WorldWideScience

Sample records for global genome organization

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

    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.

  2. Rodent malaria parasites : genome organization & comparative genomics

    Kooij, Taco W.A.

    2006-01-01

    The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P.

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

    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

  4. Organizing for Global Sourcing

    Bals, Lydia; Turkulainen, Virpi

    Research on Purchasing Organization is dominated by studies on centralization versus decentralization. While global sourcing relates to the integrated activities of purchasing and other functions in line with the company’s strategic objectives and while it has been put forward that hybrid...

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

    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

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

    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

  7. Team-based global organizations

    Zander, Lena; Butler, Christina; Mockaitis, Audra

    2015-01-01

    diversity in enhancing team creativity and performance, and 2) the sharing of knowledge in team-based organizations, while the other two themes address global team leadership: 3) the unprecedented significance of social capital for the success of global team leader roles; and 4) the link between shared......This chapter draws on a panel discussion of the future of global organizing as a team-based organization at EIBA 2014 in Uppsala, Sweden. We began by discussing contemporary developments of hybrid forms of hierarchy and teams-based organizing, but we venture to propose that as organizations become...... characterized by decreased importance of hierarchal structures, more fluidity across borders, even a possible dissolution of firm boundaries, we move towards team-based organizing as an alternative to more traditional forms of hierarchical-based organizing in global firms. To provide input for a discussion...

  8. Biology, genome organization and evolution of parvoviruses in marine shrimp

    A number of parvoviruses are now know to infect marine shrimp, and these viruses alone or in combination with other viruses have the potential to cause major losses in shrimp aquaculture globally. This review provides a comprehensive overview of the biology, genome organization, gene expression, and...

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

    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.

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

    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

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

    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.

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

    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.

  13. Genome organization, instabilities, stem cells, and cancer

    Senthil Kumar Pazhanisamy

    2009-01-01

    Full Text Available It is now widely recognized that advances in exploring genome organization provide remarkable insights on the induction and progression of chromosome abnormalities. Much of what we know about how mutations evolve and consequently transform into genome instabilities has been characterized in the spatial organization context of chromatin. Nevertheless, many underlying concepts of impact of the chromatin organization on perpetuation of multiple mutations and on propagation of chromosomal aberrations remain to be investigated in detail. Genesis of genome instabilities from accumulation of multiple mutations that drive tumorigenesis is increasingly becoming a focal theme in cancer studies. This review focuses on structural alterations evolve to raise a variety of genome instabilities that are manifested at the nucleotide, gene or sub-chromosomal, and whole chromosome level of genome. Here we explore an underlying connection between genome instability and cancer in the light of genome architecture. This review is limited to studies directed towards spatial organizational aspects of origin and propagation of aberrations into genetically unstable tumors.

  14. Genome Organization Drives Chromosome Fragility.

    Canela, Andres; Maman, Yaakov; Jung, Seolkyoung; Wong, Nancy; Callen, Elsa; Day, Amanda; Kieffer-Kwon, Kyong-Rim; Pekowska, Aleksandra; Zhang, Hongliang; Rao, Suhas S P; Huang, Su-Chen; Mckinnon, Peter J; Aplan, Peter D; Pommier, Yves; Aiden, Erez Lieberman; Casellas, Rafael; Nussenzweig, André

    2017-07-27

    In this study, we show that evolutionarily conserved chromosome loop anchors bound by CCCTC-binding factor (CTCF) and cohesin are vulnerable to DNA double strand breaks (DSBs) mediated by topoisomerase 2B (TOP2B). Polymorphisms in the genome that redistribute CTCF/cohesin occupancy rewire DNA cleavage sites to novel loop anchors. While transcription- and replication-coupled genomic rearrangements have been well documented, we demonstrate that DSBs formed at loop anchors are largely transcription-, replication-, and cell-type-independent. DSBs are continuously formed throughout interphase, are enriched on both sides of strong topological domain borders, and frequently occur at breakpoint clusters commonly translocated in cancer. Thus, loop anchors serve as fragile sites that generate DSBs and chromosomal rearrangements. VIDEO ABSTRACT. Published by Elsevier Inc.

  15. An overview on genome organization of marine organisms.

    Costantini, Maria

    2015-12-01

    In this review we will concentrate on some general genome features of marine organisms and their evolution, ranging from vertebrate to invertebrates until unicellular organisms. Before genome sequencing, the ultracentrifugation in CsCl led to high resolution of mammalian DNA (without seeing at the sequence). The analytical profile of human DNA showed that the vertebrate genome is a mosaic of isochores, typically megabase-size DNA segments that belong in a small number of families characterized by different GC levels. The recent availability of a number of fully sequenced genomes allowed mapping very precisely the isochores, based on DNA sequences. Since isochores are tightly linked to biological properties such as gene density, replication timing and recombination, the new level of detail provided by the isochore map helped the understanding of genome structure, function and evolution. This led the current level of knowledge and to further insights. Copyright © 2015. Published by Elsevier B.V.

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

    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

  17. Genomic analysis of Xenopus organizer function

    Suhai Sándor

    2006-06-01

    Full Text Available Abstract Background Studies of the Xenopus organizer have laid the foundation for our understanding of the conserved signaling pathways that pattern vertebrate embryos during gastrulation. The two primary activities of the organizer, BMP and Wnt inhibition, can regulate a spectrum of genes that pattern essentially all aspects of the embryo during gastrulation. As our knowledge of organizer signaling grows, it is imperative that we begin knitting together our gene-level knowledge into genome-level signaling models. The goal of this paper was to identify complete lists of genes regulated by different aspects of organizer signaling, thereby providing a deeper understanding of the genomic mechanisms that underlie these complex and fundamental signaling events. Results To this end, we ectopically overexpress Noggin and Dkk-1, inhibitors of the BMP and Wnt pathways, respectively, within ventral tissues. After isolating embryonic ventral halves at early and late gastrulation, we analyze the transcriptional response to these molecules within the generated ectopic organizers using oligonucleotide microarrays. An efficient statistical analysis scheme, combined with a new Gene Ontology biological process annotation of the Xenopus genome, allows reliable and faithful clustering of molecules based upon their roles during gastrulation. From this data, we identify new organizer-related expression patterns for 19 genes. Moreover, our data sub-divides organizer genes into separate head and trunk organizing groups, which each show distinct responses to Noggin and Dkk-1 activity during gastrulation. Conclusion Our data provides a genomic view of the cohorts of genes that respond to Noggin and Dkk-1 activity, allowing us to separate the role of each in organizer function. These patterns demonstrate a model where BMP inhibition plays a largely inductive role during early developmental stages, thereby initiating the suites of genes needed to pattern dorsal tissues

  18. Building a Global Responsive Organization:

    Sun, Xinbo; Cao, Yi; Li, Suxiu

    2017-01-01

    This chapter outlines the philosophic underpinnings of the self-management paradigm developed over the past three decades by China’s Haier Group, a global leader in white goods. The successful transformation of Haier from a small resource-poor firm to a dominant global giant is often attributed...... to the self-management culture established in the company by its legendary leader Zhang Ruimin. This management paradigm is a function of the humbleness displayed by Mr. Zhang Ruimin and rooted in his strong belief in the traditional Chinese philosophy of I-Ching and Daoism. We show how the hexagram of Qian...... (“qian”: humbleness, modesty) from I-Ching is linked to Mr. Zhang’s humble approach and analyze how the six parts of the hexagram of Qian are related to the six development stages of the Haier Group. These insights are used to give some thoughts to the leadership challenge associated with the creation...

  19. The Future of Global Organizing

    van Tulder, Rob; Verbeke, Alain; Drogendijk, Rian

    2015-01-01

    This research and teaching volume was composed in honour of the late Alan Rugman, a distinguished thought leader, organizer and educator in the field of international business (IB). The volume addresses Rugman’s main research focus in a career that spanned almost 40 years, namely the organizational

  20. Staffing the Global Organization: "Cultural Nomads"

    McPhail, Ruth; Fisher, Ron; Harvey, Michael; Moeller, Miriam

    2012-01-01

    This article explores the evolution of international staffing in an increasingly globalized and hypercompetitive marketplace. As the issue of staff retention becomes critical in global organizations, it is important to understand the types of managers that may be on or assigned to overseas assignments. The purpose of this article is to present a…

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

    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.

  2. Genomic organization of plant aminopropyl transferases.

    Rodríguez-Kessler, Margarita; Delgado-Sánchez, Pablo; Rodríguez-Kessler, Gabriela Theresia; Moriguchi, Takaya; Jiménez-Bremont, Juan Francisco

    2010-07-01

    Aminopropyl transferases like spermidine synthase (SPDS; EC 2.5.1.16), spermine synthase and thermospermine synthase (SPMS, tSPMS; EC 2.5.1.22) belong to a class of widely distributed enzymes that use decarboxylated S-adenosylmethionine as an aminopropyl donor and putrescine or spermidine as an amino acceptor to form in that order spermidine, spermine or thermospermine. We describe the analysis of plant genomic sequences encoding SPDS, SPMS, tSPMS and PMT (putrescine N-methyltransferase; EC 2.1.1.53). Genome organization (including exon size, gain and loss, as well as intron number, size, loss, retention, placement and phase, and the presence of transposons) of plant aminopropyl transferase genes were compared between the genomic sequences of SPDS, SPMS and tSPMS from Zea mays, Oryza sativa, Malus x domestica, Populus trichocarpa, Arabidopsis thaliana and Physcomitrella patens. In addition, the genomic organization of plant PMT genes, proposed to be derived from SPDS during the evolution of alkaloid metabolism, is illustrated. Herein, a particular conservation and arrangement of exon and intron sequences between plant SPDS, SPMS and PMT genes that clearly differs with that of ACL5 genes, is shown. The possible acquisition of the plant SPMS exon II and, in particular exon XI in the monocot SPMS genes, is a remarkable feature that allows their differentiation from SPDS genes. In accordance with our in silico analysis, functional complementation experiments of the maize ZmSPMS1 enzyme (previously considered to be SPDS) in yeast demonstrated its spermine synthase activity. Another significant aspect is the conservation of intron sequences among SPDS and PMT paralogs. In addition the existence of microsynteny among some SPDS paralogs, especially in P. trichocarpa and A. thaliana, supports duplication events of plant SPDS genes. Based in our analysis, we hypothesize that SPMS genes appeared with the divergence of vascular plants by a processes of gene duplication and the

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

    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.

  4. Evolution of Genome Organization and Epigenetic Machineries ...

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    The compact folded structure of bacterial genomic material is termed as nucleoid. The ... from pluripotent to the differentiated stage of a cell, there is a dramatic alteration both in the .... Sherratt, D.J. 2003 Bacterial Chromosome Dynamics.

  5. The genomic organization of plant pathogenicity in Fusarium species

    Rep, M.; Kistler, H.C.

    2010-01-01

    Comparative genomics is a powerful tool to infer the molecular basis of fungal pathogenicity and its evolution by identifying differences in gene content and genomic organization between fungi with different hosts or modes of infection. Through comparative analysis, pathogenicity-related chromosomes

  6. Approaching the Sequential and Three-Dimensional Organization of Genomes

    T.A. Knoch (Tobias)

    2006-01-01

    textabstractGenomes are one of the major foundations of life due to their role in information storage, process regulation and evolution. To achieve a deeper unterstanding of the human genome the three-dimensional organization of the human cell nucleus, the structural-, scaling- and dynamic

  7. Genomic Organization of Zebrafish microRNAs

    Paydar Ima

    2008-05-01

    Full Text Available Abstract Background microRNAs (miRNAs are small (~22 nt non-coding RNAs that regulate cell movement, specification, and development. Expression of miRNAs is highly regulated, both spatially and temporally. Based on direct cloning, sequence conservation, and predicted secondary structures, a large number of miRNAs have been identified in higher eukaryotic genomes but whether these RNAs are simply a subset of a much larger number of noncoding RNA families is unknown. This is especially true in zebrafish where genome sequencing and annotation is not yet complete. Results We analyzed the zebrafish genome to identify the number and location of proven and predicted miRNAs resulting in the identification of 35 new miRNAs. We then grouped all 415 zebrafish miRNAs into families based on seed sequence identity as a means to identify possible functional redundancy. Based on genomic location and expression analysis, we also identified those miRNAs that are likely to be encoded as part of polycistronic transcripts. Lastly, as a resource, we compiled existing zebrafish miRNA expression data and, where possible, listed all experimentally proven mRNA targets. Conclusion Current analysis indicates the zebrafish genome encodes 415 miRNAs which can be grouped into 44 families. The largest of these families (the miR-430 family contains 72 members largely clustered in two main locations along chromosome 4. Thus far, most zebrafish miRNAs exhibit tissue specific patterns of expression.

  8. Global features of the Alcanivorax borkumensis SK2 genome

    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...

  9. Strategic Positioning of IT in Global Organizations

    Siurdyban, Artur

    2010-01-01

    understanding of the role of IT in value creation from a business process perspective, and at the same time practitioners may use it to diagnose, communicate and plan IT positioning in their companies. The tool consists of visual maps assigning different steps of the business process management lifecycle......Executives in large global corporations are faced with a number of non-alternative decision parameters determining the strategic positioning of their IT units. These parameters include organizational structures, competence development and distribution among central and local levels, goal setting...... and type of value contributed to the organization. Although the existing body of research addresses these issues in numerous ways, the concepts have not been fully applied in practice. This paper proposes a tool for strategic positioning of IT in large global companies. It contributes to the overall...

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

    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.

  11. Globalization and Cross-Border Labor Organizing

    Ralph Armbruster

    2015-08-01

    Full Text Available The globalization of the world economy has opened up new possibilities for cross-border labor organizing. In fact, several U.S. unions are working together with unions from Mexico, Honduras, Guatemala, the Dominican Republic, Japan, South Korea, and many European nations. For example, over the last several years, UNITE (Union of Needletrades, Industrial, and Textile Employees, the AFL-CIO, and the international garment workers trade secretariat have worked directly with maquiladora workers in Honduras and the Dominican Republic. These efforts led to the formation of several labor unions and the first contracts ever negotiated in the maquiladoras in the Dominican Republic. In addition, labor rights and solidarity organizations, like the Campaign for Labor Rights, Witness for Peace, and the US/Guatemala Labor Education Project (US/GLEP, along with many other groups, have also played key roles in the formation of maquiladora unions in Nicaragua and Guatemala.

  12. cDNA structure, genomic organization and expression patterns of ...

    Visfatin was a newly identified adipocytokine, which was involved in various physiologic and pathologic processes of organisms. The cDNA structure, genomic organization and expression patterns of silver Prussian carp visfatin were described in this report. The silver Prussian carp visfatin cDNA cloned from the liver was ...

  13. Azolla--a model organism for plant genomic studies.

    Qiu, Yin-Long; Yu, Jun

    2003-02-01

    The aquatic ferns of the genus Azolla are nitrogen-fixing plants that have great potentials in agricultural production and environmental conservation. Azolla in many aspects is qualified to serve as a model organism for genomic studies because of its importance in agriculture, its unique position in plant evolution, its symbiotic relationship with the N2-fixing cyanobacterium, Anabaena azollae, and its moderate-sized genome. The goals of this genome project are not only to understand the biology of the Azolla genome to promote its applications in biological research and agriculture practice but also to gain critical insights about evolution of plant genomes. Together with the strategic and technical improvement as well as cost reduction of DNA sequencing, the deciphering of their genetic code is imminent.

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

    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.

  15. Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire

    Phillips Ruth B

    2010-10-01

    Full Text Available Abstract Background The genomes of salmonids are considered pseudo-tetraploid undergoing reversion to a stable diploid state. Given the genome duplication and extensive biological data available for salmonids, they are excellent model organisms for studying comparative genomics, evolutionary processes, fates of duplicated genes and the genetic and physiological processes associated with complex behavioral phenotypes. The evolution of the tetrapod hemoglobin genes is well studied; however, little is known about the genomic organization and evolution of teleost hemoglobin genes, particularly those of salmonids. The Atlantic salmon serves as a representative salmonid species for genomics studies. Given the well documented role of hemoglobin in adaptation to varied environmental conditions as well as its use as a model protein for evolutionary analyses, an understanding of the genomic structure and organization of the Atlantic salmon α and β hemoglobin genes is of great interest. Results We identified four bacterial artificial chromosomes (BACs comprising two hemoglobin gene clusters spanning the entire α and β hemoglobin gene repertoire of the Atlantic salmon genome. Their chromosomal locations were established using fluorescence in situ hybridization (FISH analysis and linkage mapping, demonstrating that the two clusters are located on separate chromosomes. The BACs were sequenced and assembled into scaffolds, which were annotated for putatively functional and pseudogenized hemoglobin-like genes. This revealed that the tail-to-tail organization and alternating pattern of the α and β hemoglobin genes are well conserved in both clusters, as well as that the Atlantic salmon genome houses substantially more hemoglobin genes, including non-Bohr β globin genes, than the genomes of other teleosts that have been sequenced. Conclusions We suggest that the most parsimonious evolutionary path leading to the present organization of the Atlantic salmon

  16. Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire

    2010-01-01

    Background The genomes of salmonids are considered pseudo-tetraploid undergoing reversion to a stable diploid state. Given the genome duplication and extensive biological data available for salmonids, they are excellent model organisms for studying comparative genomics, evolutionary processes, fates of duplicated genes and the genetic and physiological processes associated with complex behavioral phenotypes. The evolution of the tetrapod hemoglobin genes is well studied; however, little is known about the genomic organization and evolution of teleost hemoglobin genes, particularly those of salmonids. The Atlantic salmon serves as a representative salmonid species for genomics studies. Given the well documented role of hemoglobin in adaptation to varied environmental conditions as well as its use as a model protein for evolutionary analyses, an understanding of the genomic structure and organization of the Atlantic salmon α and β hemoglobin genes is of great interest. Results We identified four bacterial artificial chromosomes (BACs) comprising two hemoglobin gene clusters spanning the entire α and β hemoglobin gene repertoire of the Atlantic salmon genome. Their chromosomal locations were established using fluorescence in situ hybridization (FISH) analysis and linkage mapping, demonstrating that the two clusters are located on separate chromosomes. The BACs were sequenced and assembled into scaffolds, which were annotated for putatively functional and pseudogenized hemoglobin-like genes. This revealed that the tail-to-tail organization and alternating pattern of the α and β hemoglobin genes are well conserved in both clusters, as well as that the Atlantic salmon genome houses substantially more hemoglobin genes, including non-Bohr β globin genes, than the genomes of other teleosts that have been sequenced. Conclusions We suggest that the most parsimonious evolutionary path leading to the present organization of the Atlantic salmon hemoglobin genes involves

  17. HCMI Organization | Office of Cancer Genomics

    Consortium The Human Cancer Models Initiative (HCMI) was created and funded by the US National Cancer Institute, Cancer Research UK, the foundation Hubrecht Organoid Technology, and the Wellcome Sanger Institute. Together, these organizations develop policy and make programmatic decisions to contribute to the function of the HCMI. National Cancer Institute

  18. The draft genome of a termite illuminates alternative social organization

    Termites have substantial economic and ecological impact worldwide. They are also the oldest organisms living in complex societies, having evolved a caste system independent of that of eusocial Hymenoptera (ants, bees and wasps). Here we provide the first genome sequence for a termite, Zootermopsis ...

  19. Structural Genomics of Minimal Organisms: Pipeline and Results

    Kim, Sung-Hou; Shin, Dong-Hae; Kim, Rosalind; Adams, Paul; Chandonia, John-Marc

    2007-09-14

    The initial objective of the Berkeley Structural Genomics Center was to obtain a near complete three-dimensional (3D) structural information of all soluble proteins of two minimal organisms, closely related pathogens Mycoplasma genitalium and M. pneumoniae. The former has fewer than 500 genes and the latter has fewer than 700 genes. A semiautomated structural genomics pipeline was set up from target selection, cloning, expression, purification, and ultimately structural determination. At the time of this writing, structural information of more than 93percent of all soluble proteins of M. genitalium is avail able. This chapter summarizes the approaches taken by the authors' center.

  20. Mycoplasma hyopneumoniae Transcription Unit Organization: Genome Survey and Prediction

    Siqueira, Franciele Maboni; Schrank, Augusto; Schrank, Irene Silveira

    2011-01-01

    Mycoplasma hyopneumoniae is associated with swine respiratory diseases. Although gene organization and regulation are well known in many prokaryotic organisms, knowledge on mycoplasma is limited. This study performed a comparative analysis of three strains of M. hyopneumoniae (7448, J and 232), with a focus on genome organization and gene comparison for open read frame (ORF) cluster (OC) identification. An in silico analysis of gene organization demonstrated 117 OCs and 34 single ORFs in M. hyopneumoniae 7448 and J, while 116 OCs and 36 single ORFs were identified in M. hyopneumoniae 232. Genomic comparison revealed high synteny and conservation of gene order between the OCs defined for 7448 and J strains as well as for 7448 and 232 strains. Twenty-one OCs were chosen and experimentally confirmed by reverse transcription–PCR from M. hyopneumoniae 7448 genome, validating our prediction. A subset of the ORFs within an OC could be independently transcribed due to the presence of internal promoters. Our results suggest that transcription occurs in ‘run-on’ from an upstream promoter in M. hyopneumoniae, thus forming large ORF clusters (from 2 to 29 ORFs in the same orientation) and indicating a complex transcriptional organization. PMID:22086999

  1. Global Education Greenhouse: Constructing and Organizing Online Global Knowledge

    K. Kaun (Kaun); P.A. Arora (Payal)

    2010-01-01

    textabstractEducation, and the knowledge it generates, is seen as a means to effective participation in societies and economies that are affected by globalization (UNESCO). The United Nations Decade of Education for Sustainable Development (2005-2015) was declared by a Resolution of the General

  2. The footprint of metabolism in the organization of mammalian genomes

    Berná Luisa

    2012-05-01

    Full Text Available Abstract Background At present five evolutionary hypotheses have been proposed to explain the great variability of the genomic GC content among and within genomes: the mutational bias, the biased gene conversion, the DNA breakpoints distribution, the thermal stability and the metabolic rate. Several studies carried out on bacteria and teleostean fish pointed towards the critical role played by the environment on the metabolic rate in shaping the base composition of genomes. In mammals the debate is still open, and evidences have been produced in favor of each evolutionary hypothesis. Human genes were assigned to three large functional categories (as well as to the corresponding functional classes according to the KOG database: (i information storage and processing, (ii cellular processes and signaling, and (iii metabolism. The classification was extended to the organisms so far analyzed performing a reciprocal Blastp and selecting the best reciprocal hit. The base composition was calculated for each sequence of the whole CDS dataset. Results The GC3 level of the above functional categories was increasing from (i to (iii. This specific compositional pattern was found, as footprint, in all mammalian genomes, but not in frog and lizard ones. Comparative analysis of human versus both frog and lizard functional categories showed that genes involved in the metabolic processes underwent the highest GC3 increment. Analyzing the KOG functional classes of genes, again a well defined intra-genomic pattern was found in all mammals. Not only genes of metabolic pathways, but also genes involved in chromatin structure and dynamics, transcription, signal transduction mechanisms and cytoskeleton, showed an average GC3 level higher than that of the whole genome. In the case of the human genome, the genes of the aforementioned functional categories showed a high probability to be associated with the chromosomal bands. Conclusions In the light of different

  3. The DNA-encoded nucleosome organization of a eukaryotic genome.

    Kaplan, Noam; Moore, Irene K; Fondufe-Mittendorf, Yvonne; Gossett, Andrea J; Tillo, Desiree; Field, Yair; LeProust, Emily M; Hughes, Timothy R; Lieb, Jason D; Widom, Jonathan; Segal, Eran

    2009-03-19

    Nucleosome organization is critical for gene regulation. In living cells this organization is determined by multiple factors, including the action of chromatin remodellers, competition with site-specific DNA-binding proteins, and the DNA sequence preferences of the nucleosomes themselves. However, it has been difficult to estimate the relative importance of each of these mechanisms in vivo, because in vivo nucleosome maps reflect the combined action of all influencing factors. Here we determine the importance of nucleosome DNA sequence preferences experimentally by measuring the genome-wide occupancy of nucleosomes assembled on purified yeast genomic DNA. The resulting map, in which nucleosome occupancy is governed only by the intrinsic sequence preferences of nucleosomes, is similar to in vivo nucleosome maps generated in three different growth conditions. In vitro, nucleosome depletion is evident at many transcription factor binding sites and around gene start and end sites, indicating that nucleosome depletion at these sites in vivo is partly encoded in the genome. We confirm these results with a micrococcal nuclease-independent experiment that measures the relative affinity of nucleosomes for approximately 40,000 double-stranded 150-base-pair oligonucleotides. Using our in vitro data, we devise a computational model of nucleosome sequence preferences that is significantly correlated with in vivo nucleosome occupancy in Caenorhabditis elegans. Our results indicate that the intrinsic DNA sequence preferences of nucleosomes have a central role in determining the organization of nucleosomes in vivo.

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

    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 ...

  5. Anthropogenic impacts on global organic river pollution

    Wen, Y.

    2017-01-01

    Organic pollution of rivers by wastewater discharge from human activities negatively impacts people and ecosystems. Without treatment, pollution control relies on a combination of natural degradation and dilution by natural runoff to reduce downstream effects. To implement integrated water

  6. MULTILATERAL ORGANIZATIONS AND GLOBAL INEQUALITY: A ...

    Prof

    particular look at the three multilateral organizations viz IMF, World. Bank and ... The Nigerian experience with the implementation of SAP which the. IMF and ..... Devaluation of national currency and that is a reduction in the exchange value of.

  7. Hepatitis A Virus Genome Organization and Replication Strategy.

    McKnight, Kevin L; Lemon, Stanley M

    2018-04-02

    Hepatitis A virus (HAV) is a positive-strand RNA virus classified in the genus Hepatovirus of the family Picornaviridae It is an ancient virus with a long evolutionary history and multiple features of its capsid structure, genome organization, and replication cycle that distinguish it from other mammalian picornaviruses. HAV proteins are produced by cap-independent translation of a single, long open reading frame under direction of an inefficient, upstream internal ribosome entry site (IRES). Genome replication occurs slowly and is noncytopathic, with transcription likely primed by a uridylated protein primer as in other picornaviruses. Newly produced quasi-enveloped virions (eHAV) are released from cells in a nonlytic fashion in a unique process mediated by interactions of capsid proteins with components of the host cell endosomal sorting complexes required for transport (ESCRT) system. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

  8. Marine Genomics: A clearing-house for genomic and transcriptomic data of marine organisms

    Trent Harold F

    2005-03-01

    Full Text Available Abstract Background The Marine Genomics project is a functional genomics initiative developed to provide a pipeline for the curation of Expressed Sequence Tags (ESTs and gene expression microarray data for marine organisms. It provides a unique clearing-house for marine specific EST and microarray data and is currently available at http://www.marinegenomics.org. Description The Marine Genomics pipeline automates the processing, maintenance, storage and analysis of EST and microarray data for an increasing number of marine species. It currently contains 19 species databases (over 46,000 EST sequences that are maintained by registered users from local and remote locations in Europe and South America in addition to the USA. A collection of analysis tools are implemented. These include a pipeline upload tool for EST FASTA file, sequence trace file and microarray data, an annotative text search, automated sequence trimming, sequence quality control (QA/QC editing, sequence BLAST capabilities and a tool for interactive submission to GenBank. Another feature of this resource is the integration with a scientific computing analysis environment implemented by MATLAB. Conclusion The conglomeration of multiple marine organisms with integrated analysis tools enables users to focus on the comprehensive descriptions of transcriptomic responses to typical marine stresses. This cross species data comparison and integration enables users to contain their research within a marine-oriented data management and analysis environment.

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

    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...

  10. A global bioethical perspective on organ trafficking: Discrimination ...

    2017-06-21

    Jun 21, 2017 ... along with other ethical problems, is inherently discriminatory, and in many instances, the ... Although organ trafficking is a global issue and prohibited by most countries ..... Dordrecht: Springer Science and Business. Media ...

  11. A global bioethical perspective on organ trafficking: Discrimination ...

    A global bioethical perspective on organ trafficking: Discrimination, stigmatisation and the vulnerable. ... South African Journal of Bioethics and Law ... be used as an influential appeal to the world community to combat these activities together.

  12. Tracing Uganda's global primary organic pineapple value chain ...

    The organic sector is one of the fastest growing sectors globally. ... opportunity for developing countries to export high value products in the global market. ... It is clear from the study that the chain is private- sector-driven, has relatively young ...

  13. Global initiatives to tackle organ trafficking and transplant tourism.

    Bagheri, Alireza; Delmonico, Francis L

    2013-11-01

    The increasing gap between organ supply and demand has opened the door for illegal organ sale, trafficking of human organs, tissues and cells, as well as transplant tourism. Currently, underprivileged and vulnerable populations in resource-poor countries are a major source of organs for rich patient-tourists who can afford to purchase organs at home or abroad. This paper presents a summary of international initiatives, such as World Health Organization's Principle Guidelines, The Declaration of Istanbul, Asian Task Force Recommendations, as well as UNESCO's and the United Nation's initiatives against trafficking of human organs, tissues, cells, and transplant tourism. Beyond the summary, it calls for more practical measures to be taken to implement the existing guidelines and recommendations, in order to prevent exploitation of the poor as organ providers. The paper suggests that an international legally binding agreement in criminalizing organ trafficking would be a step forward to bring a change in the global picture of organ trafficking and transplant tourism.

  14. Effects of aneuploidy on genome structure, expression, and interphase organization in Arabidopsis thaliana.

    Bruno Huettel

    2008-10-01

    Full Text Available Aneuploidy refers to losses and/or gains of individual chromosomes from the normal chromosome set. The resulting gene dosage imbalance has a noticeable affect on the phenotype, as illustrated by aneuploid syndromes, including Down syndrome in humans, and by human solid tumor cells, which are highly aneuploid. Although the phenotypic manifestations of aneuploidy are usually apparent, information about the underlying alterations in structure, expression, and interphase organization of unbalanced chromosome sets is still sparse. Plants generally tolerate aneuploidy better than animals, and, through colchicine treatment and breeding strategies, it is possible to obtain inbred sibling plants with different numbers of chromosomes. This possibility, combined with the genetic and genomics tools available for Arabidopsis thaliana, provides a powerful means to assess systematically the molecular and cytological consequences of aberrant numbers of specific chromosomes. Here, we report on the generation of Arabidopsis plants in which chromosome 5 is present in triplicate. We compare the global transcript profiles of normal diploids and chromosome 5 trisomics, and assess genome integrity using array comparative genome hybridization. We use live cell imaging to determine the interphase 3D arrangement of transgene-encoded fluorescent tags on chromosome 5 in trisomic and triploid plants. The results indicate that trisomy 5 disrupts gene expression throughout the genome and supports the production and/or retention of truncated copies of chromosome 5. Although trisomy 5 does not grossly distort the interphase arrangement of fluorescent-tagged sites on chromosome 5, it may somewhat enhance associations between transgene alleles. Our analysis reveals the complex genomic changes that can occur in aneuploids and underscores the importance of using multiple experimental approaches to investigate how chromosome numerical changes condition abnormal phenotypes and

  15. Child organ trafficking: global reality and inadequate international response.

    Bagheri, Alireza

    2016-06-01

    In organ transplantation, the demand for human organs has grown far faster than the supply of organs. This has opened the door for illegal organ trade and trafficking including from children. Organized crime groups and individual organ brokers exploit the situation and, as a result, black markets are becoming more numerous and organized organ trafficking is expanding worldwide. While underprivileged and vulnerable men and women in developing countries are a major source of trafficked organs, and may themselves be trafficked for the purpose of illegal organ removal and trade, children are at especial risk of exploitation. With the confirmed cases of children being trafficked for their organs, child organ trafficking, which once called a "modern urban legend", is a sad reality in today's world. By presenting a global picture of child organ trafficking, this paper emphasizes that child organ trafficking is no longer a myth but a reality which has to be addressed. It argues that the international efforts against organ trafficking and trafficking in human beings for organ removal have failed to address child organ trafficking adequately. This chapter suggests that more orchestrated international collaboration as well as development of preventive measure and legally binding documents are needed to fight child organ trafficking and to support its victims.

  16. Gene organization inside replication domains in mammalian genomes

    Zaghloul, Lamia; Baker, Antoine; Audit, Benjamin; Arneodo, Alain

    2012-11-01

    We investigate the large-scale organization of human genes with respect to "master" replication origins that were previously identified as bordering nucleotide compositional skew domains. We separate genes in two categories depending on their CpG enrichment at the promoter which can be considered as a marker of germline DNA methylation. Using expression data in mouse, we confirm that CpG-rich genes are highly expressed in germline whereas CpG-poor genes are in a silent state. We further show that, whether tissue-specific or broadly expressed (housekeeping genes), the CpG-rich genes are over-represented close to the replication skew domain borders suggesting some coordination of replication and transcription. We also reveal that the transcription of the longest CpG-rich genes is co-oriented with replication fork progression so that the promoter of these transcriptionally active genes be located into the accessible open chromatin environment surrounding the master replication origins that border the replication skew domains. The observation of a similar gene organization in the mouse genome confirms the interplay of replication, transcription and chromatin structure as the cornerstone of mammalian genome architecture.

  17. Soil organic matter dynamics and the global carbon cycle

    Post, W.M.; Emanuel, W.R.; King, A.W.

    1992-01-01

    The large size and potentially long residence time of the soil organic matter pool make it an important component of the global carbon cycle. Net terrestrial primary production of about 60 Pg C·yr -1 is, over a several-year period of time, balanced by an equivalent flux of litter production and subsequent decomposition of detritus and soil organic matter. We will review many of the major factors that influence soil organic matter dynamics that need to be explicitly considered in development of global estimates of carbon turnover in the world's soils. We will also discuss current decomposition models that are general enough to be used to develop a representation of global soil organic matter dynamics

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

    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

  19. Approaching the sequential and three-dimensional organization of Archaea, Bacteria and Eukarya genomes. Dynamic Organization of Nuclear Function

    T.A. Knoch (Tobias); M. Göker (Markus); R. Lohner (Rudolf); J. Langowski (Jörg)

    2002-01-01

    textabstractThe largely unresolved sequential organization, i.e. the relations within DNA sequences, and its connection to the three-dimensional organization of genomes was investigated by correlation analyses of completely sequenced chromosomes from Viroids, Archaea, Bacteria, Arabidopsis

  20. Global Value Chains, Labor Organization and Private Social Standards

    Riisgaard, Lone

    2009-01-01

    This article examines the opportunities and challenges that private social standards pose for labor organizations. It explores different labor responses to private social standards in East African cut flower industries. The analysis incorporates the concept of labor agency in global value chain a...... at production sites. However, labor organizations' ability to seriously challenge the prevailing governance structure of the cut flower value chain appears extremely limited.......This article examines the opportunities and challenges that private social standards pose for labor organizations. It explores different labor responses to private social standards in East African cut flower industries. The analysis incorporates the concept of labor agency in global value chain...... analysis and reveals how retailer-driven chains offer more room for labor organizations to exercise their agency than the traditional cut flower value chains. Labor organizations have been able to influence social standard setting and implementation, and to use standards to further labor representation...

  1. Multiple Whole Genome Alignments Without a Reference Organism

    Dubchak, Inna; Poliakov, Alexander; Kislyuk, Andrey; Brudno, Michael

    2009-01-16

    Multiple sequence alignments have become one of the most commonly used resources in genomics research. Most algorithms for multiple alignment of whole genomes rely either on a reference genome, against which all of the other sequences are laid out, or require a one-to-one mapping between the nucleotides of the genomes, preventing the alignment of recently duplicated regions. Both approaches have drawbacks for whole-genome comparisons. In this paper we present a novel symmetric alignment algorithm. The resulting alignments not only represent all of the genomes equally well, but also include all relevant duplications that occurred since the divergence from the last common ancestor. Our algorithm, implemented as a part of the VISTA Genome Pipeline (VGP), was used to align seven vertebrate and sixDrosophila genomes. The resulting whole-genome alignments demonstrate a higher sensitivity and specificity than the pairwise alignments previously available through the VGP and have higher exon alignment accuracy than comparable public whole-genome alignments. Of the multiple alignment methods tested, ours performed the best at aligning genes from multigene families?perhaps the most challenging test for whole-genome alignments. Our whole-genome multiple alignments are available through the VISTA Browser at http://genome.lbl.gov/vista/index.shtml.

  2. Genomic epidemiology of global VIM-producing Enterobacteriaceae.

    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.

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

    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.

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

    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

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

    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.

  6. Are conservation organizations configured for effective adaptation to global change?

    Armsworth, Paul R.; Larson, Eric R.; Jackson, Stephen T.; Sax, Dov F.; Simonin, Paul W.; Blossey, Bernd; Green, Nancy; Lester, Liza; Klein, Mary L.; Ricketts, Taylor H.; Runge, Michael C.; Shaw, M. Rebecca

    2015-01-01

    Conservation organizations must adapt to respond to the ecological impacts of global change. Numerous changes to conservation actions (eg facilitated ecological transitions, managed relocations, or increased corridor development) have been recommended, but some institutional restructuring within organizations may also be needed. Here we discuss the capacity of conservation organizations to adapt to changing environmental conditions, focusing primarily on public agencies and nonprofits active in land protection and management in the US. After first reviewing how these organizations anticipate and detect impacts affecting target species and ecosystems, we then discuss whether they are sufficiently flexible to prepare and respond by reallocating funding, staff, or other resources. We raise new hypotheses about how the configuration of different organizations enables them to protect particular conservation targets and manage for particular biophysical changes that require coordinated management actions over different spatial and temporal scales. Finally, we provide a discussion resource to help conservation organizations assess their capacity to adapt.

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

    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...

  8. Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104

    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...

  9. CAGO: a software tool for dynamic visual comparison and correlation measurement of genome organization.

    Yi-Feng Chang

    Full Text Available CAGO (Comparative Analysis of Genome Organization is developed to address two critical shortcomings of conventional genome atlas plotters: lack of dynamic exploratory functions and absence of signal analysis for genomic properties. With dynamic exploratory functions, users can directly manipulate chromosome tracks of a genome atlas and intuitively identify distinct genomic signals by visual comparison. Signal analysis of genomic properties can further detect inconspicuous patterns from noisy genomic properties and calculate correlations between genomic properties across various genomes. To implement dynamic exploratory functions, CAGO presents each genome atlas in Scalable Vector Graphics (SVG format and allows users to interact with it using a SVG viewer through JavaScript. Signal analysis functions are implemented using R statistical software and a discrete wavelet transformation package waveslim. CAGO is not only a plotter for generating complex genome atlases, but also a platform for exploring genome atlases with dynamic exploratory functions for visual comparison and with signal analysis for comparing genomic properties across multiple organisms. The web-based application of CAGO, its source code, user guides, video demos, and live examples are publicly available and can be accessed at http://cbs.ym.edu.tw/cago.

  10. The World Health Organization and Global Health Governance: post-1990.

    Lidén, J

    2014-02-01

    This article takes a historical perspective on the changing position of WHO in the global health architecture over the past two decades. From the early 1990s a number of weaknesses within the structure and governance of the World Health Organization were becoming apparent, as a rapidly changing post Cold War world placed more complex demands on the international organizations generally, but significantly so in the field of global health. Towards the end of that decade and during the first half of the next, WHO revitalized and played a crucial role in setting global health priorities. However, over the past decade, the organization has to some extent been bypassed for funding, and it lost some of its authority and its ability to set a global health agenda. The reasons for this decline are complex and multifaceted. Some of the main factors include WHO's inability to reform its core structure, the growing influence of non-governmental actors, a lack of coherence in the positions, priorities and funding decisions between the health ministries and the ministries overseeing development assistance in several donor member states, and the lack of strong leadership of the organization. Copyright © 2013 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

  11. Principles of the Organization of the Global Economic System

    Dyatlov, Sergey A.; Bulavko, Olga A.; Balanovskaya, Anna V.; Nikitina, Natalia V.; Chudaeva, Alexandra A.

    2016-01-01

    The development of the economic system is not a spontaneous but a programmed and controlled process. Economy is always a controlled system in which there is always an appropriate subject of management. The article considers principles of the organization of the global economic system. The characteristic of the principle of "hierarchy of…

  12. Canadian Civil Society Organizations and Human Rights and Global ...

    This project aims to strengthen the capacity of Canadian civil society organizations (CSOs) to inform Canadian policy on human rights and global justice. ... in the developing world continue to face obstacles that limit their ability to establish careers and become leaders in the fields of science, technology, engineering, and ...

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

    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

  14. Global genetic response in a cancer cell: self-organized coherent expression dynamics.

    Masa Tsuchiya

    Full Text Available Understanding the basic mechanism of the spatio-temporal self-control of genome-wide gene expression engaged with the complex epigenetic molecular assembly is one of major challenges in current biological science. In this study, the genome-wide dynamical profile of gene expression was analyzed for MCF-7 breast cancer cells induced by two distinct ErbB receptor ligands: epidermal growth factor (EGF and heregulin (HRG, which drive cell proliferation and differentiation, respectively. We focused our attention to elucidate how global genetic responses emerge and to decipher what is an underlying principle for dynamic self-control of genome-wide gene expression. The whole mRNA expression was classified into about a hundred groups according to the root mean square fluctuation (rmsf. These expression groups showed characteristic time-dependent correlations, indicating the existence of collective behaviors on the ensemble of genes with respect to mRNA expression and also to temporal changes in expression. All-or-none responses were observed for HRG and EGF (biphasic statistics at around 10-20 min. The emergence of time-dependent collective behaviors of expression occurred through bifurcation of a coherent expression state (CES. In the ensemble of mRNA expression, the self-organized CESs reveals distinct characteristic expression domains for biphasic statistics, which exhibits notably the presence of criticality in the expression profile as a route for genomic transition. In time-dependent changes in the expression domains, the dynamics of CES reveals that the temporal development of the characteristic domains is characterized as autonomous bistable switch, which exhibits dynamic criticality (the temporal development of criticality in the genome-wide coherent expression dynamics. It is expected that elucidation of the biophysical origin for such critical behavior sheds light on the underlying mechanism of the control of whole genome.

  15. Genome organization of the SARS-CoV

    Xu, Jing; Hu, Jianfei; Wang, Jing

    2003-01-01

    Annotation of the genome sequence of the SARS-CoV (severe acute respiratory syndrome-associated coronavirus) is indispensable to understand its evolution and pathogenesis. We have performed a full annotation of the SARS-CoV genome sequences by using annotation programs publicly available or devel......Annotation of the genome sequence of the SARS-CoV (severe acute respiratory syndrome-associated coronavirus) is indispensable to understand its evolution and pathogenesis. We have performed a full annotation of the SARS-CoV genome sequences by using annotation programs publicly available...

  16. Assessing Summit Engagement with Other International Organizations in Global Governance

    Marina Larionova

    2016-03-01

    Full Text Available Recent decades have witnessed dramatic changes all over the world. One major trend is the proliferation and diversification of actors, forums and their arrangements to address global governance challenges, which has led to fragmentation in global governance. However, such contested multilateralism has a positive dimension, as the emergence of informal multilateral institutions claiming a major role in defining the global governance agenda creates alternatives for providing common goods. New arrangements acquire their own actorness and place in the system of global governance. In certain policy areas, there is a clear trend for the new summit institutions’ leadership. The most visible recent cases include the Group of 20 (G20, the BRICS group of Brazil, Russia, India, China and South Africa, and the Asia-Pacific Economic Cooperation (APEC forum, with APEC gaining importance regionally and globally. These new informal groupings work on their own agenda. They also engage with established international organizations to steer global governance processes. Taken together, the transformative trends in international relations, the emergence of new actors, tensions between exclusive and inclusive clubs, and demands for the legitimacy and effectiveness of the international institutions define the relevance of the study, systematization and comparative analysis of the effectiveness of this model of cooperation among international institutions. This article builds an analytical framework by undertaking three tasks. It first reviews the key concepts. Second, it argues for a rational choice institutionalist approach. Third, it puts forward a hypothesis for research: to compensate for their inefficiencies, summit institutions engage with other international organizations in a mode they regard most efficient for attainment of their goals. The modes of those institutions’ engagement with other international organizations as reflected in the leaders

  17. GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes.

    Yuan, Lina; Yu, Yang; Zhu, Yanmin; Li, Yulai; Li, Changqing; Li, Rujiao; Ma, Qin; Siu, Gilman Kit-Hang; Yu, Jun; Jiang, Taijiao; Xiao, Jingfa; Kang, Yu

    2017-01-25

    Next-generation sequencing (NGS) technologies have greatly promoted the genomic study of prokaryotes. However, highly fragmented assemblies due to short reads from NGS are still a limiting factor in gaining insights into the genome biology. Reference-assisted tools are promising in genome assembly, but tend to result in false assembly when the assigned reference has extensive rearrangements. Herein, we present GAAP, a genome assembly pipeline for scaffolding based on core-gene-defined Genome Organizational Framework (cGOF) described in our previous study. Instead of assigning references, we use the multiple-reference-derived cGOFs as indexes to assist in order and orientation of the scaffolds and build a skeleton structure, and then use read pairs to extend scaffolds, called local scaffolding, and distinguish between true and chimeric adjacencies in the scaffolds. In our performance tests using both empirical and simulated data of 15 genomes in six species with diverse genome size, complexity, and all three categories of cGOFs, GAAP outcompetes or achieves comparable results when compared to three other reference-assisted programs, AlignGraph, Ragout and MeDuSa. GAAP uses both cGOF and pair-end reads to create assemblies in genomic scale, and performs better than the currently available reference-assisted assembly tools as it recovers more assemblies and makes fewer false locations, especially for species with extensive rearranged genomes. Our method is a promising solution for reconstruction of genome sequence from short reads of NGS.

  18. Normalization of Complete Genome Characteristics: Application to Evolution from Primitive Organisms to Homo sapiens.

    Sorimachi, Kenji; Okayasu, Teiji; Ohhira, Shuji

    2015-04-01

    Normalized nucleotide and amino acid contents of complete genome sequences can be visualized as radar charts. The shapes of these charts depict the characteristics of an organism's genome. The normalized values calculated from the genome sequence theoretically exclude experimental errors. Further, because normalization is independent of both target size and kind, this procedure is applicable not only to single genes but also to whole genomes, which consist of a huge number of different genes. In this review, we discuss the applications of the normalization of the nucleotide and predicted amino acid contents of complete genomes to the investigation of genome structure and to evolutionary research from primitive organisms to Homo sapiens. Some of the results could never have been obtained from the analysis of individual nucleotide or amino acid sequences but were revealed only after the normalization of nucleotide and amino acid contents was applied to genome research. The discovery that genome structure was homogeneous was obtained only after normalization methods were applied to the nucleotide or predicted amino acid contents of genome sequences. Normalization procedures are also applicable to evolutionary research. Thus, normalization of the contents of whole genomes is a useful procedure that can help to characterize organisms.

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

    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)

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

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

    2015-06-05

    advance functional and comparative genomics of insects and other organisms.

  1. The three-dimensional genome organization of Drosophila melanogaster through data integration.

    Li, Qingjiao; Tjong, Harianto; Li, Xiao; Gong, Ke; Zhou, Xianghong Jasmine; Chiolo, Irene; Alber, Frank

    2017-07-31

    Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of three-dimensional genome structural models, it is important to integrate all available sources of experimental information about a genome's organization. It remains a major challenge to integrate such data from various complementary experimental methods. Here, we present an approach for data integration to determine a population of complete three-dimensional genome structures that are statistically consistent with data from both genome-wide chromosome conformation capture (Hi-C) and lamina-DamID experiments. Our structures resolve the genome at the resolution of topological domains, and reproduce simultaneously both sets of experimental data. Importantly, this data deconvolution framework allows for structural heterogeneity between cells, and hence accounts for the expected plasticity of genome structures. As a case study we choose Drosophila melanogaster embryonic cells, for which both data types are available. Our three-dimensional genome structures have strong predictive power for structural features not directly visible in the initial data sets, and reproduce experimental hallmarks of the D. melanogaster genome organization from independent and our own imaging experiments. Also they reveal a number of new insights about genome organization and its functional relevance, including the preferred locations of heterochromatic satellites of different chromosomes, and observations about homologous pairing that cannot be directly observed in the original Hi-C or lamina-DamID data. Our approach allows systematic integration of Hi-C and lamina-DamID data for complete three-dimensional genome structure calculation, while also explicitly considering genome structural variability.

  2. Peatland Organic Matter Chemistry Trends Over a Global Latitudinal Gradient

    Verbeke, B. A.; Hodgkins, S. B.; Carson, M. A.; Lamit, L. J.; Lilleskov, E.; Chanton, J.

    2017-12-01

    Peatlands contain a significant amount of the global soil carbon, and the climate feedback of carbon cycling within these peatland systems is still relatively unknown. Organic matter composition of peatlands plays a major role in determining carbon storage, and while high latitude peatlands seem to be the most sensitive to climate change, a global picture of peat organic matter chemistry is required to improve predictions and models of greenhouse gas emissions fueled by peatland decomposition. The objective of this research is to test the hypothesis that carbohydrate content of peatlands near the equator will be lower than high latitude peatlands, while aromatic content will be higher. As a part of the Global Peatland Microbiome Project (GPMP), around 2000 samples of peat from 10 to 70 cm across a latitudinal gradient of 79 N to 53 S were measured with Fourier transform infrared spectroscopy (FTIR) to examine the organic matter functional groups of peat. Carbohydrate and aromatic content, as determined by FTIR, are useful proxies of decomposition potential and recalcitrance, respectively. We found a highly significant relationship between carbohydrate and aromatic content, latitude, and depth. Carbohydrate content of high latitude sites were significantly greater than at sites near the equator, in contrast to aromatic content which showed the opposite trend. It is also clear that carbohydrate content decreases with depth while aromatic content increases with depth. Higher carbohydrate content at higher latitudes indicates a greater potential for lability and resultant mineralization to form the greenhouse gases, carbon dioxide and methane, whereas the composition of low latitude peatlands is consistent with their apparent stability. We speculate that the combination of low carbohydrates and high aromatics at warmer locations near the equator could foreshadow the organic matter composition of high latitude peat transitioning to a more recalcitrant form with a

  3. Functional genomics for food microbiology: Molecular mechanisms of weak organic acid preservative adaptation in yeast

    Brul, S.; Kallemeijn, W.; Smits, G.

    2008-01-01

    The recent era of genomics has offered tremendous possibilities to biology. This concise review describes the possibilities of applying (functional) genomics studies to the field of microbial food stability. In doing so, the studies on weak-organic-acid stress response in yeast are discussed by way

  4. The global distribution and dynamics of chromophoric dissolved organic matter.

    Nelson, Norman B; Siegel, David A

    2013-01-01

    Chromophoric dissolved organic matter (CDOM) is a ubiquitous component of the open ocean dissolved matter pool, and is important owing to its influence on the optical properties of the water column, its role in photochemistry and photobiology, and its utility as a tracer of deep ocean biogeochemical processes and circulation. In this review, we discuss the global distribution and dynamics of CDOM in the ocean, concentrating on developments in the past 10 years and restricting our discussion to open ocean and deep ocean (below the main thermocline) environments. CDOM has been demonstrated to exert primary control on ocean color by its absorption of light energy, which matches or exceeds that of phytoplankton pigments in most cases. This has important implications for assessing the ocean biosphere via ocean color-based remote sensing and the evaluation of ocean photochemical and photobiological processes. The general distribution of CDOM in the global ocean is controlled by a balance between production (primarily microbial remineralization of organic matter) and photolysis, with vertical ventilation circulation playing an important role in transporting CDOM to and from intermediate water masses. Significant decadal-scale fluctuations in the abundance of global surface ocean CDOM have been observed using remote sensing, indicating a potentially important role for CDOM in ocean-climate connections through its impact on photochemistry and photobiology.

  5. Composition and genomic organization of arthropod Hox clusters.

    Pace, Ryan M; Grbić, Miodrag; Nagy, Lisa M

    2016-01-01

    The ancestral arthropod is believed to have had a clustered arrangement of ten Hox genes. Within arthropods, Hox gene mutations result in transformation of segment identities. Despite the fact that variation in segment number/character was common in the diversification of arthropods, few examples of Hox gene gains/losses have been correlated with morphological evolution. Furthermore, a full appreciation of the variation in the genomic arrangement of Hox genes in extant arthropods has not been recognized, as genome sequences from each major arthropod clade have not been reported until recently. Initial genomic analysis of the chelicerate Tetranychus urticae suggested that loss of Hox genes and Hox gene clustering might be more common than previously assumed. To further characterize the genomic evolution of arthropod Hox genes, we compared the genomic arrangement and general characteristics of Hox genes from representative taxa from each arthropod subphylum. In agreement with others, we find arthropods generally contain ten Hox genes arranged in a common orientation in the genome, with an increasing number of sampled species missing either Hox3 or abdominal-A orthologs. The genomic clustering of Hox genes in species we surveyed varies significantly, ranging from 0.3 to 13.6 Mb. In all species sampled, arthropod Hox genes are dispersed in the genome relative to the vertebrate Mus musculus. Differences in Hox cluster size arise from variation in the number of intervening genes, intergenic spacing, and the size of introns and UTRs. In the arthropods surveyed, Hox gene duplications are rare and four microRNAs are, in general, conserved in similar genomic positions relative to the Hox genes. The tightly clustered Hox complexes found in the vertebrates are not evident within arthropods, and differential patterns of Hox gene dispersion are found throughout the arthropods. The comparative genomic data continue to support an ancestral arthropod Hox cluster of ten genes with

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

    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

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

    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.

  8. Self-organized global control of carbon emissions

    Zhao, Zhenyuan; Fenn, Daniel J.; Hui, Pak Ming; Johnson, Neil F.

    2010-09-01

    There is much disagreement concerning how best to control global carbon emissions. We explore quantitatively how different control schemes affect the collective emission dynamics of a population of emitting entities. We uncover a complex trade-off which arises between average emissions (affecting the global climate), peak pollution levels (affecting citizens’ everyday health), industrial efficiency (affecting the nation’s economy), frequency of institutional intervention (affecting governmental costs), common information (affecting trading behavior) and market volatility (affecting financial stability). Our findings predict that a self-organized free-market approach at the level of a sector, state, country or continent can provide better control than a top-down regulated scheme in terms of market volatility and monthly pollution peaks. The control of volatility also has important implications for any future derivative carbon emissions market.

  9. Genomic organization of a vancomycin-resistant staphylococcus aureus

    Mirani, A.Z.; Jamil, N.

    2013-01-01

    Objective: To study the genomic organization of vancomycin resistance in a local isolate of vancomycin resistant Staphylococcus aureus (VRSA). Study Design: Experimental study. Place and Duration of Study: Department of Microbiology, University of Karachi, January 2008 through December 2010. Methodology: A vancomycin-resistant Staphylococcus aureus (VRSA-CP2) isolate (MIC 16 mu g/ml) was isolated from a local hospital of Karachi. Species identification was confirmed by Gram staining, standard biochemical tests and PCR amplification of the nuc gene. The vancomycin MIC was re-confirmed by E-test. For the genetic determination of vancomycin resistance, in-vitro amplification of vanA cassette was performed by using plasmid DNA of CP2, CP2's transformant as template on MWG Thermo-Cycler. Amplified products of vanR, vanS, vanH, vanA, vanY, orf2, orf1D, orf2E, orf-Rev and IS element genes were subjected to Sanger's electrophoresis based sequence determination using specific primers. The Basic Local Alignment Search Tool (BLAST) algorithm was used to identify sequences in GenBank with similarities to the vanA cassette genes. Results: The vancomycin-resistant isolate CP2 was found to be resistant to oxacillin, chloramphenicol, erythromycin, rifampicin, gentamicin, tetracycline and ciprofloxacin, as well. The isolate CP2 revealed four bands: one of large molecular size approx 56.4 kb and three of small size approx 6.5 kb, approx 6.1 kb and approx 1.5 kb by agarose gel electrophoresis indicating the presence of 3 plasmids. The plasmid DNA of isolate CP2 was analyzed by PCR for the presence of the van cassettes with each of the vanA , vanB and vanC specific primers. It carried vanA cassette, which comprises of vanR, vanS, vanH, vanA, vanY, and orf2. The vanA cassette of isolate CP2 also carried an insertion element (IS). However, it did not show the PCR product for orf1. Vancomycin resistance was successfully transferred from the donor CP2 to a vancomycin-sensitive recipient S

  10. From hacking the human genome to editing organs.

    Tobita, Takamasa; Guzman-Lepe, Jorge; Collin de l'Hortet, Alexandra

    2015-01-01

    In the recent decades, human genome engineering has been one of the major interesting research subjects, essentially because it raises new possibilities for personalized medicine and biotechnologies. With the development of engineered nucleases such as the Zinc Finger Nucleases (ZFNs), the Transcription activator-like effector nucleases (TALENs) and more recently the Clustered Regularly Interspaced short Palindromic Repeats (CRISPR), the field of human genome edition has evolved very rapidly. Every new genetic tool is broadening the scope of applications on human tissues, even before we can completely master each of these tools. In this review, we will present the recent advances regarding human genome edition tools, we will discuss the numerous implications they have in research and medicine, and we will mention the limits and concerns about such technologies.

