic level and income inequality will help assess the potential for macro-level improvements. We extracted data for child burn mortality from the Global Burden of Disease study 2013 and combined data into 1–14 years to calculate rates at country, region and income levels. We also compiled potential lives saved. Then we examined the relationship between country level gross domestic product per capita from the World Bank and income inequality (Gini Index from the Standardized World Income Inequality Database and child burn mortality using Spearman coefficient correlations. Worldwide, the burden of child burn deaths is 2.5 per 100,000 across 103 countries with the largest burden in Sub-Saharan Africa (4.5 per 100,000. Thirty-four thousand lives could be saved yearly if all countries in the world had the same rates as the best performing group of high-income countries; the majority in low-income countries. There was a negative graded association between economic level and child burns for all countries aggregated and at regional level, but no consistent pattern existed for income inequality at regional level. The burden of child burn mortality varies by region and income level with prevention efforts needed most urgently in middle-income countries and Sub-Saharan Africa. Investment in safe living conditions and access to medical care are paramount to achieving further reductions in the global burden of preventable child burn deaths.

  19. Protected area connectivity: Shortfalls in global targets and country-level priorities.

    Science.gov (United States)

    Saura, Santiago; Bertzky, Bastian; Bastin, Lucy; Battistella, Luca; Mandrici, Andrea; Dubois, Grégoire

    2018-03-01

    Connectivity of protected areas (PAs) is crucial for meeting their conservation goals. We provide the first global evaluation of countries' progress towards Aichi Target 11 of the Convention on Biological Diversity that is to have at least 17% of the land covered by well-connected PA systems by 2020. We quantify how well the terrestrial PA systems of countries are designed to promote connectivity, using the Protected Connected (ProtConn) indicator. We refine ProtConn to focus on the part of PA connectivity that is in the power of a country to influence, i.e. not penalizing countries for PA isolation due to the sea and to foreign lands. We found that globally only 7.5% of the area of the countries is covered by protected connected lands, which is about half of the global PA coverage of 14.7%, and that only 30% of the countries currently meet the Aichi Target 11 connectivity element. These findings suggest the need for considerable efforts to improve PA connectivity globally. We further identify the main priorities for improving or sustaining PA connectivity in each country: general increase of PA coverage, targeted designation of PAs in strategic locations for connectivity, ensuring permeability of the unprotected landscapes between PAs, coordinated management of neighbouring PAs within the country, and/or transnational coordination with PAs in other countries. Our assessment provides a key contribution to evaluate progress towards global PA connectivity targets and to highlight important strengths and weaknesses of the design of PA systems for connectivity in the world's countries and regions.

  20. PROCESS OF GLOBAL SHOCKS TRANSMISSION TO DOMESTIC FOOD PRICE LEVEL: CASE OF BANGLADESH

    Directory of Open Access Journals (Sweden)

    Fakir Azmal Huda

    2014-04-01

    Full Text Available The world experienced in dramatic price surge of food commodities since mid of 2007 to 2008. It was claimed that the crisis were being mainly for backdrop of global shocks in food and energy price. But how the shocks come to domestic market from external sources is a researchable phenomenon. Surprisingly few attempts have been made to systematically analysis of shock transmission from international to domestic market. The study analyzed the effect of global commodity market factors and domestic exchange rate development on domestic food price in Bangladesh. A bi-variants co-integration approach was applied for the analysis of shock transmission. Finally an error correction model was developed. The overall magnitudes of the pass through suggest that only 46 per cent of the total world shock pass-through in domestic economy.

  1. A study on Sea Level Change for Coast of Korean Peninsular from Global Warming and Its Influences I

    Energy Technology Data Exchange (ETDEWEB)

    Cho, K.W.; Kim, J.H. [Korea Environment Institute, Seoul (Korea)

    2001-12-01

    The Third Assessment Report(2001) of the Intergovernmental Panel on Climate Change(IPCC) concluded that the global warming will be accelerated during the 21st century due to the human activities. The projected warming will increase the steric sea level rise which have large adverse effects on the natural and human systems in the coastal zone. This study intends to assess the sea level change and potential impacts of the future sea level rise on the coastal zone of the Korean Peninsula in which much socioeconomic activities have been already occurred. The contents of the present study include reviews on climate change and its impact, assessments of the current and future sea level change in the global scale and seas ne,ar Korea, and impact assessment methodology. The second year study(2002) will be focused on the impact assessment on the coastal zone of the Korea, especially on the inundation problem on human dimension due to the steric sea level rise, storm surge, and tide. Based on the tide gauge data, IPCC(2001) assessed the global average sea level rise during the 20th century is in the range of 10{approx}20cm, which is higher than that of 19th century. The contributing elements to the sea level rise are in the order of ocean thermal expansion, melting of glacier, mass balance change of the Greenland and Antarctic ice sheets, and surface and ground water storage and permafrost change. The satellite altimeter data during l990s shows higher trend than the mean trend of tide gauge data during 20th century. The recent high trend of the sea level rise by the altimetry is not clear whether it represents the recent acceleration of the global sea level the differences of the two observation methods, or short observation period of altimetry. In the 21st century, the global mean sea level is projected to increase much due to the acceleration of the warming. Based on the 35 IPCC emission scenarios, the sea level rise in the 21st century will be in the range of 9{approx}88

  2. Rosiglitazone Reduces Plasma Levels of Inflammatory and Hemostatic Biomarkers and Improves Global Endothelial Function in Habitual Heavy Smokers Without Diabetes Mellitus or Metabolic Syndrome

    Directory of Open Access Journals (Sweden)

    I-Chih Chen

    2010-02-01

    Conclusion: Rosiglitazone significantly reduces plasma levels of inflammatory and hemostatic biomarkers, and restores global endothelial dysfunction, independently from insulin sensitization, in healthy smokers.

  3. Unemployment levels after the global financial crisis linked to increase in suicides.

    Science.gov (United States)

    2013-10-23

    The 2008 global economic crisis appears to have triggered an increase in suicides, particularly among men in Europe and America. To investigate the impact of the economic crisis on international trends in suicide, researchers conducted an analysis comparing the number of suicides in 2009 with the number that would have been expected based on trends before the crisis (2000-2007). The analysis included data from 54 countries.

  4. INTERPERSONAL COMMUNICATION SKILLS,AT THE ORGANIZATIONAL LEVEL, RELEVANT IN THE CONTEXT OF GLOBALIZATION

    OpenAIRE

    Popescu Manoela; Crenicean Luminiţa Cecilia

    2013-01-01

    The approach of organizational issues as communication problems are at least one trend in era of the knowledge economy. The globalization process greatly contributes to consider the communication both as a source and as a solution to the problems faced by legal entities. The conducted study reveals, however, that interpersonal communication skills make the difference between success and failure of organizational communication. Premises of interpersonal communication skills analysis reveals co...

  5. Responsible Leadership in Global Business: A New Approach to Leadership and Its Multi-Level Outcomes

    OpenAIRE

    Voegtlin Christian; Patzer Moritz; Scherer Andreas Georg

    2012-01-01

    The article advances an understanding of responsible leadership in global business and offers an agenda for future research in this field. Our conceptualization of responsible leadership draws on deliberative practices and discursive conflict resolution combining the macro view of the business firm as a political actor with the micro view of leadership. We discuss the concept in relation to existing research in leadership. Further we propose a new model of responsible leadership that shows ho...

  6. Genome-wide siRNA Screening at Biosafety Level 4 Reveals a Crucial Role for Fibrillarin in Henipavirus Infection.

    Directory of Open Access Journals (Sweden)

    Celine Deffrasnes

    2016-03-01

    Full Text Available Hendra and Nipah viruses (genus Henipavirus, family Paramyxoviridae are highly pathogenic bat-borne viruses. The need for high biocontainment when studying henipaviruses has hindered the development of therapeutics and knowledge of the viral infection cycle. We have performed a genome-wide siRNA screen at biosafety level 4 that identified 585 human proteins required for henipavirus infection. The host protein with the largest impact was fibrillarin, a nucleolar methyltransferase that was also required by measles, mumps and respiratory syncytial viruses for infection. While not required for cell entry, henipavirus RNA and protein syntheses were greatly impaired in cells lacking fibrillarin, indicating a crucial role in the RNA replication phase of infection. During infection, the Hendra virus matrix protein co-localized with fibrillarin in cell nucleoli, and co-associated as a complex in pulldown studies, while its nuclear import was unaffected in fibrillarin-depleted cells. Mutagenesis studies showed that the methyltransferase activity of fibrillarin was required for henipavirus infection, suggesting that this enzyme could be targeted therapeutically to combat henipavirus infections.

  7. Global climate impacts of country-level primary carbonaceous aerosol from solid-fuel cookstove emissions

    International Nuclear Information System (INIS)

    Lacey, Forrest; Henze, Daven

    2015-01-01

    Cookstove use is globally one of the largest unregulated anthropogenic sources of primary carbonaceous aerosol. While reducing cookstove emissions through national-scale mitigation efforts has clear benefits for improving indoor and ambient air quality, and significant climate benefits from reduced green-house gas emissions, climate impacts associated with reductions to co-emitted black (BC) and organic carbonaceous aerosol are not well characterized. Here we attribute direct, indirect, semi-direct, and snow/ice albedo radiative forcing (RF) and associated global surface temperature changes to national-scale carbonaceous aerosol cookstove emissions. These results are made possible through the use of adjoint sensitivity modeling to relate direct RF and BC deposition to emissions. Semi- and indirect effects are included via global scaling factors, and bounds on these estimates are drawn from current literature ranges for aerosol RF along with a range of solid fuel emissions characterizations. Absolute regional temperature potentials are used to estimate global surface temperature changes. Bounds are placed on these estimates, drawing from current literature ranges for aerosol RF along with a range of solid fuel emissions characterizations. We estimate a range of 0.16 K warming to 0.28 K cooling with a central estimate of 0.06 K cooling from the removal of cookstove aerosol emissions. At the national emissions scale, countries’ impacts on global climate range from net warming (e.g., Mexico and Brazil) to net cooling, although the range of estimated impacts for all countries span zero given uncertainties in RF estimates and fuel characterization. We identify similarities and differences in the sets of countries with the highest emissions and largest cookstove temperature impacts (China, India, Nigeria, Pakistan, Bangladesh and Nepal), those with the largest temperature impact per carbon emitted (Kazakhstan, Estonia, and Mongolia), and those that would provide the

  8. Global climate impacts of country-level primary carbonaceous aerosol from solid-fuel cookstove emissions

    Science.gov (United States)

    Lacey, Forrest; Henze, Daven

    2015-11-01

    Cookstove use is globally one of the largest unregulated anthropogenic sources of primary carbonaceous aerosol. While reducing cookstove emissions through national-scale mitigation efforts has clear benefits for improving indoor and ambient air quality, and significant climate benefits from reduced green-house gas emissions, climate impacts associated with reductions to co-emitted black (BC) and organic carbonaceous aerosol are not well characterized. Here we attribute direct, indirect, semi-direct, and snow/ice albedo radiative forcing (RF) and associated global surface temperature changes to national-scale carbonaceous aerosol cookstove emissions. These results are made possible through the use of adjoint sensitivity modeling to relate direct RF and BC deposition to emissions. Semi- and indirect effects are included via global scaling factors, and bounds on these estimates are drawn from current literature ranges for aerosol RF along with a range of solid fuel emissions characterizations. Absolute regional temperature potentials are used to estimate global surface temperature changes. Bounds are placed on these estimates, drawing from current literature ranges for aerosol RF along with a range of solid fuel emissions characterizations. We estimate a range of 0.16 K warming to 0.28 K cooling with a central estimate of 0.06 K cooling from the removal of cookstove aerosol emissions. At the national emissions scale, countries’ impacts on global climate range from net warming (e.g., Mexico and Brazil) to net cooling, although the range of estimated impacts for all countries span zero given uncertainties in RF estimates and fuel characterization. We identify similarities and differences in the sets of countries with the highest emissions and largest cookstove temperature impacts (China, India, Nigeria, Pakistan, Bangladesh and Nepal), those with the largest temperature impact per carbon emitted (Kazakhstan, Estonia, and Mongolia), and those that would provide the

  9. Chromosome-level genome map provides insights into diverse defense mechanisms in the medicinal fungus Ganoderma sinense

    Science.gov (United States)

    Zhu, Yingjie; Xu, Jiang; Sun, Chao; Zhou, Shiguo; Xu, Haibin; Nelson, David R.; Qian, Jun; Song, Jingyuan; Luo, Hongmei; Xiang, Li; Li, Ying; Xu, Zhichao; Ji, Aijia; Wang, Lizhi; Lu, Shanfa; Hayward, Alice; Sun, Wei; Li, Xiwen; Schwartz, David C.; Wang, Yitao; Chen, Shilin

    2015-01-01

    Fungi have evolved powerful genomic and chemical defense systems to protect themselves against genetic destabilization and other organisms. However, the precise molecular basis involved in fungal defense remain largely unknown in Basidiomycetes. Here the complete genome sequence, as well as DNA methylation patterns and small RNA transcriptomes, was analyzed to provide a holistic overview of secondary metabolism and defense processes in the model medicinal fungus, Ganoderma sinense. We reported the 48.96 Mb genome sequence of G. sinense, consisting of 12 chromosomes and encoding 15,688 genes. More than thirty gene clusters involved in the biosynthesis of secondary metabolites, as well as a large array of genes responsible for their transport and regulation were highlighted. In addition, components of genome defense mechanisms, namely repeat-induced point mutation (RIP), DNA methylation and small RNA-mediated gene silencing, were revealed in G. sinense. Systematic bioinformatic investigation of the genome and methylome suggested that RIP and DNA methylation combinatorially maintain G. sinense genome stability by inactivating invasive genetic material and transposable elements. The elucidation of the G. sinense genome and epigenome provides an unparalleled opportunity to advance our understanding of secondary metabolism and fungal defense mechanisms. PMID:26046933

  10. Hybrid Analysis of Blue Water Consumption and Water Scarcity Implications at the Global, National, and Basin Levels in an Increasingly Globalized World.

    Science.gov (United States)

    Wang, Ranran; Zimmerman, Julie

    2016-05-17

    As the fifth global water footprint assessment, this study enhanced previous estimates of national blue water consumption (including fresh surface and groundwater) and main economic activities with (1) improved spatial and sectoral resolution and (2) quantified the impacts of virtual water trade on water use and water stress at both the national and basin level. In 2007, 1194 Gm(3) of blue water was consumed globally for human purposes. The consuming (producing) of primary and manufactured goods and services from the sectors of "Primary Crops and Livestock", "Primary Energy and Minerals", "Processed Food and Beverages", "Non-food Manufactured Products", "Electricity", "Commercial and Public Services", and "Households" accounted for 33% (91%), ∼ 0% (1%), 37% (water consumption, respectively. The considerable differences in sectoral water consumption accounted for by the two perspectives (consumption- vs production-based) highlight the significance of the water consumed indirectly, upstream in the supply chain (i.e., > 70% of total blue water consumption) while offering additional insights into the water implications of critical interconnected economic activities, such as the water-energy nexus. With 145 Gm(3) (12%) of the blue water consumption embedded in the goods and services traded internationally, 89 countries analyzed were net blue water importers at the national level. On the basin level, the impacts of virtual water trade on water stress were statistically significant for basins across the world and within 104 countries; virtual water trade mitigated water stress for the basins within 85 of the 104 countries, including all of those where there are moderate and greater water stress countrywide (except Italy).

  11. Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction.

    Directory of Open Access Journals (Sweden)

    Ellis Steven P

    2003-09-01

    Full Text Available Abstract Background Genomic studies of complex tissues pose unique analytical challenges for assessment of data quality, performance of statistical methods used for data extraction, and detection of differentially expressed genes. Ideally, to assess the accuracy of gene expression analysis methods, one needs a set of genes which are known to be differentially expressed in the samples and which can be used as a "gold standard". We introduce the idea of using sex-chromosome genes as an alternative to spiked-in control genes or simulations for assessment of microarray data and analysis methods. Results Expression of sex-chromosome genes were used as true internal biological controls to compare alternate probe-level data extraction algorithms (Microarray Suite 5.0 [MAS5.0], Model Based Expression Index [MBEI] and Robust Multi-array Average [RMA], to assess microarray data quality and to establish some statistical guidelines for analyzing large-scale gene expression. These approaches were implemented on a large new dataset of human brain samples. RMA-generated gene expression values were markedly less variable and more reliable than MAS5.0 and MBEI-derived values. A statistical technique controlling the false discovery rate was applied to adjust for multiple testing, as an alternative to the Bonferroni method, and showed no evidence of false negative results. Fourteen probesets, representing nine Y- and two X-chromosome linked genes, displayed significant sex differences in brain prefrontal cortex gene expression. Conclusion In this study, we have demonstrated the use of sex genes as true biological internal controls for genomic analysis of complex tissues, and suggested analytical guidelines for testing alternate oligonucleotide microarray data extraction protocols and for adjusting multiple statistical analysis of differentially expressed genes. Our results also provided evidence for sex differences in gene expression in the brain prefrontal cortex

  12. Global Expression Patterns of Three Festuca Species Exposed to Different Doses of Glyphosate Using the Affymetrix GeneChip Wheat Genome Array

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    Ozge Cebeci

    2009-01-01

    Full Text Available Glyphosate has been shown to act as an inhibitor of an aromatic amino acid biosynthetic pathway, while other pathways that may be affected by glyphosate are not known. Cross species hybridizations can provide a tool for elucidating biological pathways conserved among organisms. Comparative genome analyses have indicated a high level of colinearity among grass species and Festuca, on which we focus here, and showed rearrangements common to the Pooideae family. Based on sequence conservation among grass species, we selected the Affymetrix GeneChip Wheat Genome Array as a tool for the analysis of expression profiles of three Festuca (fescue species with distinctly different tolerances to varying levels of glyphosate. Differences in transcript expression were recorded upon foliar glyphosate application at 1.58 mM and 6.32 mM, representing 5% and 20%, respectively, of the recommended rate. Differences highlighted categories of general metabolic processes, such as photosynthesis, protein synthesis, stress responses, and a larger number of transcripts responded to 20% glyphosate application. Differential expression of genes encoding proteins involved in the shikimic acid pathway could not be identified by cross hybridization. Microarray data were confirmed by RT-PCR and qRT-PCR analyses. This is the first report to analyze the potential of cross species hybridization in Fescue species and the data and analyses will help extend our knowledge on the cellular processes affected by glyphosate.

  13. The Nature of Global Large-scale Sea Level Variability in Relation to Atmospheric Forcing: A Modeling Study

    Science.gov (United States)

    Fukumori, I.; Raghunath, R.; Fu, L. L.

    1996-01-01

    The relation between large-scale sea level variability and ocean circulation is studied using a numerical model. A global primitive equaiton model of the ocean is forced by daily winds and climatological heat fluxes corresponding to the period from January 1992 to February 1996. The physical nature of the temporal variability from periods of days to a year, are examined based on spectral analyses of model results and comparisons with satellite altimetry and tide gauge measurements.

  14. Global Ozone Distribution relevant to Human Health: Metrics and present day levels from the Tropospheric Ozone Assessment Report (TOAR)

    Science.gov (United States)

    Fleming, Z. L.; Doherty, R. M.; von Schneidemesser, E.; Cooper, O. R.; Malley, C.; Colette, A.; Xu, X.; Pinto, J. P.; Simpson, D.; Schultz, M. G.; Hamad, S.; Moola, R.; Solberg, S.; Feng, Z.

    2017-12-01

    Using stations from the TOAR surface ozone database, this study quantifies present-day global and regional distributions of five ozone metrics relevant for both short-term and long-term human exposure. These metrics were explored at ozone monitoring sites globally, and re-classified for this project as urban or non-urban using population densities and night-time lights. National surface ozone limit values are usually related to an annual number of exceedances of daily maximum 8-hour running mean (MDA8), with many countries not even having any ozone limit values. A discussion and comparison of exceedances in the different ozone metrics, their locations and the seasonality of exceedances provides clues as to the regions that potentially have more serious ozone health implications. Present day ozone levels (2010-2014) have been compared globally and show definite geographical differences (see Figure showing the annual 4th highest MDA8 for present day ozone for all non-urban stations). Higher ozone levels are seen in western compared to eastern US, and between southern and northern Europe, and generally higher levels in east Asia. The metrics reflective of peak concentrations show highest values in western North America, southern Europe and East Asia. A number of the metrics show similar distributions of North-South gradients, most prominent across Europe and Japan. The interquartile range of the regional ozone metrics was largest in East Asia, higher for urban stations in Asia but higher for non-urban stations in Europe and North America. With over 3000 monitoring stations included in this analysis and despite the higher densities of monitoring stations in Europe, north America and East Asia, this study provides the most comprehensive global picture to date of surface ozone levels in terms of health-relevant metrics.