  11. Lampreys as Diverse Model Organisms in the Genomics Era.

    McCauley, David W; Docker, Margaret F; Whyard, Steve; Li, Weiming

    2015-11-01

    Lampreys, one of the two surviving groups of ancient vertebrates, have become important models for study in diverse fields of biology. Lampreys (of which there are approximately 40 species) are being studied, for example, (a) to control pest sea lamprey in the North American Great Lakes and to restore declining populations of native species elsewhere; (b) in biomedical research, focusing particularly on the regenerative capability of lampreys; and (c) by developmental biologists studying the evolution of key vertebrate characters. Although a lack of genetic resources has hindered research on the mechanisms regulating many aspects of lamprey life history and development, formerly intractable questions are now amenable to investigation following the recent publication of the sea lamprey genome. Here, we provide an overview of the ways in which genomic tools are currently being deployed to tackle diverse research questions and suggest several areas that may benefit from the availability of the sea lamprey genome.

  12. Five Complete Chloroplast Genome Sequences from Diospyros: Genome Organization and Comparative Analysis.

    Fu, Jianmin; Liu, Huimin; Hu, Jingjing; Liang, Yuqin; Liang, Jinjun; Wuyun, Tana; Tan, Xiaofeng

    2016-01-01

    Diospyros is the largest genus in Ebenaceae, comprising more than 500 species with remarkable economic value, especially Diospyros kaki Thunb., which has traditionally been an important food resource in China, Korea, and Japan. Complete chloroplast (cp) genomes from D. kaki, D. lotus L., D. oleifera Cheng., D. glaucifolia Metc., and Diospyros 'Jinzaoshi' were sequenced using Illumina sequencing technology. This is the first cp genome reported in Ebenaceae. The cp genome sequences of Diospyros ranged from 157,300 to 157,784 bp in length, presenting a typical quadripartite structure with two inverted repeats each separated by one large and one small single-copy region. For each cp genome, 134 genes were annotated, including 80 protein-coding, 31 tRNA, and 4 rRNA unique genes. In all, 179 repeats and 283 single sequence repeats were identified. Four hypervariable regions, namely, intergenic region of trnQ_rps16, trnV_ndhC, and psbD_trnT, and intron of ndhA, were identified in the Diospyros genomes. Phylogenetic analyses based on the whole cp genome, protein-coding, and intergenic and intron sequences indicated that D. oleifera is closely related to D. kaki and could be used as a model plant for future research on D. kaki; to our knowledge, this is proposed for the first time. Further, these analyses together with two large deletions (301 and 140 bp) in the cp genome of D. 'Jinzaoshi', support its placement as a new species in Diospyros. Both maximum parsimony and likelihood analyses for 19 taxa indicated the basal position of Ericales in asterids and suggested that Ebenaceae is monophyletic in Ericales.

  13. Five Complete Chloroplast Genome Sequences from Diospyros: Genome Organization and Comparative Analysis.

    Jianmin Fu

    Full Text Available Diospyros is the largest genus in Ebenaceae, comprising more than 500 species with remarkable economic value, especially Diospyros kaki Thunb., which has traditionally been an important food resource in China, Korea, and Japan. Complete chloroplast (cp genomes from D. kaki, D. lotus L., D. oleifera Cheng., D. glaucifolia Metc., and Diospyros 'Jinzaoshi' were sequenced using Illumina sequencing technology. This is the first cp genome reported in Ebenaceae. The cp genome sequences of Diospyros ranged from 157,300 to 157,784 bp in length, presenting a typical quadripartite structure with two inverted repeats each separated by one large and one small single-copy region. For each cp genome, 134 genes were annotated, including 80 protein-coding, 31 tRNA, and 4 rRNA unique genes. In all, 179 repeats and 283 single sequence repeats were identified. Four hypervariable regions, namely, intergenic region of trnQ_rps16, trnV_ndhC, and psbD_trnT, and intron of ndhA, were identified in the Diospyros genomes. Phylogenetic analyses based on the whole cp genome, protein-coding, and intergenic and intron sequences indicated that D. oleifera is closely related to D. kaki and could be used as a model plant for future research on D. kaki; to our knowledge, this is proposed for the first time. Further, these analyses together with two large deletions (301 and 140 bp in the cp genome of D. 'Jinzaoshi', support its placement as a new species in Diospyros. Both maximum parsimony and likelihood analyses for 19 taxa indicated the basal position of Ericales in asterids and suggested that Ebenaceae is monophyletic in Ericales.

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

    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

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

    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.

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

    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

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

    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.

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

    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.

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

    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.

  20. Solidarity Action in Global Labor Networks. Four Cases of Workplace Organizing at Foreign Affiliates in the Global South

    Peter Wad

    2014-03-01

    Full Text Available Globalization transforms workforces of transnational corporation from predominantly home countrydominated workforces into foreign-dominated, multinational workforces. Thus, the national grounding of trade unions as the key form of labor organizing is challenged by new multinational compositions and cross-border relocations of corporate employment affecting working conditions of employees and trade unions in local places. We assume that economic globalization is characterized by expanding global corporate network of vertically and horizontally integrated (equity-based and disintegrated (nonequity-based value chains. We also assume that globalization can both impede and enable labor empowerment. Based on these premises the key question is, how can labor leverage effective power against management in global corporate networks? This question is split into two subquestions: a How can labor theoretically reorganize from national unions and industrial relations institutions into global labor networks that allow prolabor improvement in global workplaces? b How and why has labor in a globalized economy secured the core International Labor Organization (ILO international labor right to organize companies and conduct collective bargaining? The Global Labor Network perspective is adopted as an analytical framework. Empirically, a comparative case methodology is applied comprising four more or less successful industrial disputes where labor achieved the right to organize and undertake collective bargaining. The disputes took place in affiliated factories of foreign transnational corporations located in Malaysia, the Philippines, Sri Lanka, and Turkey. The conclusion is that the combination of global labor capabilities and global labor strategizing must generate strategic labor power that adequately matches the weaknesses of the counterpart’s global corporate network in order to achieve prolabor outcomes. The most efficient solidarity action was leveraged

  1. The World Health Organization and global smallpox eradication.

    Bhattacharya, S

    2008-10-01

    This article examines the multifaceted structures and complex operations of the World Health Organization and its regional offices; it also reassesses the form and the workings of the global smallpox eradication programme with which these bodies were closely linked in the 1960s and 1970s. Using the case study of South Asia, it seeks to highlight the importance of writing nuanced histories of international health campaigns through an assessment of differences between official rhetoric and practice. The article argues that the detailed examination of the implementation of policy in a variety of localities, within and across national borders, allows us to recognise the importance of the agency of field managers and workers. This analytical approach also helps us acknowledge that communities were able to influence the shape and the timing of completion of public health campaigns in myriad ways. This, in turn, can provide useful pointers for the design and management of health programmes in the contemporary world.

  2. Stable isotopic constraints on global soil organic carbon turnover

    Wang, Chao; Houlton, Benjamin Z.; Liu, Dongwei; Hou, Jianfeng; Cheng, Weixin; Bai, Edith

    2018-02-01

    Carbon dioxide release during soil organic carbon (SOC) turnover is a pivotal component of atmospheric CO2 concentrations and global climate change. However, reliably measuring SOC turnover rates on large spatial and temporal scales remains challenging. Here we use a natural carbon isotope approach, defined as beta (β), which was quantified from the δ13C of vegetation and soil reported in the literature (176 separate soil profiles), to examine large-scale controls of climate, soil physical properties and nutrients over patterns of SOC turnover across terrestrial biomes worldwide. We report a significant relationship between β and calculated soil C turnover rates (k), which were estimated by dividing soil heterotrophic respiration rates by SOC pools. ln( - β) exhibits a significant linear relationship with mean annual temperature, but a more complex polynomial relationship with mean annual precipitation, implying strong-feedbacks of SOC turnover to climate changes. Soil nitrogen (N) and clay content correlate strongly and positively with ln( - β), revealing the additional influence of nutrients and physical soil properties on SOC decomposition rates. Furthermore, a strong (R2 = 0.76; p turnover and thereby improving predictions of multiple global change influences over terrestrial C-climate feedback.

  3. A New Approach to Dissect Nuclear Organization: TALE-Mediated Genome Visualization (TGV).

    Miyanari, Yusuke

    2016-01-01

    Spatiotemporal organization of chromatin within the nucleus has so far remained elusive. Live visualization of nuclear remodeling could be a promising approach to understand its functional relevance in genome functions and mechanisms regulating genome architecture. Recent technological advances in live imaging of chromosomes begun to explore the biological roles of the movement of the chromatin within the nucleus. Here I describe a new technique, called TALE-mediated genome visualization (TGV), which allows us to visualize endogenous repetitive sequence including centromeric, pericentromeric, and telomeric repeats in living cells.

  4. Bacillus anthracis genome organization in light of whole transcriptome sequencing

    Martin, Jeffrey; Zhu, Wenhan; Passalacqua, Karla D.; Bergman, Nicholas; Borodovsky, Mark

    2010-03-22

    Emerging knowledge of whole prokaryotic transcriptomes could validate a number of theoretical concepts introduced in the early days of genomics. What are the rules connecting gene expression levels with sequence determinants such as quantitative scores of promoters and terminators? Are translation efficiency measures, e.g. codon adaptation index and RBS score related to gene expression? We used the whole transcriptome shotgun sequencing of a bacterial pathogen Bacillus anthracis to assess correlation of gene expression level with promoter, terminator and RBS scores, codon adaptation index, as well as with a new measure of gene translational efficiency, average translation speed. We compared computational predictions of operon topologies with the transcript borders inferred from RNA-Seq reads. Transcriptome mapping may also improve existing gene annotation. Upon assessment of accuracy of current annotation of protein-coding genes in the B. anthracis genome we have shown that the transcriptome data indicate existence of more than a hundred genes missing in the annotation though predicted by an ab initio gene finder. Interestingly, we observed that many pseudogenes possess not only a sequence with detectable coding potential but also promoters that maintain transcriptional activity.

  5. World Health Organization Global Disability Action Plan: The Mongolian Perspective

    Fary Khan

    2017-01-01

    Full Text Available Objective: To provide an update on disability and rehabilitation in Mongolia, and to identify potential barriers and facilitators for implementation of the World Health Organization (WHO Global Disability Action Plan (GDAP. Methods: A 4-member rehabilitation team from the Royal Melbourne Hospital conducted an intensive 6-day workshop at the Mongolian National University of Medical Sciences, for local healthcare professionals (n = 77 from medical rehabilitation facilities (urban/rural, public/private and non-governmental organizations. A modified Delphi method (interactive sessions, consensus agreement identified challenges for rehabilitation service provision and disability education and attitudes, using GDAP objectives. Results: The GDAP summary actions were considered useful for clinicians, policy-makers, government and persons with disabilities. The main challenges identified were: limited knowledge of disability services and rehabilitation within healthcare sectors; lack of coordination between sectors; geo-topographical issues; limited skilled workforces; lack of disability data, guidelines and accreditation standards; poor legislation and political commitment. The facilitators were: strong leadership; advocacy of disability-inclusive development; investment in local infrastructure/human resources; opportunities for coordination and partnerships between the healthcare sector and other stakeholders; research opportunities; and dissemination of information. Conclusion: Disability and rehabilitation is an emerging priority in Mongolia to address the rights and needs of persons with disabilities. The GDAP provides guidance to facilitate access and strengthen rehabilitation services.

  6. Genome complexity, robustness and genetic interactions in digital organisms

    Lenski, Richard E.; Ofria, Charles; Collier, Travis C.; Adami, Christoph

    1999-08-01

    Digital organisms are computer programs that self-replicate, mutate and adapt by natural selection. They offer an opportunity to test generalizations about living systems that may extend beyond the organic life that biologists usually study. Here we have generated two classes of digital organism: simple programs selected solely for rapid replication, and complex programs selected to perform mathematical operations that accelerate replication through a set of defined `metabolic' rewards. To examine the differences in their genetic architecture, we introduced millions of single and multiple mutations into each organism and measured the effects on the organism's fitness. The complex organisms are more robust than the simple ones with respect to the average effects of single mutations. Interactions among mutations are common and usually yield higher fitness than predicted from the component mutations assuming multiplicative effects; such interactions are especially important in the complex organisms. Frequent interactions among mutations have also been seen in bacteria, fungi and fruitflies. Our findings support the view that interactions are a general feature of genetic systems.

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

    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.

  8. 75 FR 28298 - Avaya Inc., Worldwide Services Group, Global Support Services (GSS) Organization, Including On...

    2010-05-20

    ...., Worldwide Services Group, Global Support Services (GSS) Organization, Including On-Site Leased Workers From..., Highlands Ranch, CO; Including Employees in Support of Avaya Inc., Worldwide Services Group, Global Support... workers of Avaya Inc., Worldwide Services Group, Global Support Services (GSS) Organization, including on...

  9. Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics

    Sze Sing-Hoi

    2005-03-01

    Full Text Available Abstract Background Chemokines and their receptors play important roles in host defense, organogenesis, hematopoiesis, and neuronal communication. Forty-two chemokines and 19 cognate receptors have been found in the human genome. Prior to this report, only 11 chicken chemokines and 7 receptors had been reported. The objectives of this study were to systematically identify chicken chemokines and their cognate receptor genes in the chicken genome and to annotate these genes and ligand-receptor binding by a comparative genomics approach. Results Twenty-three chemokine and 14 chemokine receptor genes were identified in the chicken genome. All of the chicken chemokines contained a conserved CC, CXC, CX3C, or XC motif, whereas all the chemokine receptors had seven conserved transmembrane helices, four extracellular domains with a conserved cysteine, and a conserved DRYLAIV sequence in the second intracellular domain. The number of coding exons in these genes and the syntenies are highly conserved between human, mouse, and chicken although the amino acid sequence homologies are generally low between mammalian and chicken chemokines. Chicken genes were named with the systematic nomenclature used in humans and mice based on phylogeny, synteny, and sequence homology. Conclusion The independent nomenclature of chicken chemokines and chemokine receptors suggests that the chicken may have ligand-receptor pairings similar to mammals. All identified chicken chemokines and their cognate receptors were identified in the chicken genome except CCR9, whose ligand was not identified in this study. The organization of these genes suggests that there were a substantial number of these genes present before divergence between aves and mammals and more gene duplications of CC, CXC, CCR, and CXCR subfamilies in mammals than in aves after the divergence.

  10. cDNA structure, genomic organization and expression patterns of ...

    use

    2011-11-23

    Nov 23, 2011 ... adenine dinucleotide (NAD) intermediate (Rongvaux et al., 2002). Thereupon ... in house mouse, Norway rat and human. It was not difficult to ... species in freshwater regions, and has been a new model organism in aquatic ...

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

    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

  12. The complete nucleotide sequence, genome organization, and origin of human adenovirus type 11

    Stone, Daniel; Furthmann, Anne; Sandig, Volker; Lieber, Andre

    2003-01-01

    The complete DNA sequence and transcription map of human adenovirus type 11 are reported here. This is the first published sequence for a subgenera B human adenovirus and demonstrates a genome organization highly similar to those of other human adenoviruses. All of the genes from the early, intermediate, and late regions are present in the expected locations of the genome for a human adenovirus. The genome size is 34,794 bp in length and has a GC content of 48.9%. Sequence alignment with genomes of groups A (Ad12), C (Ad5), D (Ad17), E (Simian adenovirus 25), and F (Ad40) revealed homologies of 64, 54, 68, 75, and 52%, respectively. Detailed genomic analysis demonstrated that Ads 11 and 35 are highly conserved in all areas except the hexon hypervariable regions and fiber. Similarly, comparison of Ad11 with subgroup E SAV25 revealed poor homology between fibers but high homology in proteins encoded by all other areas of the genome. We propose an evolutionary model in which functional viruses can be reconstituted following fiber substitution from one serotype to another. According to this model either the Ad11 genome is a derivative of Ad35, from which the fiber was substituted with Ad7, or the Ad35 genome is the product of a fiber substitution from Ad21 into the Ad11 genome. This model also provides a possible explanation for the origin of group E Ads, which are evolutionarily derived from a group C fiber substitution into a group B genome

  13. Global simulation of aromatic volatile organic compounds in the atmosphere

    Cabrera Perez, David; Taraborrelli, Domenico; Pozzer, Andrea

    2015-04-01

    Among the large number of chemical compounds in the atmosphere, the organic group plays a key role in the tropospheric chemistry. Specifically the subgroup called aromatics is of great interest. Aromatics are the predominant trace gases in urban areas due to high emissions, primarily by vehicle exhausts and fuel evaporation. They are also present in areas where biofuel is used (i.e residential wood burning). Emissions of aromatic compounds are a substantial fraction of the total emissions of the volatile organic compounds (VOC). Impact of aromatics on human health is very important, as they do not only contribute to the ozone formation in the urban environment, but they are also highly toxic themselves, especially in the case of benzene which is able to trigger a range of illness under long exposure, and of nitro-phenols which cause detrimental for humans and vegetation even at very low concentrations. The aim of this work is to assess the atmospheric impacts of aromatic compounds on the global scale. The main goals are: lifetime and budget estimation, mixing ratios distribution, net effect on ozone production and OH loss for the most emitted aromatic compounds (benzene, toluene, xylenes, ethylbenzene, styrene and trimethylbenzenes). For this purpose, we use the numerical chemistry and climate simulation ECHAM/MESSy Atmospheric Chemistry (EMAC) model to build the global atmospheric budget for the most emitted and predominant aromatic compounds in the atmosphere. A set of emissions was prepared in order to include biomass burning, vegetation and anthropogenic sources of aromatics into the model. A chemical mechanism based on the Master Chemical Mechanism (MCM) was developed to describe the chemical oxidation in the gas phase of these aromatic compounds. MCM have been reduced in terms of number of chemical equation and species in order to make it affordable in a 3D model. Additionally other features have been added, for instance the production of HONO via ortho

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

    You Frank M

    2010-06-01

    Full Text Available Abstract Background Physical maps employing libraries of bacterial artificial chromosome (BAC clones are essential for comparative genomics and sequencing of large and repetitive genomes such as those of the hexaploid bread wheat. The diploid ancestor of the D-genome of hexaploid wheat (Triticum aestivum, Aegilops tauschii, is used as a resource for wheat genomics. The barley diploid genome also provides a good model for the Triticeae and T. aestivum since it is only slightly larger than the ancestor wheat D genome. Gene co-linearity between the grasses can be exploited by extrapolating from rice and Brachypodium distachyon to Ae. tauschii or barley, and then to wheat. Results We report the use of Ae. tauschii for the construction of the physical map of a large distal region of chromosome arm 3DS. A physical map of 25.4 Mb was constructed by anchoring BAC clones of Ae. tauschii with 85 EST on the Ae. tauschii and barley genetic maps. The 24 contigs were aligned to the rice and B. distachyon genomic sequences and a high density SNP genetic map of barley. As expected, the mapped region is highly collinear to the orthologous chromosome 1 in rice, chromosome 2 in B. distachyon and chromosome 3H in barley. However, the chromosome scale of the comparative maps presented provides new insights into grass genome organization. The disruptions of the Ae. tauschii-rice and Ae. tauschii-Brachypodium syntenies were identical. We observed chromosomal rearrangements between Ae. tauschii and barley. The comparison of Ae. tauschii physical and genetic maps showed that the recombination rate across the region dropped from 2.19 cM/Mb in the distal region to 0.09 cM/Mb in the proximal region. The size of the gaps between contigs was evaluated by comparing the recombination rate along the map with the local recombination rates calculated on single contigs. Conclusions The physical map reported here is the first physical map using fingerprinting of a complete

  15. Long-Range Order and Fractality in the Structure and Organization of Eukaryotic Genomes

    Polychronopoulos, Dimitris; Tsiagkas, Giannis; Athanasopoulou, Labrini; Sellis, Diamantis; Almirantis, Yannis

    2014-12-01

    The late Professor J.S. Nicolis always emphasized, both in his writings and in presentations and discussions with students and friends, the relevance of a dynamical systems approach to biology. In particular, viewing the genome as a "biological text" captures the dynamical character of both the evolution and function of the organisms in the form of correlations indicating the presence of a long-range order. This genomic structure can be expressed in forms reminiscent of natural languages and several temporal and spatial traces l by the functioning of dynamical systems: Zipf laws, self-similarity and fractality. Here we review several works of our group and recent unpublished results, focusing on the chromosomal distribution of biologically active genomic components: Genes and protein-coding segments, CpG islands, transposable elements belonging to all major classes and several types of conserved non-coding genomic elements. We report the systematic appearance of power-laws in the size distribution of the distances between elements belonging to each of these types of functional genomic elements. Moreover, fractality is also found in several cases, using box-counting and entropic scaling.We present here, for the first time in a unified way, an aggregative model of the genomic dynamics which can explain the observed patterns on the grounds of known phenomena accompanying genome evolution. Our results comply with recent findings about a "fractal globule" geometry of chromatin in the eukaryotic nucleus.

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

    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

  17. Genomic organization of the canine herpesvirus US region.

    Haanes, E J; Tomlinson, C C

    1998-02-01

    Canine herpesvirus (CHV) is an alpha-herpesvirus of limited pathogenicity in healthy adult dogs and infectivity of the virus appears to be largely limited to cells of canine origin. CHV's low virulence and species specificity make it an attractive candidate for a recombinant vaccine vector to protect dogs against a variety of pathogens. As part of the analysis of the CHV genome, the authors determined the complete nucleotide sequence of the CHV US region as well as portions of the flanking inverted repeats. Seven full open reading frames (ORFs) encoding proteins larger than 100 amino acids were identified within, or partially within the CHV US: cUS2, cUS3, cUS4, cUS6, cUS7, cUS8 and cUS9; which are homologs of the herpes simplex virus type-1 US2; protein kinase; gG, gD, gI, gE; and US9 genes, respectively. An eighth ORF was identified in the inverted repeat region, cIR6, a homolog of the equine herpesvirus type-1 IR6 gene. The authors identified and mapped most of the major transcripts for the predicted CHV US ORFs by Northern analysis.

  18. Report on World Homoeopathy Summit organized by Global Homeopathy Foundation

    Eswara Das

    2015-01-01

    Full Text Available The Global Homeopathy Foundation (GHF organized the World Homoeopathy Summit (WHS at Birla Matoshree Sabhaghar, Mumbai, 400020, India on 11-12 April, 2015. Ministry of AYUSH, Central Council for Research in Homoeopathy, Central Council of Homoeopathy and Homoeopathic Pharmacopeia Laboratory were the institutional collaborators. Homoeopathic Medical Association of India, Indian Homoeopathic Medical Association and the Indian Chapter of Liga Medicorum Homeopathica Internationalis supported the event. The WHS was aimed at enhancing research aptitudes of young homoeopaths, increasing clinical proficiency of practitioners, encouraging scientists from pure and applied sciences to associate in fundamental research and also inviting government as well as non government institutions to patronize research in Homoeopathy. About 800 delegates from across the country, mainly practitioners, teaching faculties, postgraduate students, Ph.D. scholars and scientists attended the summit. Scientific sessions on nature of homoeopathic medicine, Evidence and Mechanism of its action were presented by molecular biologists, engineers, physicists, immunologists, pharmacologists, chemists, nano-technologists, zoologists, homeopaths and conventional doctors from some of the premium Universities. The conference ended with panel discussion moderated by Dr. Raj K. Manchanda and Dr. Rajesh Shah. It was recommended to encourage more scientific research and better documentation in Homoeopathy and to review the existing approaches in practice.

  19. Soil salinity decreases global soil organic carbon stocks.

    Setia, Raj; Gottschalk, Pia; Smith, Pete; Marschner, Petra; Baldock, Jeff; Setia, Deepika; Smith, Jo

    2013-11-01

    Saline soils cover 3.1% (397 million hectare) of the total land area of the world. The stock of soil organic carbon (SOC) reflects the balance between carbon (C) inputs from plants, and losses through decomposition, leaching and erosion. Soil salinity decreases plant productivity and hence C inputs to the soil, but also microbial activity and therefore SOC decomposition rates. Using a modified Rothamsted Carbon model (RothC) with a newly introduced salinity decomposition rate modifier and a plant input modifier we estimate that, historically, world soils that are currently saline have lost an average of 3.47 tSOC ha(-1) since they became saline. With the extent of saline soils predicted to increase in the future, our modelling suggests that world soils may lose 6.8 Pg SOC due to salinity by the year 2100. Our findings suggest that current models overestimate future global SOC stocks and underestimate net CO2 emissions from the soil-plant system by not taking salinity effects into account. From the perspective of enhancing soil C stocks, however, given the lower SOC decomposition rate in saline soils, salt tolerant plants could be used to sequester C in salt-affected areas. Copyright © 2012 Elsevier B.V. All rights reserved.

  20. LEMONS - A Tool for the Identification of Splice Junctions in Transcriptomes of Organisms Lacking Reference Genomes.

    Liron Levin

    Full Text Available RNA-seq is becoming a preferred tool for genomics studies of model and non-model organisms. However, DNA-based analysis of organisms lacking sequenced genomes cannot rely on RNA-seq data alone to isolate most genes of interest, as DNA codes both exons and introns. With this in mind, we designed a novel tool, LEMONS, that exploits the evolutionary conservation of both exon/intron boundary positions and splice junction recognition signals to produce high throughput splice-junction predictions in the absence of a reference genome. When tested on multiple annotated vertebrate mRNA data, LEMONS accurately identified 87% (average of the splice-junctions. LEMONS was then applied to our updated Mediterranean chameleon transcriptome, which lacks a reference genome, and predicted a total of 90,820 exon-exon junctions. We experimentally verified these splice-junction predictions by amplifying and sequencing twenty randomly selected genes from chameleon DNA templates. Exons and introns were detected in 19 of 20 of the positions predicted by LEMONS. To the best of our knowledge, LEMONS is currently the only experimentally verified tool that can accurately predict splice-junctions in organisms that lack a reference genome.

  1. [Compartmentalization of the cell nucleus and spatial organization of the genome].

    Gavrilov, A A; Razin, S V

    2015-01-01

    The eukaryotic cell nucleus is one of the most complex cell organelles. Despite the absence of membranes, the nuclear space is divided into numerous compartments where different processes in- volved in the genome activity take place. The most important nuclear compartments include nucleoli, nuclear speckles, PML bodies, Cajal bodies, histone locus bodies, Polycomb bodies, insulator bodies, transcription and replication factories. The structural basis for the nuclear compartmentalization is provided by genomic DNA that occupies most of the nuclear volume. Nuclear compartments, in turn, guide the chromosome folding by providing a platform for the spatial interaction of individual genomic loci. In this review, we discuss fundamental principles of higher order genome organization with a focus on chromosome territories and chromosome domains, as well as consider the structure and function of the key nuclear compartments. We show that the func- tional compartmentalization of the cell nucleus and genome spatial organization are tightly interconnected, and that this form of organization is highly dynamic and is based on stochastic processes.

  2. Organizing Global IS Management to Meet Competitive Challenges: Experiences from the Pharmaceutical Industry

    Bettina Schwarzer

    1995-01-01

    Despite the widely acknowledged importance information technology plays in multinational corporations, many companies lack an understanding of when and how to (re)organize global IS management. The issues of timing and organization of global IS management, however, seem to be of utmost importance in a company’s attempt to implement a new, global business strategy. Based on three case studies from the pharmaceutical industry, this paper analyzes the sequence in which business strategy, organ...

  3. In Search of a Network Organization for Innovation: A Multilevel Analysis on Transnational Corporations' Global Innovation

    Hu, Yimei

    2013-01-01

    4 explores how transnational corporations perceive and design an internal network organization to facilitate global innovation. Based on a multiple case study of three Danish transnational corporations’ global R&D organization, this paper shows three types of network organization design...... explores how an SME develops a network organization consisting of both interfirm innovation networks and an internal network organization to facilitate its global innovation strategy. Regarding the intraorganizational network organization, market mechanism is adopted to optimize internal resource...... corporations perceive/design a network organization to facilitate their global innovation? • To what extent and how can we manage a network organization? Research focus of the dissertation is on transnational corporations’ network organization for innovation. The first research question aims to clarify...

  4. Organization of plastid genomes in the freshwater red algal order Batrachospermales (Rhodophyta).

    Paiano, Monica Orlandi; Del Cortona, Andrea; Costa, Joana F; Liu, Shao-Lun; Verbruggen, Heroen; De Clerck, Olivier; Necchi, Orlando

    2018-02-01

    Little is known about genome organization in members of the order Batrachospermales, and the infra-ordinal relationship remains unresolved. Plastid (cp) genomes of seven members of the freshwater red algal order Batrachospermales were sequenced, with the following aims: (i) to describe the characteristics of cp genomes and compare these with other red algal groups; (ii) to infer the phylogenetic relationships among these members to better understand the infra-ordinal classification. Cp genomes of Batrachospermales are large, with several cases of gene loss, they are gene-dense (high gene content for the genome size and short intergenic regions) and have highly conserved gene order. Phylogenetic analyses based on concatenated nucleotide genome data roughly supports the current taxonomic system for the order. Comparative analyses confirm data for members of the class Florideophyceae that cp genomes in Batrachospermales is highly conserved, with little variation in gene composition. However, relevant new features were revealed in our study: genome sizes in members of Batrachospermales are close to the lowest values reported for Florideophyceae; differences in cp genome size within the order are large in comparison with other orders (Ceramiales, Gelidiales, Gracilariales, Hildenbrandiales, and Nemaliales); and members of Batrachospermales have the lowest number of protein-coding genes among the Florideophyceae. In terms of gene loss, apcF, which encodes the allophycocyanin beta subunit, is absent in all sequenced taxa of Batrachospermales. We reinforce that the interordinal relationships between the freshwater orders Batrachospermales and Thoreales within the Nemaliophycidae is not well resolved due to limited taxon sampling. © 2017 Phycological Society of America.

  5. Genomics dataset on unclassified published organism (patent US 7547531

    Mohammad Mahfuz Ali Khan Shawan

    2016-12-01

    Full Text Available Nucleotide (DNA sequence analysis provides important clues regarding the characteristics and taxonomic position of an organism. With the intention that, DNA sequence analysis is very crucial to learn about hierarchical classification of that particular organism. This dataset (patent US 7547531 is chosen to simplify all the complex raw data buried in undisclosed DNA sequences which help to open doors for new collaborations. In this data, a total of 48 unidentified DNA sequences from patent US 7547531 were selected and their complete sequences were retrieved from NCBI BioSample database. Quick response (QR code of those DNA sequences was constructed by DNA BarID tool. QR code is useful for the identification and comparison of isolates with other organisms. AT/GC content of the DNA sequences was determined using ENDMEMO GC Content Calculator, which indicates their stability at different temperature. The highest GC content was observed in GP445188 (62.5% which was followed by GP445198 (61.8% and GP445189 (59.44%, while lowest was in GP445178 (24.39%. In addition, New England BioLabs (NEB database was used to identify cleavage code indicating the 5, 3 and blunt end and enzyme code indicating the methylation site of the DNA sequences was also shown. These data will be helpful for the construction of the organisms’ hierarchical classification, determination of their phylogenetic and taxonomic position and revelation of their molecular characteristics.

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

    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.

  7. Draft Genome Sequence of the Model Naphthalene-Utilizing Organism Pseudomonas putida OUS82

    Tay, Martin; Roizman, Dan; Cohen, Yehuda

    2014-01-01

    Pseudomonas putida OUS82 was isolated from petrol- and oil-contaminated soil in 1992, and ever since, it has been used as a model organism to study the microbial assimilation of naphthalene and phenanthrene. Here, we report the 6.7-Mb draft genome sequence of P. putida OUS82 and analyze its...

  8. Global Account Management for Sales Organization in Multinational Companies

    Canegrati, Tino

    2009-01-01

    A Global Company is not just a Multinational Company, but on top it has developed an organizational structure, an overall governance and a set of operational decision making processes which allow running a significant percentage of business processes as a unique body across borders. Successful Global Companies have a clear setup and governance of local versus centralized decision making processes, as well as budget ownership. Corporations focused on global opportunities need to re-think their...

  9. DNA Extraction Protocols for Whole-Genome Sequencing in Marine Organisms.

    Panova, Marina; Aronsson, Henrik; Cameron, R Andrew; Dahl, Peter; Godhe, Anna; Lind, Ulrika; Ortega-Martinez, Olga; Pereyra, Ricardo; Tesson, Sylvie V M; Wrange, Anna-Lisa; Blomberg, Anders; Johannesson, Kerstin

    2016-01-01

    The marine environment harbors a large proportion of the total biodiversity on this planet, including the majority of the earths' different phyla and classes. Studying the genomes of marine organisms can bring interesting insights into genome evolution. Today, almost all marine organismal groups are understudied with respect to their genomes. One potential reason is that extraction of high-quality DNA in sufficient amounts is challenging for many marine species. This is due to high polysaccharide content, polyphenols and other secondary metabolites that will inhibit downstream DNA library preparations. Consequently, protocols developed for vertebrates and plants do not always perform well for invertebrates and algae. In addition, many marine species have large population sizes and, as a consequence, highly variable genomes. Thus, to facilitate the sequence read assembly process during genome sequencing, it is desirable to obtain enough DNA from a single individual, which is a challenge in many species of invertebrates and algae. Here, we present DNA extraction protocols for seven marine species (four invertebrates, two algae, and a marine yeast), optimized to provide sufficient DNA quality and yield for de novo genome sequencing projects.

  10. Molecular analysis and genomic organization of major DNA satellites in banana (Musa spp.).

    Čížková, Jana; Hřibová, Eva; Humplíková, Lenka; Christelová, Pavla; Suchánková, Pavla; Doležel, Jaroslav

    2013-01-01

    Satellite DNA sequences consist of tandemly arranged repetitive units up to thousands nucleotides long in head-to-tail orientation. The evolutionary processes by which satellites arise and evolve include unequal crossing over, gene conversion, transposition and extra chromosomal circular DNA formation. Large blocks of satellite DNA are often observed in heterochromatic regions of chromosomes and are a typical component of centromeric and telomeric regions. Satellite-rich loci may show specific banding patterns and facilitate chromosome identification and analysis of structural chromosome changes. Unlike many other genomes, nuclear genomes of banana (Musa spp.) are poor in satellite DNA and the information on this class of DNA remains limited. The banana cultivars are seed sterile clones originating mostly from natural intra-specific crosses within M. acuminata (A genome) and inter-specific crosses between M. acuminata and M. balbisiana (B genome). Previous studies revealed the closely related nature of the A and B genomes, including similarities in repetitive DNA. In this study we focused on two main banana DNA satellites, which were previously identified in silico. Their genomic organization and molecular diversity was analyzed in a set of nineteen Musa accessions, including representatives of A, B and S (M. schizocarpa) genomes and their inter-specific hybrids. The two DNA satellites showed a high level of sequence conservation within, and a high homology between Musa species. FISH with probes for the satellite DNA sequences, rRNA genes and a single-copy BAC clone 2G17 resulted in characteristic chromosome banding patterns in M. acuminata and M. balbisiana which may aid in determining genomic constitution in interspecific hybrids. In addition to improving the knowledge on Musa satellite DNA, our study increases the number of cytogenetic markers and the number of individual chromosomes, which can be identified in Musa.

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

    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

  12. Governance of global organic agro-food networks from Africa

    Glin, L.C.

    2014-01-01

    The increasing global concerns with regard to agro-food risks and the subsequent consumerist turn in the global food economy challenges the conventional chemical-intensive agricultural production. In fact, the post-war dominant agro-industrial development fostered the intensive use of chemical

  13. Genomic sequence and organization of two members of a human lectin gene family

    Gitt, M.A.; Barondes, S.H.

    1991-01-01

    The authors have isolated and sequenced the genomic DNA encoding a human dimeric soluble lactose-binding lectin. The gene has four exons, and its upstream region contains sequences that suggest control by glucocorticoids, heat (environmental) shock, metals, and other factors. They have also isolated and sequenced three exons of the gene encoding another human putative lectin, the existence of which was first indicated by isolation of its cDNA. Comparisons suggest a general pattern of genomic organization of members of this lectin gene family

  14. Impact of nuclear organization and chromatin structure on DNA repair and genome stability

    Batte, Amandine

    2016-01-01

    The non-random organization of the eukaryotic cell nucleus and the folding of genome in chromatin more or less condensed can influence many functions related to DNA metabolism, including genome stability. Double-strand breaks (DSBs) are the most deleterious DNA damages for the cells. To preserve genome integrity, eukaryotic cells thus developed DSB repair mechanisms conserved from yeast to human, among which homologous recombination (HR) that uses an intact homologous sequence to repair a broken chromosome. HR can be separated in two sub-pathways: Gene Conversion (GC) transfers genetic information from one molecule to its homologous and Break Induced Replication (BIR) establishes a replication fork than can proceed until the chromosome end. My doctorate work was focused on the contribution of the chromatin context and 3D genome organization on DSB repair. In S. cerevisiae, nuclear organization and heterochromatin spreading at sub-telomeres can be modified through the overexpression of the Sir3 or sir3A2Q mutant proteins. We demonstrated that reducing the physical distance between homologous sequences increased GC rates, reinforcing the notion that homology search is a limiting step for recombination. We also showed that hetero-chromatinization of DSB site fine-tunes DSB resection, limiting the loss of the DSB ends required to perform homology search and complete HR. Finally, we noticed that the presence of heterochromatin at the donor locus decreased both GC and BIR efficiencies, probably by affecting strand invasion. This work highlights new regulatory pathways of DNA repair. (author) [fr

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

    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.

  16. An Instructional Development Model for Global Organizations: The GOaL Model.

    Hara, Noriko; Schwen, Thomas M.

    1999-01-01

    Presents an instructional development model, GOaL (Global Organization Localization), for use by global organizations. Topics include gaps in language, culture, and needs; decentralized processes; collaborative efforts; predetermined content; multiple perspectives; needs negotiation; learning within context; just-in-time training; and bilingual…

  17. Beyond the network effect: towards an alternative understanding of global urban organizations

    James, P.; Verrest, H.; Gupta, J.; Pfeffer, K.; Verrest, H.; Ros-Tonen, M.

    2015-01-01

    Global organizations providing network relations for cities are bourgeoning. Organizations such as Metropolis, UN-Habitat, ICLEI - Local Governments for Sustainability, the Global Compact Cities Programme, and the C40, as well as City-to-City arrangements, have become increasingly important to

  18. 76 FR 174 - International Business Machines (IBM), Global Sales Operations Organization, Sales and...

    2011-01-03

    ... DEPARTMENT OF LABOR Employment and Training Administration [TA-W-74,575; TA-W-74,575D] International Business Machines (IBM), Global Sales Operations Organization, Sales and Distribution Business Manager Roles; One Teleworker Located in Charleston, WV; International Business Machines (IBM), Global Sales Operations Organization, Sales and...

  19. Occupancy of chromatin organizers in the Epstein-Barr virus genome.

    Holdorf, Meghan M; Cooper, Samantha B; Yamamoto, Keith R; Miranda, J J L

    2011-06-20

    The human CCCTC-binding factor, CTCF, regulates transcription of the double-stranded DNA genomes of herpesviruses. The architectural complex cohesin and RNA Polymerase II also contribute to this organization. We profiled the occupancy of CTCF, cohesin, and RNA Polymerase II on the episomal genome of the Epstein-Barr virus in a cell culture model of latent infection. CTCF colocalizes with cohesin but not RNA Polymerase II. CTCF and cohesin bind specific sequences throughout the genome that are found not just proximal to the regulatory elements of latent genes, but also near lytic genes. In addition to tracking with known transcripts, RNA Polymerase II appears at two unannotated positions, one of which lies within the latent origin of replication. The widespread occupancy profile of each protein reveals binding near or at a myriad of regulatory elements and suggests context-dependent functions. Copyright © 2011 Elsevier Inc. All rights reserved.

  20. Multilateral organizations and global inequality: A focus on IMF ...

    The paper examines issues relating to multilateral organizations, taking a particular look at the three multilateral organizations viz IMF, World Bank and WTO. It establishes that institutional and structural variables in the multilateral organizations are skewed in favour of the developed countries and this tends to entrench their ...

  1. Genomes

    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...

  2. Integrated genomics and proteomics of the Torpedo californica electric organ: concordance with the mammalian neuromuscular junction

    Mate Suzanne E

    2011-05-01

    Full Text Available Abstract Background During development, the branchial mesoderm of Torpedo californica transdifferentiates into an electric organ capable of generating high voltage discharges to stun fish. The organ contains a high density of cholinergic synapses and has served as a biochemical model for the membrane specialization of myofibers, the neuromuscular junction (NMJ. We studied the genome and proteome of the electric organ to gain insight into its composition, to determine if there is concordance with skeletal muscle and the NMJ, and to identify novel synaptic proteins. Results Of 435 proteins identified, 300 mapped to Torpedo cDNA sequences with ≥2 peptides. We identified 14 uncharacterized proteins in the electric organ that are known to play a role in acetylcholine receptor clustering or signal transduction. In addition, two human open reading frames, C1orf123 and C6orf130, showed high sequence similarity to electric organ proteins. Our profile lists several proteins that are highly expressed in skeletal muscle or are muscle specific. Synaptic proteins such as acetylcholinesterase, acetylcholine receptor subunits, and rapsyn were present in the electric organ proteome but absent in the skeletal muscle proteome. Conclusions Our integrated genomic and proteomic analysis supports research describing a muscle-like profile of the organ. We show that it is a repository of NMJ proteins but we present limitations on its use as a comprehensive model of the NMJ. Finally, we identified several proteins that may become candidates for signaling proteins not previously characterized as components of the NMJ.

  3. Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data.

    Can Alkan

    2007-09-01

    Full Text Available The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%-5% of sequence generated as part of primate genome sequencing projects consists of this material, which is fragmented or not assembled as part of published genome sequences due to its highly repetitive nature. Here, we develop computational methods to rapidly recover and categorize alpha-satellite sequences from previously uncharacterized whole-genome shotgun sequence data. We present an algorithm to computationally predict potential higher-order array structure based on paired-end sequence data and then experimentally validate its organization and distribution by experimental analyses. Using whole-genome shotgun data from the human, chimpanzee, and macaque genomes, we examine the phylogenetic relationship of these sequences and provide further support for a model for their evolution and mutation over the last 25 million years. Our results confirm fundamental differences in the dispersal and evolution of centromeric satellites in the Old World monkey and ape lineages of evolution.

  4. Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data.

    Alkan, Can; Ventura, Mario; Archidiacono, Nicoletta; Rocchi, Mariano; Sahinalp, S Cenk; Eichler, Evan E

    2007-09-01

    The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%-5% of sequence generated as part of primate genome sequencing projects consists of this material, which is fragmented or not assembled as part of published genome sequences due to its highly repetitive nature. Here, we develop computational methods to rapidly recover and categorize alpha-satellite sequences from previously uncharacterized whole-genome shotgun sequence data. We present an algorithm to computationally predict potential higher-order array structure based on paired-end sequence data and then experimentally validate its organization and distribution by experimental analyses. Using whole-genome shotgun data from the human, chimpanzee, and macaque genomes, we examine the phylogenetic relationship of these sequences and provide further support for a model for their evolution and mutation over the last 25 million years. Our results confirm fundamental differences in the dispersal and evolution of centromeric satellites in the Old World monkey and ape lineages of evolution.

  5. Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome.

    Pingault, Lise; Choulet, Frédéric; Alberti, Adriana; Glover, Natasha; Wincker, Patrick; Feuillet, Catherine; Paux, Etienne

    2015-02-10

    Because of its size, allohexaploid nature, and high repeat content, the bread wheat genome is a good model to study the impact of the genome structure on gene organization, function, and regulation. However, because of the lack of a reference genome sequence, such studies have long been hampered and our knowledge of the wheat gene space is still limited. The access to the reference sequence of the wheat chromosome 3B provided us with an opportunity to study the wheat transcriptome and its relationships to genome and gene structure at a level that has never been reached before. By combining this sequence with RNA-seq data, we construct a fine transcriptome map of the chromosome 3B. More than 8,800 transcription sites are identified, that are distributed throughout the entire chromosome. Expression level, expression breadth, alternative splicing as well as several structural features of genes, including transcript length, number of exons, and cumulative intron length are investigated. Our analysis reveals a non-monotonic relationship between gene expression and structure and leads to the hypothesis that gene structure is determined by its function, whereas gene expression is subject to energetic cost. Moreover, we observe a recombination-based partitioning at the gene structure and function level. Our analysis provides new insights into the relationships between gene and genome structure and function. It reveals mechanisms conserved with other plant species as well as superimposed evolutionary forces that shaped the wheat gene space, likely participating in wheat adaptation.

  6. Genomic organization and dynamics of repetitive DNA sequences in representatives of three Fagaceae genera.

    Alves, Sofia; Ribeiro, Teresa; Inácio, Vera; Rocheta, Margarida; Morais-Cecílio, Leonor

    2012-05-01

    Oaks, chestnuts, and beeches are economically important species of the Fagaceae. To understand the relationship between these members of this family, a deep knowledge of their genome composition and organization is needed. In this work, we have isolated and characterized several AFLP fragments obtained from Quercus rotundifolia Lam. through homology searches in available databases. Genomic polymorphisms involving some of these sequences were evaluated in two species of Quercus, one of Castanea, and one of Fagus with specific primers. Comparative FISH analysis with generated sequences was performed in interphase nuclei of the four species, and the co-immunolocalization of 5-methylcytosine was also studied. Some of the sequences isolated proved to be genus-specific, while others were present in all the genera. Retroelements, either gypsy-like of the Tat/Athila clade or copia-like, are well represented, and most are dispersed in euchromatic regions of these species with no DNA methylation associated, pointing to an interspersed arrangement of these retroelements with potential gene-rich regions. A particular gypsy-sequence is dispersed in oaks and chestnut nuclei, but its confinement to chromocenters in beech evidences genome restructuring events during evolution of Fagaceae. Several sequences generated in this study proved to be good tools to comparatively study Fagaceae genome organization.

  7. Enabling a community to dissect an organism: overview of the Neurospora functional genomics project.

    Dunlap, Jay C; Borkovich, Katherine A; Henn, Matthew R; Turner, Gloria E; Sachs, Matthew S; Glass, N Louise; McCluskey, Kevin; Plamann, Michael; Galagan, James E; Birren, Bruce W; Weiss, Richard L; Townsend, Jeffrey P; Loros, Jennifer J; Nelson, Mary Anne; Lambreghts, Randy; Colot, Hildur V; Park, Gyungsoon; Collopy, Patrick; Ringelberg, Carol; Crew, Christopher; Litvinkova, Liubov; DeCaprio, Dave; Hood, Heather M; Curilla, Susan; Shi, Mi; Crawford, Matthew; Koerhsen, Michael; Montgomery, Phil; Larson, Lisa; Pearson, Matthew; Kasuga, Takao; Tian, Chaoguang; Baştürkmen, Meray; Altamirano, Lorena; Xu, Junhuan

    2007-01-01

    A consortium of investigators is engaged in a functional genomics project centered on the filamentous fungus Neurospora, with an eye to opening up the functional genomic analysis of all the filamentous fungi. The overall goal of the four interdependent projects in this effort is to accomplish functional genomics, annotation, and expression analyses of Neurospora crassa, a filamentous fungus that is an established model for the assemblage of over 250,000 species of non yeast fungi. Building from the completely sequenced 43-Mb Neurospora genome, Project 1 is pursuing the systematic disruption of genes through targeted gene replacements, phenotypic analysis of mutant strains, and their distribution to the scientific community at large. Project 2, through a primary focus in Annotation and Bioinformatics, has developed a platform for electronically capturing community feedback and data about the existing annotation, while building and maintaining a database to capture and display information about phenotypes. Oligonucleotide-based microarrays created in Project 3 are being used to collect baseline expression data for the nearly 11,000 distinguishable transcripts in Neurospora under various conditions of growth and development, and eventually to begin to analyze the global effects of loss of novel genes in strains created by Project 1. cDNA libraries generated in Project 4 document the overall complexity of expressed sequences in Neurospora, including alternative splicing alternative promoters and antisense transcripts. In addition, these studies have driven the assembly of an SNP map presently populated by nearly 300 markers that will greatly accelerate the positional cloning of genes.

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

    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.

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

    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.

  10. A Strategic Analysis of Investment Opportunities within British Columbia's Private Healthcare Sector for a Non-Profit Genomics Research Organization

    Barclay, John W.

    2010-01-01

    Advances in the genome sciences are leading to the development of new healthcare innovations relevant to the principles of personalized medicine. Genome BC, a non-profit research organization, invests in projects that will help facilitate the integration of these innovations into the delivery of healthcare. This analysis assesses the strategic positioning of private healthcare firms in BC to be early users of such innovations. The analysis assesses the suitability of investment from Genome BC...

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

    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.

  12. Globalization and Education within Two Revolutionary Organizations in the United States of America: A Gramscian Analysis

    Holst, John D.

    2004-01-01

    This article presents the history, strategy, structure, educational practices, and globalization perspectives of two revolutionary organizations in the United States of America: the Freedom Road Socialist Organization and the League of Revolutionaries for a New America. This article relates the work of these organizations to the theory and…

  13. Human Ro60 (SSA2) genomic organization and sequence alterations, examined in cutaneous lupus erythematosus.

    Millard, T P; Ashton, G H S; Kondeatis, E; Vaughan, R W; Hughes, G R V; Khamashta, M A; Hawk, J L M; McGregor, J M; McGrath, J A

    2002-02-01

    The Ro 60 kDa protein (Ro60 or SSA2) is the major component of the Ro ribonucleoprotein (Ro RNP) complex, to which an immune response is a specific feature of several autoimmune diseases. The genomic organization and any sequence variation within the DNA encoding Ro60 are unknown. To characterize the Ro60 gene structure and to assess whether any sequence alterations might be associated with serum anti-Ro antibody in subacute cutaneous lupus erythematosus (SCLE), thus potentially providing new insight into disease pathogenesis. The cDNA sequence for Ro60 was obtained from the NCBI database and used for a BLAST search for a clone containing the entire genomic sequence. The intron-exon borders were confirmed by designing intronic primer pairs to flank each exon, which were then used to amplify genomic DNA for automated sequencing from 36 caucasian patients with SCLE (anti-Ro positive) and 49 with discoid LE (DLE, anti-Ro negative), in addition to 36 healthy caucasian controls. Heteroduplex analysis of polymerase chain reaction (PCR) products from patients and controls spanning all Ro60 exons (1-8) revealed a common bandshift in the PCR products spanning exon 7. Sequencing of the corresponding PCR products demonstrated an A > G substitution at nucleotide position 1318-7, within the consensus acceptor splice site of exon 7 (GenBank XM001901). The allele frequencies were major allele A (0.71) and minor allele G (0.29) in 72 control chromosomes, with no significant differences found between SCLE patients, DLE patients and controls. The genomic organization of the DNA encoding the Ro60 protein is described, including a common polymorphism within the consensus acceptor splice site of exon 7. Our delineation of a strategy for the genomic amplification of Ro60 forms a basis for further examination of the pathological functions of the Ro RNP in autoimmune disease.

  14. Advancing the right to health through global organizations: The potential role of a Framework Convention on Global Health.

    Friedman, Eric A; Gostin, Lawrence O; Buse, Kent

    2013-06-14

    Organizations, partnerships, and alliances form the building blocks of global governance. Global health organizations thus have the potential to play a formative role in determining the extent to which people are able to realize their right to health. This article examines how major global health organizations, such as WHO, the Global Fund to Fight AIDS, TB and Malaria, UNAIDS, and GAVI approach human rights concerns, including equality, accountability, and inclusive participation. We argue that organizational support for the right to health must transition from ad hoc and partial to permanent and comprehensive. Drawing on the literature and our knowledge of global health organizations, we offer good practices that point to ways in which such agencies can advance the right to health, covering nine areas: 1) participation and representation in governance processes; 2) leadership and organizational ethos; 3) internal policies; 4) norm-setting and promotion; 5) organizational leadership through advocacy and communication; 6) monitoring and accountability; 7) capacity building; 8) funding policies; and 9) partnerships and engagement. In each of these areas, we offer elements of a proposed Framework Convention on Global Health (FCGH), which would commit state parties to support these standards through their board membership and other interactions with these agencies. We also explain how the FCGH could incorporate these organizations into its overall financing framework, initiate a new forum where they collaborate with each other, as well as organizations in other regimes, to advance the right to health, and ensure sufficient funding for right to health capacity building. We urge major global health organizations to follow the leadership of the UN Secretary-General and UNAIDS to champion the FCGH. It is only through a rights-based approach, enshrined in a new Convention, that we can expect to achieve health for all in our lifetimes. Copyright © 2013 Friedman, Gostin

  15. Globalization of Innovation and the Rise of Network Organization

    Hu, Yimei

    2016-01-01

    ’s innovation purposes. Such organizational structure is contrast with traditional hierarchical organizational structure, and featured with flexibility, market mechanism, internal trust, etc. Secondly, a network organization refers to various forms of interorganizational designs such as strategic alliances...

  16. tracing uganda's global primary organic pineapple value chain

    ACSS

    2016-02-22

    Feb 22, 2016 ... methods were used to validate results obtained from the .... TABLE 2. Agronomic information on organic pineapple production in Uganda ..... management, which makes the value chain expensive ..... A handbook for value ...

  17. Global effects of agriculture on fluvial dissolved organic matter

    Graeber, Daniel; Boëchat, Iola; Encina, Francisco

    2015-01-01

    Agricultural land covers approximately 40% of Earth’s land surface and affects hydromorphological, biogeochemical and ecological characteristics of fluvial networks. In the northern temperate region, agriculture also strongly affects the amount and molecular composition of dissolved organic matter...

  18. The Role of Civil Society Organizations in Monitoring the Global AIDS Response.

    Smith, Julia; Mallouris, Christoforos; Lee, Kelley; Alfvén, Tobias

    2017-07-01

    Civil society organizations (CSOs) are recognized as playing an exceptional role in the global AIDS response. However, there is little detailed research to date on how they contribute to specific governance functions. This article uses Haas' framework on global governance functions to map CSO's participation in the monitoring of global commitments to the AIDS response by institutions and states. Drawing on key informant interviews and primary documents, it focuses specifically on CSO participation in Global AIDS Response Progress Reporting and in Global Fund to Fight AIDS, Tuberculosis and Malaria processes. It argues that the AIDS response is unique within global health governance, in that CSOs fulfill both formal and informal monitoring functions, and considers the strengths and weaknesses of these contributions. It concludes that future global health governance arrangements should include provisions and resources for monitoring by CSOs because their participation creates more inclusive global health governance and contributes to strengthening commitments to human rights.

  19. Global Organization of Innovation and Cooperability in Brazilian Multinationals

    Priscila Rezende da Costa

    2017-04-01

    Full Text Available Understanding the dissipation of innovations is necessary to develop them, as a company on its own does not have all the capabilities that it needs. On the contrary, they are increasingly spread over internal and external contexts, and are not developed in isolation. Most of the time, they depend on interactive, innovative processes in a global context. The aim of this study is to evaluate how the global organizational structure of innovation affects the dynamic capability of cooperation (cooperability in Brazilian multinationals (BMNs. To achieve this goal, we conducted a survey of BMNs, and a final sample of 60 companies answered a structured questionnaire. We performed statistical tests such as Factor Analysis, Cronbach's Alpha, Multiple Regression and Hierarchical Cluster, and cross-analysis of quantitative results that enabled us to create a Cooperability Model, that is, a model of local, international and global development for a dynamic capability of cooperation in BMNs. The results show that technological strengths of foreign subsidiaries and the reverse transfer of their capabilities to the parent company and technology partners affect the dynamics of cooperation in BMNs (inputs and results of cooperability. Furthermore, we detected an inverse relationship between the autonomy of foreign subsidiaries and the dynamic of cooperation in BMNs.

  20. Building a complete image of genome regulation in the model organism Escherichia coli.

    Ishihama, Akira

    2018-01-15

    The model organism, Escherichia coli, contains a total of more than 4,500 genes, but the total number of RNA polymerase (RNAP) core enzyme or the transcriptase is only about 2,000 molecules per genome. The regulatory targets of RNAP are, however, modulated by changing its promoter selectivity through two-steps of protein-protein interplay with 7 species of the sigma factor in the first step, and then 300 species of the transcription factor (TF) in the second step. Scientists working in the field of prokaryotic transcription in Japan have made considerable contributions to the elucidation of genetic frameworks and regulatory modes of the genome transcription in E. coli K-12. This review summarizes the findings by this group, first focusing on three sigma factors, the stationary-phase sigma RpoS, the heat-shock sigma RpoH, and the flagellar-chemotaxis sigma RpoF, as examples. It also presents an overview of the current state of the systematic research being carried out to identify the regulatory functions of all TFs from a single and the same bacterium E. coli K-12, using the genomic SELEX and PS-TF screening systems. All these studies have been undertaken with the aim of understanding the genome regulation in E. coli K-12 as a whole.

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

    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. Primary structure of the human follistatin precursor and its genomic organization

    Shimasaki, Shunichi; Koga, Makoto; Esch, F.

    1988-01-01

    Follistatin is a single-chain gonadal protein that specifically inhibits follicle-stimulating hormone release. By use of the recently characterized porcine follistatin cDNA as a probe to screen a human testis cDNA library and a genomic library, the structure of the complete human follistatin precursor as well as its genomic organization have been determined. Three of eight cDNA clones that were sequenced predicted a precursor with 344 amino acids, whereas the remaining five cDNA clones encoded a 317 amino acid precursor, resulting from alternative splicing of the precursor mRNA. Mature follistatins contain four contiguous domains that are encoded by precisely separated exons; three of the domains are highly similar to each other, as well as to human epidermal growth factor and human pancreatic secretory trypsin inhibitor. The genomic organization of the human follistatin is similar to that of the human epidermal growth factor gene and thus supports the notion of exon shuffling during evolution

  3. Structurally Complex Organization of Repetitive DNAs in the Genome of Cobia (Rachycentron canadum).

    Costa, Gideão W W F; Cioffi, Marcelo de B; Bertollo, Luiz A C; Molina, Wagner F

    2015-06-01

    Repetitive DNAs comprise the largest fraction of the eukaryotic genome. They include microsatellites or simple sequence repeats (SSRs), which play an important role in the chromosome differentiation among fishes. Rachycentron canadum is the only representative of the family Rachycentridae. This species has been focused on several multidisciplinary studies in view of its important potential for marine fish farming. In the present study, distinct classes of repetitive DNAs, with emphasis on SSRs, were mapped in the chromosomes of this species to improve the knowledge of its genome organization. Microsatellites exhibited a diversified distribution, both dispersed in euchromatin and clustered in the heterochromatin. The multilocus location of SSRs strengthened the heterochromatin heterogeneity in this species, as suggested by some previous studies. The colocalization of SSRs with retrotransposons and transposons pointed to a close evolutionary relationship between these repetitive sequences. A number of heterochromatic regions highlighted a greater complex organization than previously supposed, harboring a diversity of repetitive elements. In this sense, there was also evidence of colocalization of active genetic regions and different classes of repetitive DNAs in a common heterochromatic region, which offers a potential opportunity for further researches regarding the interaction of these distinct fractions in fish genomes.

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

    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)

  5. Activating Global Operating Models: The bridge from organization design to performance

    Amy Kates

    2015-07-01

    Full Text Available This article introduces the concept of activation and discusses its use in the implementation of global operating models by large multinational companies. We argue that five particular activators help set in motion the complex strategies and organizations required by global operating models.

  6. New global fire emission estimates and evaluation of volatile organic compounds

    C. Wiedinmyer; L. K. Emmons; S. K. Akagi; R. J. Yokelson; J. J. Orlando; J. A. Al-Saadi; A. J. Soja

    2010-01-01

    A daily, high-resolution, global fire emissions model has been built to estimate emissions from open burning for air quality modeling applications: The Fire INventory from NCAR (FINN version 1). The model framework uses daily fire detections from the MODIS instruments and updated emission factors, specifically for speciated non-methane organic compounds (NMOC). Global...

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

    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.

  8. Disturbances, organisms and ecosystems: a global change perspective.

    Ponge, Jean-François

    2013-04-01

    The present text exposes a theory of the role of disturbances in the assemblage and evolution of species within ecosystems, based principally, but not exclusively, on terrestrial ecosystems. Two groups of organisms, doted of contrasted strategies when faced with environmental disturbances, are presented, based on the classical r-K dichotomy, but enriched with more modern concepts from community and evolutionary ecology. Both groups participate in the assembly of known animal, plant, and microbial communities, but with different requirements about environmental fluctuations. The so-called "civilized" organisms are doted with efficient anticipatory mechanisms, allowing them to optimize from an energetic point of view their performances in a predictable environment (stable or fluctuating cyclically at the scale of life expectancy), and they developed advanced specializations in the course of evolutionary time. On the opposite side, the so-called "barbarians" are weakly efficient in a stable environment because they waste energy for foraging, growth, and reproduction, but they are well adapted to unpredictably changing conditions, in particular during major ecological crises. Both groups of organisms succeed or alternate each other in the course of spontaneous or geared successional processes, as well as in the course of evolution. The balance of "barbarians" against "civilized" strategies within communities is predicted to shift in favor of the first type under present-day anthropic pressure, exemplified among others by climate warming, land use change, pollution, and biological invasions.

  9. No boundaries: genomes, organisms, and ecological interactions responsible for divergence and reproductive isolation.

    Etges, William J

    2014-01-01

    Revealing the genetic basis of traits that cause reproductive isolation, particularly premating or sexual isolation, usually involves the same challenges as most attempts at genotype-phenotype mapping and so requires knowledge of how these traits are expressed in different individuals, populations, and environments, particularly under natural conditions. Genetic dissection of speciation phenotypes thus requires understanding of the internal and external contexts in which underlying genetic elements are expressed. Gene expression is a product of complex interacting factors internal and external to the organism including developmental programs, the genetic background including nuclear-cytotype interactions, epistatic relationships, interactions among individuals or social effects, stochasticity, and prevailing variation in ecological conditions. Understanding of genomic divergence associated with reproductive isolation will be facilitated by functional expression analysis of annotated genomes in organisms with well-studied evolutionary histories, phylogenetic affinities, and known patterns of ecological variation throughout their life cycles. I review progress and prospects for understanding the pervasive role of host plant use on genetic and phenotypic expression of reproductive isolating mechanisms in cactophilic Drosophila mojavensis and suggest how this system can be used as a model for revealing the genetic basis for species formation in organisms where speciation phenotypes are under the joint influences of genetic and environmental factors. © The American Genetic Association. 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

    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

  11. Genomic organization, transcript variants and comparative analysis of the human nucleoporin 155 (NUP155) gene

    Zhang, X.; Yang, J.; Yu, J.

    2002-01-01

    Nucleoporin 155 (Nup155) is a major component of the nuclear pore complex (NPC) involved in cellular nucleo-cytoplasmic transport. We have acquired the complete sequence and interpreted the genomic organization of the Nup155 orthologos from human (Homo sapiens) and pufferfish (Fugu rubripes), which...... complementary to RNAs of the Nup155 orthologs from Fugu and mouse. Comparative analysis of the Nup155 orthologs in many species, including H. sapiens, Mus musculus, Rattus norvegicus, F. rubripes, Arabidopsis thaliana, Drosophila melanogaster, and Saccharomyces cerevisiae, has revealed two paralogs in S...

  12. Architectural protein subclasses shape 3-D organization of genomes during lineage commitment

    Phillips-Cremins, Jennifer E.; Sauria, Michael E. G.; Sanyal, Amartya; Gerasimova, Tatiana I.; Lajoie, Bryan R.; Bell, Joshua S. K.; Ong, Chin-Tong; Hookway, Tracy A.; Guo, Changying; Sun, Yuhua; Bland, Michael J.; Wagstaff, William; Dalton, Stephen; McDevitt, Todd C.; Sen, Ranjan; Dekker, Job; Taylor, James; Corces, Victor G.

    2013-01-01

    Summary Understanding the topological configurations of chromatin may reveal valuable insights into how the genome and epigenome act in concert to control cell fate during development. Here we generate high-resolution architecture maps across seven genomic loci in embryonic stem cells and neural progenitor cells. We observe a hierarchy of 3-D interactions that undergo marked reorganization at the sub-Mb scale during differentiation. Distinct combinations of CTCF, Mediator, and cohesin show widespread enrichment in looping interactions at different length scales. CTCF/cohesin anchor long-range constitutive interactions that form the topological basis for invariant sub-domains. Conversely, Mediator/cohesin together with pioneer factors bridge shortrange enhancer-promoter interactions within and between larger sub-domains. Knockdown of Smc1 or Med12 in ES cells results in disruption of spatial architecture and down-regulation of genes found in cohesin-mediated interactions. We conclude that cell type-specific chromatin organization occurs at the sub-Mb scale and that architectural proteins shape the genome in hierarchical length scales. PMID:23706625

  13. Capturing Three-Dimensional Genome Organization in Individual Cells by Single-Cell Hi-C.

    Nagano, Takashi; Wingett, Steven W; Fraser, Peter

    2017-01-01

    Hi-C is a powerful method to investigate genome-wide, higher-order chromatin and chromosome conformations averaged from a population of cells. To expand the potential of Hi-C for single-cell analysis, we developed single-cell Hi-C. Similar to the existing "ensemble" Hi-C method, single-cell Hi-C detects proximity-dependent ligation events between cross-linked and restriction-digested chromatin fragments in cells. A major difference between the single-cell Hi-C and ensemble Hi-C protocol is that the proximity-dependent ligation is carried out in the nucleus. This allows the isolation of individual cells in which nearly the entire Hi-C procedure has been carried out, enabling the production of a Hi-C library and data from individual cells. With this new method, we studied genome conformations and found evidence for conserved topological domain organization from cell to cell, but highly variable interdomain contacts and chromosome folding genome wide. In addition, we found that the single-cell Hi-C protocol provided cleaner results with less technical noise suggesting it could be used to improve the ensemble Hi-C technique.

  14. Polytene Chromosomes - A Portrait of Functional Organization of the Drosophila Genome.

    Zykova, Tatyana Yu; Levitsky, Victor G; Belyaeva, Elena S; Zhimulev, Igor F

    2018-04-01

    This mini-review is devoted to the problem genetic meaning of main polytene chromosome structures - bands and interbands. Generally, densely packed chromatin forms black bands, moderately condensed regions form grey loose bands, whereas decondensed regions of the genome appear as interbands. Recent progress in the annotation of the Drosophila genome and epigenome has made it possible to compare the banding pattern and the structural organization of genes, as well as their activity. This was greatly aided by our ability to establish the borders of bands and interbands on the physical map, which allowed to perform comprehensive side-by-side comparisons of cytology, genetic and epigenetic maps and to uncover the association between the morphological structures and the functional domains of the genome. These studies largely conclude that interbands 5'-ends of housekeeping genes that are active across all cell types. Interbands are enriched with proteins involved in transcription and nucleosome remodeling, as well as with active histone modifications. Notably, most of the replication origins map to interband regions. As for grey loose bands adjacent to interbands, they typically host the bodies of house-keeping genes. Thus, the bipartite structure composed of an interband and an adjacent grey band functions as a standalone genetic unit. Finally, black bands harbor tissue-specific genes with narrow temporal and tissue expression profiles. Thus, the uniform and permanent activity of interbands combined with the inactivity of genes in bands forms the basis of the universal banding pattern observed in various Drosophila tissues.

  15. The genome and transcriptome of Phalaenopsis yield insights into floral organ development and flowering regulation

    Jian-Zhi Huang

    2016-05-01

    Full Text Available The Phalaenopsis orchid is an important potted flower of high economic value around the world. We report the 3.1 Gb draft genome assembly of an important winter flowering Phalaenopsis ‘KHM190’ cultivar. We generated 89.5 Gb RNA-seq and 113 million sRNA-seq reads to use these data to identify 41,153 protein-coding genes and 188 miRNA families. We also generated a draft genome for Phalaenopsis pulcherrima ‘B8802,’ a summer flowering species, via resequencing. Comparison of genome data between the two Phalaenopsis cultivars allowed the identification of 691,532 single-nucleotide polymorphisms. In this study, we reveal that the key role of PhAGL6b in the regulation of labellum organ development involves alternative splicing in the big lip mutant. Petal or sepal overexpressing PhAGL6b leads to the conversion into a lip-like structure. We also discovered that the gibberellin pathway that regulates the expression of flowering time genes during the reproductive phase change is induced by cool temperature. Our work thus depicted a valuable resource for the flowering control, flower architecture development, and breeding of the Phalaenopsis orchids.

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

    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

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

    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.

  18. Genomic organization, sequence divergence, and recombination of feline immunodeficiency virus from lions in the wild

    Pecon-Slattery, Jill; McCracken, Carrie L; Troyer, Jennifer L; VandeWoude, Sue; Roelke, Melody; Sondgeroth, Kerry; Winterbach, Christiaan; Winterbach, Hanlie; O'Brien, Stephen J

    2008-01-01

    Background Feline immunodeficiency virus (FIV) naturally infects multiple species of cat and is related to human immunodeficiency virus in humans. FIV infection causes AIDS-like disease and mortality in the domestic cat (Felis catus) and serves as a natural model for HIV infection in humans. In African lions (Panthera leo) and other exotic felid species, disease etiology introduced by FIV infection are less clear, but recent studies indicate that FIV causes moderate to severe CD4 depletion. Results In this study, comparative genomic methods are used to evaluate the full proviral genome of two geographically distinct FIV subtypes isolated from free-ranging lions. Genome organization of FIVPle subtype B (9891 bp) from lions in the Serengeti National Park in Tanzania and FIVPle subtype E (9899 bp) isolated from lions in the Okavango Delta in Botswana, both resemble FIV genome sequence from puma, Pallas cat and domestic cat across 5' LTR, gag, pol, vif, orfA, env, rev and 3'LTR regions. Comparative analyses of available full-length FIV consisting of subtypes A, B and C from FIVFca, Pallas cat FIVOma and two puma FIVPco subtypes A and B recapitulate the species-specific monophyly of FIV marked by high levels of genetic diversity both within and between species. Across all FIVPle gene regions except env, lion subtypes B and E are monophyletic, and marginally more similar to Pallas cat FIVOma than to other FIV. Sequence analyses indicate the SU and TM regions of env vary substantially between subtypes, with FIVPle subtype E more related to domestic cat FIVFca than to FIVPle subtype B and FIVOma likely reflecting recombination between strains in the wild. Conclusion This study demonstrates the necessity of whole-genome analysis to complement population/gene-based studies, which are of limited utility in uncovering complex events such as recombination that may lead to functional differences in virulence and pathogenicity. These full-length lion lentiviruses are integral to

  19. Genomic organization, sequence divergence, and recombination of feline immunodeficiency virus from lions in the wild

    Sondgeroth Kerry

    2008-02-01

    Full Text Available Abstract Background Feline immunodeficiency virus (FIV naturally infects multiple species of cat and is related to human immunodeficiency virus in humans. FIV infection causes AIDS-like disease and mortality in the domestic cat (Felis catus and serves as a natural model for HIV infection in humans. In African lions (Panthera leo and other exotic felid species, disease etiology introduced by FIV infection are less clear, but recent studies indicate that FIV causes moderate to severe CD4 depletion. Results In this study, comparative genomic methods are used to evaluate the full proviral genome of two geographically distinct FIV subtypes isolated from free-ranging lions. Genome organization of FIVPle subtype B (9891 bp from lions in the Serengeti National Park in Tanzania and FIVPle subtype E (9899 bp isolated from lions in the Okavango Delta in Botswana, both resemble FIV genome sequence from puma, Pallas cat and domestic cat across 5' LTR, gag, pol, vif, orfA, env, rev and 3'LTR regions. Comparative analyses of available full-length FIV consisting of subtypes A, B and C from FIVFca, Pallas cat FIVOma and two puma FIVPco subtypes A and B recapitulate the species-specific monophyly of FIV marked by high levels of genetic diversity both within and between species. Across all FIVPle gene regions except env, lion subtypes B and E are monophyletic, and marginally more similar to Pallas cat FIVOma than to other FIV. Sequence analyses indicate the SU and TM regions of env vary substantially between subtypes, with FIVPle subtype E more related to domestic cat FIVFca than to FIVPle subtype B and FIVOma likely reflecting recombination between strains in the wild. Conclusion This study demonstrates the necessity of whole-genome analysis to complement population/gene-based studies, which are of limited utility in uncovering complex events such as recombination that may lead to functional differences in virulence and pathogenicity. These full-length lion

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

    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.

  1. Novel rod-shaped viruses isolated from garlic, Allium sativum, possessing a unique genome organization.

    Sumi, S; Tsuneyoshi, T; Furutani, H

    1993-09-01

    Rod-shaped flexuous viruses were partially purified from garlic plants (Allium sativum) showing typical mosaic symptoms. The genome was shown to be composed of RNA with a poly(A) tail of an estimated size of 10 kb as shown by denaturing agarose gel electrophoresis. We constructed cDNA libraries and screened four independent clones, which were designated GV-A, GV-B, GV-C and GV-D, using Northern and Southern blot hybridization. Nucleotide sequence determination of the cDNAs, two of which correspond to nearly one-third of the virus genomic RNA, shows that all of these viruses possess an identical genomic structure and that also at least four proteins are encoded in the viral cDNA, their M(r)s being estimated to be 15K, 27K, 40K and 11K. The 15K open reading frame (ORF) encodes the core-like sequence of a zinc finger protein preceded by a cluster of basic amino acid residues. The 27K ORF probably encodes the viral coat protein (CP), based on both the existence of some conserved sequences observed in many other rod-shaped or flexuous virus CPs and an overall amino acid sequence similarity to potexvirus and carlavirus CPs. The 11K ORF shows significant amino acid sequence similarities to the corresponding 12K proteins of the potexviruses and carlaviruses. On the other hand, the 40K ORF product does not resemble any other plant virus gene products reported so far. The genomic organization in the 3' region of the garlic viruses resembles, but clearly differs from, that of carlaviruses. Phylogenetic analysis based upon the amino acid sequence of the viral capsid protein also indicates that the garlic viruses have a unique and distinct domain different from those of the potexvirus and carlavirus groups. The results suggest that the garlic viruses described here belong to an unclassified and new virus group closely related to the carlaviruses.

  2. Evaluation of plasmid and genomic DNA calibrants used for the quantification of genetically modified organisms.

    Caprioara-Buda, M; Meyer, W; Jeynov, B; Corbisier, P; Trapmann, S; Emons, H

    2012-07-01

    The reliable quantification of genetically modified organisms (GMOs) by real-time PCR requires, besides thoroughly validated quantitative detection methods, sustainable calibration systems. The latter establishes the anchor points for the measured value and the measurement unit, respectively. In this paper, the suitability of two types of DNA calibrants, i.e. plasmid DNA and genomic DNA extracted from plant leaves, for the certification of the GMO content in reference materials as copy number ratio between two targeted DNA sequences was investigated. The PCR efficiencies and coefficients of determination of the calibration curves as well as the measured copy number ratios for three powder certified reference materials (CRMs), namely ERM-BF415e (NK603 maize), ERM-BF425c (356043 soya), and ERM-BF427c (98140 maize), originally certified for their mass fraction of GMO, were compared for both types of calibrants. In all three systems investigated, the PCR efficiencies of plasmid DNA were slightly closer to the PCR efficiencies observed for the genomic DNA extracted from seed powders rather than those of the genomic DNA extracted from leaves. Although the mean DNA copy number ratios for each CRM overlapped within their uncertainties, the DNA copy number ratios were significantly different using the two types of calibrants. Based on these observations, both plasmid and leaf genomic DNA calibrants would be technically suitable as anchor points for the calibration of the real-time PCR methods applied in this study. However, the most suitable approach to establish a sustainable traceability chain is to fix a reference system based on plasmid DNA.

  3. Biological soil crusts: a fundamental organizing agent in global drylands

    Belnap, J.; Zhang, Y.

    2013-12-01

    Ecosystem function is profoundly affected by plant community composition, which is ultimately determined by factors that govern seed retention. Dryland ecosystems constitute ~35% of terrestrial surfaces, with most soils in these regions covered by biological soil crusts (biocrusts), a community whose autotrophs are dominated by cyanobacteria, lichens, and mosses. Studies at 550 sites revealed that plant community composition was controlled by the interaction among biocrust type, disturbance regime, and external morphology of seeds. In bare soils (due to disturbance), all seed types were present in the seedbank and plant community. As biocrusts became better developed (i.e., the cover of lichens and mosses increased), they more strongly filtered out seeds with appendages. Thus, soils under late successional biocrusts contained seedbanks dominated by smooth seeds and vascular plants growing in late successional biocrusts were dominated by those with smooth seeds. Therefore, the tension between the removal of biocrusts by soil surface disturbance and their recovery creates a shifting mosaic of plant patch types in both space and time. Because changes in vascular plant communities reverberate throughout both below ground and above ground food webs and thus affect multiple trophic levels, we propose that biocrusts are a fundamental organizing agent in drylands worldwide. Future increased demand for resources will intensify land use both temporally and spatially, resulting in an increased rate of biocrust loss across larger areas. As a result, we can expect shifts in the composition and distribution of plant communities, accompanied by concomitant changes in many aspects of dryland ecosystems. Conceptual model of shifting dryland plant mosaics through space and time. Within the large circles, soil surface type changes with time in the same space, going from bare uncrusted soil (B) to cyanobacterial biocrust (C) to lichen/moss (L/M) biocrust. Disturbance (D) drives the

  4. Organ trafficking and transplant tourism: a commentary on the global realities.

    Budiani-Saberi, D A; Delmonico, F L

    2008-05-01

    The extent of organ sales from commercial living donors (CLDs) or vendors has now become evident. At the Second Global Consultation on Human Transplantation of the World Health Organization's (WHO) in March 2007, it was estimated that organ trafficking accounts for 5-10% of the kidney transplants performed annually throughout the world. Patients with sufficient resources in need of organs may travel from one country to another to purchase a kidney (or liver) mainly from a poor person. Transplant centers in 'destination' countries have been well known to encourage the sale of organs to 'tourist' recipients from the 'client' countries.

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

    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.

  6. Chloroplast Genome Sequence of pigeonpea (Cajanus cajan (L. Millspaugh and Cajanus scarabaeoides: Genome organization and Comparison with other legumes

    Tanvi Kaila

    2016-12-01

    Full Text Available Pigeonpea (Cajanus cajan (L. Millspaugh, a diploid (2n = 22 legume crop with a genome size of 852 Mbp, serves as an important source of human dietary protein especially in South East Asian and African regions. In this study, the draft chloroplast genomes of Cajanus cajan and Cajanus scarabaeoides were sequenced. Cajanus scarabaeoides is an important species of the Cajanus gene pool and has also been used for developing promising CMS system by different groups. A male sterile genotype harbouring the Cajanus scarabaeoides cytoplasm was used for sequencing the plastid genome. The cp genome of Cajanus cajan is 152,242bp long, having a quadripartite structure with LSC of 83,455 bp and SSC of 17,871 bp separated by IRs of 25,398 bp. Similarly, the cp genome of Cajanus scarabaeoides is 152,201bp long, having a quadripartite structure in which IRs of 25,402 bp length separates 83,423 bp of LSC and 17,854 bp of SSC. The pigeonpea cp genome contains 116 unique genes, including 30 tRNA, 4 rRNA, 78 predicted protein coding genes and 5 pseudogenes. A 50kb inversion was observed in the LSC region of pigeonpea cp genome, consistent with other legumes. Comparison of cp genome with other legumes revealed the contraction of IR boundaries due to the absence of rps19 gene in the IR region. Chloroplast SSRs were mined and a total of 280 and 292 cpSSRs were identified in Cajanus scarabaeoides and Cajanus cajan respectively. RNA editing was observed at 37 sites in both Cajanus scarabaeoides and Cajanus cajan, with maximum occurrence in the ndh genes. The pigeonpea cp genome sequence would be beneficial in providing informative molecular markers which can be utilized for genetic diversity analysis and aid in understanding the plant systematics studies among major grain legumes.

  7. The elevation of radiation load on ecosystems and genome instability of organisms

    Gaziyev, A. I.; Bezlepkin, V.Q.

    2002-01-01

    prophylaxis of human disorders. Thus, it was found that the action of low-dose ionizing radiation on living organisms might induce an adaptive repair response in them aimed at decreasing the genetic consequences of the exposure. However, the potentialities of defense and repair systems of an organism are limited, so an increase in genome lesions may cause inheritable mutations, cancer and other pathologies, and death. DNA lesions caused by ionizing radiation in small and sublethal doses can essentially be repaired, whereas unrepaired lesions and errors of repair, replication, and recombination systems lead to formation of mutational changes in DNA sequences. These changes may be transmitted to daughter cells and induce genome instability in the progeny. Induced genome instability in survived somatic cells is characterized by persistence of a high level of acquired variability in many generations of these cells. Genome instability manifests itself as an increased frequency of karyotypic anomalies, chromosome and gene mutations, clonal heterogeneity, and malignant transformation in the progeny of cells exposed to DNA-damaging agents. Besides, cells with genome instability show increased amplification of genes and changes in their expression, as well as disturbances in their differentiation, delays in reproductive death and other phenotypic characters of abnormal development. Whereas some progress has been made towards knowledge of genome instability in the somatic cells of mammals, the radiation-induced genome instability in germ cells transmitted to individuals of the next generation is still not clearly understood. At the same time, evidence has been obtained which suggests that the transmission of genome instability to the somatic cells of the progeny from the germ cells of gamma - radiation-exposed parents is possible. This conclusion is based on the data on mutation frequency in the progeny of parents exposed to DNA-damaging agents. For instance, a significant increase in

  8. The global diffusion of organ transplantation: trends, drivers and policy implications.

    White, Sarah L; Hirth, Richard; Mahíllo, Beatriz; Domínguez-Gil, Beatriz; Delmonico, Francis L; Noel, Luc; Chapman, Jeremy; Matesanz, Rafael; Carmona, Mar; Alvarez, Marina; Núñez, Jose R; Leichtman, Alan

    2014-11-01

    Rising incomes, the spread of personal insurance, lifestyle factors adding to the burden of illness, ageing populations, globalization and skills transfer within the medical community have increased worldwide demand for organ transplantation. The Global Observatory on Donation and Transplantation, which was built in response to World Health Assembly resolution WHA57.18, has conducted ongoing documentation of global transplantation activities since 2007. In this paper, we use the Global Observatory's data to describe the current distribution of - and trends in - transplantation activities and to evaluate the role of health systems factors and macroeconomics in the diffusion of transplantation technology. We then consider the implications of our results for health policies relating to organ donation and transplantation. Of the World Health Organization's Member States, most now engage in organ transplantation and more than a third performed deceased donor transplantation in 2011. In general, the Member States that engage in organ transplantation have greater access to physician services and greater total health spending per capita than the Member States where organ transplantation is not performed. The provision of deceased donor transplantation was closely associated with high levels of gross national income per capita. There are several ways in which governments can support the ethical development of organ donation and transplantation programmes. Specifically, they can ensure that appropriate legislation, regulation and oversight are in place, and monitor donation and transplantation activities, practices and outcomes. Moreover, they can allocate resources towards the training of specialist physicians, surgeons and transplant coordinators, and implement a professional donor-procurement network.

  9. Cloud motions on Venus - Global structure and organization

    Limaye, S. S.; Suomi, V. E.

    1981-01-01

    Results on cloud motions on Venus obtained over a period of 3.5 days from Mariner 10 television images are presented. The implied atmosphere flow is almost zonal everywhere on the visible disk, and is in the same retrograde sense as the solid planet. Objective analysis of motions suggests the presence of jet cores (-130 m/s) and organized atmospheric waves. The longitudinal mean meridional profile of the zonal component of motion of the ultraviolet features shows presence of a midlatitude jet stream (-110 m/s). The mean zonal component is -97 m/s at the equator. The mean meridional motion at most latitudes is directed toward the pole in either hemisphere and is at least an order of magnitude smaller so that the flow is nearly zonal. A tentative conclusion from the limited coverage available from Mariner 10 is that at the level of ultraviolet features mean meridional circulation is the dominant mode of poleward angular momentum transfer as opposed to the eddy circulation.

  10. The Emergence of `Power with': The Case of a Born Global Organization

    Yan, Lin; Panteli, Niki

    Thanks to the advancement of Information and Communications Technologies, the past decade has seen the rise of Born Global organizations (Rennie, 1993; Oviatt and McDougall, 1994; Karra and Philips, 2004; Zahra, 2005). Broadly defined as ‘business organizations that, right from inception, seek to derive significant competitive advantages from the use of resources and the sales of outputs in multiple countries’ (Oviatt and McDougall, 1994: 49), Born Global organizations are small, young, and internationally dispersed. While sharing the characteristics of ‘smallness’ and ‘newness’ of Small- and Medium-sized Enterprises (SMEs), Born Global organizations also bear ‘foreignness’, similar to that of Multinational Corporations (Zahra, 2005). Born Globals therefore need to strike a balance between ‘global reach’ and ‘local touch’ as in Multinational Corporations (Bartlett and Ghoshal, 1989); yet they have to do so with scare resources and organizational uncertainty similar to SMEs, and with ‘lean’ and ‘mean’ communications afforded by ICT (e.g. Sproull and Kiesler, 1986). This study is an initial attempt to untangle the combined challenges in Born Globals’ innovative way of management. Through a longitudinal case study, we aim to explore the issue of power in a Born Global’s endeavour to manage its global knowledge via technology mediation.

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

    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.

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

    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

  13. From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptome.

    Lemay, Danielle G; Pollard, Katherine S; Martin, William F; Freeman Zadrowski, Courtneay; Hernandez, Joseph; Korf, Ian; German, J Bruce; Rijnkels, Monique

    2013-01-01

    Even in genomes lacking operons, a gene's position in the genome influences its potential for expression. The mechanisms by which adjacent genes are co-expressed are still not completely understood. Using lactation and the mammary gland as a model system, we explore the hypothesis that chromatin state contributes to the co-regulation of gene neighborhoods. The mammary gland represents a unique evolutionary model, due to its recent appearance, in the context of vertebrate genomes. An understanding of how the mammary gland is regulated to produce milk is also of biomedical and agricultural importance for human lactation and dairying. Here, we integrate epigenomic and transcriptomic data to develop a comprehensive regulatory model. Neighborhoods of mammary-expressed genes were determined using expression data derived from pregnant and lactating mice and a neighborhood scoring tool, G-NEST. Regions of open and closed chromatin were identified by ChIP-Seq of histone modifications H3K36me3, H3K4me2, and H3K27me3 in the mouse mammary gland and liver tissue during lactation. We found that neighborhoods of genes in regions of uniquely active chromatin in the lactating mammary gland, compared with liver tissue, were extremely rare. Rather, genes in most neighborhoods were suppressed during lactation as reflected in their expression levels and their location in regions of silenced chromatin. Chromatin silencing was largely shared between the liver and mammary gland during lactation, and what distinguished the mammary gland was mainly a small tissue-specific repertoire of isolated, expressed genes. These findings suggest that an advantage of the neighborhood organization is in the collective repression of groups of genes via a shared mechanism of chromatin repression. Genes essential to the mammary gland's uniqueness are isolated from neighbors, and likely have less tolerance for variation in expression, properties they share with genes responsible for an organism's survival.

  14. Integrating the genomic architecture of human nucleolar organizer regions with the biophysical properties of nucleoli.

    Mangan, Hazel; Gailín, Michael Ó; McStay, Brian

    2017-12-01

    Nucleoli are the sites of ribosome biogenesis and the largest membraneless subnuclear structures. They are intimately linked with growth and proliferation control and function as sensors of cellular stress. Nucleoli form around arrays of ribosomal gene (rDNA) repeats also called nucleolar organizer regions (NORs). In humans, NORs are located on the short arms of all five human acrocentric chromosomes. Multiple NORs contribute to the formation of large heterochromatin-surrounded nucleoli observed in most human cells. Here we will review recent findings about their genomic architecture. The dynamic nature of nucleoli began to be appreciated with the advent of photodynamic experiments using fluorescent protein fusions. We review more recent data on nucleoli in Xenopus germinal vesicles (GVs) which has revealed a liquid droplet-like behavior that facilitates nucleolar fusion. Further analysis in both XenopusGVs and Drosophila embryos indicates that the internal organization of nucleoli is generated by a combination of liquid-liquid phase separation and active processes involving rDNA. We will attempt to integrate these recent findings with the genomic architecture of human NORs to advance our understanding of how nucleoli form and respond to stress in human cells. © 2017 Federation of European Biochemical Societies.

  15. Genome organization in the nucleus: From dynamic measurements to a functional model.

    Vivante, Anat; Brozgol, Eugene; Bronshtein, Irena; Garini, Yuval

    2017-07-01

    A biological system is by definition a dynamic environment encompassing kinetic processes that occur at different length scales and time ranges. To explore this type of system, spatial information needs to be acquired at different time scales. This means overcoming significant hurdles, including the need for stable and precise labeling of the required probes and the use of state of the art optical methods. However, to interpret the acquired data, biophysical models that can account for these biological mechanisms need to be developed. The structure and function of a biological system are closely related to its dynamic properties, thus further emphasizing the importance of identifying the rules governing the dynamics that cannot be directly deduced from information on the structure itself. In eukaryotic cells, tens of thousands of genes are packed in the small volume of the nucleus. The genome itself is organized in chromosomes that occupy specific volumes referred to as chromosome territories. This organization is preserved throughout the cell cycle, even though there are no sub-compartments in the nucleus itself. This organization, which is still not fully understood, is crucial for a large number of cellular functions such as gene regulation, DNA breakage repair and error-free cell division. Various techniques are in use today, including imaging, live cell imaging and molecular methods such as chromosome conformation capture (3C) methods to better understand these mechanisms. Live cell imaging methods are becoming well established. These include methods such as Single Particle Tracking (SPT), Continuous Photobleaching (CP), Fluorescence Recovery After Photobleaching (FRAP) and Fluorescence Correlation Spectroscopy (FCS) that are currently used for studying proteins, RNA, DNA, gene loci and nuclear bodies. They provide crucial information on its mobility, reorganization, interactions and binding properties. Here we describe how these dynamic methods can be used to

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

    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

  17. Global-scale combustion sources of organic aerosols: sensitivity to formation and removal mechanisms

    Tsimpidi, Alexandra P.; Karydis, Vlassis A.; Pandis, Spyros N.; Lelieveld, Jos

    2017-06-01

    Organic compounds from combustion sources such as biomass burning and fossil fuel use are major contributors to the global atmospheric load of aerosols. We analyzed the sensitivity of model-predicted global-scale organic aerosols (OA) to parameters that control primary emissions, photochemical aging, and the scavenging efficiency of organic vapors. We used a computationally efficient module for the description of OA composition and evolution in the atmosphere (ORACLE) of the global chemistry-climate model EMAC (ECHAM/MESSy Atmospheric Chemistry). A global dataset of aerosol mass spectrometer (AMS) measurements was used to evaluate simulated primary (POA) and secondary (SOA) OA concentrations. Model results are sensitive to the emission rates of intermediate-volatility organic compounds (IVOCs) and POA. Assuming enhanced reactivity of semi-volatile organic compounds (SVOCs) and IVOCs with OH substantially improved the model performance for SOA. The use of a hybrid approach for the parameterization of the aging of IVOCs had a small effect on predicted SOA levels. The model performance improved by assuming that freshly emitted organic compounds are relatively hydrophobic and become increasingly hygroscopic due to oxidation.

  18. Visualization of genome signatures of eukaryote genomes by batch-learning self-organizing map with a special emphasis on Drosophila genomes.

    Abe, Takashi; Hamano, Yuta; Ikemura, Toshimichi

    2014-01-01

    A strategy of evolutionary studies that can compare vast numbers of genome sequences is becoming increasingly important with the remarkable progress of high-throughput DNA sequencing methods. We previously established a sequence alignment-free clustering method "BLSOM" for di-, tri-, and tetranucleotide compositions in genome sequences, which can characterize sequence characteristics (genome signatures) of a wide range of species. In the present study, we generated BLSOMs for tetra- and pentanucleotide compositions in approximately one million sequence fragments derived from 101 eukaryotes, for which almost complete genome sequences were available. BLSOM recognized phylotype-specific characteristics (e.g., key combinations of oligonucleotide frequencies) in the genome sequences, permitting phylotype-specific clustering of the sequences without any information regarding the species. In our detailed examination of 12 Drosophila species, the correlation between their phylogenetic classification and the classification on the BLSOMs was observed to visualize oligonucleotides diagnostic for species-specific clustering.

  19. A global perspective on aerosol from low-volatility organic compounds

    H. O. T. Pye

    2010-05-01

    Full Text Available Global production of organic aerosol from primary emissions of semivolatile (SVOCs and intermediate (IVOCs volatility organic compounds is estimated using the global chemical transport model, GEOS-Chem. SVOC oxidation is predicted to be a larger global source of net aerosol production than oxidation of traditional parent hydrocarbons (terpenes, isoprene, and aromatics. Using a prescribed rate constant and reduction in volatility for atmospheric oxidation, the yield of aerosol from SVOCs is predicted to be about 75% on a global, annually-averaged basis. For IVOCs, the use of a naphthalene-like surrogate with different high-NOx and low-NOx parameterizations produces a global aerosol yield of about 30%, or roughly 5 Tg/yr of aerosol. Estimates of the total global organic aerosol source presented here range between 60 and 100 Tg/yr. This range reflects uncertainty in the parameters for SVOC volatility, SVOC oxidation, SVOC emissions, and IVOC emissions, as well as wet deposition. The highest estimates result if SVOC emissions are significantly underestimated (by more than a factor of 2 or if wet deposition of the gas-phase semivolatile species is less effective than previous estimates. A significant increase in SVOC emissions, a reduction of the volatility of the SVOC emissions, or an increase in the enthalpy of vaporization of the organic aerosol all lead to an appreciable reduction of prediction/measurement discrepancy. In addition, if current primary organic aerosol (POA inventories capture only about one-half of the SVOC emission and the Henrys Law coefficient for oxidized semivolatiles is on the order of 103 M/atm, a global estimate of OA production is not inconsistent with the top-down estimate of 140 Tg/yr by (Goldstein and Galbally, 2007. Additional information is needed to constrain the emissions and treatment of SVOCs and IVOCs, which have traditionally not been included in models.

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

    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

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

    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.

  2. Development of international organizations in the context of evolution of global political system

    M A Kaverin

    2014-12-01

    Full Text Available The article analyses general regularities of development of international organizations. Dynamics of international organizations is described with the equation of biological populations’ growth and is related to the evolution of international multilateral law and world development parameters. As the result of the research, the evolution of global political system is represented with the system of international governance based on the multilateral mechanisms and the model of social structures’ types. The transformations in the system of international organizations partially confirm the hypothesis of emerging World-organism.

  3. The market of human organs: a window into a poorly understood global business.

    Surman, O S; Saidi, R; Purtilo, R; Simmerling, M; Ko, D; Burke, T F

    2008-03-01

    The global demand for human organs has set the stage for an exploding and poorly understood global business in human organs. Whenever there is demand for a product, the opportunity for business arises. The form that a business takes is dependent on a complex network of inputs and outputs, each affecting the others. Historically, the details of any specific market are drastically underestimated. Nowhere is this truer than in the market of human organs. The drivers, which propel the "goods" of human organs, form a flourishing business. Critical analysis is essential to understanding of the supply and demand sides and to determine the role of government in regulating the industry. Governmental groups have dismissed formation of a regulated market for organ sales. The concept is nonetheless a topic of active discussion, motivated by the suffering of patients in need of organs and exploitation of the victims of human trafficking. Ethical principles have been invoked on each side of the ensuing debate. Theory in the absence of sufficient data is shaky ground for enactment of new policy. The Aristotelian concept of "practical wisdom" and the pragmatism of William James illuminate the importance of scientific investigation as guide to policy formation. How will stakeholders benefit or lose? What impact might be anticipated in regard to organized medicine's social contract? What can we learn about cross-cultural differences and their effect on the global landscape?

  4. Globalization and Self-Organization in the Knowledge-Based Society

    Christian Fuchs

    2008-07-01

    Full Text Available In this paper I suggest that a theory of self-organization can be used as a consistent background theory for explaining the dynamics and logics of globalization. Globalization is not confined to the human realm, it is an attribute of all complex, self-organizing systems. Globalization in a synchronous sense means a micro-macro-link where bottom-up-emergence of new qualities in the self-reproduction of complex systems takes place, it is accompanied by a macro-micro-link of top-down-localization. A dynamic interaction between a global and a local level (glocalization results in the permanent overall self-reproduction of the system. Globalization in a diachronic sense means the emergence of a new, higher level of self-organization during a phase of instability and heavy fluctuations by order through fluctuation. Globalization is shaped by a dialectic of change and continuity: in the hierarchy that stems from emergent evolution there are both general aspects of globalization and aspects that are specific for each organizational level. Applying this general notion of globalization to society means that human globalization is both a general process that can be found in all societies and a specific process with emergent qualities in concrete phases of societal development. Globalization processes in modern society are based on structural antagonisms that result in uneven developments in the technosphere, the ecosphere, the economy, polity, and culture. The transition to Postfordist, informational capitalism has been a consequence of the development of the structural antagonisms of Fordism and has been accompanied by a new phase of globalization that has transformed the subsystems of society and has resulted in new antagonism that are an expression of general antagonisms that shape modern societies. Hence we find antagonistic tendencies of contemporary globalization in all subsystems of society that result in both risks and opportunities. Human beings

  5. Genomic Organization and Expression of Iron Metabolism Genes in the Emerging Pathogenic Mold Scedosporium apiospermum

    Yohann Le Govic

    2018-04-01

    Full Text Available The ubiquitous mold Scedosporium apiospermum is increasingly recognized as an emerging pathogen, especially among patients with underlying disorders such as immunodeficiency or cystic fibrosis (CF. Indeed, it ranks the second among the filamentous fungi colonizing the respiratory tract of CF patients. However, our knowledge about virulence factors of this fungus is still limited. The role of iron-uptake systems may be critical for establishment of Scedosporium infections, notably in the iron-rich environment of the CF lung. Two main strategies are employed by fungi to efficiently acquire iron from their host or from their ecological niche: siderophore production and reductive iron assimilation (RIA systems. The aim of this study was to assess the existence of orthologous genes involved in iron metabolism in the recently sequenced genome of S. apiospermum. At first, a tBLASTn analysis using A. fumigatus iron-related proteins as query revealed orthologs of almost all relevant loci in the S. apiospermum genome. Whereas the genes putatively involved in RIA were randomly distributed, siderophore biosynthesis and transport genes were organized in two clusters, each containing a non-ribosomal peptide synthetase (NRPS whose orthologs in A. fumigatus have been described to catalyze hydroxamate siderophore synthesis. Nevertheless, comparative genomic analysis of siderophore-related clusters showed greater similarity between S. apiospermum and phylogenetically close molds than with Aspergillus species. The expression level of these genes was then evaluated by exposing conidia to iron starvation and iron excess. The expression of several orthologs of A. fumigatus genes involved in siderophore-based iron uptake or RIA was significantly induced during iron starvation, and conversely repressed in iron excess conditions. Altogether, these results indicate that S. apiospermum possesses the genetic information required for efficient and competitive iron uptake

  6. Genome-wide comparative analysis of ABC systems in the Bdellovibrio-and-like organisms.

    Li, Nan; Chen, Huan; Williams, Henry N

    2015-05-10

    Bdellovibrio-and-like organisms (BALOs) are gram-negative, predatory bacteria with wide variations in genome sizes and GC content and ecological habitats. The ATP-binding cassette (ABC) systems have been identified in several prokaryotes, fungi and plants and have a role in transport of materials in and out of cells and in cellular processes. However, knowledge of the ABC systems of BALOs remains obscure. A total of 269 putative ABC proteins were identified in BALOs. The genes encoding these ABC systems occupy nearly 1.3% of the gene content in freshwater Bdellovibrio strains and about 0.7% in their saltwater counterparts. The proteins found belong to 25 ABC system families based on their structural characteristics and functions. Among these, 16 families function as importers, 6 as exporters and 3 are involved in various cellular processes. Eight of these 25 ABC system families were deduced to be the core set of ABC systems conserved in all BALOs. All Bacteriovorax strains have 28 or less ABC systems. On the contrary, the freshwater Bdellovibrio strains have more ABC systems, typically around 51. In the genome of Bdellovibrio exovorus JSS (CP003537.1), 53 putative ABC systems were detected, representing the highest number among all the BALO genomes examined in this study. Unexpected high numbers of ABC systems involved in cellular processes were found in all BALOs. Phylogenetic analysis suggests that the majority of ABC proteins can be assigned into many separate families with high bootstrap supports (>50%). In this study, a general framework of sequence-structure-function connections for the ABC systems in BALOs was revealed providing novel insights for future investigations. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. The copepod Tigriopus: A promising marine model organism for ecotoxicology and environmental genomics

    Raisuddin, Sheikh [Department of Chemistry and the National Research Lab of Marine Molecular and Environmental Bioscience, College of Natural Sciences, Hanyang University, Seoul 133-791 (Korea, Republic of); Kwok, Kevin W.H. [Swire Institute of Marine Science, Department of Ecology and Biodiversity, University of Hong Kong, Pokfulam, Hong Kong (China); Leung, Kenneth M.Y. [Swire Institute of Marine Science, Department of Ecology and Biodiversity, University of Hong Kong, Pokfulam, Hong Kong (China); Schlenk, Daniel [Department of Environmental Sciences, University of California, Riverside, CA 92521 (United States); Lee, Jae-Seong [Department of Chemistry and the National Research Lab of Marine Molecular and Environmental Bioscience, College of Natural Sciences, Hanyang University, Seoul 133-791 (Korea, Republic of)]. E-mail: jslee2@hanyang.ac.kr

    2007-07-20

    There is an increasing body of evidence to support the significant role of invertebrates in assessing impacts of environmental contaminants on marine ecosystems. Therefore, in recent years massive efforts have been directed to identify viable and ecologically relevant invertebrate toxicity testing models. Tigriopus, a harpacticoid copepod has a number of promising characteristics which make it a candidate worth consideration in such efforts. Tigriopus and other copepods are widely distributed and ecologically important organisms. Their position in marine food chains is very prominent, especially with regard to the transfer of energy. Copepods also play an important role in the transportation of aquatic pollutants across the food chains. In recent years there has been a phenomenal increase in the knowledge base of Tigriopus spp., particularly in the areas of their ecology, geophylogeny, genomics and their behavioural, biochemical and molecular responses following exposure to environmental stressors and chemicals. Sequences of a number of important marker genes have been studied in various Tigriopus spp., notably T. californicus and T. japonicus. These genes belong to normal biophysiological functions (e.g. electron transport system enzymes) as well as stress and toxic chemical exposure responses (heat shock protein 20, glutathione reductase, glutathione S-transferase). Recently, 40,740 expressed sequenced tags (ESTs) from T. japonicus, have been sequenced and of them, 5673 ESTs showed significant hits (E-value, >1.0E-05) to the red flour beetle Tribolium genome database. Metals and organic pollutants such as antifouling agents, pesticides, polycyclic aromatic hydrocarbons (PAH) and polychrlorinated biphenyls (PCB) have shown reproducible biological responses when tested in Tigriopus spp. Promising results have been obtained when Tigriopus was used for assessment of risk associated with exposure to endocrine-disrupting chemicals (EDCs). Application of environmental

  8. The copepod Tigriopus: A promising marine model organism for ecotoxicology and environmental genomics

    Raisuddin, Sheikh; Kwok, Kevin W.H.; Leung, Kenneth M.Y.; Schlenk, Daniel; Lee, Jae-Seong

    2007-01-01

    There is an increasing body of evidence to support the significant role of invertebrates in assessing impacts of environmental contaminants on marine ecosystems. Therefore, in recent years massive efforts have been directed to identify viable and ecologically relevant invertebrate toxicity testing models. Tigriopus, a harpacticoid copepod has a number of promising characteristics which make it a candidate worth consideration in such efforts. Tigriopus and other copepods are widely distributed and ecologically important organisms. Their position in marine food chains is very prominent, especially with regard to the transfer of energy. Copepods also play an important role in the transportation of aquatic pollutants across the food chains. In recent years there has been a phenomenal increase in the knowledge base of Tigriopus spp., particularly in the areas of their ecology, geophylogeny, genomics and their behavioural, biochemical and molecular responses following exposure to environmental stressors and chemicals. Sequences of a number of important marker genes have been studied in various Tigriopus spp., notably T. californicus and T. japonicus. These genes belong to normal biophysiological functions (e.g. electron transport system enzymes) as well as stress and toxic chemical exposure responses (heat shock protein 20, glutathione reductase, glutathione S-transferase). Recently, 40,740 expressed sequenced tags (ESTs) from T. japonicus, have been sequenced and of them, 5673 ESTs showed significant hits (E-value, >1.0E-05) to the red flour beetle Tribolium genome database. Metals and organic pollutants such as antifouling agents, pesticides, polycyclic aromatic hydrocarbons (PAH) and polychrlorinated biphenyls (PCB) have shown reproducible biological responses when tested in Tigriopus spp. Promising results have been obtained when Tigriopus was used for assessment of risk associated with exposure to endocrine-disrupting chemicals (EDCs). Application of environmental

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

    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

  10. Class and ethnicity in the global market for organs: the case of Korean cinema.

    Garden, Rebecca; Yoo Murphree, Hyon Joo

    2007-12-01

    While organ transplantation has been established in the medical imagination since the 1960s, this technology is currently undergoing a popular re-imagination in the era of global capitalism. As transplantation procedures have become routine in medical centers in non-Western and developing nations and as organ sales and transplant tourism become increasingly common, organs that function as a material resource increasingly derive from subaltern bodies. This essay explores this development as represented in Korean filmmaker Park Chan-wook's 2002 Sympathy for Mr. Vengeance, focusing on the ethnic and class characteristics of the global market in organs and possible modes of counter-logic to transplant technologies and related ethical discourses.

  11. Globalizing the Intelligent Organization: Learning Organizations, Smart Workers, (Not So) Clever Countries and the Sociological Imagination.

    Clegg, Stewart

    1999-01-01

    Contrasts exploratory learning with exploitative learning to argue for the importance of both and not just the latter. Discusses a case for organization studies that situates itself within a classical tradition of sociology. (CCM)

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

    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.

  13. Globalization of health insecurity: the World Health Organization and the new International Health Regulations.

    Aginam, Obijiofor

    2006-12-01

    The transnational spread of communicable and non-communicable diseases has opened new vistas in the discourse of global health security. Emerging and re-emerging pathogens, according to exponents of globalization of public health, disrespect the geo-political boundaries of nation-states. Despite the global ramifications of health insecurity in a globalizing world, contemporary international law still operates as a classic inter-state law within an international system exclusively founded on a coalition of nation-states. This article argues that the dynamic process of globalization has created an opportunity for the World Health Organization to develop effective synergy with a multiplicity of actors in the exercise of its legal powers. WHO's legal and regulatory strategies must transform from traditional international legal approaches to disease governance to a "post-Westphalian public health governance": the use of formal and informal sources from state and non-state actors, hard law (treaties and regulations) and soft law (recommendations and travel advisories) in global health governance. This article assesses the potential promise and problems of WHO's new International Health Regulations (IHR) as a regulatory strategy for global health governance and global health security.

  14. Uncovering the functional constraints underlying the genomic organization of the odorant-binding protein genes.

    Librado, Pablo; Rozas, Julio

    2013-01-01

    Animal olfactory systems have a critical role for the survival and reproduction of individuals. In insects, the odorant-binding proteins (OBPs) are encoded by a moderately sized gene family, and mediate the first steps of the olfactory processing. Most OBPs are organized in clusters of a few paralogs, which are conserved over time. Currently, the biological mechanism explaining the close physical proximity among OBPs is not yet established. Here, we conducted a comprehensive study aiming to gain insights into the mechanisms underlying the OBP genomic organization. We found that the OBP clusters are embedded within large conserved arrangements. These organizations also include other non-OBP genes, which often encode proteins integral to plasma membrane. Moreover, the conservation degree of such large clusters is related to the following: 1) the promoter architecture of the confined genes, 2) a characteristic transcriptional environment, and 3) the chromatin conformation of the chromosomal region. Our results suggest that chromatin domains may restrict the location of OBP genes to regions having the appropriate transcriptional environment, leading to the OBP cluster structure. However, the appropriate transcriptional environment for OBP and the other neighbor genes is not dominated by reduced levels of expression noise. Indeed, the stochastic fluctuations in the OBP transcript abundance may have a critical role in the combinatorial nature of the olfactory coding process.

  15. Genomic organization of the rat alpha 2u-globulin gene cluster.

    McFadyen, D A; Addison, W; Locke, J

    1999-05-01

    The alpha 2u-globulin are a group of similar proteins, belonging to the lipocalin superfamily of proteins, that are synthesized in a subset of secretory tissues in rats. The many alpha 2u-globulin isoforms are encoded by a multigene family that exhibits extensive homology. Despite a high degree of sequence identity, individual family members show diverse expression patterns involving complex hormonal, tissue-specific, and developmental regulation. Analysis suggests that there are approximately 20 alpha 2u-globulin genes in the rat genome. We have used fluorescence in situ hybridization (FISH) to show that the alpha 2u-globulin genes are clustered at a single site on rat Chromosome (Chr) 5 (5q22-24). Southern blots of rat genomic DNA separated by pulsed field gel electrophoresis indicated that the alpha 2u-globulin genes are contained on two NruI fragments with a total size of 880 kbp. Analysis of three P1 clones containing alpha 2u-globulin genes indicated that the alpha 2u-globulin genes are tandemly arranged in a head-to-tail fashion. The organization of the alpha 2u-globulin genes in the rat as a tandem array of single genes differs from the homologous major urinary protein genes in the mouse, which are organized as tandem arrays of divergently oriented gene pairs. The structure of these gene clusters may have consequences for the proposed function, as a pheromone transporter, for the protein products encoded by these genes.

  16. Methodological framework for World Health Organization estimates of the global burden of foodborne disease

    B. Devleesschauwer (Brecht); J.A. Haagsma (Juanita); F.J. Angulo (Frederick); D.C. Bellinger (David); D. Cole (Dana); D. Döpfer (Dörte); A. Fazil (Aamir); E.M. Fèvre (Eric); H.J. Gibb (Herman); T. Hald (Tine); M.D. Kirk (Martyn); R.J. Lake (Robin); C. Maertens De Noordhout (Charline); C. Mathers (Colin); S.A. McDonald (Scott); S.M. Pires (Sara); N. Speybroeck (Niko); M.K. Thomas (Kate); D. Torgerson; F. Wu (Felicia); A.H. Havelaar (Arie); N. Praet (Nicolas)

    2015-01-01

    textabstractBackground: The Foodborne Disease Burden Epidemiology Reference Group (FERG) was established in 2007 by the World Health Organization to estimate the global burden of foodborne diseases (FBDs). This paper describes the methodological framework developed by FERG's Computational Task Force

  17. World Health Organization Global Estimates and Regional Comparisons of the Burden of Foodborne Disease in 2010

    Havelaar, Arie H|info:eu-repo/dai/nl/072306122; Kirk, Martyn D; Torgerson, Paul R; Gibb, Herman J; Hald, Tine; Lake, Robin J; Praet, Nicolas; Bellinger, David C; de Silva, Nilanthi R; Gargouri, Neyla; Speybroeck, Niko; Cawthorne, Amy; Mathers, Colin; Stein, Claudia; Angulo, Frederick J; Devleesschauwer, Brecht

    2015-01-01

    Illness and death from diseases caused by contaminated food are a constant threat to public health and a significant impediment to socio-economic development worldwide. To measure the global and regional burden of foodborne disease (FBD), the World Health Organization (WHO) established the Foodborne

  18. Self-Organization of Genome Expression from Embryo to Terminal Cell Fate: Single-Cell Statistical Mechanics of Biological Regulation

    Alessandro Giuliani

    2017-12-01

    Full Text Available A statistical mechanical mean-field approach to the temporal development of biological regulation provides a phenomenological, but basic description of the dynamical behavior of genome expression in terms of autonomous self-organization with a critical transition (Self-Organized Criticality: SOC. This approach reveals the basis of self-regulation/organization of genome expression, where the extreme complexity of living matter precludes any strict mechanistic approach. The self-organization in SOC involves two critical behaviors: scaling-divergent behavior (genome avalanche and sandpile-type critical behavior. Genome avalanche patterns—competition between order (scaling and disorder (divergence reflect the opposite sequence of events characterizing the self-organization process in embryo development and helper T17 terminal cell differentiation, respectively. On the other hand, the temporal development of sandpile-type criticality (the degree of SOC control in mouse embryo suggests the existence of an SOC control landscape with a critical transition state (i.e., the erasure of zygote-state criticality. This indicates that a phase transition of the mouse genome before and after reprogramming (immediately after the late 2-cell state occurs through a dynamical change in a control parameter. This result provides a quantitative open-thermodynamic appreciation of the still largely qualitative notion of the epigenetic landscape. Our results suggest: (i the existence of coherent waves of condensation/de-condensation in chromatin, which are transmitted across regions of different gene-expression levels along the genome; and (ii essentially the same critical dynamics we observed for cell-differentiation processes exist in overall RNA expression during embryo development, which is particularly relevant because it gives further proof of SOC control of overall expression as a universal feature.