  15. Revisiting global mean sea level budget closure : Preliminary results from an integrative study within ESA's Climate Change Initiative -Sea level Budget Closure-Climate Change Initiative

    Science.gov (United States)

    Palanisamy, H.; Cazenave, A. A.

    2017-12-01

    The global mean sea level budget is revisited over two time periods: the entire altimetry era, 1993-2015 and the Argo/GRACE era, 2003-2015 using the version '0' of sea level components estimated by the SLBC-CCI teams. The SLBC-CCI is an European Space Agency's project on sea level budget closure using CCI products. Over the entire altimetry era, the sea level budget was performed as the sum of steric and mass components that include contributions from total land water storage, glaciers, ice sheets (Greenland and Antarctica) and total water vapor content. Over the Argo/GRACE era, it was performed as the sum of steric and GRACE based ocean mass. Preliminary budget analysis performed over the altimetry era (1993-2015) results in a trend value of 2.83 mm/yr. On comparison with the observed altimetry-based global mean sea level trend over the same period (3.03 ± 0.5 mm/yr), we obtain a residual of 0.2 mm/yr. In spite of a residual of 0.2 mm/yr, the sea level budget result obtained over the altimetry era is very promising as this has been performed using the version '0' of the sea level components. Furthermore, uncertainties are not yet included in this study as uncertainty estimation for each sea level component is currently underway. Over the Argo/GRACE era (2003-2015), the trend estimated from the sum of steric and GRACE ocean mass amounts to 2.63 mm/yr while that observed by satellite altimetry is 3.37 mm/yr, thereby leaving a residual of 0.7 mm/yr. Here an ensemble GRACE ocean mass data (mean of various available GRACE ocean mass data) was used for the estimation. Using individual GRACE data results in a residual range of 0.5 mm/yr -1.1 mm/yr. Investigations are under way to determine the cause of the vast difference between the observed sea level and the sea level obtained from steric and GRACE ocean mass. One main suspect is the impact of GRACE data gaps on sea level budget analysis due to lack of GRACE data over several months since 2011. The current action plan

  16. Impacts of Global Warming and Sea Level Rise on Service Life of Chloride-Exposed Concrete Structures

    Directory of Open Access Journals (Sweden)

    Xiao-Jian Gao

    2017-03-01

    Full Text Available Global warming will increase the rate of chloride ingress and the rate of steel corrosion of concrete structures. Furthermore, in coastal (atmospheric marine zones, sea level rise will reduce the distance of concrete structures from the coast and increase the surface chloride content. This study proposes a probabilistic model for analyzing the effects of global warming and sea level rise on the service life of coastal concrete structures. First, in the corrosion initiation stage, an improved chloride diffusion model is proposed to determine chloride concentration. The Monte Carlo method is employed to calculate the service life in the corrosion initiation stage; Second, in the corrosion propagation stage, a numerical model is proposed to calculate the rate of corrosion, probability of corrosion cracking, and service life. Third, overall service life is determined as the sum of service life in the corrosion initiation and corrosion propagation stages. After considering the impacts of global warming and sea level rise, the analysis results show that for concrete structures having a service life of 50 years, the service life decreases by about 5%.

  17. A global analysis of erosion of sandy beaches and sea-level rise: An application of DIVA

    Science.gov (United States)

    Hinkel, Jochen; Nicholls, Robert J.; Tol, Richard S. J.; Wang, Zheng B.; Hamilton, Jacqueline M.; Boot, Gerben; Vafeidis, Athanasios T.; McFadden, Loraine; Ganopolski, Andrey; Klein, Richard J. T.

    2013-12-01

    This paper presents a first assessment of the global effects of climate-induced sea-level rise on the erosion of sandy beaches, and its consequent impacts in the form of land loss and forced migration of people. We consider direct erosion on open sandy coasts and indirect erosion near selected tidal inlets and estuaries, using six global mean sea-level scenarios (in the range of 0.2-0.8 m) and six SRES socio-economic development scenarios for the 21st century. Impacts are assessed both without and with adaptation in the form of shore and beach nourishment, based on cost-benefit analysis that includes the benefits of maintaining sandy beaches for tourism. Without nourishment, global land loss would amount to about 6000-17,000 km2 during the 21st century, leading to 1.6-5.3 million people being forced to migrate and migration costs of US 300-1000 billion (not discounted). Optimal beach and shore nourishment would cost about US 65-220 billion (not discounted) during the 21st century and would reduce land loss by 8-14%, forced migration by 56-68% and the cost of forced migration by 77-84% (not discounted). The global share of erodible coast that is nourished increases from about 4% in 2000 to 18-33% in 2100, with beach nourishment being 3-4 times more frequent than shore nourishment, reflecting the importance of tourism benefits. In absolute terms, with or without nourishment, large countries with long shorelines appear to have the largest costs, but in relative terms, small island states appear most impacted by erosion. Considerable uncertainty remains due to the limited availability of basic coastal geomorphological data and models on a global scale. Future work should also further explore the effects of beach tourism, including considering sub-national distributions of beach tourists.

  18. Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes

    OpenAIRE

    Strawbridge, Rona; Dupuis, Josée; Prokopenko, Inga; Barker, Adam; Ahlqvist, Emma; Rybin, Denis; Petrie, John; Bouatia-Naji, Nabila; Dimas, Antigone; Wheeler, Eleanor; Chen, Han; Voight, Benjamin; Taneera, Jalal; Kanoni, Stavroula; Peden, John

    2011-01-01

    textabstractOBJECTIVE - Proinsulin is a precursor of mature insulin and C-peptide. Higher circulating proinsulin levels are associated with impaired b-cell function, raised glucose levels, insulin resistance, and type 2 diabetes (T2D). Studies of the insulin processing pathway could provide new insights about T2D pathophysiology. RESEARCH DESIGN AND METHODS - We have conducted a meta-analysis of genome-wide association tests of ;2.5 million genotyped or imputed single nucleotide polymorphisms...

  19. THE THEORETICAL AND METHODICAL APPROACH TO AN ASSESSMENT OF A LEVEL OF DEVELOPMENT OF THE ENTERPRISE IN CONDITIONS OF GLOBALIZATION

    Directory of Open Access Journals (Sweden)

    Tatiana Shved

    2016-11-01

    Full Text Available The subject of this article is theoretical, methodical and practical aspects of enterprise development in conditions of globalization. The purpose of this research is to provide theoretical and methodical approach to an assessment of a level of development of the enterprise, which is based on the relationship between the factors and influence, illustrating the effect of the internal and external environment of enterprises functioning, and indicates the level of development of the enterprise. Methodology. Theoretical basis of the study was the examination and rethinking of the main achievements of world and domestic science on the development of enterprises. To achieve the objectives of the research following methods were used: systemic and structural analysis for the formation of methodical approaches to the selection of the factors, influencing the development of enterprises; abstract and logical – for the formulation of conclusions and proposals; the method of valuation and expert assessments to the implementation of the proposed theoretical and methodical approach to an assessment of a level of development of the enterprise in conditions of globalization. Results of the research is the proposed theoretical and methodical to an assessment of a level of development of the enterprise in conditions of globalization, which is associated with the idea of development of the enterprise as a system with inputs–factors, influencing on the development , and outputs – indicators of the level of enterprise development within these factors. So, the chosen factors – resources, financial-economic activity, innovation and investment activities, competition, government influence, and foreign trade. Indicators that express these factors, are capital productivity, labour productivity, material efficiency within the first factor; the profitability of the activity, the coefficient of current assets, the total liquidity coefficient, financial stability

  20. Metabolic and genomic analysis elucidates strain-level variation in Microbacterium spp. isolated from chromate contaminated sediment

    Data.gov (United States)

    U.S. Environmental Protection Agency — The data is in the form of genomic sequences deposited in a public database, growth curves, and bioinformatic analysis of sequences. This dataset is associated with...

  1. Cardiovascular Diseases on the Global Agenda: The United Nations High Level Meeting, Sustainable Development Goals, and the Way Forward.

    Science.gov (United States)

    Ralston, Johanna; Reddy, K Srinath; Fuster, Valentin; Narula, Jagat

    2016-12-01

    In 2011, the United Nations (UN) organized the first ever meeting for heads of state to discuss the problem of noncommunicable diseases (NCD), including cardiovascular disease (CVD), cancer, chronic respiratory disease, and diabetes mellitus. Recognizing that these had emerged as leading causes of morbidity and mortality in the world, including in many low- and middle-income countries, advocates from government and civil society had called for increased attention and a UN response. Earlier, NCD including CVD were absent from the global health agenda in part because of their omission from the Millennium Development Goals. The UN meeting and the global advocacy response offered a game-changing opportunity to redress this omission. The World Heart Federation (WHF) played an instrumental role in the UN meeting and follow up, including inclusion of CVD in the Sustainable Development Goals. The next phase of the global CVD movement is expected through national action, including CVD roadmaps and partnering with the World Health Organization. The WHF is heavily committed to these goals and the other nongovernmental organizations invested in the mission must help take this historical mandate forward. Instrumental to this will be the engagement of people affected by or at risk of developing CVD, to draw more attention and resources to NCD and to ensure that successes to date in global policy translate into action at the national level. Copyright © 2016 World Heart Federation (Geneva). Published by Elsevier B.V. All rights reserved.

  2. Global Climate targets and future consumption level: An evaluation of the required GHG intensity

    NARCIS (Netherlands)

    Girod, B.; van Vuuren, D.P.; Hertwich, E.G.

    2013-01-01

    Discussion and analysis on international climate policy often focuses on the rather abstract level of total national and regional greenhouse gas (GHG) emissions. At some point, however, emission reductions need to be translated to consumption level. In this article, we evaluate the implications of

  3. Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle.

    Science.gov (United States)

    Shock, Jennifer L; Fischer, Kael F; DeRisi, Joseph L

    2007-01-01

    The rate of mRNA decay is an essential element of post-transcriptional regulation in all organisms. Previously, studies in several organisms found that the specific half-life of each mRNA is precisely related to its physiologic role, and plays an important role in determining levels of gene expression. We used a genome-wide approach to characterize mRNA decay in Plasmodium falciparum. We found that, globally, rates of mRNA decay increase dramatically during the asexual intra-erythrocytic developmental cycle. During the ring stage of the cycle, the average mRNA half-life was 9.5 min, but this was extended to an average of 65 min during the late schizont stage of development. Thus, a major determinant of mRNA decay rate appears to be linked to the stage of intra-erythrocytic development. Furthermore, we found specific variations in decay patterns superimposed upon the dominant trend of progressive half-life lengthening. These variations in decay pattern were frequently enriched for genes with specific cellular functions or processes. Elucidation of Plasmodium mRNA decay rates provides a key element for deciphering mechanisms of genetic control in this parasite, by complementing and extending previous mRNA abundance studies. Our results indicate that progressive stage-dependent decreases in mRNA decay rate function are a major determinant of mRNA accumulation during the schizont stage of intra-erythrocytic development. This type of genome-wide change in mRNA decay rate has not been observed in any other organism to date, and indicates that post-transcriptional regulation may be the dominant mechanism of gene regulation in P. falciparum.

  4. Physiological differences and changes in global DNA methylation levels in Agave angustifolia Haw. albino variant somaclones during the micropropagation process.

    Science.gov (United States)

    Duarte-Aké, Fátima; Castillo-Castro, Eduardo; Pool, Felipe Barredo; Espadas, Francisco; Santamaría, Jorge M; Robert, Manuel L; De-la-Peña, Clelia

    2016-12-01

    Global DNA methylation changes caused by in vitro conditions are associated with the subculturing and phenotypic variation in Agave angustifolia Haw. While the relationship between the development of albinism and in vitro culture is well documented, the role of epigenetic processes in this development leaves some important questions unanswered. During the micropropagation of Agave angustifolia Haw., we found three different phenotypes, green (G), variegated (V) and albino (A). To understand the physiological and epigenetic differences among the somaclones, we analyzed several morphophysiological parameters and changes in the DNA methylation patterns in the three phenotypes during their in vitro development. We found that under in vitro conditions, the V plantlets maintained their CAM photosynthetic capacity, while the A variant showed no pigments and lost its CAM photosynthetic ability. Epigenetic analysis revealed that global DNA methylation increased in the G phenotype during the first two subcultures. However, after that time, DNA methylation levels declined. This hypomethylation correlated with the appearance of V shoots in the G plantlets. A similar correlation occurred in the V phenotype, where an increase of 2 % in the global DNA methylation levels was correlated with the generation of A shoots in the V plantlets. This suggests that an "epigenetic stress memory" during in vitro conditions causes a chromatin shift that favors the generation of variegated and albino shoots.

  5. Has the magnitude of floods across the USA changed with global CO2 levels?

    Science.gov (United States)

    Hirsch, Robert M.; Ryberg, Karen R.

    2012-01-01

    Statistical relationships between annual floods at 200 long-term (85–127 years of record) streamgauges in the coterminous United States and the global mean carbon dioxide concentration (GMCO2) record are explored. The streamgauge locations are limited to those with little or no regulation or urban development. The coterminous US is divided into four large regions and stationary bootstrapping is used to evaluate if the patterns of these statistical associations are significantly different from what would be expected under the null hypothesis that flood magnitudes are independent of GMCO2. In none of the four regions defined in this study is there strong statistical evidence for flood magnitudes increasing with increasing GMCO2. One region, the southwest, showed a statistically significant negative relationship between GMCO2 and flood magnitudes. The statistical methods applied compensate both for the inter-site correlation of flood magnitudes and the shorter-term (up to a few decades) serial correlation of floods.

  6. Renewable energy from wind and sun. Status quo and development perspectives at the global level

    International Nuclear Information System (INIS)

    Graichen, Patrick; Grotewold, Lars; Kordowski, Klaus; Wesemann, Philipp

    2015-01-01

    The global market for renewable energy technologies has experienced strong growth since the year 2000. In 2013 newly installed electricity production plants based on renewable energy for the first time outnumbered the aggregate of newly installed plants based on coal, gas or nuclear energy. In more and more parts of the world, wind and solar energy plants are becoming the most cost-effective means of electricity production. As renewable energy resources begin to claim significant shares in the energy mix they also become more system-relevant, resulting in a need for more investment as well as regulatory changes. Due to their specific features (high capital intensity, low incremental costs, fluctuating electricity production), and in spite of the marked decline in costs, wind and solar energy are still dependent on proactive policies in support of renewable energy.

  7. Impact of management strategies on the global warming potential at the cropping system level

    International Nuclear Information System (INIS)

    Goglio, Pietro; Grant, Brian B.; Smith, Ward N.; Desjardins, Raymond L.; Worth, Devon E.; Zentner, Robert; Malhi, Sukhdev S.

    2014-01-01

    Estimating the greenhouse gas (GHG) emissions from agricultural systems is important in order to assess the impact of agriculture on climate change. In this study experimental data supplemented with results from a biophysical model (DNDC) were combined with life cycle assessment (LCA) to investigate the impact of management strategies on global warming potential of long-term cropping systems at two locations (Breton and Ellerslie) in Alberta, Canada. The aim was to estimate the difference in global warming potential (GWP) of cropping systems due to N fertilizer reduction and residue removal. Reducing the nitrogen fertilizer rate from 75 to 50 kg N ha −1 decreased on average the emissions of N 2 O by 39%, NO by 59% and ammonia volatilisation by 57%. No clear trend for soil CO 2 emissions was determined among cropping systems. When evaluated on a per hectare basis, cropping systems with residue removal required 6% more energy and had a little change in GWP. Conversely, when evaluated on the basis of gigajoules of harvestable biomass, residue removal resulted in 28% less energy requirement and 33% lower GWP. Reducing nitrogen fertilizer rate resulted in 18% less GWP on average for both functional units at Breton and 39% less GWP at Ellerslie. Nitrous oxide emissions contributed on average 67% to the overall GWP per ha. This study demonstrated that small changes in N fertilizer have a minimal impact on the productivity of the cropping systems but can still have a substantial environmental impact. - Highlights: • LCA was combined with DNDC model to estimate the GWP of a cropping system. • N 2 O, NO and NH 3 flux increased by 39% under the higher fertilizer rate. • A change from 75 to 50 kg N ha −1 reduced the GWP per ha and GJ basis by 18%. • N 2 O emissions contributed 67% to the overall GWP of the cropping system. • Small changes in N fertilizer can have a substantial environmental impact

  8. Impact of management strategies on the global warming potential at the cropping system level.

    Science.gov (United States)

    Goglio, Pietro; Grant, Brian B; Smith, Ward N; Desjardins, Raymond L; Worth, Devon E; Zentner, Robert; Malhi, Sukhdev S

    2014-08-15

    Estimating the greenhouse gas (GHG) emissions from agricultural systems is important in order to assess the impact of agriculture on climate change. In this study experimental data supplemented with results from a biophysical model (DNDC) were combined with life cycle assessment (LCA) to investigate the impact of management strategies on global warming potential of long-term cropping systems at two locations (Breton and Ellerslie) in Alberta, Canada. The aim was to estimate the difference in global warming potential (GWP) of cropping systems due to N fertilizer reduction and residue removal. Reducing the nitrogen fertilizer rate from 75 to 50 kg N ha(-1) decreased on average the emissions of N2O by 39%, NO by 59% and ammonia volatilisation by 57%. No clear trend for soil CO2 emissions was determined among cropping systems. When evaluated on a per hectare basis, cropping systems with residue removal required 6% more energy and had a little change in GWP. Conversely, when evaluated on the basis of gigajoules of harvestable biomass, residue removal resulted in 28% less energy requirement and 33% lower GWP. Reducing nitrogen fertilizer rate resulted in 18% less GWP on average for both functional units at Breton and 39% less GWP at Ellerslie. Nitrous oxide emissions contributed on average 67% to the overall GWP per ha. This study demonstrated that small changes in N fertilizer have a minimal impact on the productivity of the cropping systems but can still have a substantial environmental impact. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

  9. Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression

    Directory of Open Access Journals (Sweden)

    Vining Kelly J

    2012-01-01

    Full Text Available Abstract Background DNA cytosine methylation is an epigenetic modification that has been implicated in many biological processes. However, large-scale epigenomic studies have been applied to very few plant species, and variability in methylation among specialized tissues and its relationship to gene expression is poorly understood. Results We surveyed DNA methylation from seven distinct tissue types (vegetative bud, male inflorescence [catkin], female catkin, leaf, root, xylem, phloem in the reference tree species black cottonwood (Populus trichocarpa. Using 5-methyl-cytosine DNA immunoprecipitation followed by Illumina sequencing (MeDIP-seq, we mapped a total of 129,360,151 36- or 32-mer reads to the P. trichocarpa reference genome. We validated MeDIP-seq results by bisulfite sequencing, and compared methylation and gene expression using published microarray data. Qualitative DNA methylation differences among tissues were obvious on a chromosome scale. Methylated genes had lower expression than unmethylated genes, but genes with methylation in transcribed regions ("gene body methylation" had even lower expression than genes with promoter methylation. Promoter methylation was more frequent than gene body methylation in all tissues except male catkins. Male catkins differed in demethylation of particular transposable element categories, in level of gene body methylation, and in expression range of genes with methylated transcribed regions. Tissue-specific gene expression patterns were correlated with both gene body and promoter methylation. Conclusions We found striking differences among tissues in methylation, which were apparent at the chromosomal scale and when genes and transposable elements were examined. In contrast to other studies in plants, gene body methylation had a more repressive effect on transcription than promoter methylation.

  10. GHRSST Level 4 DMI_OI Global Foundation Sea Surface Temperature Analysis (GDS version 2)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A Group for High Resolution Sea Surface Temperature (GHRSST) Level 4 sea surface temperature analysis produced daily on an operational basis by the Danish...

  11. GHRSST Level 4 OSPO Global Nighttime Foundation Sea Surface Temperature Analysis (GDS version 2)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A Group for High Resolution Sea Surface Temperature (GHRSST) Level 4 sea surface temperature analysis produced daily on an operational basis at the Office of...

  12. GHRSST Level 4 G1SST Global Foundation Sea Surface Temperature Analysis (GDS version 1)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A Group for High Resolution Sea Surface Temperature (GHRSST) Level 4 sea surface temperature analysis produced daily on an operational basis by the JPL OurOcean...

  13. GHRSST Level 4 K10_SST Global 1 meter Sea Surface Temperature Analysis (GDS version 1)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A Group for High Resolution Sea Surface Temperature (GHRSST) Level 4 sea surface temperature analysis produced daily on an operational basis at the Naval...

  14. GHRSST Level 4 ODYSSEA Global Foundation Sea Surface Temperature Analysis (GDS version 1)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A Group for High Resolution Sea Surface Temperature (GHRSST) Level 4 sea surface temperature analysis produced daily on an operational basis at Ifremer/CERSAT...