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

    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.

  20. [The transition from 'international' to 'global' public health and the World Health Organization].

    Brown, Theodore M; Cueto, Marcos; Fee, Elizabeth

    2006-01-01

    Within the context of international public health, 'global health' seems to be emerging as a recognized term of preference. This article presents a critical analysis of the meaning and importance of 'global health' and situates its growing popularity within a historical context. A specific focus of this work is the role of the World Health Organization - WHO in both 'international' and 'global' health, and as na agent of transition from one to the other. Between 1948 and 1998, the WHO went through a period of hardship as it came up against an organizational crisis, budget cuts and a diminished status, especially when confronted with the growing influence of new, power players like the World Bank. We suggest that the WHO has responded to this changing international context by inititating its own process of restructuring and repositioning as an agent for coordinating, strategically planning and leading 'global health' initiatives.

  1. Genome Compositional Organization in Gars Shows More Similarities to Mammals than to Other Ray-Finned Fish.

    Symonová, Radka; Majtánová, Zuzana; Arias-Rodriguez, Lenin; Mořkovský, Libor; Kořínková, Tereza; Cavin, Lionel; Pokorná, Martina Johnson; Doležálková, Marie; Flajšhans, Martin; Normandeau, Eric; Ráb, Petr; Meyer, Axel; Bernatchez, Louis

    2017-11-01

    Genomic GC content can vary locally, and GC-rich regions are usually associated with increased DNA thermostability in thermophilic prokaryotes and warm-blooded eukaryotes. Among vertebrates, fish and amphibians appeared to possess a distinctly less heterogeneous AT/GC organization in their genomes, whereas cytogenetically detectable GC heterogeneity has so far only been documented in mammals and birds. The subject of our study is the gar, an ancient "living fossil" of a basal ray-finned fish lineage, known from the Cretaceous period. We carried out cytogenomic analysis in two gar genera (Atractosteus and Lepisosteus) uncovering a GC chromosomal pattern uncharacteristic for fish. Bioinformatic analysis of the spotted gar (Lepisosteus oculatus) confirmed a GC compartmentalization on GC profiles of linkage groups. This indicates a rather mammalian mode of compositional organization on gar chromosomes. Gars are thus the only analyzed extant ray-finned fishes with a GC compartmentalized genome. Since gars are cold-blooded anamniotes, our results contradict the generally accepted hypothesis that the phylogenomic onset of GC compartmentalization occurred near the origin of amniotes. Ecophysiological findings of other authors indicate a metabolic similarity of gars with mammals. We hypothesize that gars might have undergone convergent evolution with the tetrapod lineages leading to mammals on both metabolic and genomic levels. Their metabolic adaptations might have left footprints in their compositional genome evolution, as proposed by the metabolic rate hypothesis. The genome organization described here in gars sheds new light on the compositional genome evolution in vertebrates generally and contributes to better understanding of the complexities of the mechanisms involved in this process. © 2016 Wiley Periodicals, Inc.

  2. A study on international nuclear organizations and conventions for the globalization of Korean nuclear community

    Lee, Kwang Seok; Oh, Keun Bae; Lee, Byung Wook; Cho, Il Hoon; Lee, Jae Sung; Choi, Young Rok; Ko, Han Seok; Ham, Chul Hoon; Lee, Byung Woon [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of)

    1995-12-01

    The objective of this study is to analyze the current status of international nuclear organizations and conventions in systems perspective and suggest national strategies for utilizing them for the globalization of Korean nuclear community. This study analyzes the current status of international nuclear organizations such as IAEA(International Atomic Energy Agency) and international nuclear conventions related to nuclear accidents, nuclear liability, physical protection or nuclear safety. Based on the analysis, this study suggests national strategies, in general and specific terms, to utilize international nuclear organizations and conventions for the globalization of Korean nuclear community. Separately from this report this study publishes `IAEA Handbook`, which contains all about IAEA such as statute, membership, organizational structure, main activities, finance and budget, etc.. 9 tabs., 2 figs., 35 refs. (Author).

  3. A study on international nuclear organizations and conventions for the globalization of Korean nuclear community

    Lee, Kwang Seok; Oh, Keun Bae; Lee, Byung Wook; Cho, Il Hoon; Lee, Jae Sung; Choi, Young Rok; Ko, Han Seok; Ham, Chul Hoon; Lee, Byung Woon

    1995-12-01

    The objective of this study is to analyze the current status of international nuclear organizations and conventions in systems perspective and suggest national strategies for utilizing them for the globalization of Korean nuclear community. This study analyzes the current status of international nuclear organizations such as IAEA(International Atomic Energy Agency) and international nuclear conventions related to nuclear accidents, nuclear liability, physical protection or nuclear safety. Based on the analysis, this study suggests national strategies, in general and specific terms, to utilize international nuclear organizations and conventions for the globalization of Korean nuclear community. Separately from this report this study publishes 'IAEA Handbook', which contains all about IAEA such as statute, membership, organizational structure, main activities, finance and budget, etc.. 9 tabs., 2 figs., 35 refs. (Author)

  4. Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L. Genome

    Navdeep Gill

    2014-04-01

    Full Text Available Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of these repeats to that found in other food crops and model species. We also examine the expression of transposable element-related transcripts in EST databases for sunflower to determine the representation of repeats in the transcriptome and to measure their transcriptional activity. Our data confirm previous reports in suggesting that the sunflower genome is >78% repetitive. Sunflower repeats share very little similarity to other plant repeats such as those of Arabidopsis, rice, maize and wheat; overall 28% of repeats are “novel” to sunflower. The repetitive sequences appear to be randomly distributed within the sequenced BACs. Assuming the 96 BACs are representative of the genome as a whole, then approximately 5.2% of the sunflower genome comprises non TE-related genic sequence, with an average gene density of 18kbp/gene. Expression levels of these transposable elements indicate tissue specificity and differential expression in vegetative and reproductive tissues, suggesting that expressed TEs might contribute to sunflower development. The assembled BACs will also be useful for assessing the quality of several different draft assemblies of the sunflower genome and for annotating the reference sequence.

  5. Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L.) Genome

    Gill, Navdeep; Buti, Matteo; Kane, Nolan; Bellec, Arnaud; Helmstetter, Nicolas; Berges, Hélène; Rieseberg, Loren H.

    2014-01-01

    Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of these repeats to that found in other food crops and model species. We also examine the expression of transposable element-related transcripts in EST databases for sunflower to determine the representation of repeats in the transcriptome and to measure their transcriptional activity. Our data confirm previous reports in suggesting that the sunflower genome is >78% repetitive. Sunflower repeats share very little similarity to other plant repeats such as those of Arabidopsis, rice, maize and wheat; overall 28% of repeats are “novel” to sunflower. The repetitive sequences appear to be randomly distributed within the sequenced BACs. Assuming the 96 BACs are representative of the genome as a whole, then approximately 5.2% of the sunflower genome comprises non TE-related genic sequence, with an average gene density of 18kbp/gene. Expression levels of these transposable elements indicate tissue specificity and differential expression in vegetative and reproductive tissues, suggesting that expressed TEs might contribute to sunflower development. The assembled BACs will also be useful for assessing the quality of several different draft assemblies of the sunflower genome and for annotating the reference sequence. PMID:24833511

  6. The global diffusion of organ transplantation: trends, drivers and policy implications

    Hirth, Richard; Mahíllo, Beatriz; Domínguez-Gil, Beatriz; Delmonico, Francis L; Noel, Luc; Chapman, Jeremy; Matesanz, Rafael; Carmona, Mar; Alvarez, Marina; Núñez, Jose R; Leichtman, Alan

    2014-01-01

    Abstract Rising incomes, the spread of personal insurance, lifestyle factors adding to the burden of illness, ageing populations, globalization and skills transfer within the medical community have increased worldwide demand for organ transplantation. The Global Observatory on Donation and Transplantation, which was built in response to World Health Assembly resolution WHA57.18, has conducted ongoing documentation of global transplantation activities since 2007. In this paper, we use the Global Observatory’s data to describe the current distribution of – and trends in – transplantation activities and to evaluate the role of health systems factors and macroeconomics in the diffusion of transplantation technology. We then consider the implications of our results for health policies relating to organ donation and transplantation. Of the World Health Organization’s Member States, most now engage in organ transplantation and more than a third performed deceased donor transplantation in 2011. In general, the Member States that engage in organ transplantation have greater access to physician services and greater total health spending per capita than the Member States where organ transplantation is not performed. The provision of deceased donor transplantation was closely associated with high levels of gross national income per capita. There are several ways in which governments can support the ethical development of organ donation and transplantation programmes. Specifically, they can ensure that appropriate legislation, regulation and oversight are in place, and monitor donation and transplantation activities, practices and outcomes. Moreover, they can allocate resources towards the training of specialist physicians, surgeons and transplant coordinators, and implement a professional donor-procurement network. PMID:25378744

  7. Mechanisms of Formation of Secondary Organic Aerosols and Implications for Global Radiative Forcing

    Seinfeld, John H. [California Inst. of Technology (CalTech), Pasadena, CA (United States)

    2011-12-02

    Organic material constitutes about 50% of global atmospheric aerosol mass, and the dominant source of organic aerosol is the oxidation of volatile hydrocarbons, to produce secondary organic aerosol (SOA). Understanding the formation of SOA is crucial to predicting present and future climate effects of atmospheric aerosols. The goal of this program is to significantly increase our understanding of secondary organic aerosol (SOA) formation in the atmosphere. Ambient measurements indicate that the amount of SOA in the atmosphere exceeds that predicted in current models based on existing laboratory chamber data. This would suggest that either the SOA yields measured in laboratory chambers are understated or that all major organic precursors have not been identified. In this research program we are systematically exploring these possibilities.

  8. Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes

    Schnitzler Christine E

    2012-12-01

    Full Text Available Abstract Background Calcium-activated photoproteins are luciferase variants found in photocyte cells of bioluminescent jellyfish (Phylum Cnidaria and comb jellies (Phylum Ctenophora. The complete genomic sequence from the ctenophore Mnemiopsis leidyi, a representative of the earliest branch of animals that emit light, provided an opportunity to examine the genome of an organism that uses this class of luciferase for bioluminescence and to look for genes involved in light reception. To determine when photoprotein genes first arose, we examined the genomic sequence from other early-branching taxa. We combined our genomic survey with gene trees, developmental expression patterns, and functional protein assays of photoproteins and opsins to provide a comprehensive view of light production and light reception in Mnemiopsis. Results The Mnemiopsis genome has 10 full-length photoprotein genes situated within two genomic clusters with high sequence conservation that are maintained due to strong purifying selection and concerted evolution. Photoprotein-like genes were also identified in the genomes of the non-luminescent sponge Amphimedon queenslandica and the non-luminescent cnidarian Nematostella vectensis, and phylogenomic analysis demonstrated that photoprotein genes arose at the base of all animals. Photoprotein gene expression in Mnemiopsis embryos begins during gastrulation in migrating precursors to photocytes and persists throughout development in the canals where photocytes reside. We identified three putative opsin genes in the Mnemiopsis genome and show that they do not group with well-known bilaterian opsin subfamilies. Interestingly, photoprotein transcripts are co-expressed with two of the putative opsins in developing photocytes. Opsin expression is also seen in the apical sensory organ. We present evidence that one opsin functions as a photopigment in vitro, absorbing light at wavelengths that overlap with peak photoprotein light

  9. Global gene expression changes in human embryonic lung fibroblasts induced by organic extracts from respirable air particles

    Líbalová Helena

    2012-01-01

    Full Text Available Abstract Background Recently, we used cell-free assays to demonstrate the toxic effects of complex mixtures of organic extracts from urban air particles (PM2.5 collected in four localities of the Czech Republic (Ostrava-Bartovice, Ostrava-Poruba, Karvina and Trebon which differed in the extent and sources of air pollution. To obtain further insight into the biological mechanisms of action of the extractable organic matter (EOM from ambient air particles, human embryonic lung fibroblasts (HEL12469 were treated with the same four EOMs to assess changes in the genome-wide expression profiles compared to DMSO treated controls. Method For this purpose, HEL cells were incubated with subtoxic EOM concentrations of 10, 30, and 60 μg EOM/ml for 24 hours and global gene expression changes were analyzed using human whole genome microarrays (Illumina. The expression of selected genes was verified by quantitative real-time PCR. Results Dose-dependent increases in the number of significantly deregulated transcripts as well as dose-response relationships in the levels of individual transcripts were observed. The transcriptomic data did not differ substantially between the localities, suggesting that the air pollution originating mainly from various sources may have similar biological effects. This was further confirmed by the analysis of deregulated pathways and by identification of the most contributing gene modulations. The number of significantly deregulated KEGG pathways, as identified by Goeman's global test, varied, depending on the locality, between 12 to 29. The Metabolism of xenobiotics by cytochrome P450 exhibited the strongest upregulation in all 4 localities and CYP1B1 had a major contribution to the upregulation of this pathway. Other important deregulated pathways in all 4 localities were ABC transporters (involved in the translocation of exogenous and endogenous metabolites across membranes and DNA repair, the Wnt and TGF-β signaling pathways

  10. Global modelling of secondary organic aerosol in the troposphere: a sensitivity analysis

    K. Tsigaridis

    2003-01-01

    Full Text Available A global 3-dimensional chemistry/transport model able to describe O3, NOx, Volatile Organic Compounds (VOC, sulphur and NH3 chemistry has been extended to simulate the temporal and spatial distribution of primary and secondary carbonaceous aerosols in the troposphere focusing on Secondary Organic Aerosol (SOA formation. A number of global simulations have been performed to determine a possible range of annual global SOA production and investigate uncertainties associated with the model results. The studied uncertainties in the SOA budget have been evaluated to be in decreasing importance: the potentially irreversible sticking of the semi-volatile compounds on aerosols, the enthalpy of vaporization of these compounds, the partitioning of SOA on non-carbonaceous aerosols, the conversion of aerosols from hydrophobic to hydrophilic, the emissions of primary carbonaceous aerosols, the chemical fate of the first generation products and finally the activity coefficient of the condensable species. The large uncertainties associated with the emissions of VOC and the adopted simplification of chemistry have not been investigated in this study. Although not all sources of uncertainties have been investigated, according to our calculations, the above factors within the experimental range of variations could result to an overall uncertainty of about a factor of 20 in the global SOA budget. The global annual SOA production from biogenic VOC might range from 2.5 to 44.5 Tg of organic matter per year, whereas that from anthropogenic VOC ranges from 0.05 to 2.62 Tg of organic matter per year. These estimates can be considered as a lower limit, since partitioning on coarse particles like nitrate, dust or sea-salt, together with the partitioning and the dissociation of the semi-volatile products in aerosol water has been neglected. Comparison of model results to observations, where available, shows a better agreement for the upper budget estimates than for the

  11. Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions

    Balding David J

    2008-12-01

    Full Text Available Abstract Background The power of haplotype-based methods for association studies, identification of regions under selection, and ancestral inference, is well-established for diploid organisms. For polyploids, however, the difficulty of determining phase has limited such approaches. Polyploidy is common in plants and is also observed in animals. Partial polyploidy is sometimes observed in humans (e.g. trisomy 21; Down's syndrome, and it arises more frequently in some human tissues. Local changes in ploidy, known as copy number variations (CNV, arise throughout the genome. Here we present a method, implemented in the software polyHap, for the inference of haplotype phase and missing observations from polyploid genotypes. PolyHap allows each individual to have a different ploidy, but ploidy cannot vary over the genomic region analysed. It employs a hidden Markov model (HMM and a sampling algorithm to infer haplotypes jointly in multiple individuals and to obtain a measure of uncertainty in its inferences. Results In the simulation study, we combine real haplotype data to create artificial diploid, triploid, and tetraploid genotypes, and use these to demonstrate that polyHap performs well, in terms of both switch error rate in recovering phase and imputation error rate for missing genotypes. To our knowledge, there is no comparable software for phasing a large, densely genotyped region of chromosome from triploids and tetraploids, while for diploids we found polyHap to be more accurate than fastPhase. We also compare the results of polyHap to SATlotyper on an experimentally haplotyped tetraploid dataset of 12 SNPs, and show that polyHap is more accurate. Conclusion With the availability of large SNP data in polyploids and CNV regions, we believe that polyHap, our proposed method for inferring haplotypic phase from genotype data, will be useful in enabling researchers analysing such data to exploit the power of haplotype-based analyses.

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

    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.

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

    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.

  14. Looping and clustering model for the organization of protein-DNA complexes on the bacterial genome

    Walter, Jean-Charles; Walliser, Nils-Ole; David, Gabriel; Dorignac, Jérôme; Geniet, Frédéric; Palmeri, John; Parmeggiani, Andrea; Wingreen, Ned S.; Broedersz, Chase P.

    2018-03-01

    The bacterial genome is organized by a variety of associated proteins inside a structure called the nucleoid. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show that ParB proteins localize around centromere-like parS sites on the DNA to which ParB binds specifically, and spreads from there over large sections of the chromosome. Recent theoretical and experimental studies suggest that DNA-bound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this protein-DNA complex remains unclear, and a predictive quantitative theory for the distribution of ParB proteins on DNA is lacking. Here, we propose the looping and clustering model, which employs a statistical physics approach to describe protein-DNA complexes. The looping and clustering model accounts for the extrusion of DNA loops from a cluster of interacting DNA-bound proteins that is organized around a single high-affinity binding site. Conceptually, the structure of the protein-DNA complex is determined by a competition between attractive protein interactions and loop closure entropy of this protein-DNA cluster on the one hand, and the positional entropy for placing loops within the cluster on the other. Indeed, we show that the protein interaction strength determines the ‘tightness’ of the loopy protein-DNA complex. Thus, our model provides a theoretical framework for quantitatively computing the binding profiles of ParB-like proteins around a cognate (parS) binding site.

  15. Tobacco industry issues management organizations: Creating a global corporate network to undermine public health

    Malone Ruth E

    2008-01-01

    Full Text Available Abstract Background The global tobacco epidemic claims 5 million lives each year, facilitated by the ability of transnational tobacco companies to delay or thwart meaningful tobacco control worldwide. A series of cross-company tobacco industry "issues management organizations" has played an important role in coordinating and implementing common strategies to defeat tobacco control efforts at international, national, and regional levels. This study examines the development and enumerates the activities of these organizations and explores the implications of continuing industry cooperation for global public health. Methods Using a snowball sampling strategy, we collected documentary data from tobacco industry documents archives and assembled them into a chronologically organized case study. Results The International Committee on Smoking Issues (ICOSI was formed in 1977 by seven tobacco company chief executives to create common anti-tobacco control strategies and build a global network of regional and national manufacturing associations. The organization's name subsequently changed to INFOTAB. The multinational companies built the organization rapidly: by 1984, it had 69 members operating in 57 countries. INFOTAB material, including position papers and "action kits" helped members challenge local tobacco control measures and maintain tobacco-friendly environments. In 1992 INFOTAB was replaced by two smaller organizations. The Tobacco Documentation Centre, which continues to operate, distributes smoking-related information and industry argumentation to members, some produced by cross-company committees. Agro-Tobacco Services, and now Hallmark Marketing Services, assists the INFOTAB-backed and industry supported International Tobacco Growers Association in advancing claims regarding the economic importance of tobacco in developing nations. Conclusion The massive scale and scope of this industry effort illustrate how corporate interests, when

  16. Tobacco industry issues management organizations: creating a global corporate network to undermine public health.

    McDaniel, Patricia A; Intinarelli, Gina; Malone, Ruth E

    2008-01-17

    The global tobacco epidemic claims 5 million lives each year, facilitated by the ability of transnational tobacco companies to delay or thwart meaningful tobacco control worldwide. A series of cross-company tobacco industry "issues management organizations" has played an important role in coordinating and implementing common strategies to defeat tobacco control efforts at international, national, and regional levels. This study examines the development and enumerates the activities of these organizations and explores the implications of continuing industry cooperation for global public health. Using a snowball sampling strategy, we collected documentary data from tobacco industry documents archives and assembled them into a chronologically organized case study. The International Committee on Smoking Issues (ICOSI) was formed in 1977 by seven tobacco company chief executives to create common anti-tobacco control strategies and build a global network of regional and national manufacturing associations. The organization's name subsequently changed to INFOTAB. The multinational companies built the organization rapidly: by 1984, it had 69 members operating in 57 countries. INFOTAB material, including position papers and "action kits" helped members challenge local tobacco control measures and maintain tobacco-friendly environments. In 1992 INFOTAB was replaced by two smaller organizations. The Tobacco Documentation Centre, which continues to operate, distributes smoking-related information and industry argumentation to members, some produced by cross-company committees. Agro-Tobacco Services, and now Hallmark Marketing Services, assists the INFOTAB-backed and industry supported International Tobacco Growers Association in advancing claims regarding the economic importance of tobacco in developing nations. The massive scale and scope of this industry effort illustrate how corporate interests, when threatened by the globalization of public health, sidestep competitive

  17. Tobacco industry issues management organizations: Creating a global corporate network to undermine public health

    McDaniel, Patricia A; Intinarelli, Gina; Malone, Ruth E

    2008-01-01

    Background The global tobacco epidemic claims 5 million lives each year, facilitated by the ability of transnational tobacco companies to delay or thwart meaningful tobacco control worldwide. A series of cross-company tobacco industry "issues management organizations" has played an important role in coordinating and implementing common strategies to defeat tobacco control efforts at international, national, and regional levels. This study examines the development and enumerates the activities of these organizations and explores the implications of continuing industry cooperation for global public health. Methods Using a snowball sampling strategy, we collected documentary data from tobacco industry documents archives and assembled them into a chronologically organized case study. Results The International Committee on Smoking Issues (ICOSI) was formed in 1977 by seven tobacco company chief executives to create common anti-tobacco control strategies and build a global network of regional and national manufacturing associations. The organization's name subsequently changed to INFOTAB. The multinational companies built the organization rapidly: by 1984, it had 69 members operating in 57 countries. INFOTAB material, including position papers and "action kits" helped members challenge local tobacco control measures and maintain tobacco-friendly environments. In 1992 INFOTAB was replaced by two smaller organizations. The Tobacco Documentation Centre, which continues to operate, distributes smoking-related information and industry argumentation to members, some produced by cross-company committees. Agro-Tobacco Services, and now Hallmark Marketing Services, assists the INFOTAB-backed and industry supported International Tobacco Growers Association in advancing claims regarding the economic importance of tobacco in developing nations. Conclusion The massive scale and scope of this industry effort illustrate how corporate interests, when threatened by the globalization of

  18. Large differences in the genome organization of different plant Trypanosomatid parasites (Phytomonas spp.) reveal wide evolutionary divergences between taxa.

    Marín, C; Dollet, M; Pagès, M; Bastien, P

    2009-03-01

    All currently known plant trypanosomes have been grouped in the genus Phytomonas spp., although they can differ greatly in terms of both their biological properties and effects upon the host. Those parasitizing the phloem sap are specifically associated with lethal syndromes in Latin America, such as, phloem necrosis of coffee, 'Hartrot' of coconut and 'Marchitez sorpresiva' of oil palm, that inflict considerable economic losses in endemic countries. The genomic organization of one group of Phytomonas (D) considered as representative of the genus has been published previously. The present work presents the genomic structure of two representative isolates from the pathogenic phloem-restricted group (H) of Phytomonas, analyzed by pulsed field gel electrophoresis followed by hybridization with chromosome-specific DNA markers. It came as a surprise to observe an extremely different genomic organization in this group as compared with that of group D. Most notably, the chromosome number is 7 in this group (with a genome size of 10 Mb) versus 21 in the group D (totalling 25 Mb). These data unravel an unsuspected genomic diversity within plant trypanosomatids, that may justify a further debate about their division into different genera.

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

    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...

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

    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

  1. Genomes to Proteomes

    Panisko, Ellen A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Grigoriev, Igor [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Daly, Don S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Webb-Robertson, Bobbie-Jo [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baker, Scott E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2009-03-01

    Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

  2. Globalization

    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.

  3. Globalization

    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.

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

    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

  5. Chemistry of organic carbon in soil with relationship to the global carbon cycle

    Post, W.M. III.

    1988-01-01

    Various ecosystem disturbances alter the balances between production of organic matter and its decomposition and therefore change the amount of carbon in soil. The most severe perturbation is conversion of natural vegetation to cultivated crops. Conversion of natural vegetation to cultivated crops results in a lowered input of slowly decomposing material which causes a reduction in overall carbon levels. Disruption of soil matrix structure by cultivation leads to lowered physical protection of organic matter resulting in an increased net mineralization rate of soil carbon. Climate change is another perturbation that affects the amount and composition of plant production, litter inputs, and decomposition regimes but does not affect soil structure directly. Nevertheless, large changes in soil carbon storage are probable with anticipated CO 2 induced climate change, particularly in northern latitudes where anticipated climate change will be greatest (MacCracken and Luther 1985) and large amounts of soil organic matter are found. It is impossible, given the current state of knowledge of soil organic matter processes and transformations to develop detailed process models of soil carbon dynamics. Largely phenomenological models appear to be developing into predictive tools for understanding the role of soil organic matter in the global carbon cycle. In particular, these models will be useful in quantifying soil carbon changes due to human land-use and to anticipated global climate and vegetation changes. 47 refs., 7 figs., 2 tabs

  6. The maximum reservoir capacity of soils for persistent organic pollutants: implications for global cycling

    Dalla Valle, M.; Jurado, E.; Dachs, J.; Sweetman, A.J.; Jones, K.C.

    2005-01-01

    The concept of maximum reservoir capacity (MRC), the ratio of the capacities of the surface soil and of the atmospheric mixed layer (AML) to hold chemical under equilibrium conditions, is applied to selected persistent organic pollutants (POPs) in the surface 'skin' (1 mm) of soils. MRC is calculated as a function of soil organic matter (SOM) content and temperature-dependent K OA and mapped globally for selected PCB congeners (PCB-28; -153; -180) and HCB, to identify regions with a higher tendency to retain POPs. It is shown to vary over many orders of magnitude, between compounds, locations and time (seasonally/diurnally). The MRC approach emphasises the very large capacity of soils as a storage compartment for POPs. The theoretical MRC concept is compared to reality and its implications for the global cycling of POPs are discussed. Sharp gradients in soil MRC can exist in mountainous areas and between the land and ocean. Exchanges between oceans and land masses via the atmosphere is likely to be an important driver to the global cycling of these compounds, and net ocean-land transfers could occur in some areas. - Major global terrestrial sinks/stores for POPs are identified and the significance of gradients between them discussed

  7. The role of trust and leadership in the global marketing driven organization

    Chmielewski, Krzysztof J.

    2011-01-01

    The role of trust and leadership in the global marketing driven organization is discussed in this paper. The author analyzed the essence of trust, levels of trust, performance effects of trust and challenges of trust. Further, the characteristics of leadership is described as well as the essence of leadership. Current challenges facing this topic are analyzed and trends for the near future are indicated. Moreover, the author discusses the main impacts which will drive leadership in the future...

  8. American Mock World Health Organization: An Innovative Model for Student Engagement in Global Health Policy

    Lei, Mia; Acharya, Neha; Kwok Man Lee, Edith; Catherine Holcomb, Emma; Kapoor, Veronica

    2017-01-01

    ABSTRACT The American Mock World Health Organization (AMWHO) is a model for experiential-based learning and student engagement in global health diplomacy. AMWHO was established in 2014 at the University of North Carolina at Chapel Hill with a mission to engage students in health policy by providing a simulation of the World Health Assembly (WHA), the policy-forming body of the World Health Organization that sets norms and transforms the global health agenda. AMWHO conferences are designed to allow students to take their knowledge of global health beyond the classroom and practice their skills in diplomacy by assuming the role of WHA delegates throughout a 3-day weekend. Through the process of developing resolutions like those formed in the WHA, students have the unique opportunity to understand the complexities behind the conflict and compromise that ensues through the lens of a stakeholder. This article describes the structure of the first 2 AMWHO international conferences, analyzes survey results from attendees, and discusses the expansion of the organization into a multi-campus national network. The AMWHO 2014 and 2015 post-conference survey results found that 98% and 90% of participants considered the conference "good" or "better," respectively, and survey responses showed that participants considered the conference "influential" in their careers and indicated that it "allowed a paradigm shift not possible in class." PMID:28351883

  9. Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project

    Dunlap, Jay C.; Borkovich, Katherine A.; Henn, Matthew R.; Turner, Gloria E.; Sachs, Matthew S.; Glass, N. Louise; McCluskey, Kevin; Plamann, Michael; Galagan, James E.; Birren, Bruce W.; Weiss, Richard L.; Townsend, Jeffrey P.; Loros, Jennifer J.; Nelson, Mary Anne; Lambreghts, Randy

    2007-01-01

    A consortium of investigators is engaged in a functional genomics project centered on the filamentous fungus Neurospora, with an eye to opening up the functional genomic analysis of all the filamentous fungi. The overall goal of the four interdependent projects in this effort is to acccomplish functional genomics, annotation, and expression analyses of Neurospora crassa, a filamentous fungus that is an established model for the assemblage of over 250,000 species of nonyeast fungi. Building fr...

  10. Hierarchical role for transcription factors and chromatin structure in genome organization along adipogenesis

    Sarusi Portuguez, Avital; Schwartz, Michal; Siersbaek, Rasmus

    2017-01-01

    The three dimensional folding of mammalian genomes is cell type specific and difficult to alter suggesting that it is an important component of gene regulation. However, given the multitude of chromatin-associating factors, the mechanisms driving the colocalization of active chromosomal domains...... by PPARγ and Lpin1, undergoes orchestrated reorganization during adipogenesis. Coupling the dynamics of genome architecture with multiple chromatin datasets indicated that among all the transcription factors (TFs) tested, RXR is central to genome reorganization at the beginning of adipogenesis...

  11. Promoter characterization and genomic organization of the human X11β gene APBA2.

    Hao, Yan

    2012-02-15

    Overexpression of neuronal adaptor protein X11β has been shown to decrease the production of amyloid-β, a toxic peptide deposited in Alzheimer\\'s disease brains. Therefore, manipulation of the X11β level may represent a potential therapeutic strategy for Alzheimer\\'s disease. As X11β expression can be regulated at the transcription level, we determined the genomic organization and the promoter of the human X11β gene, amyloid β A4 precursor protein-binding family A member 2 (APBA2). By RNA ligase-mediated rapid amplification of cDNA ends, a single APBA2 transcription start site and the complete sequence of exon 1 were identified. The APBA2 promoter was located upstream of exon 1 and was more active in neurons. The core promoter contains several CpG dinucleotides, and was strongly suppressed by DNA methylation. In addition, mutagenesis analysis revealed a putative Pax5-binding site within the promoter. Together, APBA2 contains a potent neuronal promoter whose activity may be regulated by DNA methylation and Pax5.

  12. Genomic organization, expression, and chromosome localization of a third aurora-related kinase gene, Aie1.

    Hu, H M; Chuang, C K; Lee, M J; Tseng, T C; Tang, T K

    2000-11-01

    We previously reported two novel testis-specific serine/threonine kinases, Aie1 (mouse) and AIE2 (human), that share high amino acid identities with the kinase domains of fly aurora and yeast Ipl1. Here, we report the entire intron-exon organization of the Aie1 gene and analyze the expression patterns of Aie1 mRNA during testis development. The mouse Aie1 gene spans approximately 14 kb and contains seven exons. The sequences of the exon-intron boundaries of the Aie1 gene conform to the consensus sequences (GT/AG) of the splicing donor and acceptor sites of most eukaryotic genes. Comparative genomic sequencing revealed that the gene structure is highly conserved between mouse Aie1 and human AIE2. However, much less homology was found in the sequence outside the kinase-coding domains. The Aie1 locus was mapped to mouse chromosome 7A2-A3 by fluorescent in situ hybridization. Northern blot analysis indicates that Aie1 mRNA likely is expressed at a low level on day 14 and reaches its plateau on day 21 in the developing postnatal testis. RNA in situ hybridization indicated that the expression of the Aie1 transcript was restricted to meiotically active germ cells, with the highest levels detected in spermatocytes at the late pachytene stage. These findings suggest that Aie1 plays a role in spermatogenesis.

  13. Genome-wide organization and expression profiling of the R2R3-MYB transcription factor family in pineapple (Ananas comosus).

    Liu, Chaoyang; Xie, Tao; Chen, Chenjie; Luan, Aiping; Long, Jianmei; Li, Chuhao; Ding, Yaqi; He, Yehua

    2017-07-01

    The MYB proteins comprise one of the largest families of plant transcription factors, which are involved in various plant physiological and biochemical processes. Pineapple (Ananas comosus) is one of three most important tropical fruits worldwide. The completion of pineapple genome sequencing provides a great opportunity to investigate the organization and evolutionary traits of pineapple MYB genes at the genome-wide level. In the present study, a total of 94 pineapple R2R3-MYB genes were identified and further phylogenetically classified into 26 subfamilies, as supported by the conserved gene structures and motif composition. Collinearity analysis indicated that the segmental duplication events played a crucial role in the expansion of pineapple MYB gene family. Further comparative phylogenetic analysis suggested that there have been functional divergences of MYB gene family during plant evolution. RNA-seq data from different tissues and developmental stages revealed distinct temporal and spatial expression profiles of the AcMYB genes. Further quantitative expression analysis showed the specific expression patterns of the selected putative stress-related AcMYB genes in response to distinct abiotic stress and hormonal treatments. The comprehensive expression analysis of the pineapple MYB genes, especially the tissue-preferential and stress-responsive genes, could provide valuable clues for further function characterization. In this work, we systematically identified AcMYB genes by analyzing the pineapple genome sequence using a set of bioinformatics approaches. Our findings provide a global insight into the organization, phylogeny and expression patterns of the pineapple R2R3-MYB genes, and hence contribute to the greater understanding of their biological roles in pineapple.

  14. A sequence-based survey of the complex structural organization of tumor genomes

    Collins, Colin; Raphael, Benjamin J.; Volik, Stanislav; Yu, Peng; Wu, Chunxiao; Huang, Guiqing; Linardopoulou, Elena V.; Trask, Barbara J.; Waldman, Frederic; Costello, Joseph; Pienta, Kenneth J.; Mills, Gordon B.; Bajsarowicz, Krystyna; Kobayashi, Yasuko; Sridharan, Shivaranjani; Paris, Pamela; Tao, Quanzhou; Aerni, Sarah J.; Brown, Raymond P.; Bashir, Ali; Gray, Joe W.; Cheng, Jan-Fang; de Jong, Pieter; Nefedov, Mikhail; Ried, Thomas; Padilla-Nash, Hesed M.; Collins, Colin C.

    2008-04-03

    The genomes of many epithelial tumors exhibit extensive chromosomal rearrangements. All classes of genome rearrangements can be identified using End Sequencing Profiling (ESP), which relies on paired-end sequencing of cloned tumor genomes. In this study, brain, breast, ovary and prostate tumors along with three breast cancer cell lines were surveyed with ESP yielding the largest available collection of sequence-ready tumor genome breakpoints and providing evidence that some rearrangements may be recurrent. Sequencing and fluorescence in situ hybridization (FISH) confirmed translocations and complex tumor genome structures that include coamplification and packaging of disparate genomic loci with associated molecular heterogeneity. Comparison of the tumor genomes suggests recurrent rearrangements. Some are likely to be novel structural polymorphisms, whereas others may be bona fide somatic rearrangements. A recurrent fusion transcript in breast tumors and a constitutional fusion transcript resulting from a segmental duplication were identified. Analysis of end sequences for single nucleotide polymorphisms (SNPs) revealed candidate somatic mutations and an elevated rate of novel SNPs in an ovarian tumor. These results suggest that the genomes of many epithelial tumors may be far more dynamic and complex than previously appreciated and that genomic fusions including fusion transcripts and proteins may be common, possibly yielding tumor-specific biomarkers and therapeutic targets.

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

    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.

  16. Secondary organic aerosol in the global aerosol – chemical transport model Oslo CTM2

    I. S. A. Isaksen

    2007-11-01

    Full Text Available The global chemical transport model Oslo CTM2 has been extended to include the formation, transport and deposition of secondary organic aerosol (SOA. Precursor hydrocarbons which are oxidised to form condensible species include both biogenic species such as terpenes and isoprene, as well as species emitted predominantly by anthropogenic activities (toluene, m-xylene, methylbenzene and other aromatics. A model simulation for 2004 gives an annual global SOA production of approximately 55 Tg. Of this total, 2.5 Tg is found to consist of the oxidation products of anthropogenically emitted hydrocarbons, and about 15 Tg is formed by the oxidation products of isoprene. The global production of SOA is increased to about 69 Tg yr−1 by allowing semi-volatile species to partition to ammonium sulphate aerosol. This brings modelled organic aerosol values closer to those observed, however observations in Europe remain significantly underestimated. Allowing SOA to partition into ammonium sulphate aerosol increases the contribution of anthropogenic SOA from about 4.5% to 9.4% of the total production. Total modelled organic aerosol (OA values are found to represent a lower fraction of the measured values in winter (when primary organic aerosol (POA is the dominant OA component than in summer, which may be an indication that estimates of POA emissions are too low. Additionally, for measurement stations where the summer OA values are higher than in winter, the model generally underestimates the increase in summertime OA. In order to correctly model the observed increase in OA in summer, additional SOA sources or formation mechanisms may be necessary. The importance of NO3 as an oxidant of SOA precursors is found to vary regionally, causing up to 50%–60% of the total amount of SOA near the surface in polluted regions and less than 25% in more remote areas, if the yield of condensible oxidation products for β-pinene is used for NO3 oxidation of all terpenes

  17. Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms

    Meller Jaroslaw

    2007-03-01

    Full Text Available Abstract Background Identifying syntenic regions, i.e., blocks of genes or other markers with evolutionary conserved order, and quantifying evolutionary relatedness between genomes in terms of chromosomal rearrangements is one of the central goals in comparative genomics. However, the analysis of synteny and the resulting assessment of genome rearrangements are sensitive to the choice of a number of arbitrary parameters that affect the detection of synteny blocks. In particular, the choice of a set of markers and the effect of different aggregation strategies, which enable coarse graining of synteny blocks and exclusion of micro-rearrangements, need to be assessed. Therefore, existing tools and resources that facilitate identification, visualization and analysis of synteny need to be further improved to provide a flexible platform for such analysis, especially in the context of multiple genomes. Results We present a new tool, Cinteny, for fast identification and analysis of synteny with different sets of markers and various levels of coarse graining of syntenic blocks. Using Hannenhalli-Pevzner approach and its extensions, Cinteny also enables interactive determination of evolutionary relationships between genomes in terms of the number of rearrangements (the reversal distance. In particular, Cinteny provides: i integration of synteny browsing with assessment of evolutionary distances for multiple genomes; ii flexibility to adjust the parameters and re-compute the results on-the-fly; iii ability to work with user provided data, such as orthologous genes, sequence tags or other conserved markers. In addition, Cinteny provides many annotated mammalian, invertebrate and fungal genomes that are pre-loaded and available for analysis at http://cinteny.cchmc.org. Conclusion Cinteny allows one to automatically compare multiple genomes and perform sensitivity analysis for synteny block detection and for the subsequent computation of reversal distances

  18. Organic pollution of rivers: Combined threats of urbanization, livestock farming and global climate change.

    Wen, Yingrong; Schoups, Gerrit; van de Giesen, Nick

    2017-02-23

    Organic pollution of rivers by wastewater discharge from human activities negatively impacts people and ecosystems. Without treatment, pollution control relies on a combination of natural degradation and dilution by natural runoff to reduce downstream effects. We quantify here for the first time the global sanitation crisis through its impact on organic river pollution from the threats of (1) increasing wastewater discharge due to urbanization and intensification of livestock farming, and (2) reductions in river dilution capacity due to climate change and water extractions. Using in-stream Biochemical Oxygen Demand (BOD) as an overall indicator of organic river pollution, we calculate historical (2000) and future (2050) BOD concentrations in global river networks. Despite significant self-cleaning capacities of rivers, the number of people affected by organic pollution (BOD >5 mg/l) is projected to increase from 1.1 billion in 2000 to 2.5 billion in 2050. With developing countries disproportionately affected, our results point to a growing need for affordable wastewater solutions.

  19. Organic pollution of rivers: Combined threats of urbanization, livestock farming and global climate change

    Wen, Yingrong; Schoups, Gerrit; van de Giesen, Nick

    2017-02-01

    Organic pollution of rivers by wastewater discharge from human activities negatively impacts people and ecosystems. Without treatment, pollution control relies on a combination of natural degradation and dilution by natural runoff to reduce downstream effects. We quantify here for the first time the global sanitation crisis through its impact on organic river pollution from the threats of (1) increasing wastewater discharge due to urbanization and intensification of livestock farming, and (2) reductions in river dilution capacity due to climate change and water extractions. Using in-stream Biochemical Oxygen Demand (BOD) as an overall indicator of organic river pollution, we calculate historical (2000) and future (2050) BOD concentrations in global river networks. Despite significant self-cleaning capacities of rivers, the number of people affected by organic pollution (BOD >5 mg/l) is projected to increase from 1.1 billion in 2000 to 2.5 billion in 2050. With developing countries disproportionately affected, our results point to a growing need for affordable wastewater solutions.

  20. Structure and expression strategy of the genome of Culex pipiens densovirus, a mosquito densovirus with an ambisense organization.

    Baquerizo-Audiot, Elizabeth; Abd-Alla, Adly; Jousset, Françoise-Xavière; Cousserans, François; Tijssen, Peter; Bergoin, Max

    2009-07-01

    The genome of all densoviruses (DNVs) so far isolated from mosquitoes or mosquito cell lines consists of a 4-kb single-stranded DNA molecule with a monosense organization (genus Brevidensovirus, subfamily Densovirinae). We previously reported the isolation of a Culex pipiens DNV (CpDNV) that differs significantly from brevidensoviruses by (i) having a approximately 6-kb genome, (ii) lacking sequence homology, and (iii) lacking antigenic cross-reactivity with Brevidensovirus capsid polypeptides. We report here the sequence organization and transcription map of this virus. The cloned genome of CpDNV is 5,759 nucleotides (nt) long, and it possesses an inverted terminal repeat (ITR) of 285 nt and an ambisense organization of its genes. The nonstructural (NS) proteins NS-1, NS-2, and NS-3 are located in the 5' half of one strand and are organized into five open reading frames (ORFs) due to the split of both NS-1 and NS-2 into two ORFs. The ORF encoding capsid polypeptides is located in the 5' half of the complementary strand. The expression of NS proteins is controlled by two promoters, P7 and P17, driving the transcription of a 2.4-kb mRNA encoding NS-3 and of a 1.8-kb mRNA encoding NS-1 and NS-2, respectively. The two NS mRNAs species are spliced off a 53-nt sequence. Capsid proteins are translated from an unspliced 2.3-kb mRNA driven by the P88 promoter. CpDNV thus appears as a new type of mosquito DNV, and based on the overall organization and expression modalities of its genome, it may represent the prototype of a new genus of DNV.

  1. Globalization

    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...

  2. Recent advances in understanding secondary organic aerosol: Implications for global climate forcing: Advances in Secondary Organic Aerosol

    Shrivastava, Manish [Pacific Northwest National Laboratory, Richland Washington USA; Cappa, Christopher D. [Department of Civil and Environmental Engineering, University of California, Davis California USA; Fan, Jiwen [Pacific Northwest National Laboratory, Richland Washington USA; Goldstein, Allen H. [Department of Environmental Science, Policy and Management and Department of Civil and Environmental Engineering, University of California, Berkeley California USA; Guenther, Alex B. [Department of Earth System Science, University of California, Irvine California USA; Jimenez, Jose L. [Cooperative Institute for Research in Environmental Sciences and Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder Colorado USA; Kuang, Chongai [Brookhaven National Laboratory, Upton New York USA; Laskin, Alexander [Pacific Northwest National Laboratory, Richland Washington USA; Martin, Scot T. [School of Engineering and Applied Sciences and Department of Earth and Planetary Sciences, Harvard University, Cambridge Massachusetts USA; Ng, Nga Lee [School of Chemical and Biomolecular Engineering and School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta Georgia USA; Petaja, Tuukka [Department of Physics, University of Helsinki, Helsinki Finland; Pierce, Jeffrey R. [Department of Atmospheric Science, Colorado State University, Fort Collins Colorado USA; Rasch, Philip J. [Pacific Northwest National Laboratory, Richland Washington USA; Roldin, Pontus [Department of Physics, Lund University, Lund Sweden; Seinfeld, John H. [Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena California USA; Shilling, John [Pacific Northwest National Laboratory, Richland Washington USA; Smith, James N. [Department of Earth System Science, University of California, Irvine California USA; Thornton, Joel A. [Department of Atmospheric Sciences, University of Washington, Seattle Washington USA; Volkamer, Rainer [Cooperative Institute for Research in Environmental Sciences and Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder Colorado USA; Wang, Jian [Brookhaven National Laboratory, Upton New York USA; Worsnop, Douglas R. [Aerodyne Research, Inc., Billerica Massachusetts USA; Zaveri, Rahul A. [Pacific Northwest National Laboratory, Richland Washington USA; Zelenyuk, Alla [Pacific Northwest National Laboratory, Richland Washington USA; Zhang, Qi [Department of Environmental Toxicology, University of California, Davis California USA

    2017-06-01

    Anthropogenic emissions and land-use changes have modified atmospheric aerosol concentrations and size distributions over time. Understanding pre-industrial conditions and changes in organic aerosol due to anthropogenic activities is important because these features 1) influence estimates of aerosol radiative forcing and 2) can confound estimates of the historical response of climate to increases in greenhouse gases (e.g. the ‘climate sensitivity’). Secondary organic aerosol (SOA), formed in the atmosphere by oxidation of organic gases, represents a major fraction of global submicron-sized atmospheric organic aerosol. Over the past decade, significant advances in understanding SOA properties and formation mechanisms have occurred through a combination of laboratory and field measurements, yet current climate models typically do not comprehensively include all important SOA-relevant processes. Therefore, major gaps exist at present between current measurement-based knowledge on the one hand and model implementation of organic aerosols on the other. The critical review herein summarizes some of the important developments in understanding SOA formation that could potentially have large impacts on our understanding of aerosol radiative forcing and climate. We highlight the importance of some recently discovered processes and properties that influence the growth of SOA particles to sizes relevant for clouds and radiative forcing, including: formation of extremely low-volatility organics in the gas-phase; isoprene epoxydiols (IEPOX) multi-phase chemistry; particle-phase oligomerization; and physical properties such as viscosity. In addition, this review also highlights some of the important processes that involve interactions between natural biogenic emissions and anthropogenic emissions, such as the role of sulfate and oxides of nitrogen (NOx) on SOA formation from biogenic volatile organic compounds. Studies that relate the observed evolution of organic aerosol

  3. Spatial organization of the budding yeast genome in the cell nucleus and identification of specific chromatin interactions from multi-chromosome constrained chromatin model.

    Gürsoy, Gamze; Xu, Yun; Liang, Jie

    2017-07-01

    Nuclear landmarks and biochemical factors play important roles in the organization of the yeast genome. The interaction pattern of budding yeast as measured from genome-wide 3C studies are largely recapitulated by model polymer genomes subject to landmark constraints. However, the origin of inter-chromosomal interactions, specific roles of individual landmarks, and the roles of biochemical factors in yeast genome organization remain unclear. Here we describe a multi-chromosome constrained self-avoiding chromatin model (mC-SAC) to gain understanding of the budding yeast genome organization. With significantly improved sampling of genome structures, both intra- and inter-chromosomal interaction patterns from genome-wide 3C studies are accurately captured in our model at higher resolution than previous studies. We show that nuclear confinement is a key determinant of the intra-chromosomal interactions, and centromere tethering is responsible for the inter-chromosomal interactions. In addition, important genomic elements such as fragile sites and tRNA genes are found to be clustered spatially, largely due to centromere tethering. We uncovered previously unknown interactions that were not captured by genome-wide 3C studies, which are found to be enriched with tRNA genes, RNAPIII and TFIIS binding. Moreover, we identified specific high-frequency genome-wide 3C interactions that are unaccounted for by polymer effects under landmark constraints. These interactions are enriched with important genes and likely play biological roles.

  4. The World Health Organization Global Health Emergency Workforce: What Role Will the United States Play?

    Burkle, Frederick M

    2016-08-01

    During the May 2016 World Health Assembly of 194 member states, the World Health Organization (WHO) announced the process of developing and launching emergency medical teams as a critical component of the global health workforce concept. Over 64 countries have either launched or are in the development stages of vetting accredited teams, both international and national, to provide surge support to national health systems through WHO Regional Organizations and the delivery of emergency clinical care to sudden-onset disasters and outbreak-affected populations. To date, the United States has not yet committed to adopting the emergency medical team concept in funding and registering an international field hospital level team. This article discusses future options available for health-related nongovernmental organizations and the required educational and training requirements for health care provider accreditation. (Disaster Med Public Health Preparedness. 2016;10:531-535).

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

    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

  6. World Health Organization global policy for improvement of oral health--World Health Assembly 2007

    Petersen, Poul Erik

    2008-01-01

    The World Health Organization (WHO) Global Oral Health Programme has worked hard over the past five years to increase the awareness of oral health worldwide as an important component of general health and quality of life. Meanwhile, oral disease is still a major public health problem in high income...... countries and the burden of oral disease is growing in many low- and middle income countries. In the World Oral Health Report 2003, the WHO Global Oral Health Programme formulated the policies and the necessary actions for the improvement of oral health. The strategy is that oral disease prevention...... and the promotion of oral health needs to be integrated with chronic disease prevention and general health promotion as the risks to health are linked. The World Health Assembly (WHA) and the Executive Board (EB) are supreme governance bodies of WHO and for the first time in 25 years oral health was subject...

  7.  Project Management as a Global Trend for Organization Work

    Kampf, Constance

    in multination and global companies, understanding the power of visual rhetoric, genre and writing processes in the context of project management documentation can be an advantage for technical communicators.  In addition, project management tools and online documentation spaces are objects which cross...... Project Management as a Global Trend for Organization Work: Implications for Technical Communication Project Management tools and processes offer a visual approach to producing knowledge about a project in order to complete it.  As project management practices are used with increasing frequency......-cultural teams use to function.  This presentation will explore the potential of Project Management to be tightly integrated in Technical Communication curricula through a communications approach to project management.  Questions for discussion include: How tightly is project management integrated into different...

  8. World Health Organization Global Estimates and Regional Comparisons of the Burden of Foodborne Disease in 2010

    Havelaar, Arie H.; Kirk, Martyn D.; Torgerson, Paul R.

    2015-01-01

    parasitic helminths, were highly localised. Thus, the burden of FBD is borne particularly by children under five years old-although they represent only 9% of the global population-and people living in low-income regions of the world. These estimates are conservative, i.e., underestimates rather than......Illness and death from diseases caused by contaminated food are a constant threat to public health and a significant impediment to socio-economic development worldwide. To measure the global and regional burden of foodborne disease (FBD), the World Health Organization (WHO) established...... different burdens of FBD, with the greatest falling on the subregions in Africa, followed by the subregions in South-East Asia and the Eastern Mediterranean D subregion. Some hazards, such as non-typhoidal S. enterica, were important causes of FBD in all regions of the world, whereas others, such as certain...

  9. Ecological significance of compatible solute accumulation by micro-organisms: from single cells to global climate.

    Welsh, D T

    2000-07-01

    The osmoadaptation of most micro-organisms involves the accumulation of K(+) ions and one or more of a restricted range of low molecular mass organic solutes, collectively termed 'compatible solutes'. These solutes are accumulated to high intracellular concentrations, in order to balance the osmotic pressure of the growth medium and maintain cell turgor pressure, which provides the driving force for cell extension growth. In this review, I discuss the alternative roles which compatible solutes may also play as intracellular reserves of carbon, energy and nitrogen, and as more general stress metabolites involved in protection of cells against other environmental stresses including heat, desiccation and freezing. Thus, the evolutionary selection for the accumulation of a specific compatible solute may not depend solely upon its function during osmoadaptation, but also upon the secondary benefits its accumulation provides, such as increased tolerance of other environmental stresses prevalent in the organism's niche or even anti-herbivory or dispersal functions in the case of dimethylsulfoniopropionate (DMSP). In the second part of the review, I discuss the ecological consequences of the release of compatible solutes to the environment, where they can provide sources of compatible solutes, carbon, nitrogen and energy for other members of the micro-flora. Finally, at the global scale the metabolism of specific compatible solutes (betaines and DMSP) in brackish water, marine and hypersaline environments may influence global climate, due to the production of the trace gases, methane and dimethylsulfide (DMS) and in the case of DMS, also couple the marine and terrestrial sulfur cycles.

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

    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.

  11. Global combustion sources of organic aerosols: model comparison with 84 AMS factor-analysis data sets

    Tsimpidi, Alexandra P.; Karydis, Vlassis A.; Pandis, Spyros N.; Lelieveld, Jos

    2016-07-01

    Emissions of organic compounds from biomass, biofuel, and fossil fuel combustion strongly influence the global atmospheric aerosol load. Some of the organics are directly released as primary organic aerosol (POA). Most are emitted in the gas phase and undergo chemical transformations (i.e., oxidation by hydroxyl radical) and form secondary organic aerosol (SOA). In this work we use the global chemistry climate model ECHAM/MESSy Atmospheric Chemistry (EMAC) with a computationally efficient module for the description of organic aerosol (OA) composition and evolution in the atmosphere (ORACLE). The tropospheric burden of open biomass and anthropogenic (fossil and biofuel) combustion particles is estimated to be 0.59 and 0.63 Tg, respectively, accounting for about 30 and 32 % of the total tropospheric OA load. About 30 % of the open biomass burning and 10 % of the anthropogenic combustion aerosols originate from direct particle emissions, whereas the rest is formed in the atmosphere. A comprehensive data set of aerosol mass spectrometer (AMS) measurements along with factor-analysis results from 84 field campaigns across the Northern Hemisphere are used to evaluate the model results. Both the AMS observations and the model results suggest that over urban areas both POA (25-40 %) and SOA (60-75 %) contribute substantially to the overall OA mass, whereas further downwind and in rural areas the POA concentrations decrease substantially and SOA dominates (80-85 %). EMAC does a reasonable job in reproducing POA and SOA levels during most of the year. However, it tends to underpredict POA and SOA concentrations during winter indicating that the model misses wintertime sources of OA (e.g., residential biofuel use) and SOA formation pathways (e.g., multiphase oxidation).

  12. Recent advances in understanding secondary organic aerosol: Implications for global climate forcing

    Shrivastava, Manish; Cappa, Christopher D.; Fan, Jiwen; Goldstein, Allen H.; Guenther, Alex B.; Jimenez, Jose L.; Kuang, Chongai; Laskin, Alexander; Martin, Scot T.; Ng, Nga Lee; Petaja, Tuukka; Pierce, Jeffrey R.; Rasch, Philip J.; Roldin, Pontus; Seinfeld, John H.; Shilling, John; Smith, James N.; Thornton, Joel A.; Volkamer, Rainer; Wang, Jian; Worsnop, Douglas R.; Zaveri, Rahul A.; Zelenyuk, Alla; Zhang, Qi

    2017-06-01

    Anthropogenic emissions and land use changes have modified atmospheric aerosol concentrations and size distributions over time. Understanding preindustrial conditions and changes in organic aerosol due to anthropogenic activities is important because these features (1) influence estimates of aerosol radiative forcing and (2) can confound estimates of the historical response of climate to increases in greenhouse gases. Secondary organic aerosol (SOA), formed in the atmosphere by oxidation of organic gases, represents a major fraction of global submicron-sized atmospheric organic aerosol. Over the past decade, significant advances in understanding SOA properties and formation mechanisms have occurred through measurements, yet current climate models typically do not comprehensively include all important processes. This review summarizes some of the important developments during the past decade in understanding SOA formation. We highlight the importance of some processes that influence the growth of SOA particles to sizes relevant for clouds and radiative forcing, including formation of extremely low volatility organics in the gas phase, acid-catalyzed multiphase chemistry of isoprene epoxydiols, particle-phase oligomerization, and physical properties such as volatility and viscosity. Several SOA processes highlighted in this review are complex and interdependent and have nonlinear effects on the properties, formation, and evolution of SOA. Current global models neglect this complexity and nonlinearity and thus are less likely to accurately predict the climate forcing of SOA and project future climate sensitivity to greenhouse gases. Efforts are also needed to rank the most influential processes and nonlinear process-related interactions, so that these processes can be accurately represented in atmospheric chemistry-climate models.