  15. GHRSST Level 4 OSPO Global Foundation Sea Surface Temperature Analysis (GDS version 2)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A Group for High Resolution Sea Surface Temperature (GHRSST) Level 4 sea surface temperature analysis produced daily on an operational basis at the Office of...

  16. GHRSST Level 4 GAMSSA Global Foundation Sea Surface Temperature Analysis (GDS version 1)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A Group for High Resolution Sea Surface Temperature (GHRSST) Level 4 sea surface temperature analysis produced daily on an operational basis at the Australian Bureau...

  17. GHRSST Level 4 OSTIA Global Foundation Sea Surface Temperature Analysis (GDS versions 1 and 2)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A Group for High Resolution Sea Surface Temperature (GHRSST) Level 4 sea surface temperature analysis produced daily on an operational basis at the UK Met Office...

  18. GHRSST Level 4 UKMO Global OSTIA SST (GDS2):1

    Data.gov (United States)

    National Aeronautics and Space Administration — A GHRSST Level 4 sea surface temperature analysis produced daily on an operational basis at the UK Met Office using optimal interpolation from AVHRR, AATSR, SEVIRI,...

  19. The Unity of Application of International Law at the Global Level and the Responsibility of Judges

    OpenAIRE

    DUPUY, Pierre-Marie

    2007-01-01

    This article analyses the relationship between Courts and tribunals in the interpretation and application of international law. The goal here is of crucial importance: that of guaranteeing the unity of international law and avoid fragmentation. This relationship is considered at two levels. The first level is vertical: how do national courts perceive and react to international law? In an ideal approach, based on a federalist model, there would be an organic hierarchy insuring that nation...

  20. Coastal Adaptation Planning for Sea Level Rise and Extremes: A Global Model for Adaptation Decision-making at the Local Level Given Uncertain Climate Projections

    Science.gov (United States)

    Turner, D.

    2014-12-01

    Understanding the potential economic and physical impacts of climate change on coastal resources involves evaluating a number of distinct adaptive responses. This paper presents a tool for such analysis, a spatially-disaggregated optimization model for adaptation to sea level rise (SLR) and storm surge, the Coastal Impact and Adaptation Model (CIAM). This decision-making framework fills a gap between very detailed studies of specific locations and overly aggregate global analyses. While CIAM is global in scope, the optimal adaptation strategy is determined at the local level, evaluating over 12,000 coastal segments as described in the DIVA database (Vafeidis et al. 2006). The decision to pursue a given adaptation measure depends on local socioeconomic factors like income, population, and land values and how they develop over time, relative to the magnitude of potential coastal impacts, based on geophysical attributes like inundation zones and storm surge. For example, the model's decision to protect or retreat considers the costs of constructing and maintaining coastal defenses versus those of relocating people and capital to minimize damages from land inundation and coastal storms. Uncertain storm surge events are modeled with a generalized extreme value distribution calibrated to data on local surge extremes. Adaptation is optimized for the near-term outlook, in an "act then learn then act" framework that is repeated over the model time horizon. This framework allows the adaptation strategy to be flexibly updated, reflecting the process of iterative risk management. CIAM provides new estimates of the economic costs of SLR; moreover, these detailed results can be compactly represented in a set of adaptation and damage functions for use in integrated assessment models. Alongside the optimal result, CIAM evaluates suboptimal cases and finds that global costs could increase by an order of magnitude, illustrating the importance of adaptive capacity and coastal policy.

  1. Impact of management strategies on the global warming potential at the cropping system level

    Energy Technology Data Exchange (ETDEWEB)

    Goglio, Pietro; Grant, Brian B.; Smith, Ward N. [Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, K.W. Neatby Building, Ottawa, Ontario K1A 0C6 (Canada); Desjardins, Raymond L., E-mail: ray.desjardins@agr.gc.ca [Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, K.W. Neatby Building, Ottawa, Ontario K1A 0C6 (Canada); Worth, Devon E. [Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, K.W. Neatby Building, Ottawa, Ontario K1A 0C6 (Canada); Zentner, Robert [Swift Current Research Station, Swift Current, Saskatchewan S0E 1A0 (Canada); Malhi, Sukhdev S. [Melfort Research Farm, PO Box 1240, Melfort, Saskatchewan S0E 1A0 (Canada)

    2014-08-15

    Estimating the greenhouse gas (GHG) emissions from agricultural systems is important in order to assess the impact of agriculture on climate change. In this study experimental data supplemented with results from a biophysical model (DNDC) were combined with life cycle assessment (LCA) to investigate the impact of management strategies on global warming potential of long-term cropping systems at two locations (Breton and Ellerslie) in Alberta, Canada. The aim was to estimate the difference in global warming potential (GWP) of cropping systems due to N fertilizer reduction and residue removal. Reducing the nitrogen fertilizer rate from 75 to 50 kg N ha{sup −1} decreased on average the emissions of N{sub 2}O by 39%, NO by 59% and ammonia volatilisation by 57%. No clear trend for soil CO{sub 2} emissions was determined among cropping systems. When evaluated on a per hectare basis, cropping systems with residue removal required 6% more energy and had a little change in GWP. Conversely, when evaluated on the basis of gigajoules of harvestable biomass, residue removal resulted in 28% less energy requirement and 33% lower GWP. Reducing nitrogen fertilizer rate resulted in 18% less GWP on average for both functional units at Breton and 39% less GWP at Ellerslie. Nitrous oxide emissions contributed on average 67% to the overall GWP per ha. This study demonstrated that small changes in N fertilizer have a minimal impact on the productivity of the cropping systems but can still have a substantial environmental impact. - Highlights: • LCA was combined with DNDC model to estimate the GWP of a cropping system. • N{sub 2}O, NO and NH{sub 3} flux increased by 39% under the higher fertilizer rate. • A change from 75 to 50 kg N ha{sup −1} reduced the GWP per ha and GJ basis by 18%. • N{sub 2}O emissions contributed 67% to the overall GWP of the cropping system. • Small changes in N fertilizer can have a substantial environmental impact.

  2. Variation in genome-wide levels of meiotic recombination is established at the onset of prophase in mammalian males.

    Directory of Open Access Journals (Sweden)

    Brian Baier

    2014-01-01

    Full Text Available Segregation of chromosomes during the first meiotic division relies on crossovers established during prophase. Although crossovers are strictly regulated so that at least one occurs per chromosome, individual variation in crossover levels is not uncommon. In an analysis of different inbred strains of male mice, we identified among-strain variation in the number of foci for the crossover-associated protein MLH1. We report studies of strains with "low" (CAST/EiJ, "medium" (C3H/HeJ, and "high" (C57BL/6J genome-wide MLH1 values to define factors responsible for this variation. We utilized immunofluorescence to analyze the number and distribution of proteins that function at different stages in the recombination pathway: RAD51 and DMC1, strand invasion proteins acting shortly after double-strand break (DSB formation, MSH4, part of the complex stabilizing double Holliday junctions, and the Bloom helicase BLM, thought to have anti-crossover activity. For each protein, we identified strain-specific differences that mirrored the results for MLH1; i.e., CAST/EiJ mice had the lowest values, C3H/HeJ mice intermediate values, and C57BL/6J mice the highest values. This indicates that differences in the numbers of DSBs (as identified by RAD51 and DMC1 are translated into differences in the number of crossovers, suggesting that variation in crossover levels is established by the time of DSB formation. However, DSBs per se are unlikely to be the primary determinant, since allelic variation for the DSB-inducing locus Spo11 resulted in differences in the numbers of DSBs but not the number of MLH1 foci. Instead, chromatin conformation appears to be a more important contributor, since analysis of synaptonemal complex length and DNA loop size also identified consistent strain-specific differences; i.e., crossover frequency increased with synaptonemal complex length and was inversely related to chromatin loop size. This indicates a relationship between recombination

  3. Use of Whole-Genus Genome Sequence Data To Develop a Multilocus Sequence Typing Tool That Accurately Identifies Yersinia Isolates to the Species and Subspecies Levels

    Science.gov (United States)

    Hall, Miquette; Chattaway, Marie A.; Reuter, Sandra; Savin, Cyril; Strauch, Eckhard; Carniel, Elisabeth; Connor, Thomas; Van Damme, Inge; Rajakaruna, Lakshani; Rajendram, Dunstan; Jenkins, Claire; Thomson, Nicholas R.

    2014-01-01

    The genus Yersinia is a large and diverse bacterial genus consisting of human-pathogenic species, a fish-pathogenic species, and a large number of environmental species. Recently, the phylogenetic and population structure of the entire genus was elucidated through the genome sequence data of 241 strains encompassing every known species in the genus. Here we report the mining of this enormous data set to create a multilocus sequence typing-based scheme that can identify Yersinia strains to the species level to a level of resolution equal to that for whole-genome sequencing. Our assay is designed to be able to accurately subtype the important human-pathogenic species Yersinia enterocolitica to whole-genome resolution levels. We also report the validation of the scheme on 386 strains from reference laboratory collections across Europe. We propose that the scheme is an important molecular typing system to allow accurate and reproducible identification of Yersinia isolates to the species level, a process often inconsistent in nonspecialist laboratories. Additionally, our assay is the most phylogenetically informative typing scheme available for Y. enterocolitica. PMID:25339391

  4. A TWO LEVEL ARCHITECTURE USING CONSENSUS METHOD FOR GLOBAL DECISION MAKING AGAINST DDoS ATTACKS

    Directory of Open Access Journals (Sweden)

    S.Seetha

    2010-06-01

    Full Text Available Distributed Denial of service is a major threat to the availability of internet services. Due to the distributed, large scale nature of the Internet makes DDoS (Distributed Denial-of-Service attacks stealthy and difficult to counter. Defense against Distributed Denial- of -Service attacks is one of the hardest security problems on the Internet. Recently these network attacks have been increasing. Therefore more effective countermeasures are required to counter the threat. This requirement has motivated us to propose a novel mechanism against DDoS attack. This paper presents the design details of a distributed defense mechanism against DDoS attack. In our approach, the egress routers of the intermediate network coordinate with each other to provide the information necessary to detect and respond to the attack. Thus, a detection system based on single site will have either high positive or high negative rates. Unlike the traditional IDSs (Intrusion Detection System this method has the potential to achieve high true positive ratio. This work has been done by using consensus algorithms for exchanging the information between the detection systems. So the overall detection time would be reduced for global decision making.

  5. Global, regional, and national levels of neonatal, infant, and under-5 mortality during 1990-2013

    DEFF Research Database (Denmark)

    Wang, Haidong; Liddell, Chelsea A; Coates, Matthew M

    2014-01-01

    BACKGROUND: Remarkable financial and political efforts have been focused on the reduction of child mortality during the past few decades. Timely measurements of levels and trends in under-5 mortality are important to assess progress towards the Millennium Development Goal 4 (MDG 4) target of redu...

  6. Governing the energy challenge : Canada and Germany in a multi-level regional and global context

    International Nuclear Information System (INIS)

    Eberlein, B.; Doern, G.B.; Exeter Univ.,

    2009-01-01

    This book features essays by leading energy and public policy specialists from Canada and Germany. It originated in the Transatlantic Energy Conference which was hosted by the Canadian Centre for German and European Studies at Toronto's York University in September 2005. The conference was attended by leading energy scholars and experts from Canadian and European universities, research institutes and governmental and non-governmental organizations. The purpose of this book was to compare the dynamics of multi-level energy regulatory governance in Germany and Canada, notably the energy policy challenges that include energy security, environmental sustainability and a competitive resource economy. Many strategies to produce more efficient and sustainable energy are presented in the book. Part 1 of the book focuses on the energy industry, with particular emphasise on electricity, nuclear energy and natural gas. Part 2 of the book focuses on domestic patterns of multi-level energy governance and regulation in the two countries. As a member of the European Union, Germany is more advanced in dealing with multi-level governmental and sustainability constraints than Canada is as a member of the North American Free Trade Agreement (NAFTA). The book focuses on the influence that the energy sector and multi-level institutional arrangements have on energy governance, with particular attention to the link between environmental study, climate change issues and economic market reforms. The growing differences between NAFTA and European Union member countries were highlighted. refs., tabs., figs.

  7. Global, regional, and national levels and causes of maternal mortality during 1990-2013

    DEFF Research Database (Denmark)

    Kassebaum, Nicholas J; Bertozzi-Villa, Amelia; Coggeshall, Megan S

    2014-01-01

    BACKGROUND: The fifth Millennium Development Goal (MDG 5) established the goal of a 75% reduction in the maternal mortality ratio (MMR; number of maternal deaths per 100,000 livebirths) between 1990 and 2015. We aimed to measure levels and track trends in maternal mortality, the key causes contri...

  8. Comment on 'The Global Impacts of Extreme Sea-Level Rise: A Comprehensive Economic Assessment'

    NARCIS (Netherlands)

    Tol, R.S.J.; Nicholls, R.J.; Brown, S.; Hinkel, J.; Vafeidis, A.T.; Spencer, T.

    2016-01-01

    Pycroft et al. (Environ Resour Econ 1–29, 2015) used incorrect and outdated data to study the economic impact of sea level rise. They misinterpret some of their input data, and fail to exploit the strengths of their computable general equilibrium model and previously developed methods to study

  9. Analysis of RF thrusters with TOPICA and a global system-level model

    NARCIS (Netherlands)

    Lancellotti, V.; Vecchi, G.; Maggiora, R.; Pavarin, D.; Rocca, S.; Bramanti, C.

    2007-01-01

    Recent advances in plasma-based propulsion systems have led to the development of electromagnetic (RF) generation and acceleration systems, capable of providing highly controllable and wide-ranging exhaust velocities, and potentially enabling a wide range of missions from KWs to MWs levels. In this

  10. Probabilistic 21st and 22nd Century Sea-Level Projections at a Global Network of Tide-Gauge Sites

    Science.gov (United States)

    Kopp, Robert E.; Horton, Radley M.; Little, Christopher M.; Mitrovica, Jerry X.; Oppenheimer, Michael; Rasmussen, D. J.; Strauss, Benjamin H.; Tebaldi, Claudia

    2014-01-01

    Sea-level rise due to both climate change and non-climatic factors threatens coastal settlements, infrastructure, and ecosystems. Projections of mean global sea-level (GSL) rise provide insufficient information to plan adaptive responses; local decisions require local projections that accommodate different risk tolerances and time frames and that can be linked to storm surge projections. Here we present a global set of local sea-level (LSL) projections to inform decisions on timescales ranging from the coming decades through the 22nd century. We provide complete probability distributions, informed by a combination of expert community assessment, expert elicitation, and process modeling. Between the years 2000 and 2100, we project a very likely (90% probability) GSL rise of 0.5–1.2?m under representative concentration pathway (RCP) 8.5, 0.4–0.9?m under RCP 4.5, and 0.3–0.8?m under RCP 2.6. Site-to-site differences in LSL projections are due to varying non-climatic background uplift or subsidence, oceanographic effects, and spatially variable responses of the geoid and the lithosphere to shrinking land ice. The Antarctic ice sheet (AIS) constitutes a growing share of variance in GSL and LSL projections. In the global average and at many locations, it is the dominant source of variance in late 21st century projections, though at some sites oceanographic processes contribute the largest share throughout the century. LSL rise dramatically reshapes flood risk, greatly increasing the expected number of “1-in-10” and “1-in-100” year events.

  11. Global Strategy

    DEFF Research Database (Denmark)

    Li, Peter Ping

    2013-01-01

    Global strategy differs from domestic strategy in terms of content and process as well as context and structure. The content of global strategy can contain five key elements, while the process of global strategy can have six major stages. These are expounded below. Global strategy is influenced...... by rich and complementary local contexts with diverse resource pools and game rules at the national level to form a broad ecosystem at the global level. Further, global strategy dictates the interaction or balance between different entry strategies at the levels of internal and external networks....

  12. Measuring macro-level effects of the global economic recession on university-industry research cooperation

    Energy Technology Data Exchange (ETDEWEB)

    Azagra-Caro, J.M.; Tijssen, R.J.W.; Yegros-Yegros, A.

    2016-07-01

    The 2007/2008 financial crisis, and ensuing economic recession, had a direct negative effect on university-industry research cooperation in the OECD countries and other economies – it diminished the number of university-industry co-authored research publications (UICs) during the period 2008-13 by 7%. It also changed the relationship between national business expenditure on R&D and UIC output levels. Before the recession the relationship was negative, but became positive during the years 2008-2013. The few countries where business expenditure on R&D increased during recession saw UIC numbers rise. This moderating effect of the recession applies only to ‘domestic UICs’, where universities cooperated with business companies located in the same country. Micro-level research is needed to assess the contributing effects on large university-industry R&D consortia on both domestic and international collaboration patterns. (Author)

  13. Noiseonomics: The relationship between ambient noise levels in the sea and global economic trends

    OpenAIRE

    Frisk, George V.

    2012-01-01

    In recent years, the topic of noise in the sea and its effects on marine mammals has attracted considerable attention from both the scientific community and the general public. Since marine mammals rely heavily on acoustics as a primary means of communicating, navigating, and foraging in the ocean, any change in their acoustic environment may have an impact on their behavior. Specifically, a growing body of literature suggests that low-frequency, ambient noise levels in the open ocean increas...

  14. Optimal carbon emissions trajectories when damages depend on the rate or level of global warming

    International Nuclear Information System (INIS)

    Peck, S.C.; Teisberg, T.J.

    1994-01-01

    The authors extend earlier work with the Carbon Emissions Trajectory Assessment model (CETA) to consider a number of issues relating to the nature of optimal carbon emissions trajectories. They first explore model results when warming costs are associated with the rate of temperature rise, rather than with its level, as in earlier work. It is found that optimal trajectories are more strongly affected by the degree of non-linearity in the warming cost function than by whether the cost function is driven by the warming level or the warming rate. The authors briefly explore the implications of simple uncertainty and risk aversion for optimal emissions trajectories to be somewhat lower, but that the effect is not noticeable in the near term and not dramatic in the long term; the long term effect on the shadow price of carbon is more marked, however. Finally, they experiment with scaling up the warming cost functions until optimal policies are approximately the same as a policy of stabilising emissions at the 1990 level. Based on the results of this experiment, it is concluded that damages would have to be very high to justify anything like a stabilization policy; and even in this case, a policy allowing intertemporal variation in emissions would be better. 18 refs., 15 figs

  15. Assessing the state-level consequences of global warming: Socio-economic and energy demand impacts

    International Nuclear Information System (INIS)

    Rubin, B.M. Gailmard, S.; Marsh, D.; Septoff, A.

    1996-01-01

    The large body of research on climate change has begun to recognize a significant deficiency: the lack of analysis of the impact of climate change at a spatial level consistent with the anticipated occurrence of climate change. Climate change is likely to vary by region, while impact analysis has focused on much larger political units. Clearly, adaptation/mitigation strategies must be developed at a level consistent with political and policy-making processes. This paper specifically addresses this deficiency by identifying the potential socio-economic and energy demand consequences of climate change for subnational regions. This is accomplished via the development and application of a regional simultaneous equation, econometric simulation model that focuses on five states (Illinois, Indiana, Michigan, Ohio, and Wisconsin) in the Great Lakes region of the US. This paper presents a process for obtaining state-specific assessments of the consequences of climate change for the socio-economic system. As such, it provides an indication of which economic sectors are most sensitive to climate change for a specific state (Indiana), a set of initial mitigation/adaptation strategies for this state, and the results of testing these strategies in the policy analysis framework enabled by the model. In addition, the research demonstrates an effective methodology for assessing impacts and policy implications of climate change at a level consistent with policy making authority

  16. Measuring the global information society - explaining digital inequality by economic level and education standard

    Science.gov (United States)

    Ünver, H.

    2017-02-01

    A main focus of this research paper is to investigate on the explanation of the ‘digital inequality’ or ‘digital divide’ by economic level and education standard of about 150 countries worldwide. Inequality regarding GDP per capita, literacy and the so-called UN Education Index seem to be important factors affecting ICT usage, in particular Internet penetration, mobile phone usage and also mobile Internet services. Empirical methods and (multivariate) regression analysis with linear and non-linear functions are useful methods to measure some crucial factors of a country or culture towards becoming information and knowledge based society. Overall, the study concludes that the convergence regarding ICT usage proceeds worldwide faster than the convergence in terms of economic wealth and education in general. The results based on a large data analysis show that the digital divide is declining over more than a decade between 2000 and 2013, since more people worldwide use mobile phones and the Internet. But a high digital inequality explained to a significant extent by the functional relation between technology penetration rates, education level and average income still exists. Furthermore it supports the actions of countries at UN/G20/OECD level for providing ICT access to all people for a more balanced world in context of sustainable development by postulating that policymakers need to promote comprehensive education worldwide by means of using ICT.