  13. Site specific X-ray induced changes in organic and metal organic compounds and their influence on global radiation damage

    Heintz, Desiree Ellen

    2012-07-01

    The aim of this work was to systematically investigate the effects of specific and global X-ray radiation damage to biological samples and obtain a conclusive model to describe the underlying principles. Based on the systematic studies performed in this work, it was possible to propose two conclusive mechanisms to describe X-ray induced photoreduction and global radiation damage. The influence of chemical composition, temperature and solvent on X-ray induced photoreduction was investigated by X-ray Absorption Near Edge Spectroscopy and single crystal X-ray diffraction of two B12 cofactors - cyano- and methylcobalamin - as well as iron(II) and iron(III) complexes. The obtained results revealed that X-ray induced photoreduction is a ligand dependent process, with a redox reaction taking place within the complex. It could further be shown that selective hydrogen abstraction plays an important role in the process of X-ray induced photoreduction. Based on the experimental results of this work, a model to describe X-ray induced photoreduction of metal organic complexes could be proposed. The process of X-ray induced hydrogen abstraction was further investigated in a combined X-ray and neutron diffraction study on the amino acids L-serine and L-alanine, which were used as model compounds for proteins, and the nucleoside deoxythymidine (thymidine) as a model for DNA. A damage mechanism for L-serine could be found. It involves the abstraction of two hydrogen atoms, one from the hydroxyl group and one from the adjacent methylene group. Such a hydrogen abstraction results in the formation of a carbonyl group. X-ray diffraction measurements on cyano- and methylcobalamin as well as on three metal amino acid complexes, containing nickel(II) and copper(II), respectively, were conducted to investigate the contribution of X-ray induced photoreduction to global radiation damage. Results from these measurements combined with the results from L-serine, L-alanine and thymidine allowed

  14. Site specific X-ray induced changes in organic and metal organic compounds and their influence on global radiation damage

    Heintz, Desiree Ellen

    2012-07-15

    The aim of this work was to systematically investigate the effects of specific and global X-ray radiation damage to biological samples and obtain a conclusive model to describe the underlying principles. Based on the systematic studies performed in this work, it was possible to propose two conclusive mechanisms to describe X-ray induced photoreduction and global radiation damage. The influence of chemical composition, temperature and solvent on X-ray induced photoreduction was investigated by X-ray Absorption Near Edge Spectroscopy and single crystal X-ray diffraction of two B12 cofactors - cyano- and methylcobalamin - as well as iron(II) and iron(III) complexes. The obtained results revealed that X-ray induced photoreduction is a ligand dependent process, with a redox reaction taking place within the complex. It could further be shown that selective hydrogen abstraction plays an important role in the process of X-ray induced photoreduction. Based on the experimental results of this work, a model to describe X-ray induced photoreduction of metal organic complexes could be proposed. The process of X-ray induced hydrogen abstraction was further investigated in a combined X-ray and neutron diffraction study on the amino acids L-serine and L-alanine, which were used as model compounds for proteins, and the nucleoside deoxythymidine (thymidine) as a model for DNA. A damage mechanism for L-serine could be found. It involves the abstraction of two hydrogen atoms, one from the hydroxyl group and one from the adjacent methylene group. Such a hydrogen abstraction results in the formation of a carbonyl group. X-ray diffraction measurements on cyano- and methylcobalamin as well as on three metal amino acid complexes, containing nickel(II) and copper(II), respectively, were conducted to investigate the contribution of X-ray induced photoreduction to global radiation damage. Results from these measurements combined with the results from L-serine, L-alanine and thymidine allowed

  15. A Novel Organic Rankine Cycle System with Improved Thermal Stability and Low Global Warming Fluids

    Panesar Angad S

    2014-07-01

    Full Text Available This paper proposes a novel Organic Rankine Cycle (ORC system for long haul truck application. Rather than typical tail pipe heat recovery configurations, the proposed setup exploits the gaseous streams that are already a load on the engine cooling module. The system uses dual loops connected only by the Exhaust Gas Recirculation (EGR stream. A water blend study is conducted to identify suitable mixtures for the High Temperature (HT loop, while the Low Temperature (LT loop utilises a Low Global Warming (GWP Hydrofluoroether.

  16. Performance comparison of two efficient genomic selection methods (gsbay & MixP) applied in aquacultural organisms

    Su, Hailin; Li, Hengde; Wang, Shi; Wang, Yangfan; Bao, Zhenmin

    2017-02-01

    Genomic selection is more and more popular in animal and plant breeding industries all around the world, as it can be applied early in life without impacting selection candidates. The objective of this study was to bring the advantages of genomic selection to scallop breeding. Two different genomic selection tools MixP and gsbay were applied on genomic evaluation of simulated data and Zhikong scallop ( Chlamys farreri) field data. The data were compared with genomic best linear unbiased prediction (GBLUP) method which has been applied widely. Our results showed that both MixP and gsbay could accurately estimate single-nucleotide polymorphism (SNP) marker effects, and thereby could be applied for the analysis of genomic estimated breeding values (GEBV). In simulated data from different scenarios, the accuracy of GEBV acquired was ranged from 0.20 to 0.78 by MixP; it was ranged from 0.21 to 0.67 by gsbay; and it was ranged from 0.21 to 0.61 by GBLUP. Estimations made by MixP and gsbay were expected to be more reliable than those estimated by GBLUP. Predictions made by gsbay were more robust, while with MixP the computation is much faster, especially in dealing with large-scale data. These results suggested that both algorithms implemented by MixP and gsbay are feasible to carry out genomic selection in scallop breeding, and more genotype data will be necessary to produce genomic estimated breeding values with a higher accuracy for the industry.

  17. Genomic signatures of local directional selection in a high gene flow marine organism, the Atlantic cod (Gadus morhua)

    Eg Nielsen, Einar; Hansen, Jakob Hemmer; Poulsen, Nina Aagaard

    2009-01-01

    -associated single nucleotide polymorphisms (SNPs) for evidence of selection in local populations of Atlantic cod (Gadus morhua L.) across the species distribution. Results: Our global genome scan analysis identified eight outlier gene loci with very high statistical support, likely to be subject to directional...... selection in local demes, or closely linked to loci under selection. Likewise, on a regional south/north transect of central and eastern Atlantic populations, seven loci displayed strongly elevated levels of genetic differentiation. Selection patterns among populations appeared to be relatively widespread...

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

    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.

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

    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.

  20. Global trends in the fluorescence characteristics and distribution of marine dissolved organic matter

    Jørgensen, Linda; Stedmon, Colin; Kragh, Theis

    2011-01-01

    . These observations imply a link to dark ocean microbial remineralization and indicate that the major source of humic-like compounds is microbial turnover of organic matter. The results of the present study show that the distribution of the humic-like DOM fractions is a balance between supply from continental run off......A fraction of dissolved organic matter (DOM) is able to fluoresce. This ability has been used in the present study to investigate the characteristics and distribution of different DOM fractions. A unique global dataset revealed seven different fluorescent fractions of DOM: two humic-like, four...... in the surface layer indicate the quantitative importance of photochemical degradation as a sink of the humic-like compounds. In the dark ocean (below 200 m), significant linear relationships between humic-like DOM fluorescence and microbial activity (apparent oxygen utilization, NO3- and PO43-) were found...

  1. Global warming and environmental contaminants in aquatic organisms: the need of the etho-toxicology approach.

    Manciocco, Arianna; Calamandrei, Gemma; Alleva, Enrico

    2014-04-01

    Environmental contaminants are associated with a wide spectrum of pathological effects. Temperature increase affects ambient distribution and toxicity of these chemicals in the water environment, representing a potentially emerging problem for aquatic species with short-, medium- and long-term repercussions on human health through the food chain. We assessed peer-reviewed literature, including primary studies, review articles and organizational reports available. We focused on studies concerning toxicity of environmental pollutants within a global warming scenario. Existing knowledge on the effects that the increase of water temperature in a contaminated situation has on physiological mechanisms of aquatic organisms is presented. Altogether we consider the potential consequences for the human beings due to fish and shellfish consumption. Finally, we propose an etho-toxicological approach to study the effects of toxicants in conditions of thermal increase, using aquatic organisms as experimental models under laboratory controlled conditions. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Organized Communities as a Hybrid Form of Data Sharing: Experiences from the Global STEP Project

    Isabell Stamm

    2018-01-01

    Full Text Available With this article, I explore a new way of how social scientists can share primary qualitative data with each other. More specifically, I examine organized research communities, which are small membership groups of scholars. This hybrid form of data sharing is positioned between informal sharing through collaboration and institutionalized sharing through accessing research archives. Using the global "Successful Transgenerational Entrepreneurship Practices" (STEP project as an example, I draw attention to the pragmatic practices of data sharing in such communities. Through ongoing negotiations, organized communities can, at least temporarily, put forward sharing policies and create a culture of data sharing that elevates the re-use of qualitative data while being mindful of the data's intersubjective and processual character.

  3. Characterizing Dissolved Organic Matter and Metabolites in an Actively Serpentinizing Ophiolite Using Global Metabolomics Techniques

    Seyler, L. M.; Rempfert, K. R.; Kraus, E. A.; Spear, J. R.; Templeton, A. S.; Schrenk, M. O.

    2017-12-01

    Environmental metabolomics is an emerging approach used to study ecosystem properties. Through bioinformatic comparisons to metagenomic data sets, metabolomics can be used to study microbial adaptations and responses to varying environmental conditions. Since the techniques are highly parallel to organic geochemistry approaches, metabolomics can also provide insight into biogeochemical processes. These analyses are a reflection of metabolic potential and intersection with other organisms and environmental components. Here, we used an untargeted metabolomics approach to characterize dissolved organic carbon and aqueous metabolites from groundwater obtained from an actively serpentinizing habitat. Serpentinites are known to support microbial communities that feed off of the products of serpentinization (such as methane and H2 gas), while adapted to harsh environmental conditions such as high pH and low DIC availability. However, the biochemistry of microbial populations that inhabit these environments are understudied and are complicated by overlapping biotic and abiotic processes. The aim of this study was to identify potential sources of carbon in an environment that is depleted of soluble inorganic carbon, and to characterize the flow of metabolites and describe overlapping biogenic and abiogenic processes impacting carbon cycling in serpentinizing rocks. We applied untargeted metabolomics techniques to groundwater taken from a series of wells drilled into the Semail Ophiolite in Oman.. Samples were analyzed via quadrupole time-of-flight liquid chromatography tandem mass spectrometry (QToF-LC/MS/MS). Metabolomes and metagenomic data were imported into Progenesis QI software for statistical analysis and correlation, and metabolic networks constructed using the Genome-Linked Application for Metabolic Maps (GLAMM), a web interface tool. Further multivariate statistical analyses and quality control was performed using EZinfo. Pools of dissolved organic carbon could

  4. Global distribution of dissolved organic matter along the aquatic continuum: Across rivers, lakes and oceans.

    Massicotte, Philippe; Asmala, Eero; Stedmon, Colin; Markager, Stiig

    2017-12-31

    Based on an extensive literature survey containing more than 12,000 paired measurements of dissolved organic carbon (DOC) concentrations and absorption of chromophoric dissolved organic matter (CDOM) distributed over four continents and seven oceans, we described the global distribution and transformation of dissolved organic matter (DOM) along the aquatic continuum across rivers and lakes to oceans. A strong log-linear relationship (R 2 =0.92) between DOC concentration and CDOM absorption at 350nm was observed at a global scale, but was found to be ecosystem-dependent at local and regional scales. Our results reveal that as DOM is transported towards the oceans, the robustness of the observed relation decreases rapidly (R 2 from 0.94 to 0.44) indicating a gradual decoupling between DOC and CDOM. This likely reflects the decreased connectivity between the landscape and DOM along the aquatic continuum. To support this hypothesis, we used the DOC-specific UV absorbance (SUVA) to characterize the reactivity of the DOM pool which decreased from 4.9 to 1.7m 2 × gC -1 along the aquatic continuum. Across the continuum, a piecewise linear regression showed that the observed decrease of SUVA occurred more rapidly in freshwater ecosystems compared to marine water ecosystems, suggesting that the different degradation processes act preferentially on CDOM rather than carbon content. The observed change in the DOM characteristics along the aquatic continuum also suggests that the terrestrial DOM pool is gradually becoming less reactive, which has profound consequences on cycling of organic carbon in aquatic ecosystems. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Modeling and experimental methods to probe the link between global transcription and spatial organization of chromosomes.

    K Venkatesan Iyer

    Full Text Available Genomes are spatially assembled into chromosome territories (CT within the nucleus of living cells. Recent evidences have suggested associations between three-dimensional organization of CTs and the active gene clusters within neighboring CTs. These gene clusters are part of signaling networks sharing similar transcription factor or other downstream transcription machineries. Hence, presence of such gene clusters of active signaling networks in a cell type may regulate the spatial organization of chromosomes in the nucleus. However, given the probabilistic nature of chromosome positions and complex transcription factor networks (TFNs, quantitative methods to establish their correlation is lacking. In this paper, we use chromosome positions and gene expression profiles in interphase fibroblasts and describe methods to capture the correspondence between their spatial position and expression. In addition, numerical simulations designed to incorporate the interacting TFNs, reveal that the chromosome positions are also optimized for the activity of these networks. These methods were validated for specific chromosome pairs mapped in two distinct transcriptional states of T-Cells (naïve and activated. Taken together, our methods highlight the functional coupling between topology of chromosomes and their respective gene expression patterns.

  6. A Global Data Analysis for Representing Sediment and Particulate Organic Carbon Yield in Earth System Models

    Tan, Zeli; Leung, L. Ruby; Li, Hongyi; Tesfa, Teklu; Vanmaercke, Matthias; Poesen, Jean; Zhang, Xuesong; Lu, Hui; Hartmann, Jens

    2017-12-01

    Although sediment yield (SY) from water erosion is ubiquitous and its environmental consequences are well recognized, its impacts on the global carbon cycle remain largely uncertain. This knowledge gap is partly due to the lack of soil erosion modeling in Earth System Models (ESMs), which are important tools used to understand the global carbon cycle and explore its changes. This study analyzed sediment and particulate organic carbon yield (CY) data from 1,081 and 38 small catchments (0.1-200 km2), respectively, in different environments across the globe. Using multiple statistical analysis techniques, we explored environmental factors and hydrological processes important for SY and CY modeling in ESMs. Our results show clear correlations of high SY with traditional agriculture, seismicity and heavy storms, as well as strong correlations between SY and annual peak runoff. These highlight the potential limitation of SY models that represent only interrill and rill erosion because shallow overland flow and rill flow have limited transport capacity due to their hydraulic geometry to produce high SY. Further, our results suggest that SY modeling in ESMs should be implemented at the event scale to produce the catastrophic mass transport during episodic events. Several environmental factors such as seismicity and land management that are often not considered in current catchment-scale SY models can be important in controlling global SY. Our analyses show that SY is likely the primary control on CY in small catchments and a statistically significant empirical relationship is established to calculate SY and CY jointly in ESMs.

  7. Methodological Framework for World Health Organization Estimates of the Global Burden of Foodborne Disease.

    Brecht Devleesschauwer

    Full Text Available The Foodborne Disease Burden Epidemiology Reference Group (FERG was established in 2007 by the World Health Organization to estimate the global burden of foodborne diseases (FBDs. This paper describes the methodological framework developed by FERG's Computational Task Force to transform epidemiological information into FBD burden estimates.The global and regional burden of 31 FBDs was quantified, along with limited estimates for 5 other FBDs, using Disability-Adjusted Life Years in a hazard- and incidence-based approach. To accomplish this task, the following workflow was defined: outline of disease models and collection of epidemiological data; design and completion of a database template; development of an imputation model; identification of disability weights; probabilistic burden assessment; and estimating the proportion of the disease burden by each hazard that is attributable to exposure by food (i.e., source attribution. All computations were performed in R and the different functions were compiled in the R package 'FERG'. Traceability and transparency were ensured by sharing results and methods in an interactive way with all FERG members throughout the process.We developed a comprehensive framework for estimating the global burden of FBDs, in which methodological simplicity and transparency were key elements. All the tools developed have been made available and can be translated into a user-friendly national toolkit for studying and monitoring food safety at the local level.

  8. Critical carbon input to maintain current soil organic carbon stocks in global wheat systems.

    Wang, Guocheng; Luo, Zhongkui; Han, Pengfei; Chen, Huansheng; Xu, Jingjing

    2016-01-13

    Soil organic carbon (SOC) dynamics in croplands is a crucial component of global carbon (C) cycle. Depending on local environmental conditions and management practices, typical C input is generally required to reduce or reverse C loss in agricultural soils. No studies have quantified the critical C input for maintaining SOC at global scale with high resolution. Such information will provide a baseline map for assessing soil C dynamics under potential changes in management practices and climate, and thus enable development of management strategies to reduce C footprint from farm to regional scales. We used the soil C model RothC to simulate the critical C input rates needed to maintain existing soil C level at 0.1° × 0.1° resolution in global wheat systems. On average, the critical C input was estimated to be 2.0 Mg C ha(-1) yr(-1), with large spatial variability depending on local soil and climatic conditions. Higher C inputs are required in wheat system of central United States and western Europe, mainly due to the higher current soil C stocks present in these regions. The critical C input could be effectively estimated using a summary model driven by current SOC level, mean annual temperature, precipitation, and soil clay content.

  9. Quantified carbon input for maintaining existing soil organic carbon stocks in global wheat systems

    Wang, G.

    2017-12-01

    Soil organic carbon (SOC) dynamics in croplands is a crucial component of global carbon (C) cycle. Depending on local environmental conditions and management practices, typical C input is generally required to reduce or reverse C loss in agricultural soils. No studies have quantified the critical C input for maintaining SOC at global scale with high resolution. Such information will provide a baseline map for assessing soil C dynamics under potential changes in management practices and climate, and thus enable development of management strategies to reduce C footprint from farm to regional scales. We used the soil C model RothC to simulate the critical C input rates needed to maintain existing soil C level at 0.1°× 0.1° resolution in global wheat systems. On average, the critical C input was estimated to be 2.0 Mg C ha-1 yr-1, with large spatial variability depending on local soil and climatic conditions. Higher C inputs are required in wheat system of central United States and western Europe, mainly due to the higher current soil C stocks present in these regions. The critical C input could be effectively estimated using a summary model driven by current SOC level, mean annual temperature, precipitation, and soil clay content.

  10. A Global Data Analysis for Representing Sediment and Particulate Organic Carbon Yield in Earth System Models

    Tan, Zeli [Pacific Northwest National Laboratory, Richland WA USA; Leung, L. Ruby [Pacific Northwest National Laboratory, Richland WA USA; Li, Hongyi [Montana State University, Bozeman MT USA; Tesfa, Teklu [Pacific Northwest National Laboratory, Richland WA USA; Vanmaercke, Matthias [Département de Géographie, Université de Liège, Liege Belgium; Poesen, Jean [Department of Earth and Environmental Sciences, Division of Geography, KU Leuven, Leuven Belgium; Zhang, Xuesong [Pacific Northwest National Laboratory, Richland WA USA; Lu, Hui [Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing China; Hartmann, Jens [Institute for Geology, Center for Earth System Research and Sustainability, Universität Hamburg, Hamburg Germany

    2017-12-01

    Although sediment yield (SY) from water erosion is ubiquitous and its environmental consequences are well recognized, its impacts on the global carbon cycle remain largely uncertain. This knowledge gap is partly due to the lack of soil erosion modeling in Earth System Models (ESMs), which are important tools used to understand the global carbon cycle and explore its changes. This study analyzed sediment and particulate organic carbon yield (CY) data from 1081 and 38 small catchments (0.1-200 km27 ), respectively, in different environments across the globe. Using multiple statistical analysis techniques, we explored environmental factors and hydrological processes important for SY and CY modeling in ESMs. Our results show clear correlations of high SY with traditional agriculture, seismicity and heavy storms, as well as strong correlations between SY and annual peak runoff. These highlight the potential limitation of SY models that represent only interrill and rill erosion because shallow overland flow and rill flow have limited transport capacity due to their hydraulic geometry to produce high SY. Further, our results suggest that SY modeling in ESMs should be implemented at the event scale to produce the catastrophic mass transport during episodic events. Several environmental factors such as seismicity and land management that are often not considered in current catchment-scale SY models can be important in controlling global SY. Our analyses show that SY is likely the primary control on CY in small catchments and a statistically significant empirical relationship is established to calculate SY and CY jointly in ESMs.

  11. Present status of research activities relating global warming problems in Japan (mainly MITI and relating organizations)

    Yokoyama, O.

    1993-12-31

    Japanese government has issued action program so called {open_quotes}Action Program to Arrest Global Warming{close_quotes} for preventing global warming at Oct., 1990. According to the program, CO{sub 2} emission should be stabilized on a per capita basis in the year 2000 and beyond at about same level as in 2000 by introducing several methods such as energy conservation, improvement of energy using efficiency, expanding use of renewable energy and so on. The basic concept, target and methods are summarized. At the same time, MITI published so called {open_quotes}New Earth 21{close_quotes} project which aims remedying the earth environment modified by human activities since industrial innovation began at about 200 years ago in coming 100 years. This plan proposed yearly step of research development of technology for mitigating CO{sub 2} emission. According to the MITI`s plan, 15 institutions belonging to AIST have carrying research for developing technology of reducing emission of CO{sub 2} and other greenhouse gases, with cooperation of other research organizations such as RITE (research Institute of Innovative Technology for Earth) and NEDO (New Energy and Industrial Technology Developing Organization). Time schedule of the research development by The New Earth 21 project is summarized in Table 2. Now, in Japan, many national institutions and universities, research works relating reduction and mitigation of GHG are carried out according to this guideline.

  12. Comparison of C. elegans and C. briggsae genome sequences reveals extensive conservation of chromosome organization and synteny.

    LaDeana W Hillier

    2007-07-01

    Full Text Available To determine whether the distinctive features of Caenorhabditis elegans chromosomal organization are shared with the C. briggsae genome, we constructed a single nucleotide polymorphism-based genetic map to order and orient the whole genome shotgun assembly along the six C. briggsae chromosomes. Although these species are of the same genus, their most recent common ancestor existed 80-110 million years ago, and thus they are more evolutionarily distant than, for example, human and mouse. We found that, like C. elegans chromosomes, C. briggsae chromosomes exhibit high levels of recombination on the arms along with higher repeat density, a higher fraction of intronic sequence, and a lower fraction of exonic sequence compared with chromosome centers. Despite extensive intrachromosomal rearrangements, 1:1 orthologs tend to remain in the same region of the chromosome, and colinear blocks of orthologs tend to be longer in chromosome centers compared with arms. More strikingly, the two species show an almost complete conservation of synteny, with 1:1 orthologs present on a single chromosome in one species also found on a single chromosome in the other. The conservation of both chromosomal organization and synteny between these two distantly related species suggests roles for chromosome organization in the fitness of an organism that are only poorly understood presently.

  13. Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms.

    Gasc, Cyrielle; Peyretaillade, Eric; Peyret, Pierre

    2016-06-02

    The recent expansion of next-generation sequencing has significantly improved biological research. Nevertheless, deep exploration of genomes or metagenomic samples remains difficult because of the sequencing depth and the associated costs required. Therefore, different partitioning strategies have been developed to sequence informative subsets of studied genomes. Among these strategies, hybridization capture has proven to be an innovative and efficient tool for targeting and enriching specific biomarkers in complex DNA mixtures. It has been successfully applied in numerous areas of biology, such as exome resequencing for the identification of mutations underlying Mendelian or complex diseases and cancers, and its usefulness has been demonstrated in the agronomic field through the linking of genetic variants to agricultural phenotypic traits of interest. Moreover, hybridization capture has provided access to underexplored, but relevant fractions of genomes through its ability to enrich defined targets and their flanking regions. Finally, on the basis of restricted genomic information, this method has also allowed the expansion of knowledge of nonreference species and ancient genomes and provided a better understanding of metagenomic samples. In this review, we present the major advances and discoveries permitted by hybridization capture and highlight the potency of this approach in all areas of biology. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. Genomic Organization and Physical Mapping of Tandemly Arranged Repetitive DNAs in Sterlet (Acipenser ruthenus).

    Biltueva, Larisa S; Prokopov, Dimitry Y; Makunin, Alexey I; Komissarov, Alexey S; Kudryavtseva, Anna V; Lemskaya, Natalya A; Vorobieva, Nadezhda V; Serdyukova, Natalia A; Romanenko, Svetlana A; Gladkikh, Olga L; Graphodatsky, Alexander S; Trifonov, Vladimir A

    2017-01-01

    Acipenseriformes represent a phylogenetically basal clade of ray-finned fish characterized by unusual genomic traits, including paleopolyploid states of extant genomes with high chromosome numbers and slow rates of molecular evolution. Despite a high interest in this fish group, only a limited number of studies have been accomplished on the isolation and characterization of repetitive DNA, karyotype standardization is not yet complete, and sex chromosomes are still to be identified. Here, we applied next-generation sequencing and cluster analysis to characterize major fractions of sterlet (Acipenser ruthenus) repetitive DNA. Using FISH, we mapped 16 tandemly arranged sequences on sterlet chromosomes and found them to be unevenly distributed in the genome with a tendency to cluster in particular regions. Some of the satellite DNAs might be used as specific markers to identify individual chromosomes and their paralogs, resulting in the unequivocal identification of at least 18 chromosome pairs. Our results provide an insight into the characteristic genomic distribution of the most common sterlet repetitive sequences. Biased accumulation of repetitive DNAs in particular chromosomes makes them especially interesting for further search for cryptic sex chromosomes. Future studies of these sequences in other acipenserid species will provide new perspectives regarding the evolution of repetitive DNA within the genomes of this fish order. © 2017 S. Karger AG, Basel.

  15. Globalization

    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...

  16. Globalization

    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...

  17. Global distribution and climate forcing of marine organic aerosol: 1. Model improvements and evaluation

    N. Meskhidze

    2011-11-01

    Full Text Available Marine organic aerosol emissions have been implemented and evaluated within the National Center of Atmospheric Research (NCAR's Community Atmosphere Model (CAM5 with the Pacific Northwest National Laboratory's 7-mode Modal Aerosol Module (MAM-7. Emissions of marine primary organic aerosols (POA, phytoplankton-produced isoprene- and monoterpenes-derived secondary organic aerosols (SOA and methane sulfonate (MS are shown to affect surface concentrations of organic aerosols in remote marine regions. Global emissions of submicron marine POA is estimated to be 7.9 and 9.4 Tg yr−1, for the Gantt et al. (2011 and Vignati et al. (2010 emission parameterizations, respectively. Marine sources of SOA and particulate MS (containing both sulfur and carbon atoms contribute an additional 0.2 and 5.1 Tg yr−1, respectively. Widespread areas over productive waters of the Northern Atlantic, Northern Pacific, and the Southern Ocean show marine-source submicron organic aerosol surface concentrations of 100 ng m−3, with values up to 400 ng m−3 over biologically productive areas. Comparison of long-term surface observations of water insoluble organic matter (WIOM with POA concentrations from the two emission parameterizations shows that despite revealed discrepancies (often more than a factor of 2, both Gantt et al. (2011 and Vignati et al. (2010 formulations are able to capture the magnitude of marine organic aerosol concentrations, with the Gantt et al. (2011 parameterization attaining better seasonality. Model simulations show that the mixing state of the marine POA can impact the surface number concentration of cloud condensation nuclei (CCN. The largest increases (up to 20% in CCN (at a supersaturation (S of 0.2% number concentration are obtained over biologically productive ocean waters when marine organic aerosol is assumed to be externally mixed with sea-salt. Assuming

  18. Organic carbon burial rates in mangrove sediments: Strengthening the global budget

    Breithaupt, Joshua L.; Smoak, Joseph M.; Smith, Thomas J., III; Sanders, Christian J.; Hoare, Armando

    2012-09-01

    Mangrove wetlands exist in the transition zone between terrestrial and marine environments and as such were historically overlooked in discussions of terrestrial and marine carbon cycling. In recent decades, mangroves have increasingly been credited with producing and burying large quantities of organic carbon (OC). The amount of available data regarding OC burial in mangrove soils has more than doubled since the last primary literature review (2003). This includes data from some of the largest, most developed mangrove forests in the world, providing an opportunity to strengthen the global estimate. First-time representation is now included for mangroves in Brazil, Colombia, Malaysia, Indonesia, China, Japan, Vietnam, and Thailand, along with additional data from Mexico and the United States. Our objective is to recalculate the centennial-scale burial rate of OC at both the local and global scales. Quantification of this rate enables better understanding of the current carbon sink capacity of mangroves as well as helps to quantify and/or validate the other aspects of the mangrove carbon budget such as import, export, and remineralization. Statistical analysis of the data supports use of the geometric mean as the most reliable central tendency measurement. Our estimate is that mangrove systems bury 163 (+40; -31) g OC m-2 yr-1 (95% C.I.). Globally, the 95% confidence interval for the annual burial rate is 26.1 (+6.3; -5.1) Tg OC. This equates to a burial fraction that is 42% larger than that of the most recent mangrove carbon budget (2008), and represents 10-15% of estimated annual mangrove production. This global rate supports previous conclusions that, on a centennial time scale, 8-15% of all OC burial in marine settings occurs in mangrove systems.

  19. The global re-cycling of persistent organic pollutants is strongly retarded by soils

    Ockenden, W.A.; Breivik, Knut; Meijer, S.N.; Steinnes, Eiliv; Sweetman, A.J.; Jones, K.C

    2003-01-01

    C-rich soils of the northern hemisphere appear to be serving as sinks for POPs and preventing their transfer to the Arctic. - 'Persistent organic pollutants' (POPs) are semi-volatile, mobile in the environment and bioaccumulate. Their toxicity and propensity for long-range atmospheric transport (LRAT) has led to international bans/restrictions on their use/release. LRAT of POPs may occur by a 'single hop' or repeated temperature-driven air-surface exchange. It has been hypothesised that this will result in global fractionation and distillation - with condensation and accumulation in polar regions. Polychlorinated biphenyls (PCBs)--industrial chemicals banned/restricted in the 1970s - provide a classic illustration of POP behaviour. A latitudinally-segmented global PCB inventory has been produced, which shows that {approx}86% of the 1.3x10{sup 6} tonnes produced was used in the temperate industrial zone of the northern hemisphere. A global survey of background surface soils gives evidence for 'fractionation' of PCBs. More significantly, however, very little of the total inventory has 'made the journey' via primary emission and/or air-surface exchange and LRAT out of the heavily populated source regions, in the 70 years since PCBs were first produced. Soils generally occlude PCBs, especially soils with dynamic turnover of C/bioturbation/burial mechanisms. This limits the fraction of PCBs available for repeated air-soil exchange. The forested soils of the northern hemisphere, and other C-rich soils, appear to be playing an important role in 'protecting' the Arctic from the advective supply of POPs. Whilst investigations on POPs in remote environments are important, it is imperative that researchers also seek to better understand their release from sources, persistence in source regions, and the significant loss mechanisms/global sinks of these compounds, if they wish to predict future trends.

  20. The global re-cycling of persistent organic pollutants is strongly retarded by soils

    Ockenden, W.A.; Breivik, Knut; Meijer, S.N.; Steinnes, Eiliv; Sweetman, A.J.; Jones, K.C.

    2003-01-01

    C-rich soils of the northern hemisphere appear to be serving as sinks for POPs and preventing their transfer to the Arctic. - 'Persistent organic pollutants' (POPs) are semi-volatile, mobile in the environment and bioaccumulate. Their toxicity and propensity for long-range atmospheric transport (LRAT) has led to international bans/restrictions on their use/release. LRAT of POPs may occur by a 'single hop' or repeated temperature-driven air-surface exchange. It has been hypothesised that this will result in global fractionation and distillation - with condensation and accumulation in polar regions. Polychlorinated biphenyls (PCBs)--industrial chemicals banned/restricted in the 1970s - provide a classic illustration of POP behaviour. A latitudinally-segmented global PCB inventory has been produced, which shows that ∼86% of the 1.3x10 6 tonnes produced was used in the temperate industrial zone of the northern hemisphere. A global survey of background surface soils gives evidence for 'fractionation' of PCBs. More significantly, however, very little of the total inventory has 'made the journey' via primary emission and/or air-surface exchange and LRAT out of the heavily populated source regions, in the 70 years since PCBs were first produced. Soils generally occlude PCBs, especially soils with dynamic turnover of C/bioturbation/burial mechanisms. This limits the fraction of PCBs available for repeated air-soil exchange. The forested soils of the northern hemisphere, and other C-rich soils, appear to be playing an important role in 'protecting' the Arctic from the advective supply of POPs. Whilst investigations on POPs in remote environments are important, it is imperative that researchers also seek to better understand their release from sources, persistence in source regions, and the significant loss mechanisms/global sinks of these compounds, if they wish to predict future trends

  1. Organic carbon burial rates in mangrove sediments: strengthening the global budget

    Breithaupt, J.; Smoak, Joseph M.; Smith, Thomas J.; Sanders, Christian J.; Hoare, Armando

    2012-01-01

    Mangrove wetlands exist in the transition zone between terrestrial and marine environments and as such were historically overlooked in discussions of terrestrial and marine carbon cycling. In recent decades, mangroves have increasingly been credited with producing and burying large quantities of organic carbon (OC). The amount of available data regarding OC burial in mangrove soils has more than doubled since the last primary literature review (2003). This includes data from some of the largest, most developed mangrove forests in the world, providing an opportunity to strengthen the global estimate. First-time representation is now included for mangroves in Brazil, Colombia, Malaysia, Indonesia, China, Japan, Vietnam, and Thailand, along with additional data from Mexico and the United States. Our objective is to recalculate the centennial-scale burial rate of OC at both the local and global scales. Quantification of this rate enables better understanding of the current carbon sink capacity of mangroves as well as helps to quantify and/or validate the other aspects of the mangrove carbon budget such as import, export, and remineralization. Statistical analysis of the data supports use of the geometric mean as the most reliable central tendency measurement. Our estimate is that mangrove systems bury 163 (+40; -31) g OC m-2 yr-1 (95% C.I.). Globally, the 95% confidence interval for the annual burial rate is 26.1 (+6.3; -5.1) Tg OC. This equates to a burial fraction that is 42% larger than that of the most recent mangrove carbon budget (2008), and represents 10–15% of estimated annual mangrove production. This global rate supports previous conclusions that, on a centennial time scale, 8–15% of all OC burial in marine settings occurs in mangrove systems.

  2. Complete nucleotide sequence and genome organization of Olive latent virus 3, a new putative member of the family Tymoviridae.

    Alabdullah, Abdulkader; Minafra, Angelantonio; Elbeaino, Toufic; Saponari, Maria; Savino, Vito; Martelli, Giovanni P

    2010-09-01

    The complete nucleotide sequence and the genome organization were determined of a putative new member of the family Tymoviridae, tentatively named Olive latent virus 3 (OLV-3), recovered in southern Italy from a symptomless olive tree. The sequenced ssRNA genome comprises 7148 nucleotides excluding the poly(A) tail and contains four open reading frames (ORFs). ORF1 encodes a polyprotein of 221.6kDa in size, containing the conserved signatures of the methyltransferase (MTR), papain-like protease (PRO), helicase (HEL) and RNA-dependent RNA polymerase (RdRp) domains of the replication-associated proteins of positive-strand RNA viruses. ORF2 overlaps completely ORF1 and encodes a putative protein of 43.33kDa showing limited sequence similarity with the putative movement protein of Maize rayado fino virus (MRFV). ORF3 codes for a protein with predicted molecular mass of 28.46kDa, identified as the coat protein (CP), whereas ORF4 overlaps ORF3 and encodes a putative protein of 16kDa with sequence similarity to the p16 and p31 proteins of Citrus sudden death-associated virus (CSDaV) and Grapevine fleck virus (GFkV), respectively. Within the family Tymoviridae, OLV-3 genome has the closest identity level (49-52%) with members of the genus Marafivirus, from which, however, it differs because of the diverse genome organization and the presence of a single type of CP subunits. Copyright (c) 2010 Elsevier B.V. All rights reserved.

  3. Travelling Policies and Global Buzzwords: How International Non-Governmental Organizations and Charities Spread the Word about Early Childhood in the Global South

    Penn, Helen

    2011-01-01

    This article is based on a web-search commissioned by an international charity to review the work of international non-governmental organizations (INGOs) and charities which promote and support early childhood education and care (ECEC) in the global South. The article examines examples of such initiatives. It is suggested that there is…

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

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

    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.

  6. A survey of HK, HPt, and RR domains and their organization in two-component systems and phosphorelay proteins of organisms with fully sequenced genomes

    Baldiri Salvado

    2015-08-01

    Full Text Available Two Component Systems and Phosphorelays (TCS/PR are environmental signal transduction cascades in prokaryotes and, less frequently, in eukaryotes. The internal domain organization of proteins and the topology of TCS/PR cascades play an important role in shaping the responses of the circuits. It is thus important to maintain updated censuses of TCS/PR proteins in order to identify the various topologies used by nature and enable a systematic study of the dynamics associated with those topologies. To create such a census, we analyzed the proteomes of 7,609 organisms from all domains of life with fully sequenced and annotated genomes. To begin, we survey each proteome searching for proteins containing domains that are associated with internal signal transmission within TCS/PR: Histidine Kinase (HK, Response Regulator (RR and Histidine Phosphotranfer (HPt domains, and analyze how these domains are arranged in the individual proteins. Then, we find all types of operon organization and calculate how much more likely are proteins that contain TCS/PR domains to be coded by neighboring genes than one would expect from the genome background of each organism. Finally, we analyze if the fusion of domains into single TCS/PR proteins is more frequently observed than one might expect from the background of each proteome. We find 50 alternative ways in which the HK, HPt, and RR domains are observed to organize into single proteins. In prokaryotes, TCS/PR coding genes tend to be clustered in operons. 90% of all proteins identified in this study contain just one of the three domains, while 8% of the remaining proteins combine one copy of an HK, a RR, and/or an HPt domain. In eukaryotes, 25% of all TCS/PR proteins have more than one domain. These results might have implications for how signals are internally transmitted within TCS/PR cascades. These implications could explain the selection of the various designs in alternative circumstances.

  7. Organization and Evolution of Subtelomeric Satellite Repeats in the Potato Genome

    Torres, A.T.; Gong, Z.; Iovene, M.; Hirsch, C.D.; Buell, C.R.; Bryan, G.J.; Novák, Petr; Macas, Jiří; Jiang, J.

    2011-01-01

    Roč. 1, July 2011 (2011), s. 85-92 ISSN 2160-1836 R&D Projects: GA MŠk(CZ) LH11058 Institutional research plan: CEZ:AV0Z50510513 Keywords : Satellite sequences * Potato genome * Repeats Subject RIV: EB - Genetics ; Molecular Biology

  8. Functional organization of the genome may shape the species boundary in the house mouse

    Janoušek, Václav; Munclinger, P.; Wang, L.; Teeter, K. C.; Tucker, P. K.

    2015-01-01

    Roč. 32, č. 5 (2015), s. 1208-1220 ISSN 0737-4038 R&D Projects: GA MŠk EE2.3.20.0303 Institutional support: RVO:68081766 Keywords : hybrid zone * mouse genome * speciation Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 13.649, year: 2015

  9. Molecular cloning and genomic organization of an allatostatin preprohormone from Drosophila melanogaster

    Lenz, C; Williamson, M; Grimmelikhuijzen, C J

    2000-01-01

    The insect allatostatins are neurohormones, acting on the corpora allata (where they block the release of juvenile hormone) and on the insect gut (where they block smooth muscle contraction). We screened the "Drosophila Genome Project" database with electronic sequences corresponding to various i...

  10. Modeling soil organic carbon dynamics and their driving factors in the main global cereal cropping systems

    Wang, Guocheng; Zhang, Wen; Sun, Wenjuan; Li, Tingting; Han, Pengfei

    2017-10-01

    Changes in the soil organic carbon (SOC) stock are determined by the balance between the carbon input from organic materials and the output from the decomposition of soil C. The fate of SOC in cropland soils plays a significant role in both sustainable agricultural production and climate change mitigation. The spatiotemporal changes of soil organic carbon in croplands in response to different carbon (C) input management and environmental conditions across the main global cereal systems were studied using a modeling approach. We also identified the key variables that drive SOC changes at a high spatial resolution (0.1° × 0.1°) and over a long timescale (54 years from 1961 to 2014). A widely used soil C turnover model (RothC) and state-of-the-art databases of soil and climate variables were used in the present study. The model simulations suggested that, on a global average, the cropland SOC density increased at annual rates of 0.22, 0.45 and 0.69 Mg C ha-1 yr-1 under crop residue retention rates of 30, 60 and 90 %, respectively. Increasing the quantity of C input could enhance soil C sequestration or reduce the rate of soil C loss, depending largely on the local soil and climate conditions. Spatially, under a specific crop residue retention rate, relatively higher soil C sinks were found across the central parts of the USA, western Europe, and the northern regions of China. Relatively smaller soil C sinks occurred in the high-latitude regions of both the Northern and Southern hemispheres, and SOC decreased across the equatorial zones of Asia, Africa and America. We found that SOC change was significantly influenced by the crop residue retention rate (linearly positive) and the edaphic variable of initial SOC content (linearly negative). Temperature had weak negative effects, and precipitation had significantly negative impacts on SOC changes. The results can help guide carbon input management practices to effectively mitigate climate change through soil C

  11. Modeling soil organic carbon dynamics and their driving factors in the main global cereal cropping systems

    G. Wang

    2017-10-01

    Full Text Available Changes in the soil organic carbon (SOC stock are determined by the balance between the carbon input from organic materials and the output from the decomposition of soil C. The fate of SOC in cropland soils plays a significant role in both sustainable agricultural production and climate change mitigation. The spatiotemporal changes of soil organic carbon in croplands in response to different carbon (C input management and environmental conditions across the main global cereal systems were studied using a modeling approach. We also identified the key variables that drive SOC changes at a high spatial resolution (0.1°  ×  0.1° and over a long timescale (54 years from 1961 to 2014. A widely used soil C turnover model (RothC and state-of-the-art databases of soil and climate variables were used in the present study. The model simulations suggested that, on a global average, the cropland SOC density increased at annual rates of 0.22, 0.45 and 0.69 Mg C ha−1 yr−1 under crop residue retention rates of 30, 60 and 90 %, respectively. Increasing the quantity of C input could enhance soil C sequestration or reduce the rate of soil C loss, depending largely on the local soil and climate conditions. Spatially, under a specific crop residue retention rate, relatively higher soil C sinks were found across the central parts of the USA, western Europe, and the northern regions of China. Relatively smaller soil C sinks occurred in the high-latitude regions of both the Northern and Southern hemispheres, and SOC decreased across the equatorial zones of Asia, Africa and America. We found that SOC change was significantly influenced by the crop residue retention rate (linearly positive and the edaphic variable of initial SOC content (linearly negative. Temperature had weak negative effects, and precipitation had significantly negative impacts on SOC changes. The results can help guide carbon input management practices to

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

    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.

  13. Genomic sequence, organization and characteristics of a new nucleopolyhedrovirus isolated from Clanis bilineata larva

    Wang Yong

    2009-02-01

    Full Text Available Abstract Background Baculoviruses are well known for their potential as biological agents for controlling agricultural and forest pests. They are also widely used as expression vectors in molecular cloning studies. The genome sequences of 48 baculoviruses are currently available in NCBI databases. As the number of sequenced viral genomes increases, it is important for the authors to present sufficiently detailed analyses and annotations to advance understanding of them. In this study, the complete genome of Clanis bilineata nucleopolyhedrovirus (ClbiNPV has been sequenced and analyzed in order to understand this virus better. Results The genome of ClbiNPV contains 135,454 base pairs (bp with a G+C content of 37%, and 139 putative open reading frames (ORFs of at least 150 nucleotides. One hundred and twenty-six of these ORFs have homologues with other baculovirus genes while the other 13 are unique to ClbiNPV. The 30 baculovirus core genes are all present in ClbiNPV. Phylogenetic analysis based on the combined pif-2 and lef-8 sequences places ClbiNPV in the Group II Alphabaculoviruses. This result is consistent with the absence of gp64 from the ClbiNPV genome and the presence instead of a fusion protein gene, characteristic of Group II. Blast searches revealed that ClbiNPV encodes a photolyase-like gene sequence, which has a 1-bp deletion when compared with photolyases of other baculoviruses. This deletion disrupts the sequence into two small photolyase ORFs, designated Clbiphr-1 and Clbiphr-2, which correspond to the CPD-DNA photolyase and FAD-binding domains of photolyases, respectively. Conclusion ClbiNPV belongs to the Group II Alphabaculoviruses and is most closely related to OrleNPV, LdMNPV, TnSNPV, EcobNPV and ChchNPV. It contains a variant DNA photolyase gene, which only exists in ChchNPV, TnSNPV and SpltGV among the baculoviruses.

  14. Understanding the development of human bladder cancer by using a whole-organ genomic mapping strategy.

    Majewski, Tadeusz; Lee, Sangkyou; Jeong, Joon; Yoon, Dong-Sup; Kram, Andrzej; Kim, Mi-Sook; Tuziak, Tomasz; Bondaruk, Jolanta; Lee, Sooyong; Park, Weon-Seo; Tang, Kuang S; Chung, Woonbok; Shen, Lanlan; Ahmed, Saira S; Johnston, Dennis A; Grossman, H Barton; Dinney, Colin P; Zhou, Jain-Hua; Harris, R Alan; Snyder, Carrie; Filipek, Slawomir; Narod, Steven A; Watson, Patrice; Lynch, Henry T; Gazdar, Adi; Bar-Eli, Menashe; Wu, Xifeng F; McConkey, David J; Baggerly, Keith; Issa, Jean-Pierre; Benedict, William F; Scherer, Steven E; Czerniak, Bogdan

    2008-07-01

    The search for the genomic sequences involved in human cancers can be greatly facilitated by maps of genomic imbalances identifying the involved chromosomal regions, particularly those that participate in the development of occult preneoplastic conditions that progress to clinically aggressive invasive cancer. The integration of such regions with human genome sequence variation may provide valuable clues about their overall structure and gene content. By extension, such knowledge may help us understand the underlying genetic components involved in the initiation and progression of these cancers. We describe the development of a genome-wide map of human bladder cancer that tracks its progression from in situ precursor conditions to invasive disease. Testing for allelic losses using a genome-wide panel of 787 microsatellite markers was performed on multiple DNA samples, extracted from the entire mucosal surface of the bladder and corresponding to normal urothelium, in situ preneoplastic lesions, and invasive carcinoma. Using this approach, we matched the clonal allelic losses in distinct chromosomal regions to specific phases of bladder neoplasia and produced a detailed genetic map of bladder cancer development. These analyses revealed three major waves of genetic changes associated with growth advantages of successive clones and reflecting a stepwise conversion of normal urothelial cells into cancer cells. The genetic changes map to six regions at 3q22-q24, 5q22-q31, 9q21-q22, 10q26, 13q14, and 17p13, which may represent critical hits driving the development of bladder cancer. Finally, we performed high-resolution mapping using single nucleotide polymorphism markers within one region on chromosome 13q14, containing the model tumor suppressor gene RB1, and defined a minimal deleted region associated with clonal expansion of in situ neoplasia. These analyses provided new insights on the involvement of several non-coding sequences mapping to the region and identified

  15. Drivers of fluorescent dissolved organic matter in the global epipelagic ocean

    Catalá, T. S.

    2016-03-24

    Fluorescent dissolved organic matter (FDOM) in open surface waters (< 200 m) of the Atlantic, Pacific, and Indian oceans was analysed by excitation-emission matrix (EEM) spectroscopy and parallel factor analysis (PARAFAC). A four-component PARAFAC model was fit to the EEMs, which included two humic- (C1 and C2) and two amino acid-like (C3 and C4) components previously identified in ocean waters. Generalized-additive models (GAMs) were used to explore the environmental factors that drive the global distribution of these PARAFAC components. The explained variance for the humic-like components was substantially larger (> 70%) than for the amino acid-like components (< 35%). The environmental variables exhibiting the largest effect on the global distribution of C1 and C2 were apparent oxygen utilisation followed by chlorophyll a. Positive non-linear relationships between both predictor variables and the two humic-like PARAFAC components suggest that their distribution are biologically controlled. Compared with the dark ocean (> 200 m), the relationships of C1 and C2 with AOU indicate a higher C1/AOU and C2/AOU ratios of the humic-like substances in the dark ocean than in the surface ocean where a net effect of photobleaching is also detected. C3 (tryptophan-like) and C4 (tyrosine-like) variability was mostly dictated by salinity (S), by means of positive non-linear relationships, suggesting a primary physical control of their distributions at the global surface ocean scale that could be related to the changing evaporation-precipitation regime. Remarkably, bacterial biomass (BB) only contributed to explain a minor part of the variability of C1 and C4.

  16. Direct extraction of genomic DNA from maize with aqueous ionic liquid buffer systems for applications in genetically modified organisms analysis.

    Gonzalez García, Eric; Ressmann, Anna K; Gaertner, Peter; Zirbs, Ronald; Mach, Robert L; Krska, Rudolf; Bica, Katharina; Brunner, Kurt

    2014-12-01

    To date, the extraction of genomic DNA is considered a bottleneck in the process of genetically modified organisms (GMOs) detection. Conventional DNA isolation methods are associated with long extraction times and multiple pipetting and centrifugation steps, which makes the entire procedure not only tedious and complicated but also prone to sample cross-contamination. In recent times, ionic liquids have emerged as innovative solvents for biomass processing, due to their outstanding properties for dissolution of biomass and biopolymers. In this study, a novel, easily applicable, and time-efficient method for the direct extraction of genomic DNA from biomass based on aqueous-ionic liquid solutions was developed. The straightforward protocol relies on extraction of maize in a 10 % solution of ionic liquids in aqueous phosphate buffer for 5 min at room temperature, followed by a denaturation step at 95 °C for 10 min and a simple filtration to remove residual biopolymers. A set of 22 ionic liquids was tested in a buffer system and 1-ethyl-3-methylimidazolium dimethylphosphate, as well as the environmentally benign choline formate, were identified as ideal candidates. With this strategy, the quality of the genomic DNA extracted was significantly improved and the extraction protocol was notably simplified compared with a well-established method.

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

    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

  18. Monitoring the World Health Organization Global Target 2025 for Exclusive Breastfeeding: Experience From the United States.

    Gupta, Priya M; Perrine, Cria G; Chen, Jian; Elam-Evans, Laurie D; Flores-Ayala, Rafael

    2017-08-01

    Exclusive breastfeeding under 6 months, calculated from a single 24-hour recall among mothers of children 0 to 5 months of age, is a World Health Organization (WHO) indicator used to monitor progress on the 2025 global breastfeeding target. Many upper-middle-income and high-income countries, including the United States, do not have estimates for this indicator. Research aim: To describe the prevalence of exclusive breastfeeding under 6 months in the United States. We used a single 24-hour dietary recall from the National Health and Nutrition Examination Survey 2009-2012 to calculate the prevalence of exclusive breastfeeding under 6 months. We discuss our results in the context of routine breastfeeding surveillance, which is reported from a national survey with different methodology. Among children younger than 6 months, 24.4%, 95% confidence interval [17.6, 31.1], were exclusively breastfed the previous day. To our knowledge, this is the first estimate of the WHO indicator of exclusive breastfeeding under 6 months for the United States. This study supports the global surveillance and data strategy for reporting to the WHO on the 2025 target for exclusive breastfeeding.

  19. Data resource profile: the World Health Organization Study on global AGEing and adult health (SAGE).

    Kowal, Paul; Chatterji, Somnath; Naidoo, Nirmala; Biritwum, Richard; Fan, Wu; Lopez Ridaura, Ruy; Maximova, Tamara; Arokiasamy, Perianayagam; Phaswana-Mafuya, Nancy; Williams, Sharon; Snodgrass, J Josh; Minicuci, Nadia; D'Este, Catherine; Peltzer, Karl; Boerma, J Ties

    2012-12-01

    Population ageing is rapidly becoming a global issue and will have a major impact on health policies and programmes. The World Health Organization's Study on global AGEing and adult health (SAGE) aims to address the gap in reliable data and scientific knowledge on ageing and health in low- and middle-income countries. SAGE is a longitudinal study with nationally representative samples of persons aged 50+ years in China, Ghana, India, Mexico, Russia and South Africa, with a smaller sample of adults aged 18-49 years in each country for comparisons. Instruments are compatible with other large high-income country longitudinal ageing studies. Wave 1 was conducted during 2007-2010 and included a total of 34 124 respondents aged 50+ and 8340 aged 18-49. In four countries, a subsample consisting of 8160 respondents participated in Wave 1 and the 2002/04 World Health Survey (referred to as SAGE Wave 0). Wave 2 data collection will start in 2012/13, following up all Wave 1 respondents. Wave 3 is planned for 2014/15. SAGE is committed to the public release of study instruments, protocols and meta- and micro-data: access is provided upon completion of a Users Agreement available through WHO's SAGE website (www.who.int/healthinfo/systems/sage) and WHO's archive using the National Data Archive application (http://apps.who.int/healthinfo/systems/surveydata).

  20. Global Nursing Issues and Development: Analysis of World Health Organization Documents.

    Wong, Frances Kam Yuet; Liu, Huaping; Wang, Hui; Anderson, Debra; Seib, Charrlotte; Molasiotis, Alex

    2015-11-01

    To analyze World Health Organization (WHO) documents to identify global nursing issues and development. Qualitative content analysis. Documents published by the six WHO regions between 2007 and 2012 and with key words related to nurse/midwife or nursing/midwifery were included. Themes, categories, and subcategories were derived. The final coding reached 80% agreement among three independent coders, and the final coding for the discrepant coding was reached by consensus. Thirty-two documents from the regions of Europe (n = 19), the Americas (n = 6), the Western Pacific (n = 4), Africa (n = 1), the Eastern Mediterranean (n = 1), and Southeast Asia (n = 1) were examined. A total of 385 units of analysis dispersed in 31 subcategories under four themes were derived. The four themes derived (number of unit of analysis, %) were Management & Leadership (206, 53.5), Practice (75, 19.5), Education (70, 18.2), and Research (34, 8.8). The key nursing issues of concern at the global level are workforce, the impacts of nursing in health care, professional status, and education of nurses. International alliances can help advance nursing, but the visibility of nursing in the WHO needs to be strengthened. Organizational leadership is important in order to optimize the use of nursing competence in practice and inform policy makers regarding the value of nursing to promote people's health. © 2015 Sigma Theta Tau International.

  1. Network organization is globally atypical in autism: A graph theory study of intrinsic functional connectivity.

    Keown, Christopher L; Datko, Michael C; Chen, Colleen P; Maximo, José Omar; Jahedi, Afrooz; Müller, Ralph-Axel

    2017-01-01

    Despite abundant evidence of brain network anomalies in autism spectrum disorder (ASD), findings have varied from broad functional underconnectivity to broad overconnectivity. Rather than pursuing overly simplifying general hypotheses ('under' vs. 'over'), we tested the hypothesis of atypical network distribution in ASD (i.e., participation of unusual loci in distributed functional networks). We used a selective high-quality data subset from the ABIDE datashare (including 111 ASD and 174 typically developing [TD] participants) and several graph theory metrics. Resting state functional MRI data were preprocessed and analyzed for detection of low-frequency intrinsic signal correlations. Groups were tightly matched for available demographics and head motion. As hypothesized, the Rand Index (reflecting how similar network organization was to a normative set of networks) was significantly lower in ASD than TD participants. This was accounted for by globally reduced cohesion and density, but increased dispersion of networks. While differences in hub architecture did not survive correction, rich club connectivity (among the hubs) was increased in the ASD group. Our findings support the model of reduced network integration (connectivity with networks) and differentiation (or segregation; based on connectivity outside network boundaries) in ASD. While the findings applied at the global level, they were not equally robust across all networks and in one case (greater cohesion within ventral attention network in ASD) even reversed.