  17. Global change and relative sea level rise at Venice: what impact in term of flooding

    Energy Technology Data Exchange (ETDEWEB)

    Carbognin, Laura; Tosi, Luigi [Institute of Marine Sciences, National Research Council, Venice (Italy); Teatini, Pietro [Institute of Marine Sciences, National Research Council, Venice (Italy); University of Padova, Department of Mathematical Methods and Models for Scientific Applications, Padua (Italy); Tomasin, Alberto [Institute of Marine Sciences, National Research Council, Venice (Italy); University Ca' Foscari in Venice, Venice (Italy)

    2010-11-15

    Relative sea level rise (RSLR) due to climate change and geodynamics represents the main threat for the survival of Venice, emerging today only 90 cm above the Northern Adriatic mean sea level (msl). The 25 cm RSLR occurred over the 20th century, consisting of about 12 cm of land subsidence and 13 cm of sea level rise, has increased the flood frequency by more than seven times with severe damages to the urban heritage. Reasonable forecasts of the RSLR expected to the century end must be investigated to assess the suitability of the Mo.S.E. project planned for the city safeguarding, i.e., the closure of the lagoon inlets by mobile barriers. Here we consider three RSLR scenarios as resulting from the past sea level rise recorded in the Northern Adriatic Sea, the IPCC mid-range A1B scenario, and the expected land subsidence. Available sea level measurements show that more than 5 decades are required to compute a meaningful eustatic trend, due to pseudo-cyclic 7-8 year long fluctuations. The period from 1890 to 2007 is characterized by an average rate of 0.12 {+-} 0.01 cm/year. We demonstrate that linear regression is the most suitable model to represent the eustatic process over these 117 year. Concerning subsidence, at present Venice is sinking due to natural causes at 0.05 cm/year. The RSLR is expected to range between 17 and 53 cm by 2100, and its repercussions in terms of flooding frequency are associated here to each scenario. In particular, the frequency of tides higher than 110 cm, i.e., the value above which the gates would close the lagoon to the sea, will increase from the nowadays 4 times per year to a range between 20 and 250. These projections provide a large spread of possible conditions concerning the survival of Venice, from a moderate nuisance to an intolerable aggression. Hence, complementary solutions to Mo.S.E. may well be investigated. (orig.)

  18. Final deglaciation of the Scandinavian Ice Sheet and implications for the Holocene global sea-level budget

    Science.gov (United States)

    Cuzzone, Joshua K.; Clark, Peter U.; Carlson, Anders E.; Ullman, David J.; Rinterknecht, Vincent R.; Milne, Glenn A.; Lunkka, Juha-Pekka; Wohlfarth, Barbara; Marcott, Shaun A.; Caffee, Marc

    2016-08-01

    The last deglaciation of the Scandinavian Ice Sheet (SIS) from ∼ 21, 000 to 13,000 yr ago is well-constrained by several hundred 10Be and 14C ages. The subsequent retreat history, however, is established primarily from minimum-limiting 14C ages and incomplete Baltic-Sea varve records, leaving a substantial fraction of final SIS retreat history poorly constrained. Here we develop a high-resolution chronology for the final deglaciation of the SIS based on 79 10Be cosmogenic exposure dates sampled along three transects spanning southern to northern Sweden and Finland. Combining this new chronology with existing 10Be ages on deglaciation since the Last Glacial Maximum shows that rates of SIS margin retreat were strongly influenced by deglacial millennial-scale climate variability and its effect on surface mass balance, with regional modulation of retreat associated with dynamical controls. Ice-volume estimates constrained by our new chronology suggest that the SIS contributed ∼ 8 m sea-level equivalent to global sea-level rise between ∼14.5 ka and 10 ka. Final deglaciation was largely complete by ∼10.5 ka, with highest rates of sea-level rise occurring during the Bølling-Allerød, a 50% decrease during the Younger Dryas, and a rapid increase during the early Holocene. Combining our SIS volume estimates with estimated contributions from other remaining Northern Hemisphere ice sheets suggests that the Antarctic Ice Sheet (AIS) contributed 14.4 ± 5.9 m to global sea-level rise since ∼13 ka. This new constraint supports those studies that indicate that an ice volume of 15 m or more of equivalent sea-level rise was lost from the AIS during the last deglaciation.

  19. Chapter 6. Scaling Up Solutions to State, National and Global Levels

    Directory of Open Access Journals (Sweden)

    Daniel Kammen

    2016-12-01

    create new industries, new jobs, and further UC and California’s leadership position. Significant economic opportunities exist, such as promoting aggressive electric vehicle programs elsewhere in the world, where California-based companies could play a key role on many fronts, via electric vehicles themselves, but also through building-integrated smart meters, inverters, solar and other clean energy generation technologies. All work must include a focus on environmental justice both at home in California and through global partnerships.

  20. Ocean basin volume constraints on global sea level since the Jurassic

    Science.gov (United States)

    Seton, M.; Müller, R. D.

    2011-12-01

    Changes in the volume of the ocean basins, predominately via changes in the age-area distribution of oceanic lithosphere, have been suggested as the main driver for long-term eustatic sea-level change. As ocean lithosphere cools and thickens, ocean depth increases. The balance between the abundance of hot and buoyant crust along mid ocean ridges relative to abyssal plains is the primary driving force of long-term sea level changes. The emplacement of volcanic plateaus and chains as well as sedimentation contribute to raising eustatic sea level. Quantifying the average ocean basin depth through time primarily relies on the present day preserved seafloor spreading record, an analysis of the spatio-temporal record of plate boundary processes recorded on the continental margins adjacent to ocean basins as well as a consideration of the rules of plate tectonics, to reconstruct the history of seafloor spreading in the oceanic basins through time. This approach has been successfully applied to predict the magnitude and pattern of eustatic sea-level change since the Cretaceous (Müller et. al. 2008) but uncertainties in reconstructing mid ocean ridges and flanks increase back through time, given that we mainly depend on information preserved in preserved ocean crust. We have reconstructed the age-area distribution of oceanic lithosphere and the plate boundary configurations back to the Jurassic (200 Ma) in order to assess long-term sea-level change from amalgamation to dispersal of Pangaea. We follow the methodology presented in Müller et. al. (2008) but incorporate a new absolute plate motion model derived from Steinberger and Torsvik (2008) prior to 100 Ma, a merged Wessel et. al. (2006) and Wessel and Kroenke (2008) fixed Pacific hotspot reference frame, and a revised model for the formation of Panthalassa and the Cretaceous Pacific. Importantly, we incorporate a model for the break-up of the Ontong Java-Manihiki-Hikurangi plateaus between 120-86 Ma. We extend a

  1. Changes in the Global Hydrological Cycle: Lessons from Modeling Lake Levels at the Last Glacial Maximum

    Science.gov (United States)

    Lowry, D. P.; Morrill, C.

    2011-12-01

    Geologic evidence shows that lake levels in currently arid regions were higher and lakes in currently wet regions were lower during the Last Glacial Maximum (LGM). Current hypotheses used to explain these lake level changes include the thermodynamic hypothesis, in which decreased tropospheric water vapor coupled with patterns of convergence and divergence caused dry areas to become more wet and vice versa, the dynamic hypothesis, in which shifts in the jet stream and Inter-Tropical Convergence Zone (ITCZ) altered precipitation patterns, and the evaporation hypothesis, in which lake expansions are attributed to reduced evaporation in a colder climate. This modeling study uses the output of four climate models participating in phase 2 of the Paleoclimate Modeling Intercomparison Project (PMIP2) as input into a lake energy-balance model, in order to test the accuracy of the models and understand the causes of lake level changes. We model five lakes which include the Great Basin lakes, USA; Lake Petén Itzá, Guatemala; Lake Caçó, northern Brazil; Lake Tauca (Titicaca), Bolivia and Peru; and Lake Cari-Laufquen, Argentina. These lakes create a transect through the drylands of North America through the tropics and to the drylands of South America. The models accurately recreate LGM conditions in 14 out of 20 simulations, with the Great Basin lakes being the most robust and Lake Caçó being the least robust, due to model biases in portraying the ITCZ over South America. An analysis of the atmospheric moisture budget from one of the climate models shows that thermodynamic processes contribute most significantly to precipitation changes over the Great Basin, while dynamic processes are most significant for the other lakes. Lake Cari-Laufquen shows a lake expansion that is most likely attributed to reduced evaporation rather than changes in regional precipitation, suggesting that lake levels alone may not be the best indicator of how much precipitation this region

  2. A Global Overview of Exposure Levels and Biological Effects of Trace Elements in Penguins.

    Science.gov (United States)

    Espejo, Winfred; Celis, José E; GonzÃlez-Acuña, Daniel; Banegas, Andiranel; Barra, Ricardo; Chiang, Gustavo

    2018-01-01

    Trace elements are chemical contaminants that can be present almost anywhere on the planet. The study of trace elements in biotic matrices is a topic of great relevance for the implications that it can have on wildlife and human health. Penguins are very useful, since they live exclusively in the Southern Hemisphere and represent about 90% of the biomass of birds of the Southern Ocean. The levels of trace elements (dry weight) in different biotic matrices of penguins were reviewed here. Maps of trace element records in penguins were included. Data on exposure and effects of trace elements in penguins were collected from the literature. The most reported trace elements in penguins are aluminum, arsenic, cadmium, lead, mercury, copper, zinc, and manganese. Trace elements have been measured in 11 of the 18 species of penguins. The most studied biotic matrices are feathers and excreta. Most of the studies have been performed in Antarctica and subantarctic Islands. Little is known about the interaction among metals, which could provide better knowledge about certain mechanisms of detoxification in penguins. Future studies of trace elements in penguins must incorporate other metals such as vanadium, cobalt, nickel, and chromium. Data of metals in the species such as Eudyptes pachyrhynchus, Eudyptes moseleyi, Eudyptes sclateri, Eudyptes robustus, Eudyptes schlegeli, Spheniscus demersus, Spheniscus mendiculus, and Megadyptes antipodes are urged. It is important to correlate levels of metals in different biotic matrices with the effects on different species and in different geographic locations.

  3. Drowning of the Mississippi Delta due to insufficient sediment supply and global sea-level rise

    Science.gov (United States)

    Blum, Michael D.; Roberts, Harry H.

    2009-07-01

    Over the past few centuries, 25% of the deltaic wetlands associated with the Mississippi Delta have been lost to the ocean. Plans to protect and restore the coast call for diversions of the Mississippi River, and its associated sediment, to sustain and build new land. However, the sediment load of the Mississippi River has been reduced by 50% through dam construction in the Mississippi Basin, which could affect the effectiveness of diversion plans. Here we calculate the amount of sediment stored on the delta plain for the past 12,000 years, and find that mean storage rates necessary to construct the flood plain and delta over this period exceed modern Mississippi River sediment loads. We estimate that, in the absence of sediment input, an additional 10,000-13,500km2 will be submerged by the year 2100 owing to subsidence and sea-level rise. Sustaining existing delta surface area would require 18-24billiontons of sediment, which is significantly more than can be drawn from the Mississippi River in its current state. We conclude that significant drowning is inevitable, even if sediment loads are restored, because sea level is now rising at least three times faster than during delta-plain construction.

  4. Global sea-level rise is recognised, but flooding from anthropogenic land subsidence is ignored around northern Manila Bay, Philippines.

    Science.gov (United States)

    Rodolfo, Kelvin S; Siringan, Fernando P

    2006-03-01

    Land subsidence resulting from excessive extraction of groundwater is particularly acute in East Asian countries. Some Philippine government sectors have begun to recognise that the sea-level rise of one to three millimetres per year due to global warming is a cause of worsening floods around Manila Bay, but are oblivious to, or ignore, the principal reason: excessive groundwater extraction is lowering the land surface by several centimetres to more than a decimetre per year. Such ignorance allows the government to treat flooding as a lesser problem that can be mitigated through large infrastructural projects that are both ineffective and vulnerable to corruption. Money would be better spent on preventing the subsidence by reducing groundwater pumping and moderating population growth and land use, but these approaches are politically and psychologically unacceptable. Even if groundwater use is greatly reduced and enlightened land-use practices are initiated, natural deltaic subsidence and global sea-level rise will continue to aggravate flooding, although at substantially lower rates.

  5. Genome-wide association study for levels of total serum IgE identifies HLA-C in a Japanese population.

    Directory of Open Access Journals (Sweden)

    Yohei Yatagai

    Full Text Available Most of the previously reported loci for total immunoglobulin E (IgE levels are related to Th2 cell-dependent pathways. We undertook a genome-wide association study (GWAS to identify genetic loci responsible for IgE regulation. A total of 479,940 single nucleotide polymorphisms (SNPs were tested for association with total serum IgE levels in 1180 Japanese adults. Fine-mapping with SNP imputation demonstrated 6 candidate regions: the PYHIN1/IFI16, MHC classes I and II, LEMD2, GRAMD1B, and chr13∶60576338 regions. Replication of these candidate loci in each region was assessed in 2 independent Japanese cohorts (n = 1110 and 1364, respectively. SNP rs3130941 in the HLA-C region was consistently associated with total IgE levels in 3 independent populations, and the meta-analysis yielded genome-wide significance (P = 1.07×10(-10. Using our GWAS results, we also assessed the reproducibility of previously reported gene associations with total IgE levels. Nine of 32 candidate genes identified by a literature search were associated with total IgE levels after correction for multiple testing. Our findings demonstrate that SNPs in the HLA-C region are strongly associated with total serum IgE levels in the Japanese population and that some of the previously reported genetic associations are replicated across ethnic groups.

  6. Global, regional, and national levels and causes of maternal mortality during 1990–2013: a systematic analysis for the Global Burden of Disease Study 2013

    Science.gov (United States)

    Kassebaum, Nicholas J; Bertozzi-Villa, Amelia; Coggeshall, Megan S; Shackelford, Katya A; Steiner, Caitlyn; Heuton, Kyle R; Gonzalez-Medina, Diego; Barber, Ryan; Huynh, Chantal; Dicker, Daniel; Templin, Tara; Wolock, Timothy M; Ozgoren, Ayse Abbasoglu; Abd-Allah, Foad; Abera, Semaw Ferede; Abubakar, Ibrahim; Achoki, Tom; Adelekan, Ademola; Ademi, Zanfina; Adou, Arsène Kouablan; Adsuar, José C; Agardh, Emilie E; Akena, Dickens; Alasfoor, Deena; Alemu, Zewdie Aderaw; Alfonso-Cristancho, Rafael; Alhabib, Samia; Ali, Raghib; Al Kahbouri, Mazin J; Alla, François; Allen, Peter J; AlMazroa, Mohammad A; Alsharif, Ubai; Alvarez, Elena; Alvis-Guzmán, Nelson; Amankwaa, Adansi A; Amare, Azmeraw T; Amini, Hassan; Ammar, Walid; Antonio, Carl A T; Anwari, Palwasha; Ärnlöv, Johan; Arsenijevic, Valentina S Arsic; Artaman, Ali; Asad, Majed Masoud; Asghar, Rana J; Assadi, Reza; Atkins, Lydia S; Badawi, Alaa; Balakrishnan, Kalpana; Basu, Arindam; Basu, Sanjay; Beardsley, Justin; Bedi, Neeraj; Bekele, Tolesa; Bell, Michelle L; Bernabe, Eduardo; Beyene, Tariku J; Bhutta, Zulfiqar; Abdulhak, Aref Bin; Blore, Jed D; Basara, Berrak Bora; Bose, Dipan; Breitborde, Nicholas; Cárdenas, Rosario; Castañeda-Orjuela, Carlos A; Castro, Ruben Estanislao; Catalá-López, Ferrán; Cavlin, Alanur; Chang, Jung-Chen; Che, Xuan; Christophi, Costas A; Chugh, Sumeet S; Cirillo, Massimo; Colquhoun, Samantha M; Cooper, Leslie Trumbull; Cooper, Cyrus; da Costa Leite, Iuri; Dandona, Lalit; Dandona, Rakhi; Davis, Adrian; Dayama, Anand; Degenhardt, Louisa; De Leo, Diego; del Pozo-Cruz, Borja; Deribe, Kebede; Dessalegn, Muluken; deVeber, Gabrielle A; Dharmaratne, Samath D; Dilmen, Uğur; Ding, Eric L; Dorrington, Rob E; Driscoll, Tim R; Ermakov, Sergei Petrovich; Esteghamati, Alireza; Faraon, Emerito Jose A; Farzadfar, Farshad; Felicio, Manuela Mendonca; Fereshtehnejad, Seyed-Mohammad; de Lima, Graça Maria Ferreira; Forouzanfar, Mohammad H; França, Elisabeth B; Gaffikin, Lynne; Gambashidze, Ketevan; Gankpé, Fortuné Gbètoho; Garcia, Ana C; Geleijnse, Johanna M; Gibney, Katherine B; Giroud, Maurice; Glaser, Elizabeth L; Goginashvili, Ketevan; Gona, Philimon; González-Castell, Dinorah; Goto, Atsushi; Gouda, Hebe N; Gugnani, Harish Chander; Gupta, Rahul; Gupta, Rajeev; Hafezi-Nejad, Nima; Hamadeh, Randah Ribhi; Hammami, Mouhanad; Hankey, Graeme J; Harb, Hilda L; Havmoeller, Rasmus; Hay, Simon I; Heredia Pi, Ileana B; Hoek, Hans W; Hosgood, H Dean; Hoy, Damian G; Husseini, Abdullatif; Idrisov, Bulat T; Innos, Kaire; Inoue, Manami; Jacobsen, Kathryn H; Jahangir, Eiman; Jee, Sun Ha; Jensen, Paul N; Jha, Vivekanand; Jiang, Guohong; Jonas, Jost B; Juel, Knud; Kabagambe, Edmond Kato; Kan, Haidong; Karam, Nadim E; Karch, André; Karema, Corine Kakizi; Kaul, Anil; Kawakami, Norito; Kazanjan, Konstantin; Kazi, Dhruv S; Kemp, Andrew H; Kengne, Andre Pascal; Kereselidze, Maia; Khader, Yousef Saleh; Khalifa, Shams Eldin Ali Hassan; Khan, Ejaz Ahmed; Khang, Young-Ho; Knibbs, Luke; Kokubo, Yoshihiro; Kosen, Soewarta; Defo, Barthelemy Kuate; Kulkarni, Chanda; Kulkarni, Veena S; Kumar, G Anil; Kumar, Kaushalendra; Kumar, Ravi B; Kwan, Gene; Lai, Taavi; Lalloo, Ratilal; Lam, Hilton; Lansingh, Van C; Larsson, Anders; Lee, Jong-Tae; Leigh, James; Leinsalu, Mall; Leung, Ricky; Li, Xiaohong; Li, Yichong; Li, Yongmei; Liang, Juan; Liang, Xiaofeng; Lim, Stephen S; Lin, Hsien-Ho; Lipshultz, Steven E; Liu, Shiwei; Liu, Yang; Lloyd, Belinda K; London, Stephanie J; Lotufo, Paulo A; Ma, Jixiang; Ma, Stefan; Machado, Vasco Manuel Pedro; Mainoo, Nana Kwaku; Majdan, Marek; Mapoma, Christopher Chabila; Marcenes, Wagner; Marzan, Melvin Barrientos; Mason-Jones, Amanda J; Mehndiratta, Man Mohan; Mejia-Rodriguez, Fabiola; Memish, Ziad A; Mendoza, Walter; Miller, Ted R; Mills, Edward J; Mokdad, Ali H; Mola, Glen Liddell; Monasta, Lorenzo; de la Cruz Monis, Jonathan; Hernandez, Julio Cesar Montañez; Moore, Ami R; Moradi-Lakeh, Maziar; Mori, Rintaro; Mueller, Ulrich O; Mukaigawara, Mitsuru; Naheed, Aliya; Naidoo, Kovin S; Nand, Devina; Nangia, Vinay; Nash, Denis; Nejjari, Chakib; Nelson, Robert G; Neupane, Sudan Prasad; Newton, Charles R; Ng, Marie; Nieuwenhuijsen, Mark J; Nisar, Muhammad Imran; Nolte, Sandra; Norheim, Ole F; Nyakarahuka, Luke; Oh, In-Hwan; Ohkubo, Takayoshi; Olusanya, Bolajoko O; Omer, Saad B; Opio, John Nelson; Orisakwe, Orish Ebere; Pandian, Jeyaraj D; Papachristou, Christina; Park, Jae-Hyun; Caicedo, Angel J Paternina; Patten, Scott B; Paul, Vinod K; Pavlin, Boris Igor; Pearce, Neil; Pereira, David M; Pesudovs, Konrad; Petzold, Max; Poenaru, Dan; Polanczyk, Guilherme V; Polinder, Suzanne; Pope, Dan; Pourmalek, Farshad; Qato, Dima; Quistberg, D Alex; Rafay, Anwar; Rahimi, Kazem; Rahimi-Movaghar, Vafa; Rahman, Sajjad ur; Raju, Murugesan; Rana, Saleem M; Refaat, Amany; Ronfani, Luca; Roy, Nobhojit; Sánchez Pimienta, Tania Georgina; Sahraian, Mohammad Ali; Salomon, Joshua A; Sampson, Uchechukwu; Santos, Itamar S; Sawhney, Monika; Sayinzoga, Felix; Schneider, Ione J C; Schumacher, Austin; Schwebel, David C; Seedat, Soraya; Sepanlou, Sadaf G; Servan-Mori, Edson E; Shakh-Nazarova, Marina; Sheikhbahaei, Sara; Shibuya, Kenji; Shin, Hwashin Hyun; Shiue, Ivy; Sigfusdottir, Inga Dora; Silberberg, Donald H; Silva, Andrea P; Singh, Jasvinder A; Skirbekk, Vegard; Sliwa, Karen; Soshnikov, Sergey S; Sposato, Luciano A; Sreeramareddy, Chandrashekhar T; Stroumpoulis, Konstantinos; Sturua, Lela; Sykes, Bryan L; Tabb, Karen M; Talongwa, Roberto Tchio; Tan, Feng; Teixeira, Carolina Maria; Tenkorang, Eric Yeboah; Terkawi, Abdullah Sulieman; Thorne-Lyman, Andrew L; Tirschwell, David L; Towbin, Jeffrey A; Tran, Bach X; Tsilimbaris, Miltiadis; Uchendu, Uche S; Ukwaja, Kingsley N; Undurraga, Eduardo A; Uzun, Selen Begüm; Vallely, Andrew J; van Gool, Coen H; Vasankari, Tommi J; Vavilala, Monica S; Venketasubramanian, N; Villalpando, Salvador; Violante, Francesco S; Vlassov, Vasiliy Victorovich; Vos, Theo; Waller, Stephen; Wang, Haidong; Wang, Linhong; Wang, XiaoRong; Wang, Yanping; Weichenthal, Scott; Weiderpass, Elisabete; Weintraub, Robert G; Westerman, Ronny; Wilkinson, James D; Woldeyohannes, Solomon Meseret; Wong, John Q; Wordofa, Muluemebet Abera; Xu, Gelin; Yang, Yang C; Yano, Yuichiro; Yentur, Gokalp Kadri; Yip, Paul; Yonemoto, Naohiro; Yoon, Seok-Jun; Younis, Mustafa Z; Yu, Chuanhua; Jin, Kim Yun; El SayedZaki, Maysaa; Zhao, Yong; Zheng, Yingfeng; Zhou, Maigeng; Zhu, Jun; Zou, Xiao Nong; Lopez, Alan D; Naghavi, Mohsen; Murray, Christopher J L; Lozano, Rafael

    2014-01-01

    Summary Background The fifth Millennium Development Goal (MDG 5) established the goal of a 75% reduction in the maternal mortality ratio (MMR; number of maternal deaths per 100 000 livebirths) between 1990 and 2015. We aimed to measure levels and track trends in maternal mortality, the key causes contributing to maternal death, and timing of maternal death with respect to delivery. Methods We used robust statistical methods including the Cause of Death Ensemble model (CODEm) to analyse a database of data for 7065 site-years and estimate the number of maternal deaths from all causes in 188 countries between 1990 and 2013. We estimated the number of pregnancy-related deaths caused by HIV on the basis of a systematic review of the relative risk of dying during pregnancy for HIV-positive women compared with HIV-negative women. We also estimated the fraction of these deaths aggravated by pregnancy on the basis of a systematic review. To estimate the numbers of maternal deaths due to nine different causes, we identified 61 sources from a systematic review and 943 site-years of vital registration data. We also did a systematic review of reports about the timing of maternal death, identifying 142 sources to use in our analysis. We developed estimates for each country for 1990–2013 using Bayesian meta-regression. We estimated 95% uncertainty intervals (UIs) for all values. Findings 292 982 (95% UI 261 017–327 792) maternal deaths occurred in 2013, compared with 376 034 (343 483–407 574) in 1990. The global annual rate of change in the MMR was −0·3% (−1·1 to 0·6) from 1990 to 2003, and −2·7% (−3·9 to −1·5) from 2003 to 2013, with evidence of continued acceleration. MMRs reduced consistently in south, east, and southeast Asia between 1990 and 2013, but maternal deaths increased in much of sub-Saharan Africa during the 1990s. 2070 (1290–2866) maternal deaths were related to HIV in 2013, 0·4% (0·2–0·6) of the global total. MMR was highest in the

  7. Electric power generated by fossil fuels: Impact and environmental administration at global and local level

    International Nuclear Information System (INIS)

    Moscarella, John Paul

    1999-01-01

    An analysis is presented on the derived environmental implications of the current and future structure in the electric power market at international level. The reduced prices of the hydrocarbons determine that the fossil electricity is imposed on other generation forms, that which generates serious challenges to the companies and the governments as regards control and handling of gases emissions. By means of a comparative sample of eight electric companies of developed countries and in development, the tendencies are evaluated in the local and regional markets, as well as the environmental effects of different generating systems of electricity. The mechanism of well-known market is analyzed as activities implemented jointly (AIJ) referred to activities to be implemented jointly to combat the greenhouse gases effect. It concludes that in the short and medium term the conditions of the market will continue favoring the generation of fossil energy, reason why they should strengthen mechanisms of the climatic change control and to impel toward the long term the development of renewable and alternative energy

  8. Global genome response of Escherichia coli O157∶H7 Sakai during dynamic changes in growth kinetics induced by an abrupt downshift in water activity.

    Directory of Open Access Journals (Sweden)

    Chawalit Kocharunchitt

    Full Text Available The present study was undertaken to investigate growth kinetics and time-dependent change in global expression of Escherichia coli O157∶H7 Sakai upon an abrupt downshift in water activity (aw. Based on viable count data, shifting E. coli from aw 0.993 to aw 0.985 or less caused an apparent loss, then recovery, of culturability. Exponential growth then resumed at a rate characteristic for the aw imposed. To understand the responses of this pathogen to abrupt osmotic stress, we employed an integrated genomic and proteomic approach to characterize its cellular response during exposure to a rapid downshift but still within the growth range from aw 0.993 to aw 0.967. Of particular interest, genes and proteins with cell envelope-related functions were induced during the initial loss and subsequent recovery of culturability. This implies that cells undergo remodeling of their envelope composition, enabling them to adapt to osmotic stress. Growth at low aw, however, involved up-regulating additional genes and proteins, which are involved in the biosynthesis of specific amino acids, and carbohydrate catabolism and energy generation. This suggests their important role in facilitating growth under such stress. Finally, we highlighted the ability of E. coli to activate multiple stress responses by transiently inducing the RpoE and RpoH regulons to control protein misfolding, while simultaneously activating the master stress regulator RpoS to mediate long-term adaptation to hyperosmolality. This investigation extends our understanding of the potential mechanisms used by pathogenic E. coli to adapt, survive and grow under osmotic stress, which could potentially be exploited to aid the selection and/or development of novel strategies to inactivate this pathogen.

  9. Effect of phosphorus availability on the selection of species with different ploidy levels and genome sizes in a long-term grassland fertilization experiment.

    Science.gov (United States)

    Šmarda, Petr; Hejcman, Michal; Březinová, Alexandra; Horová, Lucie; Steigerová, Helena; Zedek, František; Bureš, Petr; Hejcmanová, Pavla; Schellberg, Jürgen

    2013-11-01

    Polyploidy and increased genome size are hypothesized to increase organismal nutrient demands, namely of phosphorus (P), which is an essential and abundant component of nucleic acids. Therefore, polyploids and plants with larger genomes are expected to be selectively disadvantaged in P-limited environments. However, this hypothesis has yet to be experimentally tested. We measured the somatic DNA content and ploidy level in 74 vascular plant species in a long-term fertilization experiment. The differences between the fertilizer treatments regarding the DNA content and ploidy level of the established species were tested using phylogeny-based statistics. The percentage and biomass of polyploid species clearly increased with soil P in particular fertilizer treatments, and a similar but weaker trend was observed for the DNA content. These increases were associated with the dominance of competitive life strategy (particularly advantageous in the P-treated plots) in polyploids and the enhanced competitive ability of dominant polyploid grasses at high soil P concentrations, indicating their increased P limitation. Our results verify the hypothesized effect of P availability on the selection of polyploids and plants with increased genome sizes, although the relative contribution of increased P demands vs increased competitiveness as causes of the observed pattern requires further evaluation. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

  10. Loss of yeast peroxiredoxin Tsa1p induces genome instability through activation of the DNA damage checkpoint and elevation of dNTP levels.

    Directory of Open Access Journals (Sweden)

    Hei-Man Vincent Tang

    2009-10-01

    Full Text Available Peroxiredoxins are a family of antioxidant enzymes critically involved in cellular defense and signaling. Particularly, yeast peroxiredoxin Tsa1p is thought to play a role in the maintenance of genome integrity, but the underlying mechanism is not understood. In this study, we took a genetic approach to investigate the cause of genome instability in tsa1Delta cells. Strong genetic interactions of TSA1 with DNA damage checkpoint components DUN1, SML1, and CRT1 were found when mutant cells were analyzed for either sensitivity to DNA damage or rate of spontaneous base substitutions. An elevation in intracellular dNTP production was observed in tsa1Delta cells. This was associated with constitutive activation of the DNA damage checkpoint as indicated by phosphorylation of Rad9/Rad53p, reduced steady-state amount of Sml1p, and induction of RNR and HUG1 genes. In addition, defects in the DNA damage checkpoint did not modulate intracellular level of reactive oxygen species, but suppressed the mutator phenotype of tsa1Delta cells. On the contrary, overexpression of RNR1 exacerbated this phenotype by increasing dNTP levels. Taken together, our findings uncover a new role of TSA1 in preventing the overproduction of dNTPs, which is a root cause of genome instability.

  11. Navigating the evidentiary turn in public health: Sensemaking strategies to integrate genomics into state-level chronic disease prevention programs.

    Science.gov (United States)

    Senier, Laura; Smollin, Leandra; Lee, Rachael; Nicoll, Lauren; Shields, Michael; Tan, Catherine

    2018-06-23

    In the past decade, healthcare delivery has faced two major disruptions: the mapping of the human genome and the rise of evidence-based practice. Sociologists have documented the paradigmatic shift towards evidence-based practice in medicine, but have yet to examine its effect on other health professions or the broader healthcare arena. This article shows how evidence-based practice is transforming public health in the United States. We present an in-depth qualitative analysis of interview, ethnographic, and archival data to show how Michigan's state public health agency has navigated the turn to evidence-based practice, as they have integrated scientific advances in genomics into their chronic disease prevention programming. Drawing on organizational theory, we demonstrate how they managed ambiguity through a combination of sensegiving and sensemaking activities. Specifically, they linked novel developments in genomics to a long-accepted public health planning model, the Core Public Health Functions. This made cutting edge advances in genomics more familiar to their peers in the state health agency. They also marshaled state-specific surveillance data to illustrate the public health burden of hereditary cancers in Michigan, and to make expert panel recommendations for genetic screening more locally relevant. Finally, they mobilized expertise to help their internal colleagues and external partners modernize conventional public health activities in chronic disease prevention. Our findings show that tools and concepts from organizational sociology can help medical sociologists understand how evidence-based practice is shaping institutions and interprofessional relations in the healthcare arena. Copyright © 2018 Elsevier Ltd. All rights reserved.

  12. Next-generation sampling: Pairing genomics with herbarium specimens provides species-level signal in Solidago (Asteraceae).

    Science.gov (United States)

    Beck, James B; Semple, John C

    2015-06-01

    The ability to conduct species delimitation and phylogeny reconstruction with genomic data sets obtained exclusively from herbarium specimens would rapidly enhance our knowledge of large, taxonomically contentious plant genera. In this study, the utility of genotyping by sequencing is assessed in the notoriously difficult genus Solidago (Asteraceae) by attempting to obtain an informative single-nucleotide polymorphism data set from a set of specimens collected between 1970 and 2010. Reduced representation libraries were prepared and Illumina-sequenced from 95 Solidago herbarium specimen DNAs, and resulting reads were processed with the nonreference Universal Network-Enabled Analysis Kit (UNEAK) pipeline. Multidimensional clustering was used to assess the correspondence between genetic groups and morphologically defined species. Library construction and sequencing were successful in 93 of 95 samples. The UNEAK pipeline identified 8470 single-nucleotide polymorphisms, and a filtered data set was analyzed for each of three Solidago subsections. Although results varied, clustering identified genomic groups that often corresponded to currently recognized species or groups of closely related species. These results suggest that genotyping by sequencing is broadly applicable to DNAs obtained from herbarium specimens. The data obtained and their biological signal suggest that pairing genomics with large-scale herbarium sampling is a promising strategy in species-rich plant groups.

  13. Observing copepods through a genomic lens

    Science.gov (United States)

    2011-01-01

    Background Copepods outnumber every other multicellular animal group. They are critical components of the world's freshwater and marine ecosystems, sensitive indicators of local and global climate change, key ecosystem service providers, parasites and predators of economically important aquatic animals and potential vectors of waterborne disease. Copepods sustain the world fisheries that nourish and support human populations. Although genomic tools have transformed many areas of biological and biomedical research, their power to elucidate aspects of the biology, behavior and ecology of copepods has only recently begun to be exploited. Discussion The extraordinary biological and ecological diversity of the subclass Copepoda provides both unique advantages for addressing key problems in aquatic systems and formidable challenges for developing a focused genomics strategy. This article provides an overview of genomic studies of copepods and discusses strategies for using genomics tools to address key questions at levels extending from individuals to ecosystems. Genomics can, for instance, help to decipher patterns of genome evolution such as those that occur during transitions from free living to symbiotic and parasitic lifestyles and can assist in the identification of genetic mechanisms and accompanying physiological changes associated with adaptation to new or physiologically challenging environments. The adaptive significance of the diversity in genome size and unique mechanisms of genome reorganization during development could similarly be explored. Genome-wide and EST studies of parasitic copepods of salmon and large EST studies of selected free-living copepods have demonstrated the potential utility of modern genomics approaches for the study of copepods and have generated resources such as EST libraries, shotgun genome sequences, BAC libraries, genome maps and inbred lines that will be invaluable in assisting further efforts to provide genomics tools for

  14. Observing copepods through a genomic lens

    Directory of Open Access Journals (Sweden)

    Johnson Stewart C

    2011-09-01

    Full Text Available Abstract Background Copepods outnumber every other multicellular animal group. They are critical components of the world's freshwater and marine ecosystems, sensitive indicators of local and global climate change, key ecosystem service providers, parasites and predators of economically important aquatic animals and potential vectors of waterborne disease. Copepods sustain the world fisheries that nourish and support human populations. Although genomic tools have transformed many areas of biological and biomedical research, their power to elucidate aspects of the biology, behavior and ecology of copepods has only recently begun to be exploited. Discussion The extraordinary biological and ecological diversity of the subclass Copepoda provides both unique advantages for addressing key problems in aquatic systems and formidable challenges for developing a focused genomics strategy. This article provides an overview of genomic studies of copepods and discusses strategies for using genomics tools to address key questions at levels extending from individuals to ecosystems. Genomics can, for instance, help to decipher patterns of genome evolution such as those that occur during transitions from free living to symbiotic and parasitic lifestyles and can assist in the identification of genetic mechanisms and accompanying physiological changes associated with adaptation to new or physiologically challenging environments. The adaptive significance of the diversity in genome size and unique mechanisms of genome reorganization during development could similarly be explored. Genome-wide and EST studies of parasitic copepods of salmon and large EST studies of selected free-living copepods have demonstrated the potential utility of modern genomics approaches for the study of copepods and have generated resources such as EST libraries, shotgun genome sequences, BAC libraries, genome maps and inbred lines that will be invaluable in assisting further efforts to

  15. Genetic basis of olfactory cognition: extremely high level of DNA sequence polymorphism in promoter regions of the human olfactory receptor genes revealed using the 1000 Genomes Project dataset.

    Science.gov (United States)

    Ignatieva, Elena V; Levitsky, Victor G; Yudin, Nikolay S; Moshkin, Mikhail P; Kolchanov, Nikolay A

    2014-01-01

    The molecular mechanism of olfactory cognition is very complicated. Olfactory cognition is initiated by olfactory receptor proteins (odorant receptors), which are activated by olfactory stimuli (ligands). Olfactory receptors are the initial player in the signal transduction cascade producing a nerve impulse, which is transmitted to the brain. The sensitivity to a particular ligand depends on the expression level of multiple proteins involved in the process of olfactory cognition: olfactory receptor proteins, proteins that participate in signal transduction cascade, etc. The expression level of each gene is controlled by its regulatory regions, and especially, by the promoter [a region of DNA about 100-1000 base pairs long located upstream of the transcription start site (TSS)]. We analyzed single nucleotide polymorphisms using human whole-genome data from the 1000 Genomes Project and revealed an extremely high level of single nucleotide polymorphisms in promoter regions of olfactory receptor genes and HLA genes. We hypothesized that the high level of polymorphisms in olfactory receptor promoters was responsible for the diversity in regulatory mechanisms controlling the expression levels of olfactory receptor proteins. Such diversity of regulatory mechanisms may cause the great variability of olfactory cognition of numerous environmental olfactory stimuli perceived by human beings (air pollutants, human body odors, odors in culinary etc.). In turn, this variability may provide a wide range of emotional and behavioral reactions related to the vast variety of olfactory stimuli.

  16. Genetic basis of olfactory cognition: extremely high level of DNA sequence polymorphism in promoter regions of the human olfactory receptor genes revealed using the 1000 Genomes Project dataset

    Directory of Open Access Journals (Sweden)

    Elena V. Ignatieva

    2014-03-01

    Full Text Available The molecular mechanism of olfactory cognition is very complicated. Olfactory cognition is initiated by olfactory receptor proteins (odorant receptors, which are activated by olfactory stimuli (ligands. Olfactory receptors are the initial player in the signal transduction cascade producing a nerve impulse, which is transmitted to the brain. The sensitivity to a particular ligand depends on the expression level of multiple proteins involved in the process of olfactory cognition: olfactory receptor proteins, proteins that participate in signal transduction cascade, etc. The expression level of each gene is controlled by its regulatory regions, and especially, by the promoter (a region of DNA about 100–1000 base pairs long located upstream of the transcription start site. We analyzed single nucleotide polymorphisms using human whole-genome data from the 1000 Genomes Project and revealed an extremely high level of single nucleotide polymorphisms in promoter regions of olfactory receptor genes and HLA genes. We hypothesized that the high level of polymorphisms in olfactory receptor promoters was responsible for the diversity in regulatory mechanisms controlling the expression levels of olfactory receptor proteins. Such diversity of regulatory mechanisms may cause the great variability of olfactory cognition of numerous environmental olfactory stimuli perceived by human beings (air pollutants, human body odors, odors in culinary etc.. In turn, this variability may provide a wide range of emotional and behavioral reactions related to the vast variety of olfactory stimuli.

  17. GHRSST Level 2P Global Bulk Sea Surface Temperature from the Advanced Very High Resolution Radiometer (AVHRR) on the NOAA-17 satellite produced by NAVO (GDS version 1)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A global Group for High Resolution Sea Surface Temperature (GHRSST) Level 2P dataset based on multi-channel sea surface temperature (SST) retrievals generated in...

  18. GHRSST Level 3P Global Subskin Sea Surface Temperature from the Advanced Very High Resolution Radiometer (AVHRR) on the MetOp-A satellite (GDS version 1)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A global Level 3 Group for HIgh Resolution Sea Surface Temperature (GHRSST) dataset from the Advanced Very High Resolution Radiometer (AVHRR) on the MetOp-A platform...

  19. GHRSST Level 2P Global Bulk Sea Surface Temperature from the Advanced Very High Resolution Radiometer (AVHRR) on the NOAA-17 satellite (GDS version 1)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A global Level 2P Group for High Resolution Sea Surface Temperature (GHRSST) dataset based on multi-channel sea surface temperature (SST) retrievals from the...

  20. GHRSST Level 4 AVHRR_OI Global Blended Sea Surface Temperature Analysis (GDS version 2) from NCEI (GDS versions 1 and 2)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A Group for High Resolution Sea Surface Temperature (GHRSST) global Level 4 sea surface temperature analysis produced daily on a 0.25 degree grid at the NOAA...

  1. GHRSST Level 2P Global Bulk Sea Surface Temperature from the Advanced Very High Resolution Radiometer (AVHRR) on the NOAA-16 satellite (GDS version 1)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A global Level 2P Group for High Resolution Sea Surface Temperature (GHRSST) dataset based on multi-channel sea surface temperature (SST) retrievals from the...