  2. Competence development organizations in project management on the basis of genomic model methodologies

    Бушуев, Сергей Дмитриевич; Рогозина, Виктория Борисовна; Ярошенко, Юрий Федерович

    2013-01-01

    The matrix technology for identification of organisational competencies in project management is presented in the article. Matrix elements are the components of organizational competence in the field of project management and project management methodology represented in the structure of the genome. The matrix model of competence in the framework of the adopted methodologies and scanning method for identifying organizational competences formalised. Proposed methods for building effective proj...

  3. Genome sequence and organization of a nucleopolyhedrovirus isolated from the smaller tea tortrix, Adoxophyes honmai

    Nakai, Madoka; Goto, Chie; Kang, Won Kyung; Shikata, Masamitsu; Luque, Teresa; Kunimi, Yasuhisa

    2003-01-01

    Adoxophyes honmai nucleopolyhedrovirus (AdhoNPV) has a distinctive pathology in A. honmai larvae, killing the host more slowly than other NPVs. To further understand the pathology of AdhoNPV, its genome was completely sequenced and compared with those of other baculoviruses. The AdhoNPV genome is 113,220 bp, with a G + C content of 35.6%. It contains 125 putative open reading frames (ORFs), of which 8 are unique to AdhoNPV, and 4 homologous regions. The other 117 ORFs display similarity to previously characterized baculovirus genes involved in early and late gene expression, DNA replication, and structural and auxiliary functions. The phylogenetic position of AdhoNPV, in relation to 15 other baculoviruses whose genomes have been completely sequenced, was assessed by three different analyses: gene sequence, gene order, and gene content. Although gene content analysis failed to support the group II NPVs, phylogenetic trees based on gene sequence and gene order showed AdhoNPV to be closely related to the group II NPVs

  4. Organization of the mitochondrial genomes of whiteflies, aphids, and psyllids (Hemiptera, Sternorrhyncha

    Baumann Paul

    2004-08-01

    Full Text Available Abstract Background With some exceptions, mitochondria within the class Insecta have the same gene content, and generally, a similar gene order allowing the proposal of an ancestral gene order. The principal exceptions are several orders within the Hemipteroid assemblage including the order Thysanoptera, a sister group of the order Hemiptera. Within the Hemiptera, there are available a number of completely sequenced mitochondrial genomes that have a gene order similar to that of the proposed ancestor. None, however, are available from the suborder Sternorryncha that includes whiteflies, psyllids and aphids. Results We have determined the complete nucleotide sequence of the mitochondrial genomes of six species of whiteflies, one psyllid and one aphid. Two species of whiteflies, one psyllid and one aphid have mitochondrial genomes with a gene order very similar to that of the proposed insect ancestor. The remaining four species of whiteflies had variations in the gene order. In all cases, there was the excision of a DNA fragment encoding for cytochrome oxidase subunit III(COIII-tRNAgly-NADH dehydrogenase subunit 3(ND3-tRNAala-tRNAarg-tRNAasn from the ancestral position between genes for ATP synthase subunit 6 and NADH dehydrogenase subunit 5. Based on the position in which all or part of this fragment was inserted, the mitochondria could be subdivided into four different gene arrangement types. PCR amplification spanning from COIII to genes outside the inserted region and sequence determination of the resulting fragments, indicated that different whitefly species could be placed into one of these arrangement types. A phylogenetic analysis of 19 whitefly species based on genes for mitochondrial cytochrome b, NADH dehydrogenase subunit 1, and 16S ribosomal DNA as well as cospeciating endosymbiont 16S and 23S ribosomal DNA indicated a clustering of species that corresponded to the gene arrangement types. Conclusions In whiteflies, the region of the

  5. Cultura organizacional brasileira pós-globalização: global ou local? Brazilian cultural organization in post-globalization: global or local?

    Rebeca Alves Chu

    2008-10-01

    Full Text Available Um dos grandes desafios para pesquisadores de gestão internacional é compreender a diversidade institucional e cultural dos ambientes de negócios nacionais. Para responder a tal desafio, os pesquisadores recorrem a agrupamentos e generalizações. Embora tal recurso metodológico apresente inegáveis méritos, pode prover quadros relativamente pobres sobre a realidade de cada país. Este artigo procura endereçar essa lacuna. Realizamos uma pesquisa exploratória sobre os traços da cultura organizacional brasileira hoje, após 17 anos de abertura econômica e transformações institucionais, as quais geraram profundos impactos na sociedade e nas organizações. Exploramos a literatura existente sobre traços da cultura organizacional brasileira e apresentamos um estudo de campo baseado em entrevistas com profissionais estrangeiros que trabalham no Brasil e com profissionais brasileiros que já trabalharam fora do país. A comparação entre os estudos anteriores e o presente estudo revela um quadro híbrido, transitório e com ressignificações, típico de um período de transição marcado pela convivência entre traços pré-globalização e traços pós-globalização.A great challenge facing international management researchers is understanding the institutional and cultural diversity of national business environments. In response to this challenge, researchers often resort to pooling and generalizations. Despite the undeniable merits of such a methodological approach, it may provide relatively poor descriptions of each country's reality. The purpose of this article is to address this gap. We carried out an exploratory research of Brazil's organizational culture today, after 17 years of economic openness and institutional changes that have led to deep impacts on society and organizations. We explored the existing literature on traits of Brazil's organizational culture and present a field study based on interviews with foreign

  6. DOMINO: development of informative molecular markers for phylogenetic and genome-wide population genetic studies in non-model organisms.

    Frías-López, Cristina; Sánchez-Herrero, José F; Guirao-Rico, Sara; Mora, Elisa; Arnedo, Miquel A; Sánchez-Gracia, Alejandro; Rozas, Julio

    2016-12-15

    The development of molecular markers is one of the most important challenges in phylogenetic and genome wide population genetics studies, especially in studies with non-model organisms. A highly promising approach for obtaining suitable markers is the utilization of genomic partitioning strategies for the simultaneous discovery and genotyping of a large number of markers. Unfortunately, not all markers obtained from these strategies provide enough information for solving multiple evolutionary questions at a reasonable taxonomic resolution. We have developed Development Of Molecular markers In Non-model Organisms (DOMINO), a bioinformatics tool for informative marker development from both next generation sequencing (NGS) data and pre-computed sequence alignments. The application implements popular NGS tools with new utilities in a highly versatile pipeline specifically designed to discover or select personalized markers at different levels of taxonomic resolution. These markers can be directly used to study the taxa surveyed for their design, utilized for further downstream PCR amplification in a broader set taxonomic scope, or exploited as suitable templates to bait design for target DNA enrichment techniques. We conducted an exhaustive evaluation of the performance of DOMINO via computer simulations and illustrate its utility to find informative markers in an empirical dataset. DOMINO is freely available from www.ub.edu/softevol/domino CONTACT: elsanchez@ub.edu or jrozas@ub.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  7. Human β satellite DNA: Genomic organization and sequence definition of a class of highly repetitive tandem DNA

    Waye, J.S.; Willard, H.F.

    1989-01-01

    The authors describe a class of human repetitive DNA, called β satellite, that, at a most fundamental level, exists as tandem arrays of diverged ∼68-base-pair monomer repeat units. The monomer units are organized as distinct subsets, each characterized by a multimeric higher-order repeat unit that is tandemly reiterated and represents a recent unit of amplification. They have cloned, characterized, and determined the sequence of two β satellite higher-order repeat units: one located on chromosome 9, the other on the acrocentric chromosomes (13, 14, 15, 21, and 22) and perhaps other sites in the genome. Analysis by pulsed-field gel electrophoresis reveals that these tandem arrays are localized in large domains that are marked by restriction fragment length polymorphisms. In total, β-satellite sequences comprise several million base pairs of DNA in the human genome. Analysis of this DNA family should permit insights into the nature of chromosome-specific and nonspecific modes of satellite DNA evolution and provide useful tools for probing the molecular organization and concerted evolution of the acrocentric chromosomes

  8. Global assessment of soil organic carbon stocks and spatial distribution of histosols: the Machine Learning approach

    Hengl, Tomislav

    2016-04-01

    Preliminary results of predicting distribution of soil organic soils (Histosols) and soil organic carbon stock (in tonnes per ha) using global compilations of soil profiles (about 150,000 points) and covariates at 250 m spatial resolution (about 150 covariates; mainly MODIS seasonal land products, SRTM DEM derivatives, climatic images, lithological and land cover and landform maps) are presented. We focus on using a data-driven approach i.e. Machine Learning techniques that often require no knowledge about the distribution of the target variable or knowledge about the possible relationships. Other advantages of using machine learning are (DOI: 10.1371/journal.pone.0125814): All rules required to produce outputs are formalized. The whole procedure is documented (the statistical model and associated computer script), enabling reproducible research. Predicted surfaces can make use of various information sources and can be optimized relative to all available quantitative point and covariate data. There is more flexibility in terms of the spatial extent, resolution and support of requested maps. Automated mapping is also more cost-effective: once the system is operational, maintenance and production of updates are an order of magnitude faster and cheaper. Consequently, prediction maps can be updated and improved at shorter and shorter time intervals. Some disadvantages of automated soil mapping based on Machine Learning are: Models are data-driven and any serious blunders or artifacts in the input data can propagate to order-of-magnitude larger errors than in the case of expert-based systems. Fitting machine learning models is at the order of magnitude computationally more demanding. Computing effort can be even tens of thousands higher than if e.g. linear geostatistics is used. Many machine learning models are fairly complex often abstract and any interpretation of such models is not trivial and require special multidimensional / multivariable plotting and data mining

  9. Evolution of organic carbon burial in the Global Ocean during the Neogene

    LI, Z.; Zhang, Y.

    2017-12-01

    Although only a small fraction of the organic carbon (OC) that rains from surface waters is eventually buried in the sediments, it is a process that controls the organic sub-cycle of the long-term carbon cycle, and the key for atmospheric O2, CO2 and nutrient cycling. Here we constrain the spatiotemporal variability of OC burial by quantifying the total organic carbon (TOC) mass accumulation rate (MAR) over the Neogene (23.0-2.6 Ma) by compiling the TOC, age model and sediment density data from sites retrieved by the Deep Sea Drilling Program, Ocean Drilling Program, and Integrated Ocean Drilling Program. We screened all available sites which yielded 80 sites with adequate data quality, covering all major ocean basins and sedimentary depositional environments. All age models are updated to the GTS 2012 timescale so the TOC MAR records from different sites are comparable. Preliminary results show a clear early Miocene peak of OC burial in many sites related to high sediment flux which might reflect the orogenic uplift and/or glacier erosion. Places that receive high influx of terrigenous inputs become "hotspots" for Neogene burial of OC. At "open ocean" sites, OC burial seems to be more impacted by marine productivity changes, with a pronounced increase during the middle Miocene "Monterey Formation" and late Miocene - early Pliocene "Biogenic Bloom". Upon the completion of the data collection, we will further explore the regional and global OC burial in the context of tectonic uplift, climate change and the evolution of primary producers and consumers during the last 23 million years of Earth history.

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

    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.

    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

    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. Analysis Of Segmental Duplications In The Pig Genome Based On Next-Generation Sequencing

    Fadista, João; Bendixen, Christian

    Segmental duplications are >1kb segments of duplicated DNA present in a genome with high sequence identity (>90%). They are associated with genomic rearrangements and provide a significant source of gene and genome evolution within mammalian genomes. Although segmental duplications have been...... extensively studied in other organisms, its analysis in pig has been hampered by the lack of a complete pig genome assembly. By measuring the depth of coverage of Illumina whole-genome shotgun sequencing reads of the Tabasco animal aligned to the latest pig genome assembly (Sus scrofa 10 – based also...... and their associated copy number alterations, focusing on the global organization of these segments and their possible functional significance in porcine phenotypes. This work provides insights into mammalian genome evolution and generates a valuable resource for porcine genomics research...

  14. Great expectations for the World Health Organization: a Framework Convention on Global Health to achieve universal health coverage.

    Ooms, G; Marten, R; Waris, A; Hammonds, R; Mulumba, M; Friedman, E A

    2014-02-01

    Establishing a reform agenda for the World Health Organization (WHO) requires understanding its role within the wider global health system and the purposes of that wider global health system. In this paper, the focus is on one particular purpose: achieving universal health coverage (UHC). The intention is to describe why achieving UHC requires something like a Framework Convention on Global Health (FCGH) that have been proposed elsewhere,(1) why WHO is in a unique position to usher in an FCGH, and what specific reforms would help enable WHO to assume this role. Copyright © 2013 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

  15. The Genome of Tolypocladium inflatum: Evolution, Organization, and Expression of the Cyclosporin Biosynthetic Gene Cluster

    Bushley, Kathryn E.; Raja, Rajani; Jaiswal, Pankaj; Cumbie, Jason S.; Nonogaki, Mariko; Boyd, Alexander E.; Owensby, C. Alisha; Knaus, Brian J.; Elser, Justin; Miller, Daniel; Di, Yanming; McPhail, Kerry L.; Spatafora, Joseph W.

    2013-01-01

    The ascomycete fungus Tolypocladium inflatum, a pathogen of beetle larvae, is best known as the producer of the immunosuppressant drug cyclosporin. The draft genome of T. inflatum strain NRRL 8044 (ATCC 34921), the isolate from which cyclosporin was first isolated, is presented along with comparative analyses of the biosynthesis of cyclosporin and other secondary metabolites in T. inflatum and related taxa. Phylogenomic analyses reveal previously undetected and complex patterns of homology between the nonribosomal peptide synthetase (NRPS) that encodes for cyclosporin synthetase (simA) and those of other secondary metabolites with activities against insects (e.g., beauvericin, destruxins, etc.), and demonstrate the roles of module duplication and gene fusion in diversification of NRPSs. The secondary metabolite gene cluster responsible for cyclosporin biosynthesis is described. In addition to genes necessary for cyclosporin biosynthesis, it harbors a gene for a cyclophilin, which is a member of a family of immunophilins known to bind cyclosporin. Comparative analyses support a lineage specific origin of the cyclosporin gene cluster rather than horizontal gene transfer from bacteria or other fungi. RNA-Seq transcriptome analyses in a cyclosporin-inducing medium delineate the boundaries of the cyclosporin cluster and reveal high levels of expression of the gene cluster cyclophilin. In medium containing insect hemolymph, weaker but significant upregulation of several genes within the cyclosporin cluster, including the highly expressed cyclophilin gene, was observed. T. inflatum also represents the first reference draft genome of Ophiocordycipitaceae, a third family of insect pathogenic fungi within the fungal order Hypocreales, and supports parallel and qualitatively distinct radiations of insect pathogens. The T. inflatum genome provides additional insight into the evolution and biosynthesis of cyclosporin and lays a foundation for further investigations of the role

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

    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.

  17. Evaluation of factors controlling global secondary organic aerosol production from cloud processes

    C. He

    2013-02-01

    Full Text Available Secondary organic aerosols (SOA exert a significant influence on ambient air quality and regional climate. Recent field, laboratorial and modeling studies have confirmed that in-cloud processes contribute to a large fraction of SOA production with large space-time heterogeneity. This study evaluates the key factors that govern the production of cloud-process SOA (SOAcld on a global scale based on the GFDL coupled chemistry-climate model AM3 in which full cloud chemistry is employed. The association between SOAcld production rate and six factors (i.e., liquid water content (LWC, total carbon chemical loss rate (TCloss, temperature, VOC/NOx, OH, and O3 is examined. We find that LWC alone determines the spatial pattern of SOAcld production, particularly over the tropical, subtropical and temperate forest regions, and is strongly correlated with SOAcld production. TCloss ranks the second and mainly represents the seasonal variability of vegetation growth. Other individual factors are essentially uncorrelated spatiotemporally to SOAcld production. We find that the rate of SOAcld production is simultaneously determined by both LWC and TCloss, but responds linearly to LWC and nonlinearly (or concavely to TCloss. A parameterization based on LWC and TCloss can capture well the spatial and temporal variability of the process-based SOAcld formation (R2 = 0.5 and can be easily applied to global three dimensional models to represent the SOA production from cloud processes.

  18. FIREX (Fire Influence on Regional and Global Environments Experiment): Measurements of Nitrogen Containing Volatile Organic Compounds

    Warneke, C.; Schwarz, J. P.; Yokelson, R. J.; Roberts, J. M.; Koss, A.; Coggon, M.; Yuan, B.; Sekimoto, K.

    2017-12-01

    A combination of a warmer, drier climate with fire-control practices over the last century have produced a situation in which we can expect more frequent fires and fires of larger magnitude in the Western U.S. and Canada. There are urgent needs to better understand the impacts of wildfire and biomass burning (BB) on the atmosphere and climate system, and for policy-relevant science to aid in the process of managing fires. The FIREX (Fire Influence on Regional and Global Environment Experiment) research effort is a multi-year, multi-agency measurement campaign focused on the impact of BB on climate and air quality from western North American wild fires, where research takes place on scales ranging from the flame-front to the global atmosphere. FIREX includes methods development and small- and large-scale laboratory and field experiments. FIREX will include: emission factor measurements from typical North American fuels in the fire science laboratory in Missoula, Montana; mobile laboratory deployments; ground site measurements at sites influenced by BB from several western states. The main FIREX effort will be a large field study with multiple aircraft and mobile labs in the fire season of 2019. One of the main advances of FIREX is the availability of various new measurement techniques that allows for smoke evaluation in unprecedented detail. The first major effort of FIREX was the fire science laboratory measurements in October 2016, where a large number of previously understudied Nitrogen containing volatile organic compounds (NVOCs) were measured using H3O+CIMS and I-CIMS instruments. The contribution of NVOCs to the total reactive Nitrogen budget and the relationship to the Nitrogen content of the fuel are investigated.

  19. Effects of screenhouse cultivation and organic materials incorporation on global warming potential in rice fields.

    Xu, Guochun; Liu, Xin; Wang, Qiangsheng; Xiong, Ruiheng; Hang, Yuhao

    2017-03-01

    Global rice production will be increasingly challenged by providing healthy food for a growing population at minimal environmental cost. In this study, a 2-year field experiment was conducted to investigate the effects of a novel rice cultivation mode (screenhouse cultivation, SHC) and organic material (OM) incorporation (wheat straw and wheat straw-based biogas residue) on methane (CH 4 ) and nitrous oxide (N 2 O) emissions and rice yields. In addition, the environmental factors and soil properties were also determined. Relative to the traditional open-field cultivation (OFC), SHC decreased the CH 4 and N 2 O emissions by 6.58-18.73 and 2.51-21.35%, respectively, and the global warming potential (GWP) was reduced by 6.49-18.65%. This trend was mainly because of lower soil temperature and higher soil redox potential in SHC. Although the rice grain yield for SHC were reduced by 2.51-4.98% compared to the OFC, the CH 4 emissions and GWP per unit of grain yield (yield-scaled CH 4 emissions and GWP) under SHC were declined. Compared to use of inorganic fertilizer only (IN), combining inorganic fertilizer with wheat straw (WS) or wheat straw-based biogas residue (BR) improved rice grain yield by 2.12-4.10 and 4.68-5.89%, respectively. However, OM incorporation enhanced CH 4 emissions and GWP, leading to higher yield-scaled CH 4 emissions and GWP in WS treatment. Due to rice yield that is relatively high, there was no obvious effect of BR treatment on them. These findings suggest that apparent environmental benefit can be realized by applying SHC and fermenting straw aerobically before its incorporation.

  20. De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis.

    Nowrousian, Minou; Stajich, Jason E; Chu, Meiling; Engh, Ines; Espagne, Eric; Halliday, Karen; Kamerewerd, Jens; Kempken, Frank; Knab, Birgit; Kuo, Hsiao-Che; Osiewacz, Heinz D; Pöggeler, Stefanie; Read, Nick D; Seiler, Stephan; Smith, Kristina M; Zickler, Denise; Kück, Ulrich; Freitag, Michael

    2010-04-08

    Filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. Thus, it is not surprising that genomes for more than 100 filamentous fungi have been sequenced, most of them by Sanger sequencing. While next-generation sequencing techniques have revolutionized genome resequencing, e.g. for strain comparisons, genetic mapping, or transcriptome and ChIP analyses, de novo assembly of eukaryotic genomes still presents significant hurdles, because of their large size and stretches of repetitive sequences. Filamentous fungi contain few repetitive regions in their 30-90 Mb genomes and thus are suitable candidates to test de novo genome assembly from short sequence reads. Here, we present a high-quality draft sequence of the Sordaria macrospora genome that was obtained by a combination of Illumina/Solexa and Roche/454 sequencing. Paired-end Solexa sequencing of genomic DNA to 85-fold coverage and an additional 10-fold coverage by single-end 454 sequencing resulted in approximately 4 Gb of DNA sequence. Reads were assembled to a 40 Mb draft version (N50 of 117 kb) with the Velvet assembler. Comparative analysis with Neurospora genomes increased the N50 to 498 kb. The S. macrospora genome contains even fewer repeat regions than its closest sequenced relative, Neurospora crassa. Comparison with genomes of other fungi showed that S. macrospora, a model organism for morphogenesis and meiosis, harbors duplications of several genes involved in self/nonself-recognition. Furthermore, S. macrospora contains more polyketide biosynthesis genes than N. crassa. Phylogenetic analyses suggest that some of these genes may have been acquired by horizontal gene transfer from a distantly related ascomycete group. Our study shows that, for typical filamentous fungi, de novo assembly of genomes from short sequence reads alone is feasible, that a mixture of Solexa and 454 sequencing substantially improves the assembly, and that the resulting data can be used for

  1. De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis.

    Minou Nowrousian

    2010-04-01

    Full Text Available Filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. Thus, it is not surprising that genomes for more than 100 filamentous fungi have been sequenced, most of them by Sanger sequencing. While next-generation sequencing techniques have revolutionized genome resequencing, e.g. for strain comparisons, genetic mapping, or transcriptome and ChIP analyses, de novo assembly of eukaryotic genomes still presents significant hurdles, because of their large size and stretches of repetitive sequences. Filamentous fungi contain few repetitive regions in their 30-90 Mb genomes and thus are suitable candidates to test de novo genome assembly from short sequence reads. Here, we present a high-quality draft sequence of the Sordaria macrospora genome that was obtained by a combination of Illumina/Solexa and Roche/454 sequencing. Paired-end Solexa sequencing of genomic DNA to 85-fold coverage and an additional 10-fold coverage by single-end 454 sequencing resulted in approximately 4 Gb of DNA sequence. Reads were assembled to a 40 Mb draft version (N50 of 117 kb with the Velvet assembler. Comparative analysis with Neurospora genomes increased the N50 to 498 kb. The S. macrospora genome contains even fewer repeat regions than its closest sequenced relative, Neurospora crassa. Comparison with genomes of other fungi showed that S. macrospora, a model organism for morphogenesis and meiosis, harbors duplications of several genes involved in self/nonself-recognition. Furthermore, S. macrospora contains more polyketide biosynthesis genes than N. crassa. Phylogenetic analyses suggest that some of these genes may have been acquired by horizontal gene transfer from a distantly related ascomycete group. Our study shows that, for typical filamentous fungi, de novo assembly of genomes from short sequence reads alone is feasible, that a mixture of Solexa and 454 sequencing substantially improves the assembly, and that the resulting data

  2. Global impacts of the meat trade on in-stream organic river pollution: the importance of spatially distributed hydrological conditions

    Wen, Yingrong; Schoups, Gerrit; van de Giesen, Nick

    2018-01-01

    In many regions of the world, intensive livestock farming has become a significant source of organic river pollution. As the international meat trade is growing rapidly, the environmental impacts of meat production within one country can occur either domestically or internationally. The goal of this paper is to quantify the impacts of the international meat trade on global organic river pollution at multiple scales (national, regional and gridded). Using the biological oxygen demand (BOD) as an overall indicator of organic river pollution, we compute the spatially distributed organic pollution in global river networks with and without a meat trade, where the without-trade scenario assumes that meat imports are replaced by local production. Our analysis reveals a reduction in the livestock population and production of organic pollutants at the global scale as a result of the international meat trade. However, the actual environmental impact of trade, as quantified by in-stream BOD concentrations, is negative; i.e. we find a slight increase in polluted river segments. More importantly, our results show large spatial variability in local (grid-scale) impacts that do not correlate with local changes in BOD loading, which illustrates: (1) the significance of accounting for the spatial heterogeneity of hydrological processes along river networks, and (2) the limited value of looking at country-level or global averages when estimating the actual impacts of trade on the environment.

  3. A global organism detection and monitoring system for non-native species

    Graham, J.; Newman, G.; Jarnevich, C.; Shory, R.; Stohlgren, T.J.

    2007-01-01

    Harmful invasive non-native species are a significant threat to native species and ecosystems, and the costs associated with non-native species in the United States is estimated at over $120 Billion/year. While some local or regional databases exist for some taxonomic groups, there are no effective geographic databases designed to detect and monitor all species of non-native plants, animals, and pathogens. We developed a web-based solution called the Global Organism Detection and Monitoring (GODM) system to provide real-time data from a broad spectrum of users on the distribution and abundance of non-native species, including attributes of their habitats for predictive spatial modeling of current and potential distributions. The four major subsystems of GODM provide dynamic links between the organism data, web pages, spatial data, and modeling capabilities. The core survey database tables for recording invasive species survey data are organized into three categories: "Where, Who & When, and What." Organisms are identified with Taxonomic Serial Numbers from the Integrated Taxonomic Information System. To allow users to immediately see a map of their data combined with other user's data, a custom geographic information system (GIS) Internet solution was required. The GIS solution provides an unprecedented level of flexibility in database access, allowing users to display maps of invasive species distributions or abundances based on various criteria including taxonomic classification (i.e., phylum or division, order, class, family, genus, species, subspecies, and variety), a specific project, a range of dates, and a range of attributes (percent cover, age, height, sex, weight). This is a significant paradigm shift from "map servers" to true Internet-based GIS solutions. The remainder of the system was created with a mix of commercial products, open source software, and custom software. Custom GIS libraries were created where required for processing large datasets

  4. The lemur revolution starts now: the genomic coming of age for a non-model organism.

    Yoder, Anne D

    2013-02-01

    Morris Goodman was a revolutionary. Together with a mere handful of like-minded scientists, Morris established himself as a leader in the molecular phylogenetic revolution of the 1960s. The effects of this revolution are most evident in this journal, which he founded in 1992. Happily for lemur biologists, one of Morris Goodman's primary interests was in reconstructing the phylogeny of the primates, including the tooth-combed Lorisifomes of Africa and Asia, and the Lemuriformes of Madagascar (collectively referred to as the suborder Strepsirrhini). This paper traces the development of molecular phylogenetic and evolutionary genetic trends and methods over the 50-year expanse of Morris Goodman's career, particularly as they apply to our understanding of lemuriform phylogeny, biogeography, and biology. Notably, this perspective reveals that the lemuriform genome is sufficiently rich in phylogenetic signal such that the very earliest molecular phylogenetic studies - many of which were conducted by Goodman himself - have been validated by contemporary studies that have exploited advanced computational methods applied to phylogenomic scale data; studies that were beyond imagining in the earliest days of phylogeny reconstruction. Nonetheless, the frontier still beckons. New technologies for gathering and analyzing genomic data will allow investigators to build upon what can now be considered a nearly-known phylogeny of the Lemuriformes in order to ask innovative questions about the evolutionary mechanisms that generate and maintain the extraordinary breadth and depth of biological diversity within this remarkable clade of primates. Copyright © 2012 Elsevier Inc. All rights reserved.

  5. Avian papillomaviruses: the parrot Psittacus erithacus papillomavirus (PePV genome has a unique organization of the early protein region and is phylogenetically related to the chaffinch papillomavirus

    Jenson A Bennett

    2002-07-01

    Full Text Available Abstract Background An avian papillomavirus genome has been cloned from a cutaneous exophytic papilloma from an African grey parrot (Psittacus erithacus. The nucleotide sequence, genome organization, and phylogenetic position of the Psittacus erithacus papillomavirus (PePV were determined. This PePV sequence represents the first complete avian papillomavirus genome defined. Results The PePV genome (7304 basepairs differs from other papillomaviruses, in that it has a unique organization of the early protein region lacking classical E6 and E7 open reading frames. Phylogenetic comparison of the PePV sequence with partial E1 and L1 sequences of the chaffinch (Fringilla coelebs papillomavirus (FPV reveals that these two avian papillomaviruses form a monophyletic cluster with a common branch that originates near the unresolved center of the papillomavirus evolutionary tree. Conclusions The PePV genome has a unique layout of the early protein region which represents a novel prototypic genomic organization for avian papillomaviruses. The close relationship between PePV and FPV, and between their Psittaciformes and Passeriformes hosts, supports the hypothesis that papillomaviruses have co-evolved and speciated together with their host species throughout evolution.

  6. Building a Sustainable Global Surgery Nonprofit Organization at an Academic Institution.

    Frisella, Margaret M

    Surgical Outreach for the Americas is a 501(c)3 nonprofit organization providing surgical care to those in need in developing countries of the Western Hemisphere. Every year since its inception in 2008, teams of surgeons, nurses, and allied health professionals have traveled to areas of need and performed primarily hernia repair surgeries for those without access to affordable health care. Surgical Outreach for the Americas (SOfA) began as a general concept based on World Health Organization statistics claiming that 11% of the global burden of disease can be resolved via surgery. Armed with this information, a group of compassionate and selfless health care professionals planned the first trip, to the Dominican Republic, in January 2009. Building on what was first just an ambition to help others, we now also train surgeons, surgery residents, and nurses in the countries we serve. To date, SOfA has successfully treated 734 patients, with 899 total surgical procedures performed (693 of these under general anesthesia). These procedures include inguinal hernia, umbilical hernia, testicular masses, orchiectomies, and various general surgical procedures. Through the efforts of a great many talented individuals and robust fundraising efforts, the SOfA message continues to gain momentum. SOfA not only considers the health and well-being of the disadvantaged through capacity-building efforts but strives to educate and improve the skills of health care professionals in the countries we visit. Our goal is to increase the number of missions each year and begin a 2-fold educational program that (a) provides surgical resident education through participation in mission work and (b) provides local surgeon education in the areas served. Copyright © 2016. Published by Elsevier Inc.

  7. Enzymology under global change: organic nitrogen turnover in alpine and sub-Arctic soils

    Weedon, J.T.; Aerts, R.; Kowalchuk, G.A.; van Bodegom, P.M.

    2011-01-01

    Understanding global change impacts on the globally important carbon storage in alpine, Arctic and sub-Arctic soils requires knowledge of the mechanisms underlying the balance between plant primary productivity and decomposition. Given that nitrogen availability limits both processes, understanding

  8. Enzymology under global change: organic nitrogen turnover in alpine and sub-Arctic soils.

    Weedon, J.T.; Aerts, R.; Kowalchuk, G.A.; van Bodegom, P.M.

    2011-01-01

    Understanding global change impacts on the globally important carbon storage in alpine, Arctic and sub-Arctic soils requires knowledge of the mechanisms underlying the balance between plant primary productivity and decomposition. Given that nitrogen availability limits both processes, understanding

  9. 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?

    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.

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

    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

  11. Linkage of genomic biomarkers to whole organism endpoints in a Toxicity Identification Evaluation (TIE).

    Aquatic organisms are exposed to many toxic chemicals and interpreting the cause and effect relationships between occurrence and impairment is difficult. Toxicity Identification Evaluation (TIE) provides a systematic approach for identifying responsible toxicants. TIE relies on ...

  12. Global organic carbon emissions from primary sources from 1960 to 2009

    Huang, Ye; Shen, Huizhong; Chen, Yilin; Zhong, Qirui; Chen, Han; Wang, Rong; Shen, Guofeng; Liu, Junfeng; Li, Bengang; Tao, Shu

    2015-12-01

    In an attempt to reduce uncertainty, global organic carbon (OC) emissions from a total of 70 sources were compiled at 0.1° × 0.1° resolution for 2007 (PKU-OC-2007) and country scale from 1960 to 2009. The compilation took advantage of a new fuel-consumption data product (PKU-Fuel-2007) and a series of newly published emission factors (EFOC) in developing countries. The estimated OC emissions were 32.9 Tg (24.1-50.6 Tg as interquartile range), of which less than one third was anthropogenic in origin. Uncertainty resulted primarily from variations in EFOC. Asia, Africa, and South America had high emissions mainly because of residential biomass fuel burning or wildfires. Per-person OC emission in rural areas was three times that of urban areas because of the relatively high EFOC of residential solid fuels. Temporal trend of anthropogenic OC emissions depended on rural population, and was influenced primarily by residential crop residue and agricultural waste burning. Both the OC/PM2.5 ratio and emission intensity, defined as quantity of OC emissions per unit of fuel consumption for all sources, of anthropogenic OC followed a decreasing trend, indicating continuous improvement in combustion efficiency and control measures.

  13. Greenhouse gas fluxes from agricultural soils under organic and non-organic management — A global meta-analysis

    Skinner, Colin; Gattinger, Andreas; Muller, Adrian; Mäder, Paul; Fließbach, Andreas; Stolze, Matthias; Ruser, Reiner; Niggli, Urs

    2014-01-01

    It is anticipated that organic farming systems provide benefits concerning soil conservation and climate protection. A literature search on measured soil-derived greenhouse gas (GHG) (nitrous oxide and methane) fluxes under organic and non-organic management from farming system comparisons was conducted and followed by a meta-analysis. Up to date only 19 studies based on field measurements could be retrieved. Based on 12 studies that cover annual measurements, it appeared with a high significance that area-scaled nitrous oxide emissions from organically managed soils are 492 ± 160 kg CO 2 eq. ha −1 a −1 lower than from non-organically managed soils. For arable soils the difference amounts to 497 ± 162 kg CO 2 eq. ha −1 a −1 . However, yield-scaled nitrous oxide emissions are higher by 41 ± 34 kg CO 2 eq. t −1 DM under organic management (arable and use). To equalize this mean difference in yield-scaled nitrous oxide emissions between both farming systems, the yield gap has to be less than 17%. Emissions from conventionally managed soils seemed to be influenced mainly by total N inputs, whereas for organically managed soils other variables such as soil characteristics seemed to be more important. This can be explained by the higher bioavailability of the synthetic N fertilisers in non-organic farming systems while the necessary mineralisation of the N sources under organic management leads to lower and retarded availability. Furthermore, a higher methane uptake of 3.2 ± 2.5 kg CO 2 eq. ha −1 a −1 for arable soils under organic management can be observed. Only one comparative study on rice paddies has been published up to date. All 19 retrieved studies were conducted in the Northern hemisphere under temperate climate. Further GHG flux measurements in farming system comparisons are required to confirm the results and close the existing knowledge gaps. - Highlights: • Lower area-scaled nitrous oxide emissions from soils managed organically compared

  14. Global patterns of organic carbon export and sequestration in the ocean (Arne Richter Award for Outstanding Young Scientists)

    Henson, S.; Sanders, R.; Madsen, E.; Le Moigne, F.; Quartly, G.

    2012-04-01

    A major term in the global carbon cycle is the ocean's biological carbon pump which is dominated by sinking of small organic particles from the surface ocean to its interior. Here we examine global patterns in particle export efficiency (PEeff), the proportion of primary production that is exported from the surface ocean, and transfer efficiency (Teff), the fraction of exported organic matter that reaches the deep ocean. This is achieved through extrapolating from in situ estimates of particulate organic carbon export to the global scale using satellite-derived data. Global scale estimates derived from satellite data show, in keeping with earlier studies, that PEeff is high at high latitudes and low at low latitudes, but that Teff is low at high latitudes and high at low latitudes. However, in contrast to the relationship observed for deep biomineral fluxes in previous studies, we find that Teff is strongly negatively correlated with opal export flux from the upper ocean, but uncorrelated with calcium carbonate export flux. We hypothesise that the underlying factor governing the spatial patterns observed in Teff is ecosystem function, specifically the degree of recycling occurring in the upper ocean, rather than the availability of calcium carbonate for ballasting. Finally, our estimate of global integrated carbon export is only 50% of previous estimates. The lack of consensus amongst different methodologies on the strength of the biological carbon pump emphasises that our knowledge of a major planetary carbon flux remains incomplete.

  15. Tracking the Global Distribution of Persistent Organic Pollutants Accounting for E-Waste Exports to Developing Regions.

    Breivik, Knut; Armitage, James M; Wania, Frank; Sweetman, Andrew J; Jones, Kevin C

    2016-01-19

    Elevated concentrations of various industrial-use Persistent Organic Pollutants (POPs), such as polychlorinated biphenyls (PCBs), have been reported in some developing areas in subtropical and tropical regions known to be destinations of e-waste. We used a recent inventory of the global generation and exports of e-waste to develop various global scale emission scenarios for industrial-use organic contaminants (IUOCs). For representative IUOCs (RIUOCs), only hypothetical emissions via passive volatilization from e-waste were considered whereas for PCBs, historical emissions throughout the chemical life-cycle (i.e., manufacturing, use, disposal) were included. The environmental transport and fate of RIUOCs and PCBs were then simulated using the BETR Global 2.0 model. Export of e-waste is expected to increase and sustain global emissions beyond the baseline scenario, which assumes no export. A comparison between model predictions and observations for PCBs in selected recipient regions generally suggests a better agreement when exports are accounted for. This study may be the first to integrate the global transport of IUOCs in waste with their long-range transport in air and water. The results call for integrated chemical management strategies on a global scale.

  16. From the chromatin interaction network to the organization of the human genome into replication N/U-domains

    Boulos, Rasha E; Julienne, Hanna; Baker, Antoine; Jensen, Pablo; Arneodo, Alain; Audit, Benjamin; Chen, Chun-Long; D'Aubenton-Carafa, Yves; Thermes, Claude; Petryk, Nataliya; Kahli, Malik; Hyrien, Olivier; Goldar, Arach

    2014-01-01

    The three-dimensional (3D) architecture of the mammalian nucleus is now being unraveled thanks to the recent development of chromatin conformation capture (3C) technologies. Here we report the results of a combined multiscale analysis of genome-wide mean replication timing and chromatin conformation data that reveal some intimate relationships between chromatin folding and human DNA replication. We previously described megabase replication N/U-domains as mammalian multiorigin replication units, and showed that their borders are ‘master’ replication initiation zones that likely initiate cascades of origin firing responsible for the stereotypic replication of these domains. Here, we demonstrate that replication N/U-domains correspond to the structural domains of self-interacting chromatin, and that their borders act as insulating regions both in high-throughput 3C (Hi-C) data and high-resolution 3C (4C) experiments. Further analyses of Hi-C data using a graph-theoretical approach reveal that N/U-domain borders are long-distance, interconnected hubs of the chromatin interaction network. Overall, these results and the observation that a well-defined ordering of chromatin states exists from N/U-domain borders to centers suggest that ‘master’ replication initiation zones are at the heart of a high-order, epigenetically controlled 3D organization of the human genome. (paper)

  17. Improving the representation of secondary organic aerosol (SOA in the MOZART-4 global chemical transport model

    A. Mahmud

    2013-07-01

    Full Text Available The secondary organic aerosol (SOA module in the Model for Ozone and Related Chemical Tracers, version 4 (MOZART-4 was updated by replacing existing two-product (2p parameters with those obtained from two-product volatility basis set (2p-VBS fits (MZ4-C1, and by treating SOA formation from the following additional volatile organic compounds (VOCs: isoprene, propene and lumped alkenes (MZ4-C2. Strong seasonal and spatial variations in global SOA distributions were demonstrated, with significant differences in the predicted concentrations between the base case and updated model simulations. Updates to the model resulted in significant increases in annual average SOA mass concentrations, particularly for the MZ4-C2 simulation in which the additional SOA precursor VOCs were treated. Annual average SOA concentrations predicted by the MZ4-C2 simulation were 1.00 ± 1.04 μg m−3 in South America, 1.57 ± 1.88 μg m−3 in Indonesia, 0.37 ± 0.27 μg m−3 in the USA, and 0.47 ± 0.29 μg m−3 in Europe with corresponding increases of 178, 406, 311 and 292% over the base-case simulation, respectively, primarily due to inclusion of isoprene. The increases in predicted SOA mass concentrations resulted in corresponding increases in SOA contributions to annual average total aerosol optical depth (AOD by ~ 1–6%. Estimated global SOA production was 5.8, 6.6 and 19.1 Tg yr−1 with corresponding burdens of 0.22, 0.24 and 0.59 Tg for the base-case, MZ4-C1 and MZ4-C2 simulations, respectively. The predicted SOA budgets fell well within reported ranges for comparable modeling studies, 6.7 to 96 Tg yr−1, but were lower than recently reported observationally constrained values, 50 to 380 Tg yr−1. For MZ4-C2, simulated SOA concentrations at the surface also were in reasonable agreement with comparable modeling studies and observations. Total organic aerosol (OA mass concentrations at the surface, however, were slightly over-predicted in Europe, Amazonian

  18. Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle.

    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.

  19. Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products.

    Holst-Jensen, Arne; Spilsberg, Bjørn; Arulandhu, Alfred J; Kok, Esther; Shi, Jianxin; Zel, Jana

    2016-07-01

    The emergence of high-throughput, massive or next-generation sequencing technologies has created a completely new foundation for molecular analyses. Various selective enrichment processes are commonly applied to facilitate detection of predefined (known) targets. Such approaches, however, inevitably introduce a bias and are prone to miss unknown targets. Here we review the application of high-throughput sequencing technologies and the preparation of fit-for-purpose whole genome shotgun sequencing libraries for the detection and characterization of genetically modified and derived products. The potential impact of these new sequencing technologies for the characterization, breeding selection, risk assessment, and traceability of genetically modified organisms and genetically modified products is yet to be fully acknowledged. The published literature is reviewed, and the prospects for future developments and use of the new sequencing technologies for these purposes are discussed.

  20. Biological Parameters and Molecular Markers of Clone CL Brener - The Reference Organism of the Trypanosoma cruzi Genome Project

    Bianca Zingales

    1997-11-01

    Full Text Available Clone CL Brener is the reference organism used in the Trypanosoma cruzi Genome Project. Some biological parameters of CL Brener were determined: (a the doubling time of epimastigote forms cultured in liver infusion-tryptose (LIT medium at 28oC is 58±13 hr; (b differentiation of epimastigotes to metacyclic trypomastigotes is obtained by incubation in LIT-20% Grace´s medium; (c trypomastigotes infect mammalian cultured cells and perform the complete intracellular cycle at 33 and 37oC; (d blood forms are highly infective to mice; (e blood forms are susceptible to nifurtimox and benznidazole. The molecular typing of CL Brener has been determined: (a isoenzymatic profiles are characteristic of zymodeme ZB; (b PCR amplification of a 24Sa ribosomal RNA sequence indicates it belongs to T. cruzi lineage 1; (c schizodeme, randomly amplified polymorphic DNA (RAPD and DNA fingerprinting analyses were performed

  1. Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua

    Mittelholzer Christian

    2009-12-01

    Full Text Available Abstract Background Marine fishes have been shown to display low levels of genetic structuring and associated high levels of gene flow, suggesting shallow evolutionary trajectories and, possibly, limited or lacking adaptive divergence among local populations. We investigated variation in 98 gene-associated single nucleotide polymorphisms (SNPs for evidence of selection in local populations of Atlantic cod (Gadus morhua L. across the species distribution. Results Our global genome scan analysis identified eight outlier gene loci with very high statistical support, likely to be subject to directional selection in local demes, or closely linked to loci under selection. Likewise, on a regional south/north transect of central and eastern Atlantic populations, seven loci displayed strongly elevated levels of genetic differentiation. Selection patterns among populations appeared to be relatively widespread and complex, i.e. outlier loci were generally not only associated with one of a few divergent local populations. Even on a limited geographical scale between the proximate North Sea and Baltic Sea populations four loci displayed evidence of adaptive evolution. Temporal genome scan analysis applied to DNA from archived otoliths from a Faeroese population demonstrated stability of the intra-population variation over 24 years. An exploratory landscape genetic analysis was used to elucidate potential effects of the most likely environmental factors responsible for the signatures of local adaptation. We found that genetic variation at several of the outlier loci was better correlated with temperature and/or salinity conditions at spawning grounds at spawning time than with geographic distance per se. Conclusion These findings illustrate that adaptive population divergence may indeed be prevalent despite seemingly high levels of gene flow, as found in most marine fishes. Thus, results have important implications for our understanding of the interplay of

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

    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...

  3. The politics of agenda setting at the global level: key informant interviews regarding the International Labour Organization Decent Work Agenda.

    Di Ruggiero, Erica; Cohen, Joanna E; Cole, Donald C

    2014-07-01

    Global labour markets continue to undergo significant transformations resulting from socio-political instability combined with rises in structural inequality, employment insecurity, and poor working conditions. Confronted by these challenges, global institutions are providing policy guidance to protect and promote the health and well-being of workers. This article provides an account of how the International Labour Organization's Decent Work Agenda contributes to the work policy agendas of the World Health Organization and the World Bank. This qualitative study involved semi-structured interviews with representatives from three global institutions--the International Labour Organization (ILO), the World Health Organization and the World Bank. Of the 25 key informants invited to participate, 16 took part in the study. Analysis for key themes was followed by interpretation using selected agenda setting theories. Interviews indicated that through the Decent Work Agenda, the International Labour Organization is shaping the global policy narrative about work among UN agencies, and that the pursuit of decent work and the Agenda were perceived as important goals with the potential to promote just policies. The Agenda was closely linked to the World Health Organization's conception of health as a human right. However, decent work was consistently identified by World Bank informants as ILO terminology in contrast to terms such as job creation and job access. The limited evidence base and its conceptual nature were offered as partial explanations for why the Agenda has yet to fully influence other global institutions. Catalytic events such as the economic crisis were identified as creating the enabling conditions to influence global work policy agendas. Our evidence aids our understanding of how an issue like decent work enters and stays on the policy agendas of global institutions, using the Decent Work Agenda as an illustrative example. Catalytic events and policy

  4. Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome.

    Hacker, William C; Li, Shuxiang; Elcock, Adrian H

    2017-07-27

    We describe structural models of the Escherichia coli chromosome in which the positions of all 4.6 million nucleotides of each DNA strand are resolved. Models consistent with two basic chromosomal orientations, differing in their positioning of the origin of replication, have been constructed. In both types of model, the chromosome is partitioned into plectoneme-abundant and plectoneme-free regions, with plectoneme lengths and branching patterns matching experimental distributions, and with spatial distributions of highly-transcribed chromosomal regions matching recent experimental measurements of the distribution of RNA polymerases. Physical analysis of the models indicates that the effective persistence length of the DNA and relative contributions of twist and writhe to the chromosome's negative supercoiling are in good correspondence with experimental estimates. The models exhibit characteristics similar to those of 'fractal globules,' and even the most genomically-distant parts of the chromosome can be physically connected, through paths combining linear diffusion and inter-segmental transfer, by an average of only ∼10 000 bp. Finally, macrodomain structures and the spatial distributions of co-expressed genes are analyzed: the latter are shown to depend strongly on the overall orientation of the chromosome. We anticipate that the models will prove useful in exploring other static and dynamic features of the bacterial chromosome. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  5. Complete nucleotide sequence and genome organization of a Chinese isolate of Tobacco vein distorting virus.

    Mo, Xiao-han; Chen, Zheng-bin; Chen, Jian-ping

    2010-12-01

    Tobacco bushy top disease is caused by tobacco bushy top virus (TBTV, a member of the genus Umbravirus) which is dependent on tobacco vein-distorting virus (TVDV) to act as a helper virus encapsidating TBTV and enabling its transmission by aphids. Isometric virions from diseased tobacco plants were purified and disease symptoms were reproduced after experimental aphid transmission. The complete genome of TVDV was determined from cloned RT-PCR products derived from viral RNA. It was 5,920 nucleotides (nts) long and had the six major open reading frames (ORFs) typical of a member of the genus Polerovirus. Sequence comparisons showed that it differed significantly from any of the other species in the genus and this was confirmed by phylogenetic analyses of the RdRp and coat protein. SDS-PAGE analysis of purified virions gave two protein bands of about 26 and 59 kDa both of which reacted strongly in Western blots with antiserum produced to prokaryotically expressed TVDV CP showing that the two forms of the TVDV CP were the only protein components of the capsid.

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

    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...

  7. Greenhouse gas fluxes from agricultural soils under organic and non-organic management — A global meta-analysis

    Skinner, Colin, E-mail: colin.skinner@fibl.org [Research Institute of Organic Agriculture (FiBL), Ackerstrasse 21, 5070 Frick (Switzerland); Gattinger, Andreas, E-mail: andreas.gattinger@fibl.org [Research Institute of Organic Agriculture (FiBL), Ackerstrasse 21, 5070 Frick (Switzerland); Muller, Adrian, E-mail: adrian.mueller@fibl.org [Research Institute of Organic Agriculture (FiBL), Ackerstrasse 21, 5070 Frick (Switzerland); Mäder, Paul, E-mail: paul.maeder@fibl.org [Research Institute of Organic Agriculture (FiBL), Ackerstrasse 21, 5070 Frick (Switzerland); Fließbach, Andreas, E-mail: andreas.fliessbach@fibl.org [Research Institute of Organic Agriculture (FiBL), Ackerstrasse 21, 5070 Frick (Switzerland); Stolze, Matthias, E-mail: matthias.stolze@fibl.org [Research Institute of Organic Agriculture (FiBL), Ackerstrasse 21, 5070 Frick (Switzerland); Ruser, Reiner, E-mail: reiner.ruser@uni-hohenheim.de [Fertilisation and Soil Matter Dynamics (340i), Institute of Crop Science, University of Hohenheim, Fruwirthstraße 20, 70599 Stuttgart (Germany); Niggli, Urs, E-mail: urs.niggli@fibl.org [Research Institute of Organic Agriculture (FiBL), Ackerstrasse 21, 5070 Frick (Switzerland)

    2014-01-01

    It is anticipated that organic farming systems provide benefits concerning soil conservation and climate protection. A literature search on measured soil-derived greenhouse gas (GHG) (nitrous oxide and methane) fluxes under organic and non-organic management from farming system comparisons was conducted and followed by a meta-analysis. Up to date only 19 studies based on field measurements could be retrieved. Based on 12 studies that cover annual measurements, it appeared with a high significance that area-scaled nitrous oxide emissions from organically managed soils are 492 ± 160 kg CO{sub 2} eq. ha{sup −1} a{sup −1} lower than from non-organically managed soils. For arable soils the difference amounts to 497 ± 162 kg CO{sub 2} eq. ha{sup −1} a{sup −1}. However, yield-scaled nitrous oxide emissions are higher by 41 ± 34 kg CO{sub 2} eq. t{sup −1} DM under organic management (arable and use). To equalize this mean difference in yield-scaled nitrous oxide emissions between both farming systems, the yield gap has to be less than 17%. Emissions from conventionally managed soils seemed to be influenced mainly by total N inputs, whereas for organically managed soils other variables such as soil characteristics seemed to be more important. This can be explained by the higher bioavailability of the synthetic N fertilisers in non-organic farming systems while the necessary mineralisation of the N sources under organic management leads to lower and retarded availability. Furthermore, a higher methane uptake of 3.2 ± 2.5 kg CO{sub 2} eq. ha{sup −1} a{sup −1} for arable soils under organic management can be observed. Only one comparative study on rice paddies has been published up to date. All 19 retrieved studies were conducted in the Northern hemisphere under temperate climate. Further GHG flux measurements in farming system comparisons are required to confirm the results and close the existing knowledge gaps. - Highlights: • Lower area-scaled nitrous

  8. Impact of Organic Amendments on Global Warming Potential of Diversified Tropical Rice Rotation Systems

    Janz, B.; Weller, S.; Kraus, D.; Wassmann, R.; Butterbach-Bahl, K.; Ralf, K.

    2017-12-01

    Paddy rice cultivation is increasingly challenged by irrigation water scarcity, which is forcing farmers to change traditional rice cultivation from flooded double-rice systems to the introduction of well-aerated upland crops during dry season. Emissions of methane (CH4) are expected to decrease, while there is a risk of increasing emissions of nitrous oxide (N2O) and decreasing soil organic carbon (SOC) stocks through volatilization in the form of carbon dioxide (CO2). We present a unique dataset of long-term continuous greenhouse gas emission measurements (CH4 and N2O) in the Philippines to assess global warming potentials (GWP) of diversified rice crop rotations including different field management practices such as straw residue application and legume intercropping. Since 2012, more than four years of CH4 and N2O emissions in double-rice cropping (R-R) and paddy rice rotations diversified with either maize (R-M) or aerobic rice (R-A) during dry season have been collected. Introduction of upland crops reduced irrigation water use and CH4 emissions by 66-81% and 95-99%, respectively. Although dry season N2O emissions increased twice- to threefold in the diversified systems, the strong reduction of CH4 led to a significantly lower annual GWP (CH4 + N2O) as compared to the traditional R-R system. Diversified crop management practices were first implemented during land-preparation for dry season 2015 where i) 6 t/ha rice straw was returned to the field and ii) mungbean was grown as a cover-crop between dry and wet season in addition to rice straw application. The input of organic material (straw and mungbean) led to higher substrate availability for methanogens during the following season. Therefore, GWP was 9-39% higher following straw incorporation than the control treatment. This increase was mainly driven by additional CH4 emissions. Even more, mungbean intercropping further increased GWPs, whereby the increment was highest in R-R rotation (88%) and lowest in R

  9. Unsolvable Problems of Biology: It Is Impossible to Create Two Identical Organisms, to Defeat Cancer, or to Map Organisms onto Their Genomes.

    Sverdlov, E D

    2018-04-01

    The review is devoted to unsolvable problems of biology. 1) Problems unsolvable due to stochastic mutations occurring during DNA replication that make it impossible to create two identical organisms or even two identical complex cells (Sverdlov, E. D. (2009) Biochemistry (Moscow), 74, 939-944) and to "defeat" cancer. 2) Problems unsolvable due to multiple interactions in complex systems leading to the appearance of unpredictable emergent properties that prevent establishment of unambiguous relationships between the genetic architecture and phenotypic manifestation of the genome and make impossible to predict with certainty responses of the organism, its parts, or pathological processes to external factors. 3) Problems unsolvable because of the uncertainty principle and observer effect in biology, due to which it is impossible to obtain adequate information about cells in their tissue microenvironment by isolating and analyzing individual cells. In particular, we cannot draw conclusions on the properties of stem cells in their niches based on the properties of stem cell cultures. A strategy is proposed for constructing the pattern most closely approximated to the relationship of genotypes with their phenotypes by designing networks of intermediate phenotypes (endophenotypes).

  10. Bidirectional global spontaneous network activity precedes the canonical unidirectional circuit organization in the developing hippocampus.

    Shi, Yulin; Ikrar, Taruna; Olivas, Nicholas D; Xu, Xiangmin

    2014-06-15

    Spontaneous network activity is believed to sculpt developing neural circuits. Spontaneous giant depolarizing potentials (GDPs) were first identified with single-cell recordings from rat CA3 pyramidal neurons, but here we identify and characterize a large-scale spontaneous network activity we term global network activation (GNA) in the developing mouse hippocampal slices, which is measured macroscopically by fast voltage-sensitive dye imaging. The initiation and propagation of GNA in the mouse is largely GABA-independent and dominated by glutamatergic transmission via AMPA receptors. Despite the fact that signal propagation in the adult hippocampus is strongly unidirectional through the canonical trisynaptic circuit (dentate gyrus [DG] to CA3 to CA1), spontaneous GNA in the developing hippocampus originates in distal CA3 and propagates both forward to CA1 and backward to DG. Photostimulation-evoked GNA also shows prominent backward propagation in the developing hippocampus from CA3 to DG. Mouse GNA is strongly correlated to electrophysiological recordings of highly localized single-cell and local field potential events. Photostimulation mapping of neural circuitry demonstrates that the enhancement of local circuit connections to excitatory pyramidal neurons occurs over the same time course as GNA and reveals the underlying pathways accounting for GNA backward propagation from CA3 to DG. The disappearance of GNA coincides with a transition to the adult-like unidirectional circuit organization at about 2 weeks of age. Taken together, our findings strongly suggest a critical link between GNA activity and maturation of functional circuit connections in the developing hippocampus. Copyright © 2013 Wiley Periodicals, Inc.

  11. Genome interplay in the grain transcriptome of hexaploid bread wheat.

    Pfeifer, Matthias; Kugler, Karl G; Sandve, Simen R; Zhan, Bujie; Rudi, Heidi; Hvidsten, Torgeir R; Mayer, Klaus F X; Olsen, Odd-Arne

    2014-07-18

    Allohexaploid bread wheat (Triticum aestivum L.) provides approximately 20% of calories consumed by humans. Lack of genome sequence for the three homeologous and highly similar bread wheat genomes (A, B, and D) has impeded expression analysis of the grain transcriptome. We used previously unknown genome information to analyze the cell type-specific expression of homeologous genes in the developing wheat grain and identified distinct co-expression clusters reflecting the spatiotemporal progression during endosperm development. We observed no global but cell type- and stage-dependent genome dominance, organization of the wheat genome into transcriptionally active chromosomal regions, and asymmetric expression in gene families related to baking quality. Our findings give insight into the transcriptional dynamics and genome interplay among individual grain cell types in a polyploid cereal genome. Copyright © 2014, American Association for the Advancement of Science.