  2. GHRSST Level 2P 1 m Depth Global Sea Surface Temperature from the Visible Infrared Imaging Radiometer Suite (VIIRS) on the Suomi NPP satellite (GDS version 2)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A global Group for High Resolution Sea Surface Temperature (GHRSST) Level 2P dataset based on retrievals from the Visible Infrared Imaging Radiometer Suite (VIIRS)....

  3. China’s Role at Global and Regional Levels from the Perspective of Trade and FDI Flows

    Directory of Open Access Journals (Sweden)

    Iulia Monica Oehler-Șincai

    2010-01-01

    Full Text Available Taking into consideration its economic scale and growth potential, we can assert that China represents a regional as well a global player. Gradually, its growth model centred on exports becomes one based on innovation in which exports have a complementary role. Our objective is to reflect China’s role in the field of trade and FDI at regional and global level as well as its transformation into an economy centred on innovation. Following this rationale, the present paper is structured around four main sections, as follows. First, we bring to the forefront the impact of the financial and economic crisis on the Chinese economy and on two of its growth engines: the internal demand and exports. Second, we present China’s trade in goods as one of the main engines of its economic growth. Third, we demonstrate that China represents the linkage between the Eastern, Southern and South-Eastern Asian countries through FDI flows. Fourth, we reflect how China becomes gradually an economy centred on innovation.

  4. Coral indicators of past sea-level change: A global repository of U-series dated benchmarks

    Science.gov (United States)

    Hibbert, Fiona D.; Rohling, Eelco J.; Dutton, Andrea; Williams, Felicity H.; Chutcharavan, Peter M.; Zhao, Cheng; Tamisiea, Mark E.

    2016-08-01

    Fossil corals provide valuable data for reconstructing past sea levels, as they are often well preserved in the fossil record and can be dated with U-series methods. Here we present a global and internally consistent database of Usbnd Th dated fossil coral sea-level indicators, including full consideration of all (known) associated uncertainties (both vertical and chronological). We include carefully determined taxon-specific depth distributions, rather than blanket depth uncertainty terms as used in most previous work. This is based on a synthesis of extensive modern ecological information on depth ranges. These ranges are found to be spatially variable (between ocean basins, between regions, and on sub-regional scales) because depth itself is not limiting - instead, depth distributions arise from complex physical, chemical, and biological interactions with coral-reef growth, distribution, and composition. One of the main causes for recognition of the greater depth-variability of coral taxa has been the routine inclusion of deep-diving and ROV surveys in coral ecological studies over the past few decades, which has broken through the "shallow-water" bias of early surveys by adding frequent observations on deeper occurrences (although more are needed). It is also clear from our assessment that coral habitat-depth distributions must be determined on the species level to reduce uncertainties in reconstructions of past sea levels, and that application to sea-level studies then requires these studies also to identify fossil corals to the species level. Samples identified only to the genus level give rise to wide uncertainties in habitat depth and, hence, sea level. Our database contains extensive metadata to assist evaluations of dating quality, as well as geomorphic and stratigraphic metadata. We demonstrate with examples how such metadata can help to evaluate sea-level reconstructions, for example by identifying outlier points. One example discusses the Last

  5. Efficient globally optimal segmentation of cells in fluorescence microscopy images using level sets and convex energy functionals.

    Science.gov (United States)

    Bergeest, Jan-Philip; Rohr, Karl

    2012-10-01

    In high-throughput applications, accurate and efficient segmentation of cells in fluorescence microscopy images is of central importance for the quantification of protein expression and the understanding of cell function. We propose an approach for segmenting cell nuclei which is based on active contours using level sets and convex energy functionals. Compared to previous work, our approach determines the global solution. Thus, the approach does not suffer from local minima and the segmentation result does not depend on the initialization. We consider three different well-known energy functionals for active contour-based segmentation and introduce convex formulations of these functionals. We also suggest a numeric approach for efficiently computing the solution. The performance of our approach has been evaluated using fluorescence microscopy images from different experiments comprising different cell types. We have also performed a quantitative comparison with previous segmentation approaches. Copyright © 2012 Elsevier B.V. All rights reserved.

  6. Reconciling past changes in Earth's rotation with 20th century global sea-level rise: Resolving Munk's enigma.

    Science.gov (United States)

    Mitrovica, Jerry X; Hay, Carling C; Morrow, Eric; Kopp, Robert E; Dumberry, Mathieu; Stanley, Sabine

    2015-12-01

    In 2002, Munk defined an important enigma of 20th century global mean sea-level (GMSL) rise that has yet to be resolved. First, he listed three canonical observations related to Earth's rotation [(i) the slowing of Earth's rotation rate over the last three millennia inferred from ancient eclipse observations, and changes in the (ii) amplitude and (iii) orientation of Earth's rotation vector over the last century estimated from geodetic and astronomic measurements] and argued that they could all be fit by a model of ongoing glacial isostatic adjustment (GIA) associated with the last ice age. Second, he demonstrated that prevailing estimates of the 20th century GMSL rise (~1.5 to 2.0 mm/year), after correction for the maximum signal from ocean thermal expansion, implied mass flux from ice sheets and glaciers at a level that would grossly misfit the residual GIA-corrected observations of Earth's rotation. We demonstrate that the combination of lower estimates of the 20th century GMSL rise (up to 1990) improved modeling of the GIA process and that the correction of the eclipse record for a signal due to angular momentum exchange between the fluid outer core and the mantle reconciles all three Earth rotation observations. This resolution adds confidence to recent estimates of individual contributions to 20th century sea-level change and to projections of GMSL rise to the end of the 21st century based on them.

  7. Nature of global large-scale sea level variability in relation to atmospheric forcing: A modeling study

    Science.gov (United States)

    Fukumori, Ichiro; Raghunath, Ramanujam; Fu, Lee-Lueng

    1998-03-01

    The relation between large-scale sea level variability and ocean circulation is studied using a numerical model. A global primitive equation model of the ocean is forced by daily winds and climatological heat fluxes corresponding to the period from January 1992 to January 1994. The physical nature of sea level's temporal variability from periods of days to a year is examined on the basis of spectral analyses of model results and comparisons with satellite altimetry and tide gauge measurements. The study elucidates and diagnoses the inhomogeneous physics of sea level change in space and frequency domain. At midlatitudes, large-scale sea level variability is primarily due to steric changes associated with the seasonal heating and cooling cycle of the surface layer. In comparison, changes in the tropics and high latitudes are mainly wind driven. Wind-driven variability exhibits a strong latitudinal dependence in itself. Wind-driven changes are largely baroclinic in the tropics but barotropic at higher latitudes. Baroclinic changes are dominated by the annual harmonic of the first baroclinic mode and is largest off the equator; variabilities associated with equatorial waves are smaller in comparison. Wind-driven barotropic changes exhibit a notable enhancement over several abyssal plains in the Southern Ocean, which is likely due to resonant planetary wave modes in basins semienclosed by discontinuities in potential vorticity. Otherwise, barotropic sea level changes are typically dominated by high frequencies with as much as half the total variance in periods shorter than 20 days, reflecting the frequency spectra of wind stress curl. Implications of the findings with regards to analyzing observations and data assimilation are discussed.

  8. Global distribution and seasonal variability of coastal low-level jets derived from ERA-Interim reanalysis

    Directory of Open Access Journals (Sweden)

    Raza Ranjha

    2013-08-01

    Full Text Available A low-level wind maximum is often found over the oceans near many coasts around the world. These Coastal Low-Level Jets (CLLJs play an important role in the coastal weather and have significant impacts on regional climate and ecology as well as on a number of human activities. The presence of CLLJs is related to various local circumstances such as land-sea temperature contrasts, upwelling, coastal terrain, orientation of the coast, and so on, but also to the large-scale atmospheric dynamics. This makes studies of CLLJs not only interesting but also challenging. In this study, based on ERA-Interim reanalysis data, the global distribution, spatio-temporal structure and the seasonal variability of CLLJs are documented. Seasonal data from 1980 to 2011 are used to identify areas where CLLJs are frequently found in the lowest 2 km, following criteria based on the vertical profiles of wind speed and temperature. The results are analysed to highlight the fundamental aspects and distinctive features of the CLLJs across the globe, including their occurrence rate, jet height, maximum wind speed and horizontal extent. Global maps of CLLJs are constructed for the summer and winter seasons. The west coasts of North America, the Iberian Peninsula, north-western Africa and the south-eastern coast of the Arabian Peninsula make up the Northern Hemispheric CLLJ regions, while the west coasts of South America, Australia, and southern Africa comprise the South Hemispheric equivalents. The existence and characteristics of CLLJs along the southern coast of Oman and the western coast of the Iberian Peninsula regions are also discussed, not fully envisaged before in the context of CLLJs. The highest occurrence of CLLJs is found during the summer in both hemispheres, and the coast of Oman has the globally highest CLLJ frequency, with also the highest maximum wind speeds. The most commonly found CLLJ has a maximum wind speed between 9 and 15 m s−1, and occurs at

  9. Systems-level analysis of age-related macular degeneration reveals global biomarkers and phenotype-specific functional networks

    Science.gov (United States)

    2012-01-01

    Background Age-related macular degeneration (AMD) is a leading cause of blindness that affects the central region of the retinal pigmented epithelium (RPE), choroid, and neural retina. Initially characterized by an accumulation of sub-RPE deposits, AMD leads to progressive retinal degeneration, and in advanced cases, irreversible vision loss. Although genetic analysis, animal models, and cell culture systems have yielded important insights into AMD, the molecular pathways underlying AMD's onset and progression remain poorly delineated. We sought to better understand the molecular underpinnings of this devastating disease by performing the first comparative transcriptome analysis of AMD and normal human donor eyes. Methods RPE-choroid and retina tissue samples were obtained from a common cohort of 31 normal, 26 AMD, and 11 potential pre-AMD human donor eyes. Transcriptome profiles were generated for macular and extramacular regions, and statistical and bioinformatic methods were employed to identify disease-associated gene signatures and functionally enriched protein association networks. Selected genes of high significance were validated using an independent donor cohort. Results We identified over 50 annotated genes enriched in cell-mediated immune responses that are globally over-expressed in RPE-choroid AMD phenotypes. Using a machine learning model and a second donor cohort, we show that the top 20 global genes are predictive of AMD clinical diagnosis. We also discovered functionally enriched gene sets in the RPE-choroid that delineate the advanced AMD phenotypes, neovascular AMD and geographic atrophy. Moreover, we identified a graded increase of transcript levels in the retina related to wound response, complement cascade, and neurogenesis that strongly correlates with decreased levels of phototransduction transcripts and increased AMD severity. Based on our findings, we assembled protein-protein interactomes that highlight functional networks likely to be

  10. The complete mitochondrial genome of the styloperlid stonefly species Styloperla spinicercia Wu (Insecta: Plecoptera) with family-level phylogenetic analyses of the Pteronarcyoidea.

    Science.gov (United States)

    Wang, Ying; Cao, Jinjun; Li, Weihai

    2017-03-13

    We present the complete mitochondrial (mt) genome sequence of the stonefly, Styloperla spinicercia Wu, 1935 (Plecoptera: Styloperlidae), the type species of the genus Styloperla and the first complete mt genome for the family Styloperlidae. The genome is circular, 16,129 base pairs long, has an A+T content of 70.7%, and contains 37 genes including the large and small ribosomal RNA (rRNA) subunits, 13 protein coding genes (PCGs), 22 tRNA genes and a large non-coding region (CR). All of the PCGs use the standard initiation codon ATN except ND1 and ND5, which start with TTG and GTG. Twelve of the PCGs stop with conventional terminal codons TAA and TAG, except ND5 which shows an incomplete terminator signal T. All tRNAs have the classic clover-leaf structures with the dihydrouridine (DHU) arm of tRNASer(AGN) forming a simple loop. Secondary structures of the two ribosomal RNAs are presented with reference to previous models. The structural elements and the variable numbers of tandem repeats are described within the control region. Phylogenetic analyses using both Bayesian (BI) and Maximum Likelihood (ML) methods support the previous hypotheses regarding family level relationships within the Pteronarcyoidea. The genetic distance calculated based on 13 PCGs and two rRNAs between Styloperla sp. and S. spinicercia is provided and interspecific divergence is discussed.

  11. Cenozoic global sea level, sequences, and the New Jersey transect: Results from coastal plain and continental slope drilling

    Science.gov (United States)

    Miller, K.G.; Mountain, Gregory S.; Browning, J.V.; Kominz, M.; Sugarman, P.J.; Christie-Blick, N.; Katz, M.E.; Wright, J.D.

    1998-01-01

    The New Jersey Sea Level Transect was designed to evaluate the relationships among global sea level (eustatic) change, unconformity-bounded sequences, and variations in subsidence, sediment supply, and climate on a passive continental margin. By sampling and dating Cenozoic strata from coastal plain and continental slope locations, we show that sequence boundaries correlate (within ??0.5 myr) regionally (onshore-offshore) and interregionally (New Jersey-Alabama-Bahamas), implicating a global cause. Sequence boundaries correlate with ??18O increases for at least the past 42 myr, consistent with an ice volume (glacioeustatic) control, although a causal relationship is not required because of uncertainties in ages and correlations. Evidence for a causal connection is provided by preliminary Miocene data from slope Site 904 that directly link ??18O increases with sequence boundaries. We conclude that variation in the size of ice sheets has been a primary control on the formation of sequence boundaries since ~42 Ma. We speculate that prior to this, the growth and decay of small ice sheets caused small-amplitude sea level changes (changes on mid-ocean ridges. Although our results are consistent with the general number and timing of Paleocene to middle Miocene sequences published by workers at Exxon Production Research Company, our estimates of sea level amplitudes are substantially lower than theirs. Lithofacies patterns within sequences follow repetitive, predictable patterns: (1) coastal plain sequences consist of basal transgressive sands overlain by regressive highstand silts and quartz sands; and (2) although slope lithofacies variations are subdued, reworked sediments constitute lowstand deposits, causing the strongest, most extensive seismic reflections. Despite a primary eustatic control on sequence boundaries, New Jersey sequences were also influenced by changes in tectonics, sediment supply, and climate. During the early to middle Eocene, low siliciclastic and

  12. Genome-wide analysis suggests high level of microsynteny and purifying selection affect the evolution of EIN3/EIL family in Rosaceae.

    Science.gov (United States)

    Cao, Yunpeng; Han, Yahui; Meng, Dandan; Li, Dahui; Jin, Qing; Lin, Yi; Cai, Yongping

    2017-01-01

    The ethylene-insensitive3/ethylene-insensitive3-like ( EIN3/EIL ) proteins are a type of nuclear-localized protein with DNA-binding activity in plants. Although the EIN3/EIL gene family has been studied in several plant species, little is known about comprehensive study of the EIN3/EIL gene family in Rosaceae. In this study, ten, five, four, and five EIN3/EIL genes were identified in the genomes of pear ( Pyrus bretschneideri ), mei ( Prunus mume ), peach ( Prunus persica ) and strawberry ( Fragaria vesca ), respectively. Twenty-eight chromosomal segments of EIL/EIN3 gene family were found in four Rosaceae species, and these segments could form seven orthologous or paralogous groups based on interspecies or intraspecies gene colinearity (microsynteny) analysis. Moreover, the highly conserved regions of microsynteny were found in four Rosaceae species. Subsequently it was found that both whole genome duplication and tandem duplication events significantly contributed to the EIL/EIN3 gene family expansion. Gene expression analysis of the EIL/EIN3 genes in the pear revealed subfunctionalization for several PbEIL genes derived from whole genome duplication. It is noteworthy that according to environmental selection pressure analysis, the strong purifying selection should dominate the maintenance of the EIL/EIN3 gene family in four Rosaceae species. These results provided useful information on Rosaceae EIL/EIN3 genes, as well as insights into the evolution of this gene family in four Rosaceae species. Furthermore, high level of microsynteny in the four Rosaceae plants suggested that a large-scale genome duplication event in the EIL/EIN3 gene family was predated to speciation.

  13. Genome-wide analysis suggests high level of microsynteny and purifying selection affect the evolution of EIN3/EIL family in Rosaceae

    Directory of Open Access Journals (Sweden)

    Yunpeng Cao

    2017-05-01

    Full Text Available The ethylene-insensitive3/ethylene-insensitive3-like (EIN3/EIL proteins are a type of nuclear-localized protein with DNA-binding activity in plants. Although the EIN3/EIL gene family has been studied in several plant species, little is known about comprehensive study of the EIN3/EIL gene family in Rosaceae. In this study, ten, five, four, and five EIN3/EIL genes were identified in the genomes of pear (Pyrus bretschneideri, mei (Prunus mume, peach (Prunus persica and strawberry (Fragaria vesca, respectively. Twenty-eight chromosomal segments of EIL/EIN3 gene family were found in four Rosaceae species, and these segments could form seven orthologous or paralogous groups based on interspecies or intraspecies gene colinearity (microsynteny analysis. Moreover, the highly conserved regions of microsynteny were found in four Rosaceae species. Subsequently it was found that both whole genome duplication and tandem duplication events significantly contributed to the EIL/EIN3 gene family expansion. Gene expression analysis of the EIL/EIN3 genes in the pear revealed subfunctionalization for several PbEIL genes derived from whole genome duplication. It is noteworthy that according to environmental selection pressure analysis, the strong purifying selection should dominate the maintenance of the EIL/EIN3 gene family in four Rosaceae species. These results provided useful information on Rosaceae EIL/EIN3 genes, as well as insights into the evolution of this gene family in four Rosaceae species. Furthermore, high level of microsynteny in the four Rosaceae plants suggested that a large-scale genome duplication event in the EIL/EIN3 gene family was predated to speciation.

  14. Global Climate Change Consequences Changing the Middle Sea Level in the Brazilian Coast: Impacts on Ceará State

    Science.gov (United States)

    Lacerda, E. G.; Pires, L. B. M.; Pinto, V. K. E.

    2015-12-01

    Since the Industrial Revolution, man started to generate increasing amounts of waste and pollutants, which on a large scale in the long term is causing a series of climate change consequences, both globally as well as locally. One of the many effects of these changes has been reflected in the ocean levels, depending on various factors. Thus, the population living in coastal areas suffers from the negative effects of the advancement of ocean waters. The coast of northeastern Brazil is an example of this, especially the state of Ceará coast. The state of Ceará has 573 km of coastline, a region that has suffered extensive erosion, in which the Middle Sea Level (MSL) changes exert a significant influence. The coastal plain is a strip of land of small extent, with an average width of 2.5 km, formed depending on the availability of high sediment stocks provided through the action of wind, marine, or river processes, individually in combination with each other. In many beaches it is observed that the strip of beach is narrow due to the presence of topographic elevations carved into sharp cliffs. Between periods of high tide and low tide, often rocky beach features are observed that have recently formed. The waves control the stretches of beach which are mostly sandy. This paper presents a survey about the evidence already apparent on the rise in the MSL and correlates it with the advance of the sea on the coast of Ceará, as well as assesses the possible consequences of this process. Therefore, a literature search was conducted in relevant scientific publications. The data used are from the station "Global Sea Level Observing System - GLOSS" which maintains a tide gauge installed in Ceará in Fortaleza. The analyses show that the phenomenon has caused a lot of inconvenience to the people, streets have disappeared, as well as several buildings located along the coast. The sea advances destroyed beaches and have promoted an accelerated level of erosion, changing the

  15. Complete genome sequence of the myxobacterium Sorangium cellulosum

    DEFF Research Database (Denmark)

    Schneiker, S; Perlova, O; Kaiser, O

    2007-01-01

    The genus Sorangium synthesizes approximately half of the secondary metabolites isolated from myxobacteria, including the anti-cancer metabolite epothilone. We report the complete genome sequence of the model Sorangium strain S. cellulosum Soce56, which produces several natural products and has...... morphological and physiological properties typical of the genus. The circular genome, comprising 13,033,779 base pairs, is the largest bacterial genome sequenced to date. No global synteny with the genome of Myxococcus xanthus is apparent, revealing an unanticipated level of divergence between...... these myxobacteria. A large percentage of the genome is devoted to regulation, particularly post-translational phosphorylation, which probably supports the strain's complex, social lifestyle. This regulatory network includes the highest number of eukaryotic protein kinase-like kinases discovered in any organism...

  16. Climate-model induced differences in the 21st century global and regional glacier contributions to sea-level rise

    NARCIS (Netherlands)

    Giesen, R.H.|info:eu-repo/dai/nl/304831603; Oerlemans, J.|info:eu-repo/dai/nl/06833656X

    2013-01-01

    The large uncertainty in future global glacier volume projections partly results from a substantial range in future climate conditions projected by global climate models. This study addresses the effect of global and regional differences in climate input data on the projected twenty-first century

  17. Preterm-associated visual impairment and estimates of retinopathy of prematurity at regional and global levels for 2010

    Science.gov (United States)

    Blencowe, Hannah; Lawn, Joy E.; Vazquez, Thomas; Fielder, Alistair; Gilbert, Clare

    2013-01-01

    Background: Retinopathy of prematurity (ROP) is a leading cause of potentially avoidable childhood blindness worldwide. We estimated ROP burden at the global and regional levels to inform screening and treatment programs, research, and data priorities. Methods: Systematic reviews and meta-analyses were undertaken to estimate the risk of ROP and subsequent visual impairment for surviving preterm babies by level of neonatal care, access to ROP screening, and treatment. A compartmental model was used to estimate ROP cases and numbers of visually impaired survivors. Results: In 2010, an estimated 184,700 (uncertainty range: 169,600–214,500) preterm babies developed any stage of ROP, 20,000 (15,500–27,200) of whom became blind or severely visually impaired from ROP, and a further 12,300 (8,300–18,400) developed mild/moderate visual impairment. Sixty-five percent of those visually impaired from ROP were born in middle-income regions; 6.2% (4.3–8.9%) of all ROP visually impaired infants were born at >32-wk gestation. Visual impairment from other conditions associated with preterm birth will affect larger numbers of survivors. Conclusion: Improved care, including oxygen delivery and monitoring, for preterm babies in all facility settings would reduce the number of babies affected with ROP. Improved data tracking and coverage of locally adapted screening/treatment programs are urgently required. PMID:24366462

  18. Global Estimates of Average Ground-Level Fine Particulate Matter Concentrations from Satellite-Based Aerosol Optical Depth

    Science.gov (United States)

    Van Donkelaar, A.; Martin, R. V.; Brauer, M.; Kahn, R.; Levy, R.; Verduzco, C.; Villeneuve, P.

    2010-01-01

    Exposure to airborne particles can cause acute or chronic respiratory disease and can exacerbate heart disease, some cancers, and other conditions in susceptible populations. Ground stations that monitor fine particulate matter in the air (smaller than 2.5 microns, called PM2.5) are positioned primarily to observe severe pollution events in areas of high population density; coverage is very limited, even in developed countries, and is not well designed to capture long-term, lower-level exposure that is increasingly linked to chronic health effects. In many parts of the developing world, air quality observation is absent entirely. Instruments aboard NASA Earth Observing System satellites, such as the MODerate resolution Imaging Spectroradiometer (MODIS) and the Multi-angle Imaging SpectroRadiometer (MISR), monitor aerosols from space, providing once daily and about once-weekly coverage, respectively. However, these data are only rarely used for health applications, in part because the can retrieve the amount of aerosols only summed over the entire atmospheric column, rather than focusing just on the near-surface component, in the airspace humans actually breathe. In addition, air quality monitoring often includes detailed analysis of particle chemical composition, impossible from space. In this paper, near-surface aerosol concentrations are derived globally from the total-column aerosol amounts retrieved by MODIS and MISR. Here a computer aerosol simulation is used to determine how much of the satellite-retrieved total column aerosol amount is near the surface. The five-year average (2001-2006) global near-surface aerosol concentration shows that World Health Organization Air Quality standards are exceeded over parts of central and eastern Asia for nearly half the year.

  19. Twentieth-century global-mean sea level rise: Is the whole greater than the sum of the parts?

    Science.gov (United States)

    Gregory, J.M.; White, N.J.; Church, J.A.; Bierkens, M.F.P.; Box, J.E.; Van den Broeke, M.R.; Cogley, J.G.; Fettweis, X.; Hanna, E.; Huybrechts, P.; Konikow, Leonard F.; Leclercq, P.W.; Marzeion, B.; Oerlemans, J.; Tamisiea, M.E.; Wada, Y.; Wake, L.M.; Van de Wal, R.S.W.

    2013-01-01

    Confidence in projections of global-mean sea level rise (GMSLR) depends on an ability to account for GMSLR during the twentieth century. There are contributions from ocean thermal expansion, mass loss from glaciers and ice sheets, groundwater extraction, and reservoir impoundment. Progress has been made toward solving the “enigma” of twentieth-century GMSLR, which is that the observed GMSLR has previously been found to exceed the sum of estimated contributions, especially for the earlier decades. The authors propose the following: thermal expansion simulated by climate models may previously have been underestimated because of their not including volcanic forcing in their control state; the rate of glacier mass loss was larger than previously estimated and was not smaller in the first half than in the second half of the century; the Greenland ice sheet could have made a positive contribution throughout the century; and groundwater depletion and reservoir impoundment, which are of opposite sign, may have been approximately equal in magnitude. It is possible to reconstruct the time series of GMSLR from the quantified contributions, apart from a constant residual term, which is small enough to be explained as a long-term contribution from the Antarctic ice sheet. The reconstructions account for the observation that the rate of GMSLR was not much larger during the last 50 years than during the twentieth century as a whole, despite the increasing anthropogenic forcing. Semiempirical methods for projecting GMSLR depend on the existence of a relationship between global climate change and the rate of GMSLR, but the implication of the authors' closure of the budget is that such a relationship is weak or absent during the twentieth century.

  20. Ecological Genomics of Marine Picocyanobacteria†

    Science.gov (United States)

    Scanlan, D. J.; Ostrowski, M.; Mazard, S.; Dufresne, A.; Garczarek, L.; Hess, W. R.; Post, A. F.; Hagemann, M.; Paulsen, I.; Partensky, F.

    2009-01-01

    Summary: Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus numerically dominate the picophytoplankton of the world ocean, making a key contribution to global primary production. Prochlorococcus was isolated around 20 years ago and is probably the most abundant photosynthetic organism on Earth. The genus comprises specific ecotypes which are phylogenetically distinct and differ markedly in their photophysiology, allowing growth over a broad range of light and nutrient conditions within the 45°N to 40°S latitudinal belt that they occupy. Synechococcus and Prochlorococcus are closely related, together forming a discrete picophytoplankton clade, but are distinguishable by their possession of dissimilar light-harvesting apparatuses and differences in cell size and elemental composition. Synechococcus strains have a ubiquitous oceanic distribution compared to that of Prochlorococcus strains and are characterized by phylogenetically discrete lineages with a wide range of pigmentation. In this review, we put our current knowledge of marine picocyanobacterial genomics into an environmental context and present previously unpublished genomic information arising from extensive genomic comparisons in order to provide insights into the adaptations of these marine microbes to their environment and how they are reflected at the genomic level. PMID:19487728

  1. Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank.

    Science.gov (United States)

    Prlic, Andreas; Kalro, Tara; Bhattacharya, Roshni; Christie, Cole; Burley, Stephen K; Rose, Peter W

    2016-12-15

    The Protein Data Bank (PDB) now contains more than 120,000 three-dimensional (3D) structures of biological macromolecules. To allow an interpretation of how PDB data relates to other publicly available annotations, we developed a novel data integration platform that maps 3D structural information across various datasets. This integration bridges from the human genome across protein sequence to 3D structure space. We developed novel software solutions for data management and visualization, while incorporating new libraries for web-based visualization using SVG graphics. The new views are available from http://www.rcsb.org and software is available from https://github.com/rcsb/. andreas.prlic@rcsb.orgSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  2. Impacts of climate change on European hydrology at 1.5, 2 and 3 degrees mean global warming above preindustrial level

    NARCIS (Netherlands)

    Donnelly, Chantal; Greuell, Wouter; Andersson, Jafet; Gerten, Dieter; Pisacane, Giovanna; Roudier, Philippe; Ludwig, Fulco

    2017-01-01

    Impacts of climate change at 1.5, 2 and 3 °C mean global warming above preindustrial level are investigated and compared for runoff, discharge and snowpack in Europe. Ensembles of climate projections representing each of the warming levels were assembled to describe the hydro-meteorological climate

  3. Salivary Alpha Amylase and Cortisol Levels in Children with Global Developmental Delay and Their Relation with the Expectation of Dental Care and Behavior during the Intervention

    Science.gov (United States)

    dos Santos, Marcio Jose Possari; Bernabe, Daniel Galera; Nakamune, Ana Claudia de Melo Stevanato; Perri, Silvia Helena Venturoli; de Aguiar, Sandra Maria Herondina Coelho Avila; de Oliveira, Sandra Helena Penha

    2012-01-01

    The purpose of this study was to analyze the alpha-amylase (sAA) and cortisol levels in children with Global developmental delay (GDD) before and after dental treatment and its association with the children's behavior during treatment. The morning salivary cortisol levels and activity of sAA of 33 children with GDD were evaluated before and after…

  4. Comparative genomic analysis of Campylobacter jejuni associated with Guillain-Barré and Miller Fisher syndromes: neuropathogenic and enteritis-associated isolates can share high levels of genomic similarity

    Directory of Open Access Journals (Sweden)

    Endtz Hubert P

    2007-10-01

    Full Text Available Abstract Background Campylobacter jejuni infection represents the most frequent antecedent infection triggering the onset of the neuropathic disorders Guillain-Barré syndrome (GBS and Miller Fisher syndrome (MFS. Although sialylated ganglioside-mimicking lipo-oligosaccharide (LOS structures are the strongest neuropathogenic determinants in C. jejuni, they do not appear to be the only requirement for a neuropathic outcome since strains capable of their production have been isolated from patients with uncomplicated cases of enteritis. Consequently, other pathogen and/or host-related factors contribute to the onset of neurological complications. We have used comparative genomic hybridization to perform a detailed genomic comparison of strains isolated from GBS/MFS and enteritis-only patients. Our dataset, in which the gene conservation profile for 1712 genes was assayed in 102 strains, including 56 neuropathogenic isolates, represents the largest systematic search for C. jejuni factors associated with GBS/MFS to date and has allowed us to analyze the genetic background of neuropathogenic C. jejuni strains with an unprecedented level of resolution. Results The majority of GBS/MFS strains can be assigned to one of six major lineages, suggesting that several genetic backgrounds can result in a neuropathogenic phenotype. A statistical analysis of gene conservation rates revealed that although genes involved in the sialylation of LOS structures were significantly associated with neuropathogenic strains, still many enteritis-control strains both bear these genes and share remarkable levels of genomic similarity with their neuropathogenic counterparts. Two capsule biosynthesis genes (Cj1421c and Cj1428c showed higher conservation rates among neuropathogenic strains compared to enteritis-control strains. Any potential involvement of these genes in neuropathogenesis must be assessed. A single gene (HS:3 Cj1135 had a higher conservation rate among enteritis

  5. Improved estimates of global sea level change from Ice Sheets, glaciers and land water storage using GRACE

    Science.gov (United States)

    Velicogna, I.; Hsu, C. W.; Ciraci, E.; Sutterley, T. C.

    2015-12-01

    We use observations of time variable gravity from GRACE to estimate mass changes for the Antarctic and Greenland Ice Sheets, the Glaciers and Ice Caps (GIC) and land water storage for the time period 2002-2015 and evaluate their total contribution to sea level. We calculate regional sea level changes from these present day mass fluxes using an improved scaling factor for the GRACE data that accounts for the spatial and temporal variability of the observed signal. We calculate a separate scaling factor for the annual and the long-term components of the GRACE signal. To estimate the contribution of the GIC, we use a least square mascon approach and we re-analyze recent inventories to optimize the distribution of mascons and recover the GRACE signal more accurately. We find that overall, Greenland controls 43% of the global trend in eustatic sea level rise, 16% for Antarctica and 29% for the GIC. The contribution from the GIC is dominated by the mass loss of the Canadian Arctic Archipelago, followed by Alaska, Patagonia and the High Mountains of Asia. We report a marked increase in mass loss for the Canadian Arctic Archipelago. In Greenland, following the 2012 high summer melt, years 2013 and 2014 have slowed down the increase in mass loss, but our results will be updated with summer 2015 observations at the meeting. In Antarctica, the mass loss is still on the rise with increased contributions from the Amundsen Sea sector and surprisingly from the Wilkes Land sector of East Antarctica, including Victoria Land. Conversely, the Queen Maud Land sector experienced a large snowfall in 2009-2013 and has now resumed to a zero mass gain since 2013. We compare sea level changes from these GRACE derived mass fluxes after including the atmospheric and ocean loading signal with sea level change from satellite radar altimetry (AVISO) corrected for steric signal of the ocean using Argo measurements and find an excellent agreement in amplitude, phase and trend in these estimates

  6. Is climate predictable?. Fear of global warming and rise of sea levels; Laesst sich das Klima in die Karten schauen?. Globale Erwaermung und Anstieg des Meeresspiegels befuerchtet

    Energy Technology Data Exchange (ETDEWEB)

    Grassl, H [Weltorganisation fuer Meteorologie (WMO), Genf (Switzerland)

    1995-02-01

    Scientific warnings of world-wide climate changes through human activities were voiced even as long ago as 100 years before now. A chain of evidence reaching into our time has since turned up. With the first UN world climate conference in 1979, climate change became a concern of climatologists all over the world. Many scientists fear that man has already triggered global warming by emissions of trace gases into the atmosphere. (orig.) [Deutsch] Wissenschaftliche Warnungen vor weltweiten Klimaveraenderungen durch den Menschen reichen inzwischen rund 100 Jahre zurueck. Seither fuehrt eine Kette von Befunden bis in unsere Zeit. Mit der ersten UN-Weltklimakonferenz im Jahr 1979 wurden sie zu einem internationalen Anliegen der Klimatologie. Viele Wissenschaftler befuerchten, dass der Mensch mit Emissionen von Spurengasen in die Atmosphaere eine globale Erwaermung bereits angestossen hat. (orig.)

  7. A cohort study evaluating the implications of biology, weight status and socioeconomic level on global self-esteem competence among female African-American adolescents.

    Science.gov (United States)

    Powell-Young, Yolanda M; Zabaleta, Jovanny; Velasco-Gonzalez, Cruz; Sothern, Melinda S

    2013-07-01

    The link between obesity and self-esteem among minority youth has received minimal empirical evaluation. This study aims to describe the magnitude of risk that body mass index, household income, and transitional age have on global self-esteem levels among African-American adolescents. These analyses were conducted on cross-sectional data obtained from 264 urban-dwelling African-American females between 14 and 18 years of age. Survey data on global self-esteem levels, transitory age, and socioeconomic levels were collected using self-administered questionnaires. Measured height and weight values were used to calculate and categorize weight status according to body mass index. Logistic regression models examined the probability of reporting less than average levels of global self-esteem. Adolescent African-American females residing in low-income households were 10 times more likely to report lower global self-esteem scores than those individuals from more affluent households (95% CI: 1.94, 60.19, p self-esteem among participants in this study. Household income appears to be the greatest predictor of global self-esteem levels. Further research in this area is needed to fully elucidate precursors for psychological health vulnerability and facilitate intervention development.

  8. A Cohort Study Evaluating the Implications of Biology, Weight Status and Socioeconomic Level on Global Self-Esteem Competence Among Female African-American Adolescents

    Science.gov (United States)

    Powell-Young, Yolanda M.; Zabaleta, Jovanny; Velasco-Gonzalez, Cruz; Sothern, Melinda S.

    2014-01-01

    The link between obesity and self-esteem among minority youth has received minimal empirical evaluation. This study aims to describe the magnitude of risk that body mass index, household income, and transitional age have on global self-esteem levels among African-American adolescents. These analyses were conducted on cross-sectional data obtained from 264 urban-dwelling African-American females between 14 and 18 years of age. Survey data on global self-esteem levels, transitory age, and socioeconomic levels were collected using self-administered questionnaires. Measured height and weight values were used to calculate and categorize weight status according to body mass index. Logistic regression models examined the probability of reporting less than average levels of global self-esteem. Adolescent African-American females residing in low-income households were 10 times more likely to report lower global self-esteem scores than those individuals from more affluent households (95% CI: 1.94, 60.19, p self-esteem among participants in this study. Household income appears to be the greatest predictor of global self-esteem levels. Further research in this area is needed to fully elucidate precursors for psychological health vulnerability and facilitate intervention development. PMID:24218867

  9. Global metabolic analyses identify key differences in metabolite levels between polymyxin-susceptible and polymyxin-resistant Acinetobacter baumannii.

    Science.gov (United States)

    Maifiah, Mohd Hafidz Mahamad; Cheah, Soon-Ee; Johnson, Matthew D; Han, Mei-Ling; Boyce, John D; Thamlikitkul, Visanu; Forrest, Alan; Kaye, Keith S; Hertzog, Paul; Purcell, Anthony W; Song, Jiangning; Velkov, Tony; Creek, Darren J; Li, Jian

    2016-02-29

    Multidrug-resistant Acinetobacter baumannii presents a global medical crisis and polymyxins are used as the last-line therapy. This study aimed to identify metabolic differences between polymyxin-susceptible and polymyxin-resistant A. baumannii using untargeted metabolomics. The metabolome of each A. baumannii strain was measured using liquid chromatography-mass spectrometry. Multivariate and univariate statistics and pathway analyses were employed to elucidate metabolic differences between the polymyxin-susceptible and -resistant A. baumannii strains. Significant differences were identified between the metabolic profiles of the polymyxin-susceptible and -resistant A. baumannii strains. The lipopolysaccharide (LPS) deficient, polymyxin-resistant 19606R showed perturbation in specific amino acid and carbohydrate metabolites, particularly pentose phosphate pathway (PPP) and tricarboxylic acid (TCA) cycle intermediates. Levels of nucleotides were lower in the LPS-deficient 19606R. Furthermore, 19606R exhibited a shift in its glycerophospholipid profile towards increased abundance of short-chain lipids compared to the parent polymyxin-susceptible ATCC 19606. In contrast, in a pair of clinical isolates 03-149.1 (polymyxin-susceptible) and 03-149.2 (polymyxin-resistant, due to modification of lipid A), minor metabolic differences were identified. Notably, peptidoglycan biosynthesis metabolites were significantly depleted in both of the aforementioned polymyxin-resistant strains. This is the first comparative untargeted metabolomics study to show substantial differences in the metabolic profiles of the polymyxin-susceptible and -resistant A. baumannii.

  10. 100% energy supply coverage with renewable energy. Requirements for its implementation at the global, national and municipal level

    International Nuclear Information System (INIS)

    Rogall, Holger

    2014-01-01

    This book presents itself as a systematic, easily understandable introduction into the requirements for an energy supply based 100% on renewable energy. Its main focus is on the strategic paths that must be followed for this purpose in the realms of business, technology and governmental policy. It highlights the opportunities and impediments on the way, analysing in the process the roles of political, economic and civil society players from the global down to the municipal level. Starting out from the present state of discussion on the German energy transition it investigates the strengths and weak points of efficiency technologies and renewable energies available today and elaborates a strategic path for developing the necessary infrastructure. In awareness of the fact that 100% coverage will not come about from market mechanisms alone it explores the ecological crash barriers that need to be set up in addition. This is followed by chapters on the roles, interests and means of those players who can exert influence on the framing of the relevant political and legal instruments as well as their means of pursuing their interests. The book thus contributes to clarifying the possibilities of and impediments to achieving an energy supply system based 100% on renewable energy.

  11. Individual to Community-Level Faunal Responses to Environmental Change from a Marine Fossil Record of Early Miocene Global Warming

    Science.gov (United States)

    Belanger, Christina L.

    2012-01-01

    Modern climate change has a strong potential to shift earth systems and biological communities into novel states that have no present-day analog, leaving ecologists with no observational basis to predict the likely biotic effects. Fossil records contain long time-series of past environmental changes outside the range of modern observation, which are vital for predicting future ecological responses, and are capable of (a) providing detailed information on rates of ecological change, (b) illuminating the environmental drivers of those changes, and (c) recording the effects of environmental change on individual physiological rates. Outcrops of Early Miocene Newport Member of the Astoria Formation (Oregon) provide one such time series. This record of benthic foraminiferal and molluscan community change from continental shelf depths spans a past interval environmental change (∼20.3-16.7 mya) during which the region warmed 2.1–4.5°C, surface productivity and benthic organic carbon flux increased, and benthic oxygenation decreased, perhaps driven by intensified upwelling as on the modern Oregon coast. The Newport Member record shows that (a) ecological responses to natural environmental change can be abrupt, (b) productivity can be the primary driver of faunal change during global warming, (c) molluscs had a threshold response to productivity change while foraminifera changed gradually, and (d) changes in bivalve body size and growth rates parallel changes in taxonomic composition at the community level, indicating that, either directly or indirectly through some other biological parameter, the physiological tolerances of species do influence community change. Ecological studies in modern and fossil records that consider multiple ecological levels, environmental parameters, and taxonomic groups can provide critical information for predicting future ecological change and evaluating species vulnerability. PMID:22558424

  12. The genomic-level heritabilities of preparedness and plasticity in human life history: the strategic differentiation and integration of genetic transmissibilities

    Directory of Open Access Journals (Sweden)

    Michael Anthony Woodley of Menie

    2015-04-01

    Full Text Available The Continuous Parameter Estimation Model is applied to develop individual genomic-level heritabilities for the latent hierarchical structure and developmental dynamics of Life History (LH strategy LH strategies relate to the allocations of bioenergetic resources into different domains of fitness. LH has moderate to high population-level heritability in humans, both at the level of the high-order Super-K Factor and the lower-order factors, the K-Factor, Covitality Factor, and General Factor of Personality (GFP. Several important questions remain unexplored. We developed measures of genome-level heritabilities employing an American sample of 316 monozygotic (MZ and 274 dizygotic (DZ twin dyads and a Swedish sample of 863 MZ and 475 DZ twin dyads. This novel heritability index measures individual genetic transmissibility, therefore opening new avenues for analyzing complex interactions among heritable traits inaccessible to standard structural equations methods. For these samples: (1 moderate to high heritability of factor loadings of Super-K on its lower-order factors is demonstrated, evidencing biological preparedness, genetic accommodation, and the gene-culture coevolution of biased epigenetic rules of development; (2 moderate to high heritability of the magnitudes of the effect of the higher-order factors upon their loadings on their constituent factors, evidencing genetic constraints upon phenotypic plasticity; and (3 that heritability of the LH factors, of factor loadings, and of the magnitudes of the correlations among factors are weaker among those with slower LH speeds, demonstrating that inter-individual variation in transmissibility is a function of individual socioecological selection pressures.