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

    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.

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

    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.

  14. IMPACT OF GLOBAL WARMING ON LIFE: LIFE ON EARTH FROM SINGLE-CELLULAR ORGANISMS TO MULTICELLULAR ORGANISMS

    Kartikey Gupta [Grade X, Mayura School, Jaipur (India)

    2008-09-30

    Wherever we look, life can be seen...so many different forms of life, that is, uncountable varieties of animals and plants occupy the whole world today! But, where and how did it all start? The story of evolution is one of the most interesting theories ever put forward. It refers to - the way that simple and small living things eventually changed into much more functional and bigger beings, in course of time. Charles Darwin had explored this mystery, and had provided the reason- Evolution. Evolution is changing of life forms into more functional ones with respect to their changing environment. However, as odd as it may sound, evolution and extinction are closely linked. Because, the better evolved species survives, and throughout the timeline of evolution, there have been many extinction waves. They were all occurred naturally thus proving that the very process of extinction is natural. The earth has seen many variations of global temperature; it has suffered various ice ages, which had also many a times threatened to eradicate most life from the planet. But, every time life has found a way to go on. Therefore, whatever life we see today has resulted from the ongoing long process of evolution. After millions of years, finally we humans have come into existence, and today are the leading species of the world. But, we may possibly be very close to another major extinction wave, the root causes of which are both natural and man-made, but the part played by the latter is much more than the former. Global Warming has now started affecting all kinds of life on the planet, and it is our responsibility as the leading and most intellectual species to try to save our earth. A study reveals that 60% Indian people do not actually know about Global Warming, and that the number of youth aware of Global Warming and Its impacts are much more than the number of adults. About 75% Indians believe that it is the sole responsibility of the government to solve the problems related to

  15. How do natural, uncultivated microbes interact with organic matter? Insights from single cell genomics and metagenomics

    Lloyd, Karen; Bird, Jordan; Schreiber, Lars

    Abstract Since most of the microbes in marine sediments remain uncultured, little is known about the mechanisms by which these natural communities degrade organic matter (OM). Likewise, little is known about the make-up of labile OM in marine sediments beyond general functional classes such as pr......Abstract Since most of the microbes in marine sediments remain uncultured, little is known about the mechanisms by which these natural communities degrade organic matter (OM). Likewise, little is known about the make-up of labile OM in marine sediments beyond general functional classes...... such as proteins, carbohydrates, and lipids, measured as monomers. However, microbes have complex interactions with specific polymers within these functional classes, which can be indicated by a microbe's enzymatic toolkit. We ...

  16. De novo mutations in the genome organizer CTCF cause intellectual disability

    Gregor, Anne; Oti, Martin; Kouwenhoven, Evelyn N

    2013-01-01

    An increasing number of genes involved in chromatin structure and epigenetic regulation has been implicated in a variety of developmental disorders, often including intellectual disability. By trio exome sequencing and subsequent mutational screening we now identified two de novo frameshift...... mutations and one de novo missense mutation in CTCF in individuals with intellectual disability, microcephaly, and growth retardation. Furthermore, an individual with a larger deletion including CTCF was identified. CTCF (CCCTC-binding factor) is one of the most important chromatin organizers in vertebrates...... and is involved in various chromatin regulation processes such as higher order of chromatin organization, enhancer function, and maintenance of three-dimensional chromatin structure. Transcriptome analyses in all three individuals with point mutations revealed deregulation of genes involved in signal transduction...

  17. Molecular Analysis and Genomic Organization of Major DNA Satellites in Banana (Musa spp.)

    Čížková, Jana; Hřibová, Eva; Humplíková, Lenka; Christelová, Pavla; Suchánková, Pavla; Doležel, Jaroslav

    2013-01-01

    Roč. 8, č. 1 (2013) E-ISSN 1932-6203 R&D Projects: GA AV ČR KJB500380901; GA MŠk(CZ) LG12021 Grant - others:GA MŠk(CZ) ED0007/01/01 Program:ED Institutional research plan: CEZ:AV0Z50380511 Keywords : IN-SITU HYBRIDIZATION * LARGE-SCALE ORGANIZATION * RIBOSOMAL-RNA GENES Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.534, year: 2013

  18. Genomic organization and the tissue distribution of alternatively spliced isoforms of the mouse Spatial gene

    Mattei Marie-Geneviève

    2004-07-01

    Full Text Available Abstract Background The stromal component of the thymic microenvironment is critical for T lymphocyte generation. Thymocyte differentiation involves a cascade of coordinated stromal genes controlling thymocyte survival, lineage commitment and selection. The "Stromal Protein Associated with Thymii And Lymph-node" (Spatial gene encodes a putative transcription factor which may be involved in T-cell development. In the testis, the Spatial gene is also expressed by round spermatids during spermatogenesis. Results The Spatial gene maps to the B3-B4 region of murine chromosome 10 corresponding to the human syntenic region 10q22.1. The mouse Spatial genomic DNA is organised into 10 exons and is alternatively spliced to generate two short isoforms (Spatial-α and -γ and two other long isoforms (Spatial-δ and -ε comprising 5 additional exons on the 3' site. Here, we report the cloning of a new short isoform, Spatial-β, which differs from other isoforms by an additional alternative exon of 69 bases. This new exon encodes an interesting proline-rich signature that could confer to the 34 kDa Spatial-β protein a particular function. By quantitative TaqMan RT-PCR, we have shown that the short isoforms are highly expressed in the thymus while the long isoforms are highly expressed in the testis. We further examined the inter-species conservation of Spatial between several mammals and identified that the protein which is rich in proline and positive amino acids, is highly conserved. Conclusions The Spatial gene generates at least five alternative spliced variants: three short isoforms (Spatial-α, -β and -γ highly expressed in the thymus and two long isoforms (Spatial-δ and -ε highly expressed in the testis. These alternative spliced variants could have a tissue specific function.

  19. U1 snDNA clusters in grasshoppers: chromosomal dynamics and genomic organization

    Anjos, A; Ruiz-Ruano, F J; Camacho, J P M; Loreto, V; Cabrero, J; de Souza, M J; Cabral-de-Mello, D C

    2015-01-01

    The spliceosome, constituted by a protein set associated with small nuclear RNA (snRNA), is responsible for mRNA maturation through intron removal. Among snRNA genes, U1 is generally a conserved repetitive sequence. To unveil the chromosomal/genomic dynamics of this multigene family in grasshoppers, we mapped U1 genes by fluorescence in situ hybridization in 70 species belonging to the families Proscopiidae, Pyrgomorphidae, Ommexechidae, Romaleidae and Acrididae. Evident clusters were observed in all species, indicating that, at least, some U1 repeats are tandemly arrayed. High conservation was observed in the first four families, with most species carrying a single U1 cluster, frequently located in the third or fourth longest autosome. By contrast, extensive variation was observed among Acrididae, from a single chromosome pair carrying U1 to all chromosome pairs carrying it, with occasional occurrence of two or more clusters in the same chromosome. DNA sequence analysis in Eyprepocnemis plorans (species carrying U1 clusters on seven different chromosome pairs) and Locusta migratoria (carrying U1 in a single chromosome pair) supported the coexistence of functional and pseudogenic lineages. One of these pseudogenic lineages was truncated in the same nucleotide position in both species, suggesting that it was present in a common ancestor to both species. At least in E. plorans, this U1 snDNA pseudogenic lineage was associated with 5S rDNA and short interspersed elements (SINE)-like mobile elements. Given that we conclude in grasshoppers that the U1 snDNA had evolved under the birth-and-death model and that its intragenomic spread might be related with mobile elements. PMID:25248465

  20. Cloning, functional characterization and genomic organization of 1,8-cineole synthases from Lavandula.

    Demissie, Zerihun A; Cella, Monica A; Sarker, Lukman S; Thompson, Travis J; Rheault, Mark R; Mahmoud, Soheil S

    2012-07-01

    Several members of the genus Lavandula produce valuable essential oils (EOs) that are primarily constituted of the low molecular weight isoprenoids, particularly monoterpenes. We isolated over 8,000 ESTs from the glandular trichomes of L. x intermedia flowers (where bulk of the EO is synthesized) to facilitate the discovery of genes that control the biosynthesis of EO constituents. The expression profile of these ESTs in L. x intermedia and its parents L. angustifolia and L. latifolia was established using microarrays. The resulting data highlighted a differentially expressed, previously uncharacterized cDNA with strong homology to known 1,8-cineole synthase (CINS) genes. The ORF, excluding the transit peptide, of this cDNA was expressed in E. coli, purified by Ni-NTA agarose affinity chromatography and functionally characterized in vitro. The ca. 63 kDa bacterially produced recombinant protein, designated L. x intermedia CINS (LiCINS), converted geranyl diphosphate (the linear monoterpene precursor) primarily to 1,8-cineole with K ( m ) and k ( cat ) values of 5.75 μM and 8.8 × 10(-3) s(-1), respectively. The genomic DNA of CINS in the studied Lavandula species had identical exon-intron architecture and coding sequences, except for a single polymorphic nucleotide in the L. angustifolia ortholog which did not alter protein function. Additional nucleotide variations restricted to L. angustifolia introns were also observed, suggesting that LiCINS was most likely inherited from L. latifolia. The LiCINS mRNA levels paralleled the 1,8-cineole content in mature flowers of the three lavender species, and in developmental stages of L. x intermedia inflorescence indicating that the production of 1,8 cineole in Lavandula is most likely controlled through transcriptional regulation of LiCINS.

  1. The role of non-governmental organizations in global health diplomacy: negotiating the Framework Convention on Tobacco Control.

    Lencucha, Raphael; Kothari, Anita; Labonté, Ronald

    2011-09-01

    The Framework Convention on Tobacco Control (FCTC) is an exemplar result of global health diplomacy, based on its global reach (binding on all World Health Organization member nations) and its negotiation process. The FCTC negotiations are one of the first examples of various states and non-state entities coming together to create a legally binding tool to govern global health. They have demonstrated that diplomacy, once consigned to interactions among state officials, has witnessed the dilution of its state-centric origins with the inclusion of non-governmental organizations (NGOs) in the diplomacy process. To engage in the discourse of global health diplomacy, NGO diplomats are immediately presented with two challenges: to convey the interests of larger publics and to contribute to inter-state negotiations in a predominantly state-centric system of governance that are often diluted by pressures from private interests or mercantilist self-interest on the part of the state itself. How do NGOs manage these challenges within the process of global health diplomacy itself? What roles do, and can, they play in achieving new forms of global health diplomacy? This paper addresses these questions through presentation of findings from a study of the roles assumed by one group of non-governmental actors (the Canadian NGOs) in the FCTC negotiations. The findings presented are drawn from a larger grounded theory study. Qualitative data were collected from 34 public documents and 18 in-depth interviews with participants from the Canadian government and Canadian NGOs. This analysis yielded five key activities or roles of the Canadian NGOs during the negotiation of the FCTC: monitoring, lobbying, brokering knowledge, offering technical expertise and fostering inclusion. This discussion begins to address one of the key goals of global health diplomacy, namely 'the challenges facing health diplomacy and how they have been addressed by different groups and at different levels of

  2. Identification, characterization and metagenome analysis of oocyte-specific genes organized in clusters in the mouse genome

    Vaiman Daniel

    2005-05-01

    Full Text Available Abstract Background Genes specifically expressed in the oocyte play key roles in oogenesis, ovarian folliculogenesis, fertilization and/or early embryonic development. In an attempt to identify novel oocyte-specific genes in the mouse, we have used an in silico subtraction methodology, and we have focused our attention on genes that are organized in genomic clusters. Results In the present work, five clusters have been studied: a cluster of thirteen genes characterized by an F-box domain localized on chromosome 9, a cluster of six genes related to T-cell leukaemia/lymphoma protein 1 (Tcl1 on chromosome 12, a cluster composed of a SPErm-associated glutamate (E-Rich (Speer protein expressed in the oocyte in the vicinity of four unknown genes specifically expressed in the testis on chromosome 14, a cluster composed of the oocyte secreted protein-1 (Oosp-1 gene and two Oosp-related genes on chromosome 19, all three being characterized by a partial N-terminal zona pellucida-like domain, and another small cluster of two genes on chromosome 19 as well, composed of a TWIK-Related spinal cord K+ channel encoding-gene, and an unknown gene predicted in silico to be testis-specific. The specificity of expression was confirmed by RT-PCR and in situ hybridization for eight and five of them, respectively. Finally, we showed by comparing all of the isolated and clustered oocyte-specific genes identified so far in the mouse genome, that the oocyte-specific clusters are significantly closer to telomeres than isolated oocyte-specific genes are. Conclusion We have studied five clusters of genes specifically expressed in female, some of them being also expressed in male germ-cells. Moreover, contrarily to non-clustered oocyte-specific genes, those that are organized in clusters tend to map near chromosome ends, suggesting that this specific near-telomere position of oocyte-clusters in rodents could constitute an evolutionary advantage. Understanding the biological

  3. Single-cell Hi-C bridges microscopy and genome-wide sequencing approaches to study 3D chromatin organization.

    Ulianov, Sergey V; Tachibana-Konwalski, Kikue; Razin, Sergey V

    2017-10-01

    Recent years have witnessed an explosion of the single-cell biochemical toolbox including chromosome conformation capture (3C)-based methods that provide novel insights into chromatin spatial organization in individual cells. The observations made with these techniques revealed that topologically associating domains emerge from cell population averages and do not exist as static structures in individual cells. Stochastic nature of the genome folding is likely to be biologically relevant and may reflect the ability of chromatin fibers to adopt a number of alternative configurations, some of which could be transiently stabilized and serve regulatory purposes. Single-cell Hi-C approaches provide an opportunity to analyze chromatin folding in rare cell types such as stem cells, tumor progenitors, oocytes, and totipotent cells, contributing to a deeper understanding of basic mechanisms in development and disease. Here, we review key findings of single-cell Hi-C and discuss possible biological reasons and consequences of the inferred dynamic chromatin spatial organization. © 2017 WILEY Periodicals, Inc.

  4. Genome-Wide Identification, Phylogeny, and Expression Analysis of ARF Genes Involved in Vegetative Organs Development in Switchgrass

    Jianli Wang

    2018-01-01

    Full Text Available Auxin response factors (ARFs have been reported to play vital roles during plant growth and development. In order to reveal specific functions related to vegetative organs in grasses, an in-depth study of the ARF gene family was carried out in switchgrass (Panicum virgatum L., a warm-season C4 perennial grass that is mostly used as bioenergy and animal feedstock. A total of 47 putative ARF genes (PvARFs were identified in the switchgrass genome (2n = 4x = 36, 42 of which were anchored to the seven pairs of chromosomes and found to be unevenly distributed. Sixteen PvARFs were predicted to be potential targets of small RNAs (microRNA160 and 167. Phylogenetically speaking, PvARFs were divided into seven distinct subgroups based on the phylogeny, exon/intron arrangement, and conserved motif distribution. Moreover, 15 pairs of PvARFs have different temporal-spatial expression profiles in vegetative organs (2nd, 3rd, and 4th internode and leaves, which implies that different PvARFs have specific functions in switchgrass growth and development. In addition, at least 14 pairs of PvARFs respond to naphthylacetic acid (NAA treatment, which might be helpful for us to study on auxin response in switchgrass. The comprehensive analysis, described here, will facilitate the future functional analysis of ARF genes in grasses.

  5. Genome Sequence of Pseudomonas sp. Strain Chol1, a Model Organism for the Degradation of Bile Salts and Other Steroid Compounds

    Holert, Johannes; Alam, Intikhab; Larsen, Michael; Antunes, Andre; Bajic, Vladimir B.; Stingl, Ulrich; Philipp, Bodo

    2013-01-01

    Bacterial degradation of steroid compounds is of high ecological and biotechnological relevance. Pseudomonas sp. strain Chol1 is a model organism for studying the degradation of the steroid compound cholate. Its draft genome sequence is presented and reveals one gene cluster responsible for the metabolism of steroid compounds.

  6. The genomic organization of four b-1,4-endoglucanase genes in plant-parasitic cyst nematodes and its evolutionary implications.

    Yan, Y.; Smant, G.; Stokkermans, J.P.W.G.; Qin Ling,; Baum, T.J.; Schots, A.; Davis, E.L.

    1998-01-01

    The genomic organization of genes encoding -1,4-endoglucanases (cellulases) from the plant-parasitic cyst nematodes Heterodera glycines and Globodera rostochiensis (HG-eng1, Hg-eng2, GR-eng1, and GR-eng2) was investigated. HG-eng1 and GR-eng1 both contained eight introns and structural domains of

  7. Genome Sequence of Pseudomonas sp. Strain Chol1, a Model Organism for the Degradation of Bile Salts and Other Steroid Compounds

    Holert, Johannes

    2013-01-15

    Bacterial degradation of steroid compounds is of high ecological and biotechnological relevance. Pseudomonas sp. strain Chol1 is a model organism for studying the degradation of the steroid compound cholate. Its draft genome sequence is presented and reveals one gene cluster responsible for the metabolism of steroid compounds.

  8. Rice sHsp genes: genomic organization and expression profiling under stress and development

    Grover Anil

    2009-08-01

    Full Text Available Abstract Background Heat shock proteins (Hsps constitute an important component in the heat shock response of all living systems. Among the various plant Hsps (i.e. Hsp100, Hsp90, Hsp70 and Hsp20, Hsp20 or small Hsps (sHsps are expressed in maximal amounts under high temperature stress. The characteristic feature of the sHsps is the presence of α-crystallin domain (ACD at the C-terminus. sHsps cooperate with Hsp100/Hsp70 and co-chaperones in ATP-dependent manner in preventing aggregation of cellular proteins and in their subsequent refolding. Database search was performed to investigate the sHsp gene family across rice genome sequence followed by comprehensive expression analysis of these genes. Results We identified 40 α-crystallin domain containing genes in rice. Phylogenetic analysis showed that 23 out of these 40 genes constitute sHsps. The additional 17 genes containing ACD clustered with Acd proteins of Arabidopsis. Detailed scrutiny of 23 sHsp sequences enabled us to categorize these proteins in a revised scheme of classification constituting of 16 cytoplasmic/nuclear, 2 ER, 3 mitochondrial, 1 plastid and 1 peroxisomal genes. In the new classification proposed herein nucleo-cytoplasmic class of sHsps with 9 subfamilies is more complex in rice than in Arabidopsis. Strikingly, 17 of 23 rice sHsp genes were noted to be intronless. Expression analysis based on microarray and RT-PCR showed that 19 sHsp genes were upregulated by high temperature stress. Besides heat stress, expression of sHsp genes was up or downregulated by other abiotic and biotic stresses. In addition to stress regulation, various sHsp genes were differentially upregulated at different developmental stages of the rice plant. Majority of sHsp genes were expressed in seed. Conclusion We identified twenty three sHsp genes and seventeen Acd genes in rice. Three nucleocytoplasmic sHsp genes were found only in monocots. Analysis of expression profiling of sHsp genes revealed

  9. Genomics of Banana and Plantain (Musa spp.), Major Staple Crops in the Tropics

    Roux, N.; Baurens, F.C.; Dolezel, J.; Hribova, E.; Heslop-Harrison, P.; Town, C.; Sasaki, T.; Matsumoto, T.; Aert, R.; Remy, S.; Souza, M.T.; Lagoda, P.

    2008-01-01

    This chapter on Musa (banana and plantain) genomics covers the latest information on activities and resources developed by the Global Musa Genomics Consortium. Section 4.1 describes the morphology of the plant, its socio-economical importance and usefulness as an experimental organism. Section 4.2

  10. Spatiotemporal models of global soil organic carbon stock to support land degradation assessments at regional and global scales: limitations, challenges and opportunities

    Hengl, Tomislav; Heuvelink, Gerard; Sanderman, Jonathan; MacMillan, Robert

    2017-04-01

    There is an increasing interest in fitting and applying spatiotemporal models that can be used to assess and monitor soil organic carbon stocks (SOCS), for example, in support of the '4 pourmille' initiative aiming at soil carbon sequestration towards climate change adaptation and mitigation and UN's Land Degradation Neutrality indicators and similar degradation assessment projects at regional and global scales. The land cover mapping community has already produced several spatiotemporal data sets with global coverage and at relatively fine resolution e.g. USGS MODIS land cover annual maps for period 2000-2014; European Space Agency land cover maps at 300 m resolution for the year 2000, 2005 and 2010; Chinese GlobeLand30 dataset available for years 2000 and 2010; Columbia University's WRI GlobalForestWatch with deforestation maps at 30 m resolution for the period 2000-2016 (Hansen et al. 2013). These data sets can be used for land degradation assessment and scenario testing at global and regional scales (Wei et al 2014). Currently, however, no compatible global spatiotemporal data sets exist on status of soil quality and/or soil health (Powlson et al. 2013). This paper describes an initial effort to devise and evaluate a procedure for mapping spatio-temporal changes in SOC stocks using a complete stack of soil forming factors (climate, relief, land cover, land use, lithology and living organisms) represented mainly through remote sensing based time series of Earth images. For model building we used some 75,000 geo-referenced soil profiles and a stacks space-time covariates (land cover, land use, biomass, climate) at two standard resolutions: (1) 10 km resolution with data available for period 1920-2014 and (2) 1000 m resolution with data available for period 2000-2014. The initial results show that, although it is technically feasible to produce space time estimates of SOCS that demonstrate the procedure, the estimates are relatively uncertain (<45% of variation

  11. Exploring Patterns of Soil Organic Matter Decomposition with Students and the Public Through the Global Decomposition Project (GDP)

    Wood, J. H.; Natali, S.

    2014-12-01

    The Global Decomposition Project (GDP) is a program designed to introduce and educate students and the general public about soil organic matter and decomposition through a standardized protocol for collecting, reporting, and sharing data. This easy-to-use hands-on activity focuses on questions such as "How do environmental conditions control decomposition of organic matter in soil?" and "Why do some areas accumulate organic matter and others do not?" Soil organic matter is important to local ecosystems because it affects soil structure, regulates soil moisture and temperature, and provides energy and nutrients to soil organisms. It is also important globally because it stores a large amount of carbon, and when microbes "eat", or decompose organic matter they release greenhouse gasses such as carbon dioxide and methane into the atmosphere, which affects the earth's climate. The protocol describes a commonly used method to measure decomposition using a paper made of cellulose, a component of plant cell walls. Participants can receive pre-made cellulose decomposition bags, or make decomposition bags using instructions in the protocol and easily obtained materials (e.g., window screen and lignin-free paper). Individual results will be shared with all participants and the broader public through an online database. We will present decomposition bag results from a research site in Alaskan tundra, as well as from a middle-school-student led experiment in California. The GDP demonstrates how scientific methods can be extended to educate broader audiences, while at the same time, data collected by students and the public can provide new insight into global patterns of soil decomposition. The GDP provides a pathway for scientists and educators to interact and reach meaningful education and research goals.

  12. The politics of agenda setting at the global level: key informant interviews regarding the International Labour Organization Decent Work Agenda

    2014-01-01

    Background Global labour markets continue to undergo significant transformations resulting from socio-political instability combined with rises in structural inequality, employment insecurity, and poor working conditions. Confronted by these challenges, global institutions are providing policy guidance to protect and promote the health and well-being of workers. This article provides an account of how the International Labour Organization’s Decent Work Agenda contributes to the work policy agendas of the World Health Organization and the World Bank. Methods This qualitative study involved semi-structured interviews with representatives from three global institutions – the International Labour Organization (ILO), the World Health Organization and the World Bank. Of the 25 key informants invited to participate, 16 took part in the study. Analysis for key themes was followed by interpretation using selected agenda setting theories. Results Interviews indicated that through the Decent Work Agenda, the International Labour Organization is shaping the global policy narrative about work among UN agencies, and that the pursuit of decent work and the Agenda were perceived as important goals with the potential to promote just policies. The Agenda was closely linked to the World Health Organization’s conception of health as a human right. However, decent work was consistently identified by World Bank informants as ILO terminology in contrast to terms such as job creation and job access. The limited evidence base and its conceptual nature were offered as partial explanations for why the Agenda has yet to fully influence other global institutions. Catalytic events such as the economic crisis were identified as creating the enabling conditions to influence global work policy agendas. Conclusions Our evidence aids our understanding of how an issue like decent work enters and stays on the policy agendas of global institutions, using the Decent Work Agenda as an illustrative

  13. Organizing SOCOM for Cross-Functional and Geographic Area Operations in the Global War on Terrorism

    Cabanas, Kevin A

    2005-01-01

    .... The first organization would plan, direct, and execute direct-action type operations designed to defeat the terrorist threat, while the second organization would plan, direct, and execute long-term...

  14. Global change-driven effects on dissolved organic matter composition: Implications for food webs of northern lakes.

    Creed, Irena F; Bergström, Ann-Kristin; Trick, Charles G; Grimm, Nancy B; Hessen, Dag O; Karlsson, Jan; Kidd, Karen A; Kritzberg, Emma; McKnight, Diane M; Freeman, Erika C; Senar, Oscar E; Andersson, Agneta; Ask, Jenny; Berggren, Martin; Cherif, Mehdi; Giesler, Reiner; Hotchkiss, Erin R; Kortelainen, Pirkko; Palta, Monica M; Vrede, Tobias; Weyhenmeyer, Gesa A

    2018-03-15

    Northern ecosystems are experiencing some of the most dramatic impacts of global change on Earth. Rising temperatures, hydrological intensification, changes in atmospheric acid deposition and associated acidification recovery, and changes in vegetative cover are resulting in fundamental changes in terrestrial-aquatic biogeochemical linkages. The effects of global change are readily observed in alterations in the supply of dissolved organic matter (DOM)-the messenger between terrestrial and lake ecosystems-with potentially profound effects on the structure and function of lakes. Northern terrestrial ecosystems contain substantial stores of organic matter and filter or funnel DOM, affecting the timing and magnitude of DOM delivery to surface waters. This terrestrial DOM is processed in streams, rivers, and lakes, ultimately shifting its composition, stoichiometry, and bioavailability. Here, we explore the potential consequences of these global change-driven effects for lake food webs at northern latitudes. Notably, we provide evidence that increased allochthonous DOM supply to lakes is overwhelming increased autochthonous DOM supply that potentially results from earlier ice-out and a longer growing season. Furthermore, we assess the potential implications of this shift for the nutritional quality of autotrophs in terms of their stoichiometry, fatty acid composition, toxin production, and methylmercury concentration, and therefore, contaminant transfer through the food web. We conclude that global change in northern regions leads not only to reduced primary productivity but also to nutritionally poorer lake food webs, with discernible consequences for the trophic web to fish and humans. © 2018 John Wiley & Sons Ltd.

  15. Global monitoring of Salmonella serovar distribution from the World Health Organization Global Foodborne Infections Network Country Data Bank: results of quality assured laboratories from 2001 to 2007.

    Hendriksen, Rene S; Vieira, Antonio R; Karlsmose, Susanne; Lo Fo Wong, Danilo M A; Jensen, Arne B; Wegener, Henrik C; Aarestrup, Frank M

    2011-08-01

    Salmonella enterica is commonly acquired from contaminated food and is an important cause of illness worldwide. Interventions are needed to control Salmonella; subtyping Salmonella by serotyping is useful for targeting such interventions. We, therefore, analyzed the global distribution of the 15 most frequently identified serovars of Salmonella isolated from humans from 2001 to 2007 in laboratories from 37 countries that participated in World Health Organization Global Foodborne Infections Network and demonstrated serotyping proficiency in the Global Foodborne Infections Network External Quality Assurance System. In all regions throughout the study period, with the exception of the Oceania and North American regions, Salmonella serovars Enteritidis and Typhimurium ranked as the most common and second most common serovar, respectively. In the North American and Oceania (Australia and New Zealand) regions, Salmonella serovar Typhimurium was the most common serovar reported, and Salmonella serovar Enteritidis was the second most common serovar. During the study period, the proportion of Salmonella isolates reported from humans that were Salmonella serovar Enteritidis was 43.5% (range: 40.6% [2007] to 44.9% [2003]), and Salmonella serovar Typhimurium was 17.1% (range: 15% [2007] to 18.9% [2001]). Salmonella serovars Newport (mainly observed in Latin and North American and European countries), Infantis (dominating in all regions), Virchow (mainly observed in Asian, European, and Oceanic countries), Hadar (profound in European countries), and Agona (intense in Latin and North American and European countries) were also frequently isolated with an overall proportion of 3.5%, 1.8%, 1.5%, 1.5%, and 0.8%, respectively. There were large differences in the most commonly isolated serovars between regions, but lesser differences between countries within the same region. The results also highlight the complexity of the global epidemiology of Salmonella and the need and importance

  16. British American Tobacco on Facebook: undermining article 13 of the global World Health Organization Framework Convention on Tobacco Control

    Freeman, Becky; Chapman, Simon

    2010-01-01

    Background The World Health Organization Framework Convention on Tobacco Control (WHO FCTC) bans all forms of tobacco advertising, promotion and sponsorship. The comprehensiveness of this ban has yet to be tested by online social networking media such as Facebook. In this paper, the activities of employees of the transnational tobacco company, British American Tobacco, (BAT) on Facebook and the type of content associated with two globally popular BAT brands (Dunhill and Lucky Strike) are mapp...

  17. Waste Picker Organizations and Their Contribution to the Circular Economy: Two Case Studies from a Global South Perspective

    Jutta Gutberlet

    2017-09-01

    Full Text Available The discussion on the circular economy (CE has attracted a rising interest within global policy and business as a way of increasing the sustainability of production and consumption. Yet the literature mostly portrays a Global North perspective. There is a diverse spectrum of community-based organizations playing important roles in resource recovery and transformation, particularly, but not only, in Global South countries, providing innovative examples for grassroots involvement in waste management and in the CE. This article proposes to add a Southern lens, situated in the context of waste picker organizations, to the concept of CE. The discursive framework in this article couples ecological economy (EE with social/solidarity economy (SSE, focusing not only on environmental sustainability but also on social, economic, political and cultural dimensions involved in production, consumption and discard. We acknowledge that grassroots movements contribute to policy making and improve urban waste management systems. The paper outlines two empirical studies (Argentina, Brazil that illustrate how waste picker organizations perform selective waste collection services, engage with municipalities and industries, and practice the CE. The research reveals that social and political facets need to be added to the debate about the CE, linking environmental management and policy with community development and recognizing waste pickers as protagonists in the CE. Our findings emphasize a need for a change of persisting inequalities in public policy by recognizing the importance of popular waste management praxis and knowledge, ultimately redefining the CE.

  18. Whole-brain structural topology in adult attention-deficit/hyperactivity disorder: Preserved global – disturbed local network organization

    Justina Sidlauskaite

    2015-01-01

    Full Text Available Prior studies demonstrate altered organization of functional brain networks in attention-deficit/hyperactivity disorder (ADHD. However, the structural underpinnings of these functional disturbances are poorly understood. In the current study, we applied a graph-theoretic approach to whole-brain diffusion magnetic resonance imaging data to investigate the organization of structural brain networks in adults with ADHD and unaffected controls using deterministic fiber tractography. Groups did not differ in terms of global network metrics — small-worldness, global efficiency and clustering coefficient. However, there were widespread ADHD-related effects at the nodal level in relation to local efficiency and clustering. The affected nodes included superior occipital, supramarginal, superior temporal, inferior parietal, angular and inferior frontal gyri, as well as putamen, thalamus and posterior cerebellum. Lower local efficiency of left superior temporal and supramarginal gyri was associated with higher ADHD symptom scores. Also greater local clustering of right putamen and lower local clustering of left supramarginal gyrus correlated with ADHD symptom severity. Overall, the findings indicate preserved global but altered local network organization in adult ADHD implicating regions underpinning putative ADHD-related neuropsychological deficits.

  19. Whole-brain structural topology in adult attention-deficit/hyperactivity disorder: Preserved global - disturbed local network organization.

    Sidlauskaite, Justina; Caeyenberghs, Karen; Sonuga-Barke, Edmund; Roeyers, Herbert; Wiersema, Jan R

    2015-01-01

    Prior studies demonstrate altered organization of functional brain networks in attention-deficit/hyperactivity disorder (ADHD). However, the structural underpinnings of these functional disturbances are poorly understood. In the current study, we applied a graph-theoretic approach to whole-brain diffusion magnetic resonance imaging data to investigate the organization of structural brain networks in adults with ADHD and unaffected controls using deterministic fiber tractography. Groups did not differ in terms of global network metrics - small-worldness, global efficiency and clustering coefficient. However, there were widespread ADHD-related effects at the nodal level in relation to local efficiency and clustering. The affected nodes included superior occipital, supramarginal, superior temporal, inferior parietal, angular and inferior frontal gyri, as well as putamen, thalamus and posterior cerebellum. Lower local efficiency of left superior temporal and supramarginal gyri was associated with higher ADHD symptom scores. Also greater local clustering of right putamen and lower local clustering of left supramarginal gyrus correlated with ADHD symptom severity. Overall, the findings indicate preserved global but altered local network organization in adult ADHD implicating regions underpinning putative ADHD-related neuropsychological deficits.

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

    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.

  1. The problem of induced genomic instability in the child organism under conditions of long-term effect of small radiation doses

    Suskov, I.I.; Kuz'mina, N.S.

    2001-01-01

    The phenomenological aspects of the genomic instability induced in the descendants of the multi-divided cells having been exposed to the radiation are examined. It is demonstrated that the regularity of the genomic instability induction do not correspond to the classical conception of the radiation genetics (hit principle and target theory). The mechanisms and the biological significance of this new genetic phenomenon in the child organism under conditions of low-intensive effect of small-dose radiation and its connection with the state of health are discussed [ru

  2. Genomic Organization, Phylogenetic Comparison and Differential Expression of the SBP-Box Family Genes in Grape

    Hou, Hongmin; Li, Jun; Gao, Min; Singer, Stacy D.; Wang, Hao; Mao, Linyong; Fei, Zhangjun; Wang, Xiping

    2013-01-01

    Background The SBP-box gene family is specific to plants and encodes a class of zinc finger-containing transcription factors with a broad range of functions. Although SBP-box genes have been identified in numerous plants including green algae, moss, silver birch, snapdragon, Arabidopsis, rice and maize, there is little information concerning SBP-box genes, or the corresponding miR156/157, function in grapevine. Methodology/Principal Findings Eighteen SBP-box gene family members were identified in Vitis vinifera, twelve of which bore sequences that were complementary to miRNA156/157. Phylogenetic reconstruction demonstrated that plant SBP-domain proteins could be classified into seven subgroups, with the V. vinifera SBP-domain proteins being more closely related to SBP-domain proteins from dicotyledonous angiosperms than those from monocotyledonous angiosperms. In addition, synteny analysis between grape and Arabidopsis demonstrated that homologs of several grape SBP genes were found in corresponding syntenic blocks of Arabidopsis. Expression analysis of the grape SBP-box genes in various organs and at different stages of fruit development in V. quinquangularis ‘Shang-24’ revealed distinct spatiotemporal patterns. While the majority of the grape SBP-box genes lacking a miR156/157 target site were expressed ubiquitously and constitutively, most genes bearing a miR156/157 target site exhibited distinct expression patterns, possibly due to the inhibitory role of the microRNA. Furthermore, microarray data mining and quantitative real-time RT-PCR analysis identified several grape SBP-box genes that are potentially involved in the defense against biotic and abiotic stresses. Conclusion The results presented here provide a further understanding of SBP-box gene function in plants, and yields additional insights into the mechanism of stress management in grape, which may have important implications for the future success of this crop. PMID:23527172

  3. The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation

    Zhou Bai-Cheng

    2010-04-01

    Full Text Available Abstract Background Zunongwangia profunda SM-A87, which was isolated from deep-sea sediment, is an aerobic, gram-negative bacterium that represents a new genus of Flavobacteriaceae. This is the first sequenced genome of a deep-sea bacterium from the phylum Bacteroidetes. Results The Z. profunda SM-A87 genome has a single 5 128 187-bp circular chromosome with no extrachromosomal elements and harbors 4 653 predicted protein-coding genes. SM-A87 produces a large amount of capsular polysaccharides and possesses two polysaccharide biosynthesis gene clusters. It has a total of 130 peptidases, 61 of which have signal peptides. In addition to extracellular peptidases, SM-A87 also has various extracellular enzymes for carbohydrate, lipid and DNA degradation. These extracellular enzymes suggest that the bacterium is able to hydrolyze organic materials in the sediment, especially carbohydrates and proteinaceous organic nitrogen. There are two clustered regularly interspaced short palindromic repeats in the genome, but their spacers do not match any sequences in the public sequence databases. SM-A87 is a moderate halophile. Our protein isoelectric point analysis indicates that extracellular proteins have lower predicted isoelectric points than intracellular proteins. SM-A87 accumulates organic osmolytes in the cell, so its extracelluar proteins are more halophilic than its intracellular proteins. Conclusion Here, we present the first complete genome of a deep-sea sedimentary bacterium from the phylum Bacteroidetes. The genome analysis shows that SM-A87 has some common features of deep-sea bacteria, as well as an important capacity to hydrolyze sedimentary organic nitrogen.

  4. Fine organization of genomic regions tagged to the 5S rDNA locus of the bread wheat 5B chromosome.

    Sergeeva, Ekaterina M; Shcherban, Andrey B; Adonina, Irina G; Nesterov, Michail A; Beletsky, Alexey V; Rakitin, Andrey L; Mardanov, Andrey V; Ravin, Nikolai V; Salina, Elena A

    2017-11-14

    The multigene family encoding the 5S rRNA, one of the most important structurally-functional part of the large ribosomal subunit, is an obligate component of all eukaryotic genomes. 5S rDNA has long been a favored target for cytological and phylogenetic studies due to the inherent peculiarities of its structural organization, such as the tandem arrays of repetitive units and their high interspecific divergence. The complex polyploid nature of the genome of bread wheat, Triticum aestivum, and the technically difficult task of sequencing clusters of tandem repeats mean that the detailed organization of extended genomic regions containing 5S rRNA genes remains unclear. This is despite the recent progress made in wheat genomic sequencing. Using pyrosequencing of BAC clones, in this work we studied the organization of two distinct 5S rDNA-tagged regions of the 5BS chromosome of bread wheat. Three BAC-clones containing 5S rDNA were identified in the 5BS chromosome-specific BAC-library of Triticum aestivum. Using the results of pyrosequencing and assembling, we obtained six 5S rDNA- containing contigs with a total length of 140,417 bp, and two sets (pools) of individual 5S rDNA sequences belonging to separate, but closely located genomic regions on the 5BS chromosome. Both regions are characterized by the presence of approximately 70-80 copies of 5S rDNA, however, they are completely different in their structural organization. The first region contained highly diverged short-type 5S rDNA units that were disrupted by multiple insertions of transposable elements. The second region contained the more conserved long-type 5S rDNA, organized as a single tandem array. FISH using probes specific to both 5S rDNA unit types showed differences in the distribution and intensity of signals on the chromosomes of polyploid wheat species and their diploid progenitors. A detailed structural organization of two closely located 5S rDNA-tagged genomic regions on the 5BS chromosome of bread

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

    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.

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

    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

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

    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 ...

  8. Structural organization of poliovirus RNA replication is mediated by viral proteins of the P2 genomic region

    Bienz, K.; Egger, D.; Troxler, M.; Pasamontes, L.

    1990-01-01

    Transcriptionally active replication complexes bound to smooth membrane vesicles were isolated from poliovirus-infected cells. In electron microscopic, negatively stained preparations, the replication complex appeared as an irregularly shaped, oblong structure attached to several virus-induced vesicles of a rosettelike arrangement. Electron microscopic immunocytochemistry of such preparations demonstrated that the poliovirus replication complex contains the proteins coded by the P2 genomic region (P2 proteins) in a membrane-associated form. In addition, the P2 proteins are also associated with viral RNA, and they can be cross-linked to viral RNA by UV irradiation. Guanidine hydrochloride prevented the P2 proteins from becoming membrane bound but did not change their association with viral RNA. The findings allow the conclusion that the protein 2C or 2C-containing precursor(s) is responsible for the attachment of the viral RNA to the vesicular membrane and for the spatial organization of the replication complex necessary for its proper functioning in viral transcription. A model for the structure of the viral replication complex and for the function of the 2C-containing P2 protein(s) and the vesicular membranes is proposed

  9. dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms.

    Puritz, Jonathan B; Hollenbeck, Christopher M; Gold, John R

    2014-01-01

    Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially for non-model organisms with large effective population sizes and high levels of genetic polymorphism. dDocent is an analysis pipeline with a user-friendly, command-line interface designed to process individually barcoded RADseq data (with double cut sites) into informative SNPs/Indels for population-level analyses. The pipeline, written in BASH, uses data reduction techniques and other stand-alone software packages to perform quality trimming and adapter removal, de novo assembly of RAD loci, read mapping, SNP and Indel calling, and baseline data filtering. Double-digest RAD data from population pairings of three different marine fishes were used to compare dDocent with Stacks, the first generally available, widely used pipeline for analysis of RADseq data. dDocent consistently identified more SNPs shared across greater numbers of individuals and with higher levels of coverage. This is due to the fact that dDocent quality trims instead of filtering, incorporates both forward and reverse reads (including reads with INDEL polymorphisms) in assembly, mapping, and SNP calling. The pipeline and a comprehensive user guide can be found at http://dDocent.wordpress.com.

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

    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.

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

    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.

  12. The family Rhabdoviridae: Mono- and bipartite negative-sense RNA viruses with diverse genome organization and common evolutionary origins

    Dietzgen, Ralf G.; Kondo, Hideki; Goodin, Michael M.; Kurath, Gael; Vasilakis, Nikos

    2017-01-01

    The family Rhabdoviridae consists of mostly enveloped, bullet-shaped or bacilliform viruses with a negative-sense, single-stranded RNA genome that infect vertebrates, invertebrates or plants. This ecological diversity is reflected by the diversity and complexity of their genomes. Five canonical structural protein genes are conserved in all rhabdoviruses, but may be overprinted, overlapped or interspersed with several novel and diverse accessory genes. This review gives an overview of the characteristics and diversity of rhabdoviruses, their taxonomic classification, replication mechanism, properties of classical rhabdoviruses such as rabies virus and rhabdoviruses with complex genomes, rhabdoviruses infecting aquatic species, and plant rhabdoviruses with both mono- and bipartite genomes.

  13. Working together for global health goals: The United States Agency for International Development and faith-based organizations

    Clydette L Powell

    2014-01-01

    Full Text Available For many years, and before the term “FBO” was used for faith-based organizations, the United States Agency for International Development (USAID has supported the work of FBOs in global health and development. The Agency has long recognized the impact of FBOs within that development space, because these organizations are often well positioned to reach the hard-to-reach and to go the last mile because of their strong ties to the community. Moreover, FBOs deliver a substantial percentage of the health services in some developing countries. Faith partners, whether Catholic, Protestant, Buddhist, Hindu, Muslim, or other, have an important role to play as implementers in global health and to support global efforts towards achieving the Millennium Development Goals (MDGs in health. In addition, partnerships at national and international levels are key to the success of US Presidential Initiatives in the developing world, such as President’s Emergency Plan for AIDS Relief (PEPFAR and President’s Malaria Initiative (PMI. FBOs also have an important voice in policy and strategy formulation. Among other international donors, USAID support has been of great importance to the work of FBOs, thereby helping host nations to achieve goals in ending preventable child and maternal deaths, improving communicable disease control and prevention, and by supporting the construction and renovation of hospitals and health facilities where service delivery is most needed. The development literature is replete with examples of the work of FBOs made possible through access to resources. This paper focuses on some of the work supported by USAID in global health initiatives in order to reach complementary goals and achieve significant public health advances. Given the vastness of the topic, not all the global health initiatives involving FBOs supported by USAID are included here; the reader is encouraged to access the USAID website and USAID implementing partners for

  14. Sequence analysis of the PIP5K locus in Eimeria maxima provides further evidence for eimerian genome plasticity and segmental organization.

    Song, B K; Pan, M Z; Lau, Y L; Wan, K L

    2014-07-29

    Commercial flocks infected by Eimeria species parasites, including Eimeria maxima, have an increased risk of developing clinical or subclinical coccidiosis; an intestinal enteritis associated with increased mortality rates in poultry. Currently, infection control is largely based on chemotherapy or live vaccines; however, drug resistance is common and vaccines are relatively expensive. The development of new cost-effective intervention measures will benefit from unraveling the complex genetic mechanisms that underlie host-parasite interactions, including the identification and characterization of genes encoding proteins such as phosphatidylinositol 4-phosphate 5-kinase (PIP5K). We previously identified a PIP5K coding sequence within the E. maxima genome. In this study, we analyzed two bacterial artificial chromosome clones presenting a ~145-kb E. maxima (Weybridge strain) genomic region spanning the PIP5K gene locus. Sequence analysis revealed that ~95% of the simple sequence repeats detected were located within regions comparable to the previously described feature-rich segments of the Eimeria tenella genome. Comparative sequence analysis with the orthologous E. maxima (Houghton strain) region revealed a moderate level of conserved synteny. Unique segmental organizations and telomere-like repeats were also observed in both genomes. A number of incomplete transposable elements were detected and further scrutiny of these elements in both orthologous segments revealed interesting nesting events, which may play a role in facilitating genome plasticity in E. maxima. The current analysis provides more detailed information about the genome organization of E. maxima and may help to reveal genotypic differences that are important for expression of traits related to pathogenicity and virulence.

  15. STRING 8--a global view on proteins and their functional interactions in 630 organisms

    Jensen, Lars Juhl; Kuhn, Michael; Stark, Manuel

    2008-01-01

    Functional partnerships between proteins are at the core of complex cellular phenotypes, and the networks formed by interacting proteins provide researchers with crucial scaffolds for modeling, data reduction and annotation. STRING is a database and web resource dedicated to protein-protein inter......Functional partnerships between proteins are at the core of complex cellular phenotypes, and the networks formed by interacting proteins provide researchers with crucial scaffolds for modeling, data reduction and annotation. STRING is a database and web resource dedicated to protein......-protein interactions, including both physical and functional interactions. It weights and integrates information from numerous sources, including experimental repositories, computational prediction methods and public text collections, thus acting as a meta-database that maps all interaction evidence onto a common set...... of genomes and proteins. The most important new developments in STRING 8 over previous releases include a URL-based programming interface, which can be used to query STRING from other resources, improved interaction prediction via genomic neighborhood in prokaryotes, and the inclusion of protein structures...

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

    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.

  17. Implementing CRM System in a Global Organization National vs. Organizational Culture

    Frygell, Linda; Hedman, Jonas; Carlsson, Sven

    2017-01-01

    global subsidiaries, and has planned the implementation well, the implementation was not a complete success. The study has identified that the cultural factor are important, but not stressed enough in the current CRM literature. Understanding the difference between the organizational culture in which...

  18. Turnover time of fluorescent dissolved organic matter in the dark global ocean

    Catalá, Teresa Serrano; Reche, Isabel; Fuentes-Lema, Antonio

    2015-01-01

    with a turnover time of 379±103 years is also detected. We propose the use of DOM fluorescence to study the cycling of resistant DOM that is preserved at centennial timescales and could represent a mechanism of carbon sequestration (humic-like fraction) and the decaying DOM injected into the dark global ocean......, where it decreases at centennial timescales (tyrosine-like fraction)...

  19. Global modeling of secondary organic aerosol formation from aromatic hydrocarbons: high- vs. low-yield pathways

    D. K. Henze

    2008-05-01

    Full Text Available Formation of SOA from the aromatic species toluene, xylene, and, for the first time, benzene, is added to a global chemical transport model. A simple mechanism is presented that accounts for competition between low and high-yield pathways of SOA formation, wherein secondary gas-phase products react further with either nitric oxide (NO or hydroperoxy radical (HO2 to yield semi- or non-volatile products, respectively. Aromatic species yield more SOA when they react with OH in regions where the [NO]/[HO2] ratios are lower. The SOA yield thus depends upon the distribution of aromatic emissions, with biomass burning emissions being in areas with lower [NO]/[HO2] ratios, and the reactivity of the aromatic with respect to OH, as a lower initial reactivity allows transport away from industrial source regions, where [NO]/[HO2] ratios are higher, to more remote regions, where this ratio is lower and, hence, the ultimate yield of SOA is higher. As a result, benzene is estimated to be the most important aromatic species with regards to global formation of SOA, with a total production nearly equal that of toluene and xylene combined. Global production of SOA from aromatic sources via the mechanisms identified here is estimated at 3.5 Tg/yr, resulting in a global burden of 0.08 Tg, twice as large as previous estimates. The contribution of these largely anthropogenic sources to global SOA is still small relative to biogenic sources, which are estimated to comprise 90% of the global SOA burden, about half of which comes from isoprene. Uncertainty in these estimates owing to factors ranging from the atmospheric relevance of chamber conditions to model deficiencies result in an estimated range of SOA production from aromatics of 2–12 Tg/yr. Though this uncertainty range affords a significant anthropogenic contribution to global SOA, it is evident from comparisons to recent observations that additional pathways for

  20. Short interspersed nuclear elements (SINEs) are abundant in Solanaceae and have a family-specific impact on gene structure and genome organization.

    Seibt, Kathrin M; Wenke, Torsten; Muders, Katja; Truberg, Bernd; Schmidt, Thomas

    2016-05-01

    Short interspersed nuclear elements (SINEs) are highly abundant non-autonomous retrotransposons that are widespread in plants. They are short in size, non-coding, show high sequence diversity, and are therefore mostly not or not correctly annotated in plant genome sequences. Hence, comparative studies on genomic SINE populations are rare. To explore the structural organization and impact of SINEs, we comparatively investigated the genome sequences of the Solanaceae species potato (Solanum tuberosum), tomato (Solanum lycopersicum), wild tomato (Solanum pennellii), and two pepper cultivars (Capsicum annuum). Based on 8.5 Gbp sequence data, we annotated 82 983 SINE copies belonging to 10 families and subfamilies on a base pair level. Solanaceae SINEs are dispersed over all chromosomes with enrichments in distal regions. Depending on the genome assemblies and gene predictions, 30% of all SINE copies are associated with genes, particularly frequent in introns and untranslated regions (UTRs). The close association with genes is family specific. More than 10% of all genes annotated in the Solanaceae species investigated contain at least one SINE insertion, and we found genes harbouring up to 16 SINE copies. We demonstrate the involvement of SINEs in gene and genome evolution including the donation of splice sites, start and stop codons and exons to genes, enlargement of introns and UTRs, generation of tandem-like duplications and transduction of adjacent sequence regions. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

  1. First cellular approach of the effects of global warming on groundwater organisms: a study of the HSP70 gene expression.

    Colson-Proch, Céline; Morales, Anne; Hervant, Frédéric; Konecny, Lara; Moulin, Colette; Douady, Christophe J

    2010-05-01

    Whereas the consequences of global warming at population or community levels are well documented, studies at the cellular level are still scarce. The study of the physiological or metabolic effects of such small increases in temperature (between +2 degrees C and +6 degrees C) is difficult because they are below the amplitude of the daily or seasonal thermal variations occurring in most environments. In contrast, subterranean biotopes are highly thermally buffered (+/-1 degrees C within a year), and underground water organisms could thus be particularly well suited to characterise cellular responses of global warming. To this purpose, we studied genes encoding chaperone proteins of the HSP70 family in amphipod crustaceans belonging to the ubiquitous subterranean genus Niphargus. An HSP70 sequence was identified in eight populations of two complexes of species of the Niphargus genus (Niphargus rhenorhodanensis and Niphargus virei complexes). Expression profiles were determined for one of these by reverse transcription and quantitative polymerase chain reaction, confirming the inducible nature of this gene. An increase in temperature of 2 degrees C seemed to be without effect on N. rhenorhodanensis physiology, whereas a heat shock of +6 degrees C represented an important thermal stress for these individuals. Thus, this study shows that although Niphargus individuals do not undergo any daily or seasonal thermal variations in underground water, they display an inducible HSP70 heat shock response. This controlled laboratory-based physiological experiment constitutes a first step towards field investigations of the cellular consequences of global warming on subterranean organisms.

  2. Genome Analyses of Icelandic Strains of Sulfolobus islandicus, Model Organisms for Genetic and Virus-Host Interaction Studies

    Guo, Li; Brügger, Kim; Liu, Chao

    2011-01-01

    The genomes of two Sulfolobus islandicus strains obtained from Icelandic solfataras were sequenced and analyzed. Strain REY15A is a host for a versatile genetic toolbox. It exhibits a genome of minimal size, is stable genetically, and is easy to grow and manipulate. Strain HVE10/4 shows a broad h...

  3. The evolution of human rights in World Health Organization policy and the future of human rights through global health governance.

    Meier, B M; Onzivu, W

    2014-02-01

    The World Health Organization (WHO) was intended to serve at the forefront of efforts to realize human rights to advance global health, and yet this promise of a rights-based approach to health has long been threatened by political constraints in international relations, organizational resistance to legal discourses, and medical ambivalence toward human rights. Through legal research on international treaty obligations, historical research in the WHO organizational archives, and interview research with global health stakeholders, this research examines WHO's contributions to (and, in many cases, negligence of) the rights-based approach to health. Based upon such research, this article analyzes the evolving role of WHO in the development and implementation of human rights for global health, reviews the current state of human rights leadership in the WHO Secretariat, and looks to future institutions to reclaim the mantle of human rights as a normative framework for global health governance. Copyright © 2013 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

  4. Cephalopod genomics

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria......, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described...

  5. Drivers of fluorescent dissolved organic matter in the global epipelagic ocean

    Catalá , T. S.; Á lvarez-Salgado, X. A.; Otero, J.; Iuculano, F.; Companys, B.; Horstkotte, B.; Romera-Castillo, C.; Nieto-Cid, M.; Latasa, M.; Moran, Xose Anxelu G.; Gasol, J. M.; Marrasé , C.; Stedmon, C. A.; Reche, I.

    2016-01-01

    Fluorescent dissolved organic matter (FDOM) in open surface waters (< 200 m) of the Atlantic, Pacific, and Indian oceans was analysed by excitation-emission matrix (EEM) spectroscopy and parallel factor analysis (PARAFAC). A four-component PARAFAC

  6. Chromophoric Dissolved Organic Material, Aqua MODIS, NPP, 0.05 degrees, Global, Science Quality

    National Oceanic and Atmospheric Administration, Department of Commerce — MODIS data is used to develop an index of the amount of chromophoric dissolved organic material (CDOM) in the surface waters. CDOM absorbs heavily in the blue...

  7. FLUIDIZED BED STEAM REFORMING MINERALIZATION FOR HIGH ORGANIC AND NITRATE WASTE STREAMS FOR THE GLOBAL NUCLEAR ENERGY PARTNERSHIP

    Jantzen, C; Michael Williams, M

    2008-01-11

    Waste streams that may be generated by the Global Nuclear Energy Partnership (GNEP) Advanced Energy Initiative may contain significant quantities of organics (0-53 wt%) and/or nitrates (0-56 wt%). Decomposition of high nitrate streams requires reducing conditions, e.g. organic additives such as sugar or coal, to reduce the NO{sub x} in the off-gas to N{sub 2} to meet the Clean Air Act (CAA) standards during processing. Thus, organics will be present during waste form stabilization regardless of which GNEP processes are chosen, e.g. organics in the feed or organics for nitrate destruction. High organic containing wastes cannot be stabilized with the existing HLW Best Developed Available Technology (BDAT) which is HLW vitrification (HLVIT) unless the organics are removed by preprocessing. Alternative waste stabilization processes such as Fluidized Bed Steam Reforming (FBSR) operate at moderate temperatures (650-750 C) compared to vitrification (1150-1300 C). FBSR converts organics to CAA compliant gases, creates no secondary liquid waste streams, and creates a stable mineral waste form that is as durable as glass. For application to the high Cs-137 and Sr-90 containing GNEP waste streams a single phase mineralized Cs-mica phase was made by co-reacting illite clay and GNEP simulated waste. The Cs-mica accommodates up to 30% wt% Cs{sub 2}O and all the GNEP waste species, Ba, Sr, Rb including the Cs-137 transmutation to Ba-137. For reference, the cesium mineral pollucite (CsAlSi{sub 2}O{sub 6}), currently being studied for GNEP applications, can only be fabricated at {ge} 1000 C. Pollucite mineralization creates secondary aqueous waste streams and NO{sub x}. Pollucite is not tolerant of high concentrations of Ba, Sr or Rb and forces the divalent species into different mineral host phases. The pollucite can accommodate up to 33% wt% Cs{sub 2}O.