  13. Musa sebagai Model Genom

    Directory of Open Access Journals (Sweden)

    RITA MEGIA

    2005-12-01

    Full Text Available During the meeting in Arlington, USA in 2001, the scientists grouped in PROMUSA agreed with the launching of the Global Musa Genomics Consortium. The Consortium aims to apply genomics technologies to the improvement of this important crop. These genome projects put banana as the third model species after Arabidopsis and rice that will be analyzed and sequenced. Comparing to Arabidopsis and rice, banana genome provides a unique and powerful insight into structural and in functional genomics that could not be found in those two species. This paper discussed these subjects-including the importance of banana as the fourth main food in the world, the evolution and biodiversity of this genetic resource and its parasite.

  14. Identifying the Impact of E-Selen on the Sterile Medfly Ceratitis capitata at the Genomic Level Using DNA Profile

    International Nuclear Information System (INIS)

    Zaghloul, Y.S.

    2014-01-01

    The antioxidant E-Selen is an exogenous antioxidant containing both selenium and vitamin E. It was added to the larval artificial diets of the Mediterranean fruit fly, Ceratitis capitata in various concentrations (0.1, 0.3, 0.5 and 1.5 mg) prior to irradiation in order to obtain fully competent males. The produced full grown pupae were exposed to gamma rays at a dose rate of 90 Gy. Biological assessment of two E-Selen concentrations 0.3 and 0.5 mg were found to ameliorate the fitness of the sterile insects as well as to increase significantly most of their amino acids content. The study of the PCR patterns of normal and irradiated C. capitata undertaken or not different doses of E-Selen prior to irradiation and contained in the larval diets induced some modifications to the DNA profiles. The appearance of some new bands and disappearance of others were frequently encountered during this investigation. The appearance of bands was attributed to a repair mechanism that occurs in the irradiated DNA. However, the similarity in the DNA patterns of the homogenate pupal of C. capitata was due to the irradiation-induced damage may be in genome regions other than the regions of study

  15. Complete mitochondrial genome of Clistocoeloma sinensis (Brachyura: Grapsoidea): Gene rearrangements and higher-level phylogeny of the Brachyura.

    Science.gov (United States)

    Xin, Zhao-Zhe; Liu, Yu; Zhang, Dai-Zhen; Chai, Xin-Yue; Wang, Zheng-Fei; Zhang, Hua-Bin; Zhou, Chun-Lin; Tang, Bo-Ping; Liu, Qiu-Ning

    2017-06-23

    Deciphering the animal mitochondrial genome (mitogenome) is very important to understand their molecular evolution and phylogenetic relationships. In this study, the complete mitogenome of Clistocoeloma sinensis was determined. The mitogenome of C. sinensis was 15,706 bp long, and its A+T content was 75.7%. The A+T skew of the mitogenome of C. sinensis was slightly negative (-0.020). All the transfer RNA genes had the typical cloverleaf structure, except for the trnS1 gene, which lacked a dihydroxyuridine arm. The two ribosomal RNA genes had 80.2% A+T content. The A+T-rich region spanned 684 bp. The gene order within the complete mitogenome of C. sinensis was identical to the pancrustacean ground pattern except for the translocation of trnH. Additionally, the gene order of trnI-trnQ-trnM in the pancrustacean ground pattern becomes trnQ-trnI-trnM in C. sinensis. Our phylogenetic analysis showed that C. sinensis and Sesarmops sinensis cluster together with high nodal support values, indicating that C. sinensis and S. sinensis have a sister group relationship. The results support that C. sinensis belongs to Grapsoidea, Sesarmidae. Our findings also indicate that Varunidae and Sesarmidae species share close relationships. Thus, mitogenomes are likely to be valuable tools for systematics in other groups of Crustacea.

  16. Genome-Wide Analysis of the World's Sheep Breeds Reveals High Levels of Historic Mixture and Strong Recent Selection

    Science.gov (United States)

    Kijas, James W.; Lenstra, Johannes A.; Hayes, Ben; Boitard, Simon; Porto Neto, Laercio R.; San Cristobal, Magali; Servin, Bertrand; McCulloch, Russell; Whan, Vicki; Gietzen, Kimberly; Paiva, Samuel; Barendse, William; Ciani, Elena; Raadsma, Herman; McEwan, John; Dalrymple, Brian

    2012-01-01

    Through their domestication and subsequent selection, sheep have been adapted to thrive in a diverse range of environments. To characterise the genetic consequence of both domestication and selection, we genotyped 49,034 SNP in 2,819 animals from a diverse collection of 74 sheep breeds. We find the majority of sheep populations contain high SNP diversity and have retained an effective population size much higher than most cattle or dog breeds, suggesting domestication occurred from a broad genetic base. Extensive haplotype sharing and generally low divergence time between breeds reveal frequent genetic exchange has occurred during the development of modern breeds. A scan of the genome for selection signals revealed 31 regions containing genes for coat pigmentation, skeletal morphology, body size, growth, and reproduction. We demonstrate the strongest selection signal has occurred in response to breeding for the absence of horns. The high density map of genetic variability provides an in-depth view of the genetic history for this important livestock species. PMID:22346734

  17. Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection.

    Directory of Open Access Journals (Sweden)

    James W Kijas

    2012-02-01

    Full Text Available Through their domestication and subsequent selection, sheep have been adapted to thrive in a diverse range of environments. To characterise the genetic consequence of both domestication and selection, we genotyped 49,034 SNP in 2,819 animals from a diverse collection of 74 sheep breeds. We find the majority of sheep populations contain high SNP diversity and have retained an effective population size much higher than most cattle or dog breeds, suggesting domestication occurred from a broad genetic base. Extensive haplotype sharing and generally low divergence time between breeds reveal frequent genetic exchange has occurred during the development of modern breeds. A scan of the genome for selection signals revealed 31 regions containing genes for coat pigmentation, skeletal morphology, body size, growth, and reproduction. We demonstrate the strongest selection signal has occurred in response to breeding for the absence of horns. The high density map of genetic variability provides an in-depth view of the genetic history for this important livestock species.

  18. Genetic predictors of response to serotonergic and noradrenergic antidepressants in major depressive disorder: a genome-wide analysis of individual-level data and a meta-analysis.

    Directory of Open Access Journals (Sweden)

    Katherine E Tansey

    Full Text Available It has been suggested that outcomes of antidepressant treatment for major depressive disorder could be significantly improved if treatment choice is informed by genetic data. This study aims to test the hypothesis that common genetic variants can predict response to antidepressants in a clinically meaningful way.The NEWMEDS consortium, an academia-industry partnership, assembled a database of over 2,000 European-ancestry individuals with major depressive disorder, prospectively measured treatment outcomes with serotonin reuptake inhibiting or noradrenaline reuptake inhibiting antidepressants and available genetic samples from five studies (three randomized controlled trials, one part-randomized controlled trial, and one treatment cohort study. After quality control, a dataset of 1,790 individuals with high-quality genome-wide genotyping provided adequate power to test the hypotheses that antidepressant response or a clinically significant differential response to the two classes of antidepressants could be predicted from a single common genetic polymorphism. None of the more than half million genetic markers significantly predicted response to antidepressants overall, serotonin reuptake inhibitors, or noradrenaline reuptake inhibitors, or differential response to the two types of antidepressants (genome-wide significance p<5×10(-8. No biological pathways were significantly overrepresented in the results. No significant associations (genome-wide significance p<5×10(-8 were detected in a meta-analysis of NEWMEDS and another large sample (STAR*D, with 2,897 individuals in total. Polygenic scoring found no convergence among multiple associations in NEWMEDS and STAR*D.No single common genetic variant was associated with antidepressant response at a clinically relevant level in a European-ancestry cohort. Effects specific to particular antidepressant drugs could not be investigated in the current study. Please see later in the article for the

  19. Combating a Global Threat to a Clonal Crop: Banana Black Sigatoka Pathogen Pseudocercospora fijiensis (Synonym Mycosphaerella fijiensis Genomes Reveal Clues for Disease Control.

    Directory of Open Access Journals (Sweden)

    Rafael E Arango Isaza

    2016-08-01

    Full Text Available Black Sigatoka or black leaf streak disease, caused by the Dothideomycete fungus Pseudocercospora fijiensis (previously: Mycosphaerella fijiensis, is the most significant foliar disease of banana worldwide. Due to the lack of effective host resistance, management of this disease requires frequent fungicide applications, which greatly increase the economic and environmental costs to produce banana. Weekly applications in most banana plantations lead to rapid evolution of fungicide-resistant strains within populations causing disease-control failures throughout the world. Given its extremely high economic importance, two strains of P. fijiensis were sequenced and assembled with the aid of a new genetic linkage map. The 74-Mb genome of P. fijiensis is massively expanded by LTR retrotransposons, making it the largest genome within the Dothideomycetes. Melting-curve assays suggest that the genomes of two closely related members of the Sigatoka disease complex, P. eumusae and P. musae, also are expanded. Electrophoretic karyotyping and analyses of molecular markers in P. fijiensis field populations showed chromosome-length polymorphisms and high genetic diversity. Genetic differentiation was also detected using neutral markers, suggesting strong selection with limited gene flow at the studied geographic scale. Frequencies of fungicide resistance in fungicide-treated plantations were much higher than those in untreated wild-type P. fijiensis populations. A homologue of the Cladosporium fulvum Avr4 effector, PfAvr4, was identified in the P. fijiensis genome. Infiltration of the purified PfAVR4 protein into leaves of the resistant banana variety Calcutta 4 resulted in a hypersensitive-like response. This result suggests that Calcutta 4 could carry an unknown resistance gene recognizing PfAVR4. Besides adding to our understanding of the overall Dothideomycete genome structures, the P. fijiensis genome will aid in developing fungicide treatment schedules

  20. Combating a Global Threat to a Clonal Crop: Banana Black Sigatoka Pathogen Pseudocercospora fijiensis (Synonym Mycosphaerella fijiensis) Genomes Reveal Clues for Disease Control.

    Science.gov (United States)

    Arango Isaza, Rafael E; Diaz-Trujillo, Caucasella; Dhillon, Braham; Aerts, Andrea; Carlier, Jean; Crane, Charles F; V de Jong, Tristan; de Vries, Ineke; Dietrich, Robert; Farmer, Andrew D; Fortes Fereira, Claudia; Garcia, Suzana; Guzman, Mauricio; Hamelin, Richard C; Lindquist, Erika A; Mehrabi, Rahim; Quiros, Olman; Schmutz, Jeremy; Shapiro, Harris; Reynolds, Elizabeth; Scalliet, Gabriel; Souza, Manoel; Stergiopoulos, Ioannis; Van der Lee, Theo A J; De Wit, Pierre J G M; Zapater, Marie-Françoise; Zwiers, Lute-Harm; Grigoriev, Igor V; Goodwin, Stephen B; Kema, Gert H J

    2016-08-01

    Black Sigatoka or black leaf streak disease, caused by the Dothideomycete fungus Pseudocercospora fijiensis (previously: Mycosphaerella fijiensis), is the most significant foliar disease of banana worldwide. Due to the lack of effective host resistance, management of this disease requires frequent fungicide applications, which greatly increase the economic and environmental costs to produce banana. Weekly applications in most banana plantations lead to rapid evolution of fungicide-resistant strains within populations causing disease-control failures throughout the world. Given its extremely high economic importance, two strains of P. fijiensis were sequenced and assembled with the aid of a new genetic linkage map. The 74-Mb genome of P. fijiensis is massively expanded by LTR retrotransposons, making it the largest genome within the Dothideomycetes. Melting-curve assays suggest that the genomes of two closely related members of the Sigatoka disease complex, P. eumusae and P. musae, also are expanded. Electrophoretic karyotyping and analyses of molecular markers in P. fijiensis field populations showed chromosome-length polymorphisms and high genetic diversity. Genetic differentiation was also detected using neutral markers, suggesting strong selection with limited gene flow at the studied geographic scale. Frequencies of fungicide resistance in fungicide-treated plantations were much higher than those in untreated wild-type P. fijiensis populations. A homologue of the Cladosporium fulvum Avr4 effector, PfAvr4, was identified in the P. fijiensis genome. Infiltration of the purified PfAVR4 protein into leaves of the resistant banana variety Calcutta 4 resulted in a hypersensitive-like response. This result suggests that Calcutta 4 could carry an unknown resistance gene recognizing PfAVR4. Besides adding to our understanding of the overall Dothideomycete genome structures, the P. fijiensis genome will aid in developing fungicide treatment schedules to combat this

  1. Does Climate Literacy Matter? A Case Study of U.S. Students' Level of Concern about Anthropogenic Global Warming

    Science.gov (United States)

    Bedford, Daniel

    2016-01-01

    Educators seeking to address global warming in their classrooms face numerous challenges, including the question of whether student opinions about anthropogenic global warming (AGW) can change in response to increased knowledge about the climate system. This article analyzes survey responses from 458 students at a primarily undergraduate…

  2. Future Coastal Population Growth and Exposure to Sea-Level Rise and Coastal Flooding - A Global Assessment

    Science.gov (United States)

    Neumann, Barbara; Vafeidis, Athanasios T.; Zimmermann, Juliane; Nicholls, Robert J.

    2015-01-01

    Coastal zones are exposed to a range of coastal hazards including sea-level rise with its related effects. At the same time, they are more densely populated than the hinterland and exhibit higher rates of population growth and urbanisation. As this trend is expected to continue into the future, we investigate how coastal populations will be affected by such impacts at global and regional scales by the years 2030 and 2060. Starting from baseline population estimates for the year 2000, we assess future population change in the low-elevation coastal zone and trends in exposure to 100-year coastal floods based on four different sea-level and socio-economic scenarios. Our method accounts for differential growth of coastal areas against the land-locked hinterland and for trends of urbanisation and expansive urban growth, as currently observed, but does not explicitly consider possible displacement or out-migration due to factors such as sea-level rise. We combine spatially explicit estimates of the baseline population with demographic data in order to derive scenario-driven projections of coastal population development. Our scenarios show that the number of people living in the low-elevation coastal zone, as well as the number of people exposed to flooding from 1-in-100 year storm surge events, is highest in Asia. China, India, Bangladesh, Indonesia and Viet Nam are estimated to have the highest total coastal population exposure in the baseline year and this ranking is expected to remain largely unchanged in the future. However, Africa is expected to experience the highest rates of population growth and urbanisation in the coastal zone, particularly in Egypt and sub-Saharan countries in Western and Eastern Africa. The results highlight countries and regions with a high degree of exposure to coastal flooding and help identifying regions where policies and adaptive planning for building resilient coastal communities are not only desirable but essential. Furthermore, we

  3. Future coastal population growth and exposure to sea-level rise and coastal flooding--a global assessment.

    Science.gov (United States)

    Neumann, Barbara; Vafeidis, Athanasios T; Zimmermann, Juliane; Nicholls, Robert J

    2015-01-01

    Coastal zones are exposed to a range of coastal hazards including sea-level rise with its related effects. At the same time, they are more densely populated than the hinterland and exhibit higher rates of population growth and urbanisation. As this trend is expected to continue into the future, we investigate how coastal populations will be affected by such impacts at global and regional scales by the years 2030 and 2060. Starting from baseline population estimates for the year 2000, we assess future population change in the low-elevation coastal zone and trends in exposure to 100-year coastal floods based on four different sea-level and socio-economic scenarios. Our method accounts for differential growth of coastal areas against the land-locked hinterland and for trends of urbanisation and expansive urban growth, as currently observed, but does not explicitly consider possible displacement or out-migration due to factors such as sea-level rise. We combine spatially explicit estimates of the baseline population with demographic data in order to derive scenario-driven projections of coastal population development. Our scenarios show that the number of people living in the low-elevation coastal zone, as well as the number of people exposed to flooding from 1-in-100 year storm surge events, is highest in Asia. China, India, Bangladesh, Indonesia and Viet Nam are estimated to have the highest total coastal population exposure in the baseline year and this ranking is expected to remain largely unchanged in the future. However, Africa is expected to experience the highest rates of population growth and urbanisation in the coastal zone, particularly in Egypt and sub-Saharan countries in Western and Eastern Africa. The results highlight countries and regions with a high degree of exposure to coastal flooding and help identifying regions where policies and adaptive planning for building resilient coastal communities are not only desirable but essential. Furthermore, we

  4. Future coastal population growth and exposure to sea-level rise and coastal flooding--a global assessment.

    Directory of Open Access Journals (Sweden)

    Barbara Neumann

    Full Text Available Coastal zones are exposed to a range of coastal hazards including sea-level rise with its related effects. At the same time, they are more densely populated than the hinterland and exhibit higher rates of population growth and urbanisation. As this trend is expected to continue into the future, we investigate how coastal populations will be affected by such impacts at global and regional scales by the years 2030 and 2060. Starting from baseline population estimates for the year 2000, we assess future population change in the low-elevation coastal zone and trends in exposure to 100-year coastal floods based on four different sea-level and socio-economic scenarios. Our method accounts for differential growth of coastal areas against the land-locked hinterland and for trends of urbanisation and expansive urban growth, as currently observed, but does not explicitly consider possible displacement or out-migration due to factors such as sea-level rise. We combine spatially explicit estimates of the baseline population with demographic data in order to derive scenario-driven projections of coastal population development. Our scenarios show that the number of people living in the low-elevation coastal zone, as well as the number of people exposed to flooding from 1-in-100 year storm surge events, is highest in Asia. China, India, Bangladesh, Indonesia and Viet Nam are estimated to have the highest total coastal population exposure in the baseline year and this ranking is expected to remain largely unchanged in the future. However, Africa is expected to experience the highest rates of population growth and urbanisation in the coastal zone, particularly in Egypt and sub-Saharan countries in Western and Eastern Africa. The results highlight countries and regions with a high degree of exposure to coastal flooding and help identifying regions where policies and adaptive planning for building resilient coastal communities are not only desirable but essential

  5. Rice Genome Research: Current Status and Future Perspectives

    Directory of Open Access Journals (Sweden)

    Bin Han

    2008-11-01

    Full Text Available Rice ( L. is the leading genomics system among the crop plants. The sequence of the rice genome, the first cereal plant genome, was published in 2005. This review summarizes progress made in rice genome annotations, comparative genomics, and functional genomics researches. It also maps out the status of rice genomics globally and provides a vision of future research directions and resource building.

  6. Consequences of 1.5 °C and 2 °C global warming levels for temperature and precipitation changes over Central Africa

    Science.gov (United States)

    Pokam Mba, Wilfried; Longandjo, Georges-Noel T.; Moufouma-Okia, Wilfran; Bell, Jean-Pierre; James, Rachel; Vondou, Derbetini A.; Haensler, Andreas; Fotso-Nguemo, Thierry C.; Merlin Guenang, Guy; Djiotang Tchotchou, Angennes Lucie; Kamsu-Tamo, Pierre H.; Takong, Ridick R.; Nikulin, Grigory; Lennard, Christopher J.; Dosio, Alessandro

    2018-05-01

    Discriminating climate impacts between 1.5 °C and 2 °C warming levels is particularly important for Central Africa, a vulnerable region where multiple biophysical, political, and socioeconomic stresses interact to constrain the region’s adaptive capacity. This study uses an ensemble of 25 transient Regional Climate Model (RCM) simulations from the CORDEX initiative, forced with the Repre