  8. Understanding dissolved organic matter reactivity in a global context: tribute to Dr. George Aiken's many contributions

    McKnight, Diane

    2017-04-01

    As Dr. George Aiken emphasized throughout his distinguished research career, the diversity of sources of dissolved organic material (DOM) is associated with a diversity of dissolved organic compounds with a range of chemistries and reactivities that are present in the natural environment. From a limnological perspective, dissolved organic matter (DOM) can originate from allochthonous sources on the landscape which drains into a lake, river, wetland, coastal region, or other aquatic ecosystem, or from autochthonous sources within the given aquatic ecosystem. In many landscapes, the precursor organic materials that contribute to the DOM of the associated aquatic ecosystem can be derived from diverse sources, e.g. terrestrial plants, plant litter, organic material in different soil horizons, and the products of microbial growth and decay. Yet, through his focus on the underlying chemical processes a clear, chemically robust foundation for understanding DOM reactivity has emerged from Aiken's research. These processes include the enhancement in solubility due to ionized carboxylic acid functional groups and the reactions of organic sulfur groups with mercury. This approach has advanced understand of carbon cycling in the lakes of the Mars-like barren landscapes of the McMurdo Dry Valleys in Antarctica and the rivers draining the warming tundra of the Arctic.

  9. New Economy And Global Challenge: Winning Model Of Successful Small Business Organizations

    Mirjana Radovic Markovic

    2007-01-01

    The old principles no longer work in the age of Globalization. Businesses have reached the old model's limits with respect to complexity and speed. The real problem is a ruinously dysfunctional mismatch between today's business environment and the classic business model. Namely, the wrong model may transform a company into the vehicle of its own death. Great shifts - genuine and radical transformation- have been shaping the economy and business environment in recent decades. Technology, espec...

  10. Speciation of anthropogenic emissions of non-methane volatile organic compounds: a global gridded data set for 1970–2012

    G. Huang

    2017-06-01

    Full Text Available Non-methane volatile organic compounds (NMVOCs include a large number of chemical species which differ significantly in their chemical characteristics and thus in their impacts on ozone and secondary organic aerosol formation. It is important that chemical transport models (CTMs simulate the chemical transformation of the different NMVOC species in the troposphere consistently. In most emission inventories, however, only total NMVOC emissions are reported, which need to be decomposed into classes to fit the requirements of CTMs. For instance, the Emissions Database for Global Atmospheric Research (EDGAR provides spatially resolved global anthropogenic emissions of total NMVOCs. In this study the EDGAR NMVOC inventory was revised and extended in time and in sectors. Moreover the new version of NMVOC emission data in the EDGAR database were disaggregated on a detailed sector resolution to individual species or species groups, thus enhancing the usability of the NMVOC emission data by the modelling community. Region- and source-specific speciation profiles of NMVOC species or species groups are compiled and mapped to EDGAR processes (detailed resolution of sectors, with corresponding quality codes specifying the quality of the mapping. Individual NMVOC species in different profiles are aggregated to 25 species groups, in line with the common classification of the Global Emissions Initiative (GEIA. Global annual grid maps with a resolution of 0.1°  ×  0.1° for the period 1970–2012 are produced by sector and species. Furthermore, trends in NMVOC composition are analysed, taking road transport and residential sources in Germany and the United Kingdom (UK as examples.

  11. Visuospatial working memory in children with autism: the effect of a semantic global organization.

    Mammarella, Irene C; Giofrè, David; Caviola, Sara; Cornoldi, Cesare; Hamilton, Colin

    2014-06-01

    It has been reported that individuals with Autism Spectrum Disorders (ASD) perceive visual scenes as a sparse set of details rather than as a congruent and meaningful unit, failing in the extraction of the global configuration of the scene. In the present study, children with ASD were compared with typically developing (TD) children, in a visuospatial working memory task, the Visual Patterns Test (VPT). The VPT array was manipulated to vary the semantic affordance of the pattern, high semantic (global) vs. low semantic; temporal parameters were also manipulated within the change detection protocol. Overall, there was no main effect associated with Group, however there was a significant effect associated with Semantics, which was further qualified by an interaction between the Group and Semantic factors; there was only a significant effect of semantics in the TD group. The findings are discussed in light of the weak central coherence theory where the ASD group are unable to make use of long term memory semantics in order to construct global representations of the array. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. MIPS plant genome information resources.

    Spannagl, Manuel; Haberer, Georg; Ernst, Rebecca; Schoof, Heiko; Mayer, Klaus F X

    2007-01-01

    The Munich Institute for Protein Sequences (MIPS) has been involved in maintaining plant genome databases since the Arabidopsis thaliana genome project. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable data sets for model plant genomes as a backbone against which experimental data, for example from high-throughput functional genomics, can be organized and evaluated. In addition, model genomes also form a scaffold for comparative genomics, and much can be learned from genome-wide evolutionary studies.

  13. Global Expression Patterns of Three Festuca Species Exposed to Different Doses of Glyphosate Using the Affymetrix GeneChip Wheat Genome Array

    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.

  14. Global warming potential of material fractions occurring in source-separated organic household waste treated by anaerobic digestion or incineration under different framework conditions

    Naroznova, Irina; Møller, Jacob; Scheutz, Charlotte

    2016-01-01

    This study compared the environmental profiles of anaerobic digestion (AD) and incineration, in relation to global warming potential (GWP), for treating individual material fractions that may occur in source-separated organic household waste (SSOHW). Different framework conditions representative...

  15. GLOBAL CONSULTATION ON ESTABLISHMENT A UNIFIED SURVEILLANCE SYSTEM FOR DONATION AND TRANSPLANTATION OF ORGANS, TISSUES AND CELLS OF HUMAN ORIGIN

    O. V. Orlova

    2011-01-01

    Full Text Available From from February 7th to 9th 2011, the World Health Organization (WHO, the Italian National Transplant Cen- tre and the EU-funded Project «Vigilance and Surveillance of Substances of Human Origin» joined forces to organise a major global consultation that took place in Bologna, Italy. The scope of the project included organs, tissues and cells for transplantation and for assisted reproduction. The participants represented regulatory and non-regulatory government agencies, professional societies and scientific and clinical specialities from all WHO regions. The meeting explored the work already carried out on-line and agreed on priorities for the future deve- lopment of the Project «Vigilance and Surveillance of Substances of Human Origin». 

  16. Building Resilience in Families, Communities, and Organizations: A Training Program in Global Mental Health and Psychosocial Support.

    Saul, Jack; Simon, Winnifred

    2016-12-01

    This article describes the Summer Institute in Global Mental Health and Psychosocial Support, a brief immersion training program for mental health, health, and allied professionals who work with populations that have endured severe adversities and trauma, such as domestic and political violence, extreme poverty, armed conflict, epidemics, and natural disasters. The course taught participants to apply collaborative and contextually sensitive approaches to enhance social connectedness and resilience in families, communities, and organizations. This article presents core training principles and vignettes which illustrate how those engaging in such interventions must: (1) work in the context of a strong and supportive organization; (2) appreciate the complexity of the systems with which they are engaging; and (3) be open to the possibilities for healing and transformation. The program utilized a combination of didactic presentations, hands-on interactive exercises, case studies, and experiential approaches to organizational team building and staff stress management. © 2016 Family Process Institute.

  17. The role of extreme orbits in the global organization of periodic regions in parameter space for one dimensional maps

    da Costa, Diogo Ricardo; Hansen, Matheus; Guarise, Gustavo; Medrano-T, Rene O.; Leonel, Edson D.

    2016-04-01

    We show that extreme orbits, trajectories that connect local maximum and minimum values of one dimensional maps, play a major role in the parameter space of dissipative systems dictating the organization for the windows of periodicity, hence producing sets of shrimp-like structures. Here we solve three fundamental problems regarding the distribution of these sets and give: (i) their precise localization in the parameter space, even for sets of very high periods; (ii) their local and global distributions along cascades; and (iii) the association of these cascades to complicate sets of periodicity. The extreme orbits are proved to be a powerful indicator to investigate the organization of windows of periodicity in parameter planes. As applications of the theory, we obtain some results for the circle map and perturbed logistic map. The formalism presented here can be extended to many other different nonlinear and dissipative systems.

  18. Editorial for the special issue dedicated to GOPV (Global Organic Photovoltaics Conference)

    Krebs, Frederik C

    2012-01-01

    and USA dedicated to the topic of OPV that attract participants from both the USA and Europe but relatively few from Asia. It is naïve to believe that OPV should not become a global effort and that developments would accelerate faster by maintaining this geographical imbalance. The aim with the GOPV......, degradation, stability, thermo-mechanical properties, roll-to-roll processing, manufacture and industrial aspects of the field. It is my hope that you will enjoy reading this extract from the GOPV conference that comprised 48 oral presentations, 24 poster presentations and had 114 participants from 18...

  19. Global Health Security Demands a Strong International Health Regulations Treaty and Leadership From a Highly Resourced World Health Organization.

    Burkle, Frederick M

    2015-10-01

    If the Ebola tragedy of West Africa has taught us anything, it should be that the 2005 International Health Regulations (IHR) Treaty, which gave unprecedented authority to the World Health Organization (WHO) to provide global public health security during public health emergencies of international concern, has fallen severely short of its original goal. After encouraging successes with the 2003 severe acute respiratory syndrome (SARS) pandemic, the intent of the legally binding Treaty to improve the capacity of all countries to detect, assess, notify, and respond to public health threats has shamefully lapsed. Despite the granting of 2-year extensions in 2012 to countries to meet core surveillance and response requirements, less than 20% of countries have complied. Today it is not realistic to expect that these gaps will be solved or narrowed in the foreseeable future by the IHR or the WHO alone under current provisions. The unfortunate failures that culminated in an inadequate response to the Ebola epidemic in West Africa are multifactorial, including funding, staffing, and poor leadership decisions, but all are reversible. A rush by the Global Health Security Agenda partners to fill critical gaps in administrative and operational areas has been crucial in the short term, but questions remain as to the real priorities of the G20 as time elapses and critical gaps in public health protections and infrastructure take precedence over the economic and security needs of the developed world. The response from the Global Outbreak Alert and Response Network and foreign medical teams to Ebola proved indispensable to global health security, but both deserve stronger strategic capacity support and institutional status under the WHO leadership granted by the IHR Treaty. Treaties are the most successful means the world has in preventing, preparing for, and controlling epidemics in an increasingly globalized world. Other options are not sustainable. Given the gravity of ongoing

  20. Biological responses of two marine organisms of ecological relevance to on-going ocean acidification and global warming.

    Gomiero, A; Bellerby, R G J; Manca Zeichen, M; Babbini, L; Viarengo, A

    2018-05-01

    Recently, there has been a growing concern that climate change may rapidly and extensively alter global ecosystems with unknown consequences for terrestrial and aquatic life. While considerable emphasis has been placed on terrestrial ecology consequences, aquatic environments have received relatively little attention. Limited knowledge is available on the biological effects of increments of seawater temperature and pH decrements on key ecological species, i.e., primary producers and/or organisms representative of the basis of the trophic web. In the present study, we addressed the biological effects of global warming and ocean acidification on two model organisms, the microbenthic marine ciliate Euplotes crassus and the green alga Dunaliella tertiocleta using a suite of high level ecological endpoint tests and sub-lethal stress measures. Organisms were exposed to combinations of pH and temperature (TR1: 7.9 [pH], 25.5 °C and TR2: 7.8 [pH], 27,0 °C) simulating two possible environmental scenarios predicted to occur in the habitats of the selected species before the end of this century. The outcomes of the present study showed that the tested scenarios did not induce a significant increment of mortality on protozoa. Under the most severe exposure conditions, sub-lethal stress indices show that pH homeostatic mechanisms have energetic costs that divert energy from essential cellular processes and functions. The marine protozoan exhibited significant impairment of the lysosomal compartment and early signs of oxidative stress under these conditions. Similarly, significant impairment of photosynthetic efficiency and an increment in lipid peroxidation were observed in the autotroph model organism held under the most extreme exposure condition tested. Copyright © 2018 Elsevier Ltd. All rights reserved.

  1. The Global Organic Food Market and Transformation: A Conceptual Theoretical Framework

    Rasmussen, Ole Horn

    of organic agriculture. In the conclusion the study is presenting a basis for indicators that can be used for comparative studies. It is underlined that the indicators are tentative and that they have to be tested and adjusted in future studies.   The report is written by Ole Horn Rasmussen that for four...

  2. Organic pollution of rivers : Combined threats of urbanization, livestock farming and global climate change

    Wen, Y.; Schoups, G.H.W.; van de Giesen, N.C.

    2017-01-01

    Organic pollution of rivers by wastewater discharge from human activities negatively impacts people and ecosystems. Without treatment, pollution control relies on a combination of natural degradation and dilution by natural runoff to reduce downstream effects. We quantify here for the first time

  3. Drivers of fluorescent dissolved organic matter in the global epipelagic ocean

    Catalá, T.S.; Álvarez-Salgado, X. A.; Otero, J.

    2016-01-01

    Fluorescent dissolved organic matter (FDOM) in open surface waters (< 200 m) of the Atlantic, Pacific, and Indian oceans was analysed by excitation-emission matrix (EEM) spectroscopy and parallel factor analysis (PARAFAC). A four-component PARAFAC model was fit to the EEMs, which included two hum...

  4. The Grand Challenges of Organ Banking: Proceedings from the first global summit on complex tissue cryopreservation.

    Lewis, Jedediah K; Bischof, John C; Braslavsky, Ido; Brockbank, Kelvin G M; Fahy, Gregory M; Fuller, Barry J; Rabin, Yoed; Tocchio, Alessandro; Woods, Erik J; Wowk, Brian G; Acker, Jason P; Giwa, Sebastian

    2016-04-01

    The first Organ Banking Summit was convened from Feb. 27 - March 1, 2015 in Palo Alto, CA, with events at Stanford University, NASA Research Park, and Lawrence Berkeley National Labs. Experts at the summit outlined the potential public health impact of organ banking, discussed the major remaining scientific challenges that need to be overcome in order to bank organs, and identified key opportunities to accelerate progress toward this goal. Many areas of public health could be revolutionized by the banking of organs and other complex tissues, including transplantation, oncofertility, tissue engineering, trauma medicine and emergency preparedness, basic biomedical research and drug discovery - and even space travel. Key remaining scientific sub-challenges were discussed including ice nucleation and growth, cryoprotectant and osmotic toxicities, chilling injury, thermo-mechanical stress, the need for rapid and uniform rewarming, and ischemia/reperfusion injury. A variety of opportunities to overcome these challenge areas were discussed, i.e. preconditioning for enhanced stress tolerance, nanoparticle rewarming, cyroprotectant screening strategies, and the use of cryoprotectant cocktails including ice binding agents. Copyright © 2015.

  5. The family Rhabdoviridae: mono- and bipartite negative-sense RNA viruses with diverse genome organization and common evolutionary origins.

    Dietzgen, Ralf G; Kondo, Hideki; Goodin, Michael M; Kurath, Gael; Vasilakis, Nikos

    2017-01-02

    The family Rhabdoviridae consists of mostly enveloped, bullet-shaped or bacilliform viruses with a negative-sense, single-stranded RNA genome that infect vertebrates, invertebrates or plants. This ecological diversity is reflected by the diversity and complexity of their genomes. Five canonical structural protein genes are conserved in all rhabdoviruses, but may be overprinted, overlapped or interspersed with several novel and diverse accessory genes. This review gives an overview of the characteristics and diversity of rhabdoviruses, their taxonomic classification, replication mechanism, properties of classical rhabdoviruses such as rabies virus and rhabdoviruses with complex genomes, rhabdoviruses infecting aquatic species, and plant rhabdoviruses with both mono- and bipartite genomes. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. The family Rhabdoviridae: mono- and bipartite negative-sense RNA viruses with diverse genome organization and common evolutionary origins

    Dietzgen, Ralf G.; Kondo, Hideki; Goodin, Michael M.; Kurath, Gael; Vasilakis, Nikos

    2016-01-01

    The family Rhabdoviridae consists of mostly enveloped, bullet-shaped or bacilliform viruses with a negative-sense, single-stranded RNA genome that infect vertebrates, invertebrates or plants. This ecological diversity is reflected by the diversity and complexity of their genomes. Five canonical structural protein genes are conserved in all rhabdoviruses, but may be overprinted, overlapped or interspersed with several novel and diverse accessory genes. This review gives an overview of the char...

  7. Genome-wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium.

    Humira Sonah

    Full Text Available Plant genomes are complex and contain large amounts of repetitive DNA including microsatellites that are distributed across entire genomes. Whole genome sequences of several monocot and dicot plants that are available in the public domain provide an opportunity to study the origin, distribution and evolution of microsatellites, and also facilitate the development of new molecular markers. In the present investigation, a genome-wide analysis of microsatellite distribution in monocots (Brachypodium, sorghum and rice and dicots (Arabidopsis, Medicago and Populus was performed. A total of 797,863 simple sequence repeats (SSRs were identified in the whole genome sequences of six plant species. Characterization of these SSRs revealed that mono-nucleotide repeats were the most abundant repeats, and that the frequency of repeats decreased with increase in motif length both in monocots and dicots. However, the frequency of SSRs was higher in dicots than in monocots both for nuclear and chloroplast genomes. Interestingly, GC-rich repeats were the dominant repeats only in monocots, with the majority of them being present in the coding region. These coding GC-rich repeats were found to be involved in different biological processes, predominantly binding activities. In addition, a set of 22,879 SSR markers that were validated by e-PCR were developed and mapped on different chromosomes in Brachypodium for the first time, with a frequency of 101 SSR markers per Mb. Experimental validation of 55 markers showed successful amplification of 80% SSR markers in 16 Brachypodium accessions. An online database 'BraMi' (Brachypodium microsatellite markers of these genome-wide SSR markers was developed and made available in the public domain. The observed differential patterns of SSR marker distribution would be useful for studying microsatellite evolution in a monocot-dicot system. SSR markers developed in this study would be helpful for genomic studies in Brachypodium

  8. 'Preparing ourselves to become an international organization': Thailand Tobacco Monopoly's regional and global strategies.

    MacKenzie, Ross; Ross, Hana; Lee, Kelley

    2017-03-01

    The Thailand Tobacco Monopoly (TTM) controlled the country's tobacco industry from its formation in the 1940s, until the government dropped restrictions on imported cigarettes in the late 1980s in response to pressure from the United States. The TTM has since competed with transnational tobacco companies (TTCs) in a semi-monopoly market in which TTCs have steadily increased their market share. Coupled with a decline in national smoking prevalence, the result of Thailand's stringent tobacco control agenda, the TTM now accounts for a diminishing share of a contracting market. In response, the monopoly has looked to regional trade liberalisation, and proximity to markets with some of the world's highest smoking rates to expand its operations. Expansion strategies have gone largely unrealised however, and the TTM effectively remains a domestic operation. Using TTM publications, market and trade reports, industry publications, tobacco industry documents and other resources, this paper analyses TTM expansion strategies, and the limited extent to which they have been achieved. This inability to expand its operations has left the monopoly potentially vulnerable to global strategies of its transnational competitors. This article is part of the special issue 'The Emergence of Asian Tobacco Companies: Implications for Global Health Governance'.

  9. Dissolved organic carbon in the precipitation of Seoul, Korea: Implications for global wet depositional flux of fossil-fuel derived organic carbon

    Yan, Ge; Kim, Guebuem

    2012-11-01

    Precipitation was sampled in Seoul over a one-year period from 2009 to 2010 to investigate the sources and fluxes of atmospheric dissolved organic carbon (DOC). The concentrations of DOC varied from 15 μM to 780 μM, with a volume-weighted average of 94 μM. On the basis of correlation analysis using the commonly acknowledged tracers, such as vanadium, the combustion of fossil-fuels was recognized to be the dominant source. With the aid of air mass backward trajectory analyses, we concluded that the primary fraction of DOC in our precipitation samples originated locally in Korea, albeit the frequent long-range transport from eastern and northeastern China might contribute substantially. In light of the relatively invariant organic carbon to sulfur mass ratios in precipitation over Seoul and other urban regions around the world, the global magnitude of wet depositional DOC originating from fossil-fuels was calculated to be 36 ± 10 Tg C yr-1. Our study further underscores the potentially significant environmental impacts that might be brought about by this anthropogenically derived component of organic carbon in the atmosphere.

  10. The draft genome of Mycobacterium aurum , a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae

    Jody Phelan

    2015-01-01

    Full Text Available Mycobacterium aurum (M. aurum is an environmental mycobacteria that has previously been used in studies of anti-mycobacterial drugs due to its fast growth rate and low pathogenicity. The M. aurum genome has been sequenced and assembled into 46 contigs, with a total length of 6.02 Mb containing 5684 annotated protein-coding genes. A phylogenetic analysis using whole genome alignments positioned M. aurum close to Mycobacterium vaccae and Mycobacterium vanbaalenii, within a clade related to fast-growing mycobacteria. Large-scale genomic rearrangements were identified by comparing the M. aurum genome to those of Mycobacterium tuberculosis and Mycobacterium leprae. M. aurum orthologous genes implicated in resistance to anti-tuberculosis drugs in M. tuberculosis were observed. The sequence identity at the DNA level varied from 68.6% for pncA (pyrazinamide drug-related to 96.2% for rrs (streptomycin, capreomycin. We observed two homologous genes encoding the catalase-peroxidase enzyme (katG that is associated with resistance to isoniazid. Similarly, two emb B homologues were identified in the M. aurum genome. In addition to describing for the first time the genome of M. aurum , this work provides a resource to aid the use of M. aurum in studies to develop improved drugs for the pathogenic mycobacteria M. tuberculosis and M. leprae.

  11. The draft genome of Mycobacterium aurum, a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae

    Phelan, Jody

    2015-06-04

    Mycobacterium aurum (M. aurum) is an environmental mycobacteria that has previously been used in studies of anti-mycobacterial drugs due to its fast growth rate and low pathogenicity. The M. aurum genome has been sequenced and assembled into 46 contigs, with a total length of 6.02 Mb containing 5684 annotated protein-coding genes. A phylogenetic analysis using whole genome alignments positioned M. aurum close to Mycobacterium vaccae and Mycobacterium vanbaalenii, within a clade related to fast-growing mycobacteria. Large-scale genomic rearrangements were identified by comparing the M. aurum genome to those of Mycobacterium tuberculosis and Mycobacterium leprae. M. aurum orthologous genes implicated in resistance to anti-tuberculosis drugs in M. tuberculosis were observed. The sequence identity at the DNA level varied from 68.6% for pncA (pyrazinamide drug-related) to 96.2% for rrs (streptomycin, capreomycin). We observed two homologous genes encoding the catalase-peroxidase enzyme (katG) that is associated with resistance to isoniazid. Similarly, two embB homologues were identified in the M. aurum genome. In addition to describing for the first time the genome of M. aurum, this work provides a resource to aid the use of M. aurum in studies to develop improved drugs for the pathogenic mycobacteria M. tuberculosis and M. leprae.

  12. The draft genome of Mycobacterium aurum, a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae

    Phelan, Jody; Maitra, Arundhati; McNerney, Ruth; Nair, Mridul; Gupta, Antima; Coll, Francesc; Pain, Arnab; Bhakta, Sanjib; Clark, Taane G.

    2015-01-01

    Mycobacterium aurum (M. aurum) is an environmental mycobacteria that has previously been used in studies of anti-mycobacterial drugs due to its fast growth rate and low pathogenicity. The M. aurum genome has been sequenced and assembled into 46 contigs, with a total length of 6.02 Mb containing 5684 annotated protein-coding genes. A phylogenetic analysis using whole genome alignments positioned M. aurum close to Mycobacterium vaccae and Mycobacterium vanbaalenii, within a clade related to fast-growing mycobacteria. Large-scale genomic rearrangements were identified by comparing the M. aurum genome to those of Mycobacterium tuberculosis and Mycobacterium leprae. M. aurum orthologous genes implicated in resistance to anti-tuberculosis drugs in M. tuberculosis were observed. The sequence identity at the DNA level varied from 68.6% for pncA (pyrazinamide drug-related) to 96.2% for rrs (streptomycin, capreomycin). We observed two homologous genes encoding the catalase-peroxidase enzyme (katG) that is associated with resistance to isoniazid. Similarly, two embB homologues were identified in the M. aurum genome. In addition to describing for the first time the genome of M. aurum, this work provides a resource to aid the use of M. aurum in studies to develop improved drugs for the pathogenic mycobacteria M. tuberculosis and M. leprae.

  13. The draft genome of Mycobacterium aurum, a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae.

    Phelan, Jody; Maitra, Arundhati; McNerney, Ruth; Nair, Mridul; Gupta, Antima; Coll, Francesc; Pain, Arnab; Bhakta, Sanjib; Clark, Taane G

    2015-09-01

    Mycobacterium aurum (M. aurum) is an environmental mycobacteria that has previously been used in studies of anti-mycobacterial drugs due to its fast growth rate and low pathogenicity. The M. aurum genome has been sequenced and assembled into 46 contigs, with a total length of 6.02Mb containing 5684 annotated protein-coding genes. A phylogenetic analysis using whole genome alignments positioned M. aurum close to Mycobacterium vaccae and Mycobacterium vanbaalenii, within a clade related to fast-growing mycobacteria. Large-scale genomic rearrangements were identified by comparing the M. aurum genome to those of Mycobacterium tuberculosis and Mycobacterium leprae. M. aurum orthologous genes implicated in resistance to anti-tuberculosis drugs in M. tuberculosis were observed. The sequence identity at the DNA level varied from 68.6% for pncA (pyrazinamide drug-related) to 96.2% for rrs (streptomycin, capreomycin). We observed two homologous genes encoding the catalase-peroxidase enzyme (katG) that is associated with resistance to isoniazid. Similarly, two embB homologues were identified in the M. aurum genome. In addition to describing for the first time the genome of M. aurum, this work provides a resource to aid the use of M. aurum in studies to develop improved drugs for the pathogenic mycobacteria M. tuberculosis and M. leprae. Copyright © 2015 Asian-African Society for Mycobacteriology. Published by Elsevier Ltd. All rights reserved.

  14. Utility of sequenced genomes for microsatellite marker development in non-model organisms: a case study of functionally important genes in nine-spined sticklebacks (Pungitius pungitius

    Shimada Yukinori

    2010-05-01

    Full Text Available Abstract Background Identification of genes involved in adaptation and speciation by targeting specific genes of interest has become a plausible strategy also for non-model organisms. We investigated the potential utility of available sequenced fish genomes to develop microsatellite (cf. simple sequence repeat, SSR markers for functionally important genes in nine-spined sticklebacks (Pungitius pungitius, as well as cross-species transferability of SSR primers from three-spined (Gasterosteus aculeatus to nine-spined sticklebacks. In addition, we examined the patterns and degree of SSR conservation between these species using their aligned sequences. Results Cross-species amplification success was lower for SSR markers located in or around functionally important genes (27 out of 158 than for those randomly derived from genomic (35 out of 101 and cDNA (35 out of 87 libraries. Polymorphism was observed at a large proportion (65% of the cross-amplified loci independently of SSR type. To develop SSR markers for functionally important genes in nine-spined sticklebacks, SSR locations were surveyed in or around 67 target genes based on the three-spined stickleback genome and these regions were sequenced with primers designed from conserved sequences in sequenced fish genomes. Out of the 81 SSRs identified in the sequenced regions (44,084 bp, 57 exhibited the same motifs at the same locations as in the three-spined stickleback. Di- and trinucleotide SSRs appeared to be highly conserved whereas mononucleotide SSRs were less so. Species-specific primers were designed to amplify 58 SSRs using the sequences of nine-spined sticklebacks. Conclusions Our results demonstrated that a large proportion of SSRs are conserved in the species that have diverged more than 10 million years ago. Therefore, the three-spined stickleback genome can be used to predict SSR locations in the nine-spined stickleback genome. While cross-species utility of SSR primers is limited due

  15. Functional Annotation, Genome Organization and Phylogeny of the Grapevine (Vitis vinifera Terpene Synthase Gene Family Based on Genome Assembly, FLcDNA Cloning, and Enzyme Assays

    Toub Omid

    2010-10-01

    Full Text Available Abstract Background Terpenoids are among the most important constituents of grape flavour and wine bouquet, and serve as useful metabolite markers in viticulture and enology. Based on the initial 8-fold sequencing of a nearly homozygous Pinot noir inbred line, 89 putative terpenoid synthase genes (VvTPS were predicted by in silico analysis of the grapevine (Vitis vinifera genome assembly 1. The finding of this very large VvTPS family, combined with the importance of terpenoid metabolism for the organoleptic properties of grapevine berries and finished wines, prompted a detailed examination of this gene family at the genomic level as well as an investigation into VvTPS biochemical functions. Results We present findings from the analysis of the up-dated 12-fold sequencing and assembly of the grapevine genome that place the number of predicted VvTPS genes at 69 putatively functional VvTPS, 20 partial VvTPS, and 63 VvTPS probable pseudogenes. Gene discovery and annotation included information about gene architecture and chromosomal location. A dense cluster of 45 VvTPS is localized on chromosome 18. Extensive FLcDNA cloning, gene synthesis, and protein expression enabled functional characterization of 39 VvTPS; this is the largest number of functionally characterized TPS for any species reported to date. Of these enzymes, 23 have unique functions and/or phylogenetic locations within the plant TPS gene family. Phylogenetic analyses of the TPS gene family showed that while most VvTPS form species-specific gene clusters, there are several examples of gene orthology with TPS of other plant species, representing perhaps more ancient VvTPS, which have maintained functions independent of speciation. Conclusions The highly expanded VvTPS gene family underpins the prominence of terpenoid metabolism in grapevine. We provide a detailed experimental functional annotation of 39 members of this important gene family in grapevine and comprehensive information

  16. Developing global competitiveness by assessing organized retail productivity using data envelopment analysis

    Mehrotra, A.

    2009-01-01

    Full Text Available The purpose of this paper was to find out (using Regression, Data Envelopment Analysis and Sensitivity Analysis how efficiently some of the top organized India retail companies have been performing relative to each other over the years and thereby to identify factors that help increase the efficiency of a retail company. The study was conducted based on the analysis of data downloaded from Prowess database for five Indian retail companies for the time period 2000-2007. The paper is deemed to be helpful to enable Indian retail companies gain a competitive advantage in the face of increased competition being faced in the emerging organized retail sector in India. The findings brought forth Advertising and Marketing expenses as the significant performance determining factors to be paid attention to.

  17. Tracing global biogeochemical cycles and meridional overturning circulation using chromophoric dissolved organic matter

    Nelson, Norman B.; Siegel, David A.; Carlson, Craig A.; Swan, Chantal M.

    2010-02-01

    Basin-scale distributions of light absorption by chromophoric dissolved organic matter (CDOM) are positively correlated (R2 > 0.8) with apparent oxygen utilization (AOU) within the top kilometer of the Pacific and Indian Oceans. However, a much weaker correspondence is found for the Atlantic (R2 organic matter from sinking particles. The observed meridional-depth sections of CDOM result from a balance between biogeochemical processes (autochthonous production and solar bleaching) and the meridional overturning circulation. Rapid mixing in the Atlantic dilutes CDOM in the interior and implies that the time scale for CDOM accumulation is greater than ˜50 years. CDOM emerges as a unique tracer for diagnosing changes in biogeochemistry and the overturning circulation, similar to dissolved oxygen, with the additional feature that it can be quantified from satellite observation.

  18. Global energy governance: trade, infrastructure, and the diffusion of international organizations

    Leonardo Baccini; Veronica Lenzi; Paul W. Thurner

    2013-01-01

    Why do states choose to join and form international governmental organizations (IGOs) that regulate energy policy? In this article we make three specific contributions to the literature on international cooperation and diffusion. First, we show that countries form and join energy IGOs in response to memberships previously gained by direct competitors among oil and gas producers and consumers. Moreover, we demonstrate that energy IGOs diffuse among countries that share oil and gas pipelines. F...

  19. Whole genome analysis of a schistosomiasis-transmitting freshwater snail

    Adema, Coen M; Hillier, LaDeana W; Jones, Catherine S; Loker, Eric S; Knight, Matty; Minx, Patrick; Oliveira, Guilherme; Raghavan, Nithya; Shedlock, Andrew; do Amaral, Laurence Rodrigues; Arican-Goktas, Halime D; Assis, Juliana G; Baba, Elio Hideo; Baron, Olga L; Bayne, Christopher J; Bickham-Wright, Utibe; Biggar, Kyle K; Blouin, Michael; Bonning, Bryony C; Botka, Chris; Bridger, Joanna M; Buckley, Katherine M; Buddenborg, Sarah K; Lima Caldeira, Roberta; Carleton, Julia; Carvalho, Omar S; Castillo, Maria G; Chalmers, Iain W; Christensens, Mikkel; Clifton, Sandra; Cosseau, Celine; Coustau, Christine; Cripps, Richard M; Cuesta-Astroz, Yesid; Cummins, Scott F; di Stephano, Leon; Dinguirard, Nathalie; Duval, David; Emrich, Scott; Feschotte, Cédric; Feyereisen, Rene; FitzGerald, Peter; Fronick, Catrina; Fulton, Lucinda; Galinier, Richard; Gava, Sandra G; Geusz, Michael; Geyer, Kathrin K; Giraldo-Calderón, Gloria I; de Souza Gomes, Matheus; Gordy, Michelle A; Gourbal, Benjamin; Grunau, Christoph; Hanington, Patrick C; Hoffmann, Karl F; Hughes, Daniel; Humphries, Judith; Jackson, Daniel J; Jannotti-Passos, Liana K; de Jesus Jeremias, Wander; Jobling, Susan; Kamel, Bishoy; Kapusta, Aurélie; Kaur, Satwant; Koene, Joris M; Kohn, Andrea B; Lawson, Dan; Lawton, Scott P; Liang, D.C.; Limpanont, Yanin; Liu, Sijun; Lockyer, Anne E; Lovato, TyAnna L; Ludolf, Fernanda; Magrini, Vince; McManus, Donald P; Medina, Monica; Misra, Milind; Mitta, Guillaume; Mkoji, Gerald M; Montague, Michael J; Montelongo, Cesar; Moroz, Leonid L; Munoz-Torres, Monica C; Niazi, Umar; Noble, Leslie R; Oliveira, Francislon S; Pais, Fabiano S; Papenfuss, Anthony T; Peace, Rob; Pena, Janeth J; Pila, Emmanuel A; Quelais, Titouan; Raney, Brian J; Rast, Jonathan P; Rollinson, David; Rosse, Izinara C; Rotgans, Bronwyn; Routledge, Edwin J; Ryan, Kathryn M; Scholte, Larissa L S; Storey, Kenneth B; Swain, Martin; Tennessen, Jacob A; Tomlinson, Chad; Trujillo, Damian L; Volpi, Emanuela V; Walker, Anthony J; Wang, Tianfang; Wannaporn, Ittiprasert; Warren, Wesley C; Wu, Xiao-Jun; Yoshino, Timothy P; Yusuf, Mohammed; Zhang, Si-Ming; Zhao, Min; Wilson, Richard K

    2017-01-01

    Biomphalaria snails are instrumental in transmission of the human blood fluke Schistosoma mansoni. With the World Health Organization's goal to eliminate schistosomiasis as a global health problem by 2025, there is now renewed emphasis on snail control. Here, we characterize the genome of

  20. Whole genome analysis of a schistosomiasis-transmitting freshwater snail

    Adema, Coen M; Hillier, Ladeana W; Jones, Catherine S

    2017-01-01

    Biomphalaria snails are instrumental in transmission of the human blood fluke Schistosoma mansoni. With the World Health Organization's goal to eliminate schistosomiasis as a global health problem by 2025, there is now renewed emphasis on snail control. Here, we characterize the genome of Biompha...

  1. Spam nation the inside story of organized cybercrime-from global epidemic to your front door

    Krebs, Brian

    2014-01-01

    In Spam Nation, investigative journalist and cybersecurity expert Brian Krebs unmasks the criminal masterminds driving some of the biggest spam and hacker operations targeting Americans and their bank accounts. Tracing the rise, fall, and alarming resurrection of the digital mafia behind the two largest spam pharmacies-and countless viruses, phishing, and spyware attacks-he delivers the first definitive narrative of the global spam problem and its threat to consumers everywhere. Blending cutting-edge research, investigative reporting, and firsthand interviews, this terrifying true story reveals how we unwittingly invite these digital thieves into our lives every day. From unassuming computer programmers right next door to digital mobsters like "Cosma"-who unleashed a massive malware attack that has stolen thousands of Americans' logins and passwords-Krebs uncovers the shocking lengths to which these people will go to profit from our data and our wallets. Not only are hundreds of thousands of Americans expos...

  2. Primary Prevention Is? A Global Perspective on How Organizations Engaging Men in Preventing Gender-Based Violence Conceptualize and Operationalize Their Work.

    Storer, Heather L; Casey, Erin A; Carlson, Juliana; Edleson, Jeffrey L; Tolman, Richard M

    2016-02-01

    Engaging men in addressing violence against women (VAW) has become a strategy in the global prevention of gender-based violence. Concurrently, Western public health frameworks have been utilized to guide prevention agendas worldwide. Using qualitative methods, this study describes how global anti-violence organizations that partner with men conceptualize primary prevention in their work. Findings suggest that "primary prevention" is not a fixed term in the context of VAW and that front-line prevention work challenges rigidly delineated distinctions between levels of prevention. Much can be learned from global organizations' unique and contextualized approaches to the prevention of VAW. © The Author(s) 2015.

  3. The Role Of Leadership Inside Organizations In The Context Of Globalization

    Dan Păuna

    2013-05-01

    Full Text Available Any organization, irrespective of the field, needs skilled leaders who have a vision and confidence in action.The leader plays various roles and the key issue is to determine how they influence the performance of the team they coordinate. The research method used was the mathematical modeling applied to the example of a team. The aim of the research is to identify the cooperation method in order to improve workers’ performance but also to minimize the possible conflicts which can affect the level of performance. The results of this research led us to conclusions regarding the characteristics of the team leader.

  4. A global hotspot for dissolved organic carbon in hypermaritime watersheds of coastal British Columbia

    A. A. Oliver

    2017-08-01

    Full Text Available The perhumid region of the coastal temperate rainforest (CTR of Pacific North America is one of the wettest places on Earth and contains numerous small catchments that discharge freshwater and high concentrations of dissolved organic carbon (DOC directly to the coastal ocean. However, empirical data on the flux and composition of DOC exported from these watersheds are scarce. We established monitoring stations at the outlets of seven catchments on Calvert and Hecate islands, British Columbia, which represent the rain-dominated hypermaritime region of the perhumid CTR. Over several years, we measured stream discharge, stream water DOC concentration, and stream water dissolved organic-matter (DOM composition. Discharge and DOC concentrations were used to calculate DOC fluxes and yields, and DOM composition was characterized using absorbance and fluorescence spectroscopy with parallel factor analysis (PARAFAC. The areal estimate of annual DOC yield in water year 2015 was 33.3 Mg C km−2 yr−1, with individual watersheds ranging from an average of 24.1 to 37.7 Mg C km−2 yr−1. This represents some of the highest DOC yields to be measured at the coastal margin. We observed seasonality in the quantity and composition of exports, with the majority of DOC export occurring during the extended wet period (September–April. Stream flow from catchments reacted quickly to rain inputs, resulting in rapid export of relatively fresh, highly terrestrial-like DOM. DOC concentration and measures of DOM composition were related to stream discharge and stream temperature and correlated with watershed attributes, including the extent of lakes and wetlands, and the thickness of organic and mineral soil horizons. Our discovery of high DOC yields from these small catchments in the CTR is especially compelling as they deliver relatively fresh, highly terrestrial organic matter directly to the coastal ocean. Hypermaritime landscapes are common on the

  5. A global hotspot for dissolved organic carbon in hypermaritime watersheds of coastal British Columbia

    Oliver, Allison A.; Tank, Suzanne E.; Giesbrecht, Ian; Korver, Maartje C.; Floyd, William C.; Sanborn, Paul; Bulmer, Chuck; Lertzman, Ken P.

    2017-08-01

    The perhumid region of the coastal temperate rainforest (CTR) of Pacific North America is one of the wettest places on Earth and contains numerous small catchments that discharge freshwater and high concentrations of dissolved organic carbon (DOC) directly to the coastal ocean. However, empirical data on the flux and composition of DOC exported from these watersheds are scarce. We established monitoring stations at the outlets of seven catchments on Calvert and Hecate islands, British Columbia, which represent the rain-dominated hypermaritime region of the perhumid CTR. Over several years, we measured stream discharge, stream water DOC concentration, and stream water dissolved organic-matter (DOM) composition. Discharge and DOC concentrations were used to calculate DOC fluxes and yields, and DOM composition was characterized using absorbance and fluorescence spectroscopy with parallel factor analysis (PARAFAC). The areal estimate of annual DOC yield in water year 2015 was 33.3 Mg C km-2 yr-1, with individual watersheds ranging from an average of 24.1 to 37.7 Mg C km-2 yr-1. This represents some of the highest DOC yields to be measured at the coastal margin. We observed seasonality in the quantity and composition of exports, with the majority of DOC export occurring during the extended wet period (September-April). Stream flow from catchments reacted quickly to rain inputs, resulting in rapid export of relatively fresh, highly terrestrial-like DOM. DOC concentration and measures of DOM composition were related to stream discharge and stream temperature and correlated with watershed attributes, including the extent of lakes and wetlands, and the thickness of organic and mineral soil horizons. Our discovery of high DOC yields from these small catchments in the CTR is especially compelling as they deliver relatively fresh, highly terrestrial organic matter directly to the coastal ocean. Hypermaritime landscapes are common on the British Columbia coast, suggesting that

  6. Plant STAND P-loop NTPases: a current perspective of genome distribution, evolution, and function : Plant STAND P-loop NTPases: genomic organization, evolution, and molecular mechanism models contribute broadly to plant pathogen defense.

    Arya, Preeti; Acharya, Vishal

    2018-02-01

    STAND P-loop NTPase is the common weapon used by plant and other organisms from all three kingdoms of life to defend themselves against pathogen invasion. The purpose of this study is to review comprehensively the latest finding of plant STAND P-loop NTPase related to their genomic distribution, evolution, and their mechanism of action. Earlier, the plant STAND P-loop NTPase known to be comprised of only NBS-LRRs/AP-ATPase/NB-ARC ATPase. However, recent finding suggests that genome of early green plants comprised of two types of STAND P-loop NTPases: (1) mammalian NACHT NTPases and (2) NBS-LRRs. Moreover, YchF (unconventional G protein and members of P-loop NTPase) subfamily has been reported to be exceptionally involved in biotic stress (in case of Oryza sativa), thereby a novel member of STAND P-loop NTPase in green plants. The lineage-specific expansion and genome duplication events are responsible for abundance of plant STAND P-loop NTPases; where "moderate tandem and low segmental duplication" trajectory followed in majority of plant species with few exception (equal contribution of tandem and segmental duplication). Since the past decades, systematic research is being investigated into NBS-LRR function supported the direct recognition of pathogen or pathogen effectors by the latest models proposed via 'integrated decoy' or 'sensor domains' model. Here, we integrate the recently published findings together with the previous literature on the genomic distribution, evolution, and distinct models proposed for functional molecular mechanism of plant STAND P-loop NTPases.

  7. High resolution linkage maps of the model organism Petunia reveal substantial synteny decay with the related genome of tomato.

    Bossolini, Eligio; Klahre, Ulrich; Brandenburg, Anna; Reinhardt, Didier; Kuhlemeier, Cris

    2011-04-01

    Two linkage maps were constructed for the model plant Petunia. Mapping populations were obtained by crossing the wild species Petunia axillaris subsp. axillaris with Petunia inflata, and Petunia axillaris subsp. parodii with Petunia exserta. Both maps cover the seven chromosomes of Petunia, and span 970 centimorgans (cM) and 700 cM of the genomes, respectively. In total, 207 markers were mapped. Of these, 28 are multilocus amplified fragment length polymorphism (AFLP) markers and 179 are gene-derived markers. For the first time we report on the development and mapping of 83 Petunia microsatellites. The two maps retain the same marker order, but display significant differences of recombination frequencies at orthologous mapping intervals. A complex pattern of genomic rearrangements was detected with the related genome of tomato (Solanum lycopersicum), indicating that synteny between Petunia and other Solanaceae crops has been considerably disrupted. The newly developed markers will facilitate the genetic characterization of mutants and ecological studies on genetic diversity and speciation within the genus Petunia. The maps will provide a powerful tool to link genetic and genomic information and will be useful to support sequence assembly of the Petunia genome.

  8. The mitochondrial genome of the stingless bee Melipona bicolor (Hymenoptera, Apidae, Meliponini: sequence, gene organization and a unique tRNA translocation event conserved across the tribe Meliponini

    Daniela Silvestre

    2008-01-01

    Full Text Available At present a complete mtDNA sequence has been reported for only two hymenopterans, the Old World honey bee, Apis mellifera and the sawfly Perga condei. Among the bee group, the tribe Meliponini (stingless bees has some distinction due to its Pantropical distribution, great number of species and large importance as main pollinators in several ecosystems, including the Brazilian rain forest. However few molecular studies have been conducted on this group of bees and few sequence data from mitochondrial genomes have been described. In this project, we PCR amplified and sequenced 78% of the mitochondrial genome of the stingless bee Melipona bicolor (Apidae, Meliponini. The sequenced region contains all of the 13 mitochondrial protein-coding genes, 18 of 22 tRNA genes, and both rRNA genes (one of them was partially sequenced. We also report the genome organization (gene content and order, gene translation, genetic code, and other molecular features, such as base frequencies, codon usage, gene initiation and termination. We compare these characteristics of M. bicolor to those of the mitochondrial genome of A. mellifera and other insects. A highly biased A+T content is a typical characteristic of the A. mellifera mitochondrial genome and it was even more extreme in that of M. bicolor. Length and compositional differences between M. bicolor and A. mellifera genes were detected and the gene order was compared. Eleven tRNA gene translocations were observed between these two species. This latter finding was surprising, considering the taxonomic proximity of these two bee tribes. The tRNA Lys gene translocation was investigated within Meliponini and showed high conservation across the Pantropical range of the tribe.

  9. The role of extreme orbits in the global organization of periodic regions in parameter space for one dimensional maps

    Costa, Diogo Ricardo da, E-mail: diogo_cost@hotmail.com [Departamento de Física, UNESP – Universidade Estadual Paulista, Av. 24A, 1515, Bela Vista, 13506-900, Rio Claro, SP (Brazil); Hansen, Matheus [Departamento de Física, UNESP – Universidade Estadual Paulista, Av. 24A, 1515, Bela Vista, 13506-900, Rio Claro, SP (Brazil); Instituto de Física, Univ. São Paulo, Rua do Matão, Cidade Universitária, 05314-970, São Paulo – SP (Brazil); Guarise, Gustavo [Departamento de Física, UNESP – Universidade Estadual Paulista, Av. 24A, 1515, Bela Vista, 13506-900, Rio Claro, SP (Brazil); Medrano-T, Rene O. [Departamento de Ciências Exatas e da Terra, UNIFESP – Universidade Federal de São Paulo, Rua São Nicolau, 210, Centro, 09913-030, Diadema, SP (Brazil); Department of Mathematics, Imperial College London, London SW7 2AZ (United Kingdom); Leonel, Edson D. [Departamento de Física, UNESP – Universidade Estadual Paulista, Av. 24A, 1515, Bela Vista, 13506-900, Rio Claro, SP (Brazil); Abdus Salam International Center for Theoretical Physics, Strada Costiera 11, 34151 Trieste (Italy)

    2016-04-22

    We show that extreme orbits, trajectories that connect local maximum and minimum values of one dimensional maps, play a major role in the parameter space of dissipative systems dictating the organization for the windows of periodicity, hence producing sets of shrimp-like structures. Here we solve three fundamental problems regarding the distribution of these sets and give: (i) their precise localization in the parameter space, even for sets of very high periods; (ii) their local and global distributions along cascades; and (iii) the association of these cascades to complicate sets of periodicity. The extreme orbits are proved to be a powerful indicator to investigate the organization of windows of periodicity in parameter planes. As applications of the theory, we obtain some results for the circle map and perturbed logistic map. The formalism presented here can be extended to many other different nonlinear and dissipative systems. - Highlights: • Extreme orbits and the organization of periodic regions in parameter space. • One-dimensional dissipative mappings. • The circle map and also a time perturbed logistic map were studied.

  10. The role of extreme orbits in the global organization of periodic regions in parameter space for one dimensional maps

    Costa, Diogo Ricardo da; Hansen, Matheus; Guarise, Gustavo; Medrano-T, Rene O.; Leonel, Edson D.

    2016-01-01

    We show that extreme orbits, trajectories that connect local maximum and minimum values of one dimensional maps, play a major role in the parameter space of dissipative systems dictating the organization for the windows of periodicity, hence producing sets of shrimp-like structures. Here we solve three fundamental problems regarding the distribution of these sets and give: (i) their precise localization in the parameter space, even for sets of very high periods; (ii) their local and global distributions along cascades; and (iii) the association of these cascades to complicate sets of periodicity. The extreme orbits are proved to be a powerful indicator to investigate the organization of windows of periodicity in parameter planes. As applications of the theory, we obtain some results for the circle map and perturbed logistic map. The formalism presented here can be extended to many other different nonlinear and dissipative systems. - Highlights: • Extreme orbits and the organization of periodic regions in parameter space. • One-dimensional dissipative mappings. • The circle map and also a time perturbed logistic map were studied.

  11. Chloroplast Genome of the Folk Medicine and Vegetable Plant Talinum paniculatum (Jacq.) Gaertn.: Gene Organization, Comparative and Phylogenetic Analysis.

    Liu, Xia; Li, Yuan; Yang, Hongyuan; Zhou, Boyang

    2018-04-09

    The complete chloroplast (cp) genome of Talinum paniculatum (Caryophyllale), a source of pharmaceutical efficacy similar to ginseng, and a widely distributed and planted edible vegetable, were sequenced and analyzed. The cp genome size of T. paniculatum is 156,929 bp, with a pair of inverted repeats (IRs) of 25,751 bp separated by a large single copy (LSC) region of 86,898 bp and a small single copy (SSC) region of 18,529 bp. The genome contains 83 protein-coding genes, 37 transfer RNA (tRNA) genes, eight ribosomal RNA (rRNA) genes and four pseudogenes. Fifty one (51) repeat units and ninety two (92) simple sequence repeats (SSRs) were found in the genome. The pseudogene rpl23 (Ribosomal protein L23) was insert AATT than other Caryophyllale species by sequence alignment, which located in IRs region. The gene of trnK-UUU (tRNA-Lys) and rpl16 (Ribosomal protein L16) have larger introns in T. paniculatum , and the existence of matK (maturase K) genes, which usually located in the introns of trnK-UUU , rich sequence divergence in Caryophyllale. Complete cp genome comparison with other eight Caryophyllales species indicated that the differences between T. paniculatum and P. oleracea were very slight, and the most highly divergent regions occurred in intergenic spacers. Comparisons of IR boundaries among nine Caryophyllales species showed that T. paniculatum have larger IRs region and the contraction is relatively slight. The phylogenetic analysis among 35 Caryophyllales species and two outgroup species revealed that T. paniculatum and P. oleracea do not belong to the same family. All these results give good opportunities for future identification, barcoding of Talinum species, understanding the evolutionary mode of Caryophyllale cp genome and molecular breeding of T. paniculatum with high pharmaceutical efficacy.

  12. The Global Sustainability Index: An Instrument For Assessing The Progress Towards The Sustainable Organization

    Grecu, Valentin

    2015-09-01

    There is rarely an optimal solution in sustainable development but most frequently a need to build compromises between conflicting aspects such as economic, social and environmental ones and different expectations of stakeholders. Moreover, information is rarely available and precise. This paper will focus on how to use indicators to monitor sustainable development, integrating the information provided by many of them into a complex general sustainability index. Having this general indicator is essential for decision makers as it is very complicated to evaluate the performance of the organization based on multiple indicators. The objective of this paper is to find mathematical algorithms for simplifying the decision-making process by offering an instrument for the evaluation of the sustainability progress.

  13. The role of calcifying organisms in the global CO sub 2 cycle

    Kayanne, H; Miyachi, S [Geological Survey of Japan, Tsukuba (Japan)

    1991-11-01

    The increase in atmospheric CO{sub 2} is recognised as a serious problem. The coral reefs of the Japanese islands fix 2.2 kg CO{sub 2}/m per year as organic carbon and 2.1 kg CO{sub 2}/m per year as calcium carbonate. The potential CO{sub 2} fixation of the Ryukyu reefs is 1.4 per cent of CO{sub 2} emission from Japan. Technology is being established to enhance the rate of CO{sub 2} fixation. Calcareous algae also play an important role in the calcification, and the mass culture of marine unicellular coccolith former is under investigation in Japan. 4 refs., 3 boxes.

  14. Characteristics of global organic matrix in normal and pimpled chicken eggshells.

    Liu, Z; Song, L; Zhang, F; He, W; Linhardt, R J

    2017-10-01

    The organic matrix from normal and pimpled calcified chicken eggshells were dissociated into acid-insoluble, water-insoluble, and facultative-soluble (both acid- and water-soluble) components, to understand the influence of shell matrix on eggshell qualities. A linear correlation was shown among these 3 matrix components in normal eggshells but was not observed in pimpled eggshells. In pimpled eggshells, the percentage contents of all 4 groups of matrix (the total matrix, acid-insoluble matrix, water-insoluble matrix, and facultative-soluble matrix) were significantly higher than that in normal eggshells. The amounts of both total matrix and acid-insoluble matrix in individual pimpled calcified shells were high, even though their weight was much lower than a normal eggshell. In both normal and pimpled eggshells, the calcified eggshell weight and shell thickness significantly and positively correlated with the amounts of all 4 groups of matrix in an individual calcified shell. In normal eggshells, the calcified shell thickness and shell breaking strength showed no significant correlations with the percentage contents of all 4 groups of matrix. In normal eggshells, only the shell membrane weight significantly correlated with the constituent ratios of both acid-insoluble matrix and facultative-soluble matrix in the whole matrix. In pimpled eggshells, 3 variables (calcified shell weight, shell thickness, and breaking strength) were significantly correlated with the constituent proportions of both acid-insoluble matrix and facultative-matrix. This study suggests that mechanical properties of normal eggshells may not linearly depend on the organic matrix content in the calcified eggshells and that pimpled eggshells might result by the disequilibrium enrichment of some proteins with negative effects. © 2017 Poultry Science Association Inc.

  15. The complete chloroplast genome sequence of the chlorophycean green alga Scenedesmus obliquus reveals a compact gene organization and a biased distribution of genes on the two DNA strands

    de Cambiaire, Jean-Charles; Otis, Christian; Lemieux, Claude; Turmel, Monique

    2006-01-01

    Background The phylum Chlorophyta contains the majority of the green algae and is divided into four classes. While the basal position of the Prasinophyceae is well established, the divergence order of the Ulvophyceae, Trebouxiophyceae and Chlorophyceae (UTC) remains uncertain. The five complete chloroplast DNA (cpDNA) sequences currently available for representatives of these classes display considerable variability in overall structure, gene content, gene density, intron content and gene order. Among these genomes, that of the chlorophycean green alga Chlamydomonas reinhardtii has retained the least ancestral features. The two single-copy regions, which are separated from one another by the large inverted repeat (IR), have similar sizes, rather than unequal sizes, and differ radically in both gene contents and gene organizations relative to the single-copy regions of prasinophyte and ulvophyte cpDNAs. To gain insights into the various changes that underwent the chloroplast genome during the evolution of chlorophycean green algae, we have sequenced the cpDNA of Scenedesmus obliquus, a member of a distinct chlorophycean lineage. Results The 161,452 bp IR-containing genome of Scenedesmus features single-copy regions of similar sizes, encodes 96 genes, i.e. only two additional genes (infA and rpl12) relative to its Chlamydomonas homologue and contains seven group I and two group II introns. It is clearly more compact than the four UTC algal cpDNAs that have been examined so far, displays the lowest proportion of short repeats among these algae and shows a stronger bias in clustering of genes on the same DNA strand compared to Chlamydomonas cpDNA. Like the latter genome, Scenedesmus cpDNA displays only a few ancestral gene clusters. The two chlorophycean genomes share 11 gene clusters that are not found in previously sequenced trebouxiophyte and ulvophyte cpDNAs as well as a few genes that have an unusual structure; however, their single-copy regions differ

  16. Observing copepods through a genomic lens

    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

  17. Observing copepods through a genomic lens

    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